Student
Student--Faculty Programs
2012 Abstract Book
STUDENT-FACULTY PROGRAMS
2012 Abstract Book
This document contains the abstracts of the research projects
conducted by students in all programs coordinated by Caltech’s
Student-Faculty Programs Office for the summer of 2012.
Table of Contents
Summer Undergraduate Research Fellowships (SURF)
1
MURF Undergraduate Research Fellowships
115
Amgen Scholars Program
121
Laser Interferometer Gravitational-Wave Observatory (LIGO)
131
NASA/JPL Programs
 Planetary Geology and Geophysics
Undergraduate Research Program (PGGURP)
 The National Space Grant College
and Fellowship Program (Space Grant)
 Undergraduate Student Research Program (USRP)
 JPL Student Internship Program (JPLSIP)
141
SURF
SUMMER UNDERGRADUATE
RESEARCH FELLOWSHIPS
S
U
R
F
-Olefin Polymerization of Group 4 Metal Complexes Containing Amido-Pyridine-Phenoxide Ligands
Tonia Ahmed
Mentors: John Bercaw and Rachel Klet
The annual world production of polyolefins is in excess of 70 billion kilograms. Because of the huge demand for
polyolefins, finding processes for producing polymers with specific molecular weights and microstructures continues
to be an important industrial and academic goal. Several amido-pyridine-phenoxide ligands were synthesized with
variants to the R-group on the amido arm. These ligands were metalated with titanium, zirconium, and hafnium
and then tested for propylene polymerization activity. The identity of these compounds was confirmed by 1H and
13
C nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry. The
microstructures of the polypropylene produced were investigated using 13C NMR spectroscopy.
Investigating Brain Activity Differences Between 2D and 3D Dynamic Face Stimuli Using Functional
Magnetic Resonance Imaging
Curie Ahn
Mentors: Ralph Adolphs and Laura Loesch
Traditionally, social psychology and neuroscience studies have used carefully-controlled pre-recorded visual stimuli
as an alternative to more ecologically valid live stimuli. To better understand social cognition, we believe it is
important to better simulate social interaction. We hypothesize that if social stimuli are made to feel more
immersive or real, social attention will be increased, and we will observe greater activation in areas of the brain
associated with social cognition and emotion. One novel way of making a stimulus more real is making use of 3D
technology, and adding additional depth cues to existing 2D images. Increasing the size of an image to be closer to
life-sized can also make it more life-like. If either of these manipulations can make an artificial stimuli feel more
immersive, subjects may consider the social information in the stimuli to be of greater importance. Functional
magnetic resonance imaging will be used to assess differing neural responses to these stimulus types. In our
experiment, subjects will complete a one-back attentional task while viewing pre-recorded dynamic social stimuli in
a 2 (Depth: 2D, 3D) x 2 (Size: small, large) blocked design. We expect that the amygdala, insula, superior
temporal sulcus, and other social attention network regions will show a greater activation as the stimuli become
more immersive, such that the large 3D stimuli elicit the greatest effect.
Frequency Precision and Spiral Pattern Formation in Lattices of Coupled Oscillators With Reactive
Coupling
John-Mark A. Allen
Mentor: Michael C. Cross
The dynamics of a two-dimensional lattice of limit-cycle oscillators each subject to independent noise sources is
studied in the phase reduction limit in the presence of reactive coupling between nearest-neighbour oscillators.
Specifically, the noise properties of an entrained solution featuring a spiral pattern in phase are sought. Analysis in
the continuum limit of the equations of motion allows approximate frequency precision and entrained frequencies
to be found. Direct simulation is then used to check the validity of these results. The noise properties are then
compared to those of target patterns in the same lattice and analysed in terms of their suitability for constructing
high-precision frequency sources out of coupled nanomechanical oscillators.
Mechanical Size Effects in Fe Nanoparticles
Eli Alster
Mentors: Eugen Rabkin and Julia R. Greer
Metals sized on the order of nanometers often produce mechanical size effects, property differences from bulk due
to external scale rather than internal structure. In order to investigate the relationship between dimensionality and
size effects, iron thin film deposited on a sapphire substrate underwent dewetting to produce iron nanoparticles –
particles nanometers in size in all three dimensions. The nanoparticles were indented plastically using an adapted
atomic force microscope (AFM) that enabled high resolution in-situ topographical imaging of the indented particles.
These nanoindentation results are compared to indentation of the nondewetted iron thin film and bulk iron.
Differences in deformation mechanisms are expected between gold nanoparticles (studies previously) and the
present work, as a result of their fundamental differences in lattice structure: gold is fcc (face-centered cubic) while
iron is bcc (body-centered cubic).
Peptide-Based Capture Agents: High-Affinity, High-Specificity Cancer-Targeting Agents
Belen Alvarez-Villalonga
Mentors: James Heath, Arundhati Nag, and Samir Das
High-affinity, high-specificity capture agents are important clinical diagnostics tools. Peptide-based capture agents
can be less expensive and more reliable than the antibodies that are commonly used. The current project focuses
on developing a cyclic peptide capture agent against the phospho Ser474 region of Akt2 kinase, a protein that is
activated, over-expressed, or mutated in various types of cancer. To create such a capture agent, a 32mer
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fragment from the relevant C terminal region of Akt2 was synthesized and screened with a cyclic peptide library.
The hit peptide sequences were obtained by sequencing them with the Edman Peptide Sequencer. The best four
sequences were remade on resin. These candidates were then tested in an Enzyme Linked ImmunoSorbent Assay
against the 32mer phosphopeptide. A scrambled 32mer peptide was used as a control. A promising cyclic peptide
candidate was found that binds selectively to the target phosphopeptide and not the control peptide; however, the
binding affinity seems to be low. Further optimization of this peptide is being done, to increase the affinity of the
cyclic peptide to the target phosphopeptide, while retaining the specificity. The optimized candidate shall then be
tested for binding to the full-length active protein containing the phospho-Ser474.
The Propagation of Coronal Mass Ejections
Keshav Amla
Mentors: Paulett C. Liewer and Eric M. DeJong
A Coronal Mass Ejection (CME) is an event in which the Sun explosively discharges a cloud of plasma and magnetic
field from its corona. These CMEs are a major driver of space weather and much of geomagnetic activity on
planets. The focus of this project was to further advance the study of the way these CMEs propagate from the Sun.
Using imaging data from NASA’s twin Solar TErrestrial RElations Observatory (STEREO) satellites, we sought to
determine the trajectories of a large list of CMEs for which we had clear in situ data at various spacecraft. We
applied the Graduated Cylindrical Shell (GCS) model to track the trajectory of the CMEs using Coronagraph images
and the Rtsccguicloud GCS modeling software. Using difference images, which are generated by subtracting an
image from the subsequent image, of the Coronagraph and Heliographic Imager data and the Solar Angle Time Plot
CME tracking software suite, we determined the elongation vs. time track of each CME and then fit these tracks
using the Fixed-Phi and Harmonic Mean models to determine the CME trajectories. For the three different models,
we compared the predictions for CME arrival times and velocities at the spacecraft with the actual in situ data
observed at these satellites.
Cryogenic MKID Testing Stage for MUSIC
Da An
Mentor: Sunil Golwala
This paper discusses the retrofit of both the cryogenic multistage dewar and the testing stage for the microwave
kinetic inductance detectors (MKIDs), as part of the Multicolor Submillimeter Inductance Camera (MUSIC)
instrument. Details presented include the design, implementation, and performance calculations for each part. The
MKID testing stage, located inside the dewar, sits at about 250 mK, which is the operating temperature of the
MUSIC focal plane. To achieve and maintain this temperature, the dewar buffers the heat loads of various
components through the use of intermediate temperature stages of approximately 350 mK, 4.2 K, and 77 K. These
stages also act as heat sinks for the optical window filters, which only transmit wavelengths in the (sub)millimeter
range. The retrofit results in a reduced heat load on the testing stage, a wider viewing angle for input radiation,
and more space to maneuver within the dewar.
Study of the Jovian Atmosphere in the Near Infrared
Kimberly Andersen
Mentors: Glenn Orton and Robert West
The goal of my SURF internship this summer was to analyze images and spectra of Jupiter that were taken at the
NASA Infrared Telescope Facility with the SpeX instrument at infrared wavelengths between 0.8 and 2.5 microns.
The purpose is to learn about the vertical and horizontal distribution of haze in Jupiter's stratosphere with latitude
coverage from pole to pole. The results of this analysis can be used to estimate radiative heating rates for
stratospheric circulation models of Jupiter. The first step was to calibrate the spectral images, however, wavelength
calibration was much more difficult than first anticipated because calibration software had to be generated from
scratch. I first attempted to use an Argon calibration spectrum, but lack of a reference spectrum caused this to be
unsuccessful. I then compared the infrared transmission spectrum of Earth's atmosphere to spectra of Jupiter's
moon Europa and a bright star. I had little success with the Europa spectrum but I was able to roughly match the
atmospheric transmission spectrum to absorption lines in the stellar spectra. Additional refinements in calibration
are still necessary and will require more analysis after the end of my internship.
The Bacterial Capsular Polysaccharide PSA and Its Antimicrobrial Properties Through
Immunomodulation of the Mammalian Innate Immune System
Phoebe Ann
Mentors: Sarkis Mazmanian and Arya Khosravi
Conventional antibiotics nonspecifically target bacteria within the mammalian body. In doing so, they initially kill
pathogens as desired but also eradicate symbiotic microbes and augment bacterial resistance. Thus, continual
utilization of antibiotics not only creates ideal environments for opportunistic infection, but also inherently relegates
itself to futility. Conversely, immunomodulatory molecules which enhance host immune function to resist infection
may be a more effective treatment, as shown by the promising capsular Polysaccharide A (PSA) of the prominent
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human symbiont Bacteroides fragilis. We thus hypothesize that PSA primes macrophages of innate immunity to
reduce infection by other bacteria. Listeria monocytogenes (L. monocytogenes) is utilized as this other bacterium,
since it is well characterized and easily manipulated. Raw macrophages from an immortal mouse macrophagal cell
line are stimulated with PSA and infected with L. Monocytogenes. Measurement of listericidal activity over 8 hours
shows that PSA enhances macrophage listericidal activity. Furthermore, Griess assays show that PSA-stimulated
macrophages secrete higher levels of NO, an essential mediator of L. monocytogenes clearance. Ultimately,
elucidation of the mechanism by which PSA protects against infection may lead to development of a novel, natural
therapeutic PSA which resists pathogenesis via the host’s own immunity.
NMR-Based Conformational Analysis of the Monoconjugate Acid of N,N,N’,N’Tetramethylethylenediamine Oxide (TMEDO) and N,N-Dimethylsuccinamic Acid (DMSA) in a Lyotropic
Solution for Dihedral Angle Calculations
Ben K. Arbeiter
Mentors: John D. Roberts, William Carroll, and Bright Emenike
Pharmaceutical drug function and potency depends on a molecule’s conformational state to correctly bond to an
active site. This experiment focused on conformational analysis of N,N,N’,N’-tetramethylethylenediamine oxide
(TMEDO) as a gauche standard (nearly 100% gauche) and N,N-Dimethylsuccinamic acid (DMSA) via NMR
spectroscopy. Previous computational modeling found the dihedral angle to be 60° and 180°. The goal of this
project is to examine whether these angles can be experimentally determined from dipolar coulpings using the
Hasnoot-Altona equation. This equation relates coupling constants to dihedral angles. In order to observe 1H nucleinuclei interactions through space instead of through bonds, Lyotropic solutions, composed primarily of
Myristyltrimethylammonium bromide and Decyl alcohol, were used to orient compounds within the magnetic field
to reduce time-averaging effects of rapid conformational state changes. Analysis of spectra using Adept Scientific’s
gNMR produced scalar and dipolar couplings that were used in calculations for the fraction gauche and dihedral
angle, respectively. The dihedral angle of TMEDO was found to deviate from the traditional 60 degrees, at 85° ± 4°
with a fraction gauche of 95% ± 5%. DMSA was found to have a fraction gauche of 64% ± 4%. Further research
will analyze similar compounds for comparison.
A Table-Top Demonstration of an Exact Mechanical Analog of a Magnetic Mirror
Patricio Arrangoiz
Mentor: Paul M. Bellan
Long thought of as a peculiarity of electromagnetism, the well-known phenomenon of magnetic mirroring can now
be understood as a property of any 2D Hamiltonian system having fast oscillatory motion in one direction and slow
motion in the other. This property has recently been shown to apply to a much wider class of multidimensional
systems with a periodic variable [R.J. Perkins and P.M. Bellan, PRL 105, 124301 (2010)]. The purpose of this
project is to build a table-top system that is an exact mechanical analog of a magnetic mirror. The system involves
a small ball that is set in rolling motion on a saddle-like surface. The surface has a downhill parabolic profile (slow
direction), with a groove of parabolic cross-section (fast direction) that narrows as one moves away from the
center of the hill. The dynamics of the system is such that the adiabatic invariance effectively produces a return
force opposing gravity. This return force prevents the ball from falling and makes it oscillate about the top of the
hill. The surface was successfully machined using CNC microstepping on aluminum, and the mirroring effect was
observed.
Evaluation of Oxygen Transport in Ceria Through Electrical Conductivity Relaxation
Arun S. Asundi
Mentors: Sossina M. Haile and Chirranjeevi Balaji Gopal
Water splitting through the thermochemical cycling of the non-stoichiometric oxide ceria, CeO2-δ, is a promising
method of hydrogen fuel production. The rate of hydrogen fuel production is determined by the rate of oxygen
transport through ceria. The objective of this project was to determine the kinetic parameters that govern oxygen
transport in doped and undoped ceria, namely the bulk oxygen diffusivity, DO, and the surface reaction constant,
kS. This was done through conductivity relaxation experiments. The conductivity of ceria is a function of the oxygen
non-stoichiometry, δ, which in turn is a function of the oxygen partial pressure, pO2, and temperature, T. Upon
imposing a small step change in pO2 at a constant temperature, ceria relaxes to a new equilibrium nonstoichiometry at a rate governed by DO and kS. This relaxation was tracked by measuring the electrical conductivity
over time. The kinetic parameters were then extracted by fitting the conductivity relaxation data to theoretical
equations. This conductivity relaxation method was also used to study the effect of dopants on oxygen transport in
zirconia-substituted ceria.
3
Measuring the Selectivity of Cell-Selective BONCAT
Lydia Atangcho
Mentors: David A. Tirrell and John D. Bagert
Characterizing a cell’s proteome, the set of proteins produced at any given time, is crucial for understanding
biological processes and the role of particular proteins in cell behavior. Members of the Tirrell lab have developed a
method called bioorthogonal noncanonical amino acid tagging (BONCAT) that focuses proteomic analysis onto the
subset of a cell’s newly synthesized proteins. In this approach, noncanonical amino acids (ncAAs) are pulsed into
cell culture and subsequently incorporated into natural cellular protein synthesis, labeling newly made proteins.
Cell-selective BONCAT expands upon this method and allows the labeling of proteins from a specific cell strain or
type in a mixture of cells. Target cells are manipulated to express a mutant aminoacyl tRNA synthetase which
allows only these cells to incorporate the ncAA azidonorleucine (ANL) into protein synthesis. Newly synthesized
proteins containing ANL can be ligated to chemical probes for visualization or affinity enrichment. Although cellselective BONCAT is well established, the extent of specificity has not been measured. In my research, I measure
the precise selectivity of cell-selective BONCAT which will determine the extent to which this method is applicable.
Improvement and Calibration of a Model for Seismic Noise Generated by Sediment Transport in Rivers
Sarun Atiganyanun
Mentor: Victor C. Tsai
Measuring seismic noise is a promising way to study sediment flux in rivers, and thus a simple physical model for
the seismic noise generated by sediment transport in rivers has been proposed. However, further improvement and
calibration must be made to the model before it can be used. The project has identified two methods of improving
and calibrating the model. One is to reconstruct the model, using fewer assumptions that were used originally. The
other one is to include a Love wave into the model where only a Rayleigh wave was included previously. Our
reconstruction which assumes homogeneity of the Earth's layers has shown that the contribution of the Rayleigh
wave to the seismic noise is less significant than it was previously predicted, while our incorporation of the Love
wave has shown that the Love wave's contribution is more significant than that of the Rayleigh wave by at least the
factor of three. These results suggest that further research should be pursued to compare experimental data with
our model to evaluate the model's validity and limitation.
Correlation of Psychophysiological Measurements and Neural Responses to Live Social Gaze
Vineet Augustine
Mentors: Ralph Adolphs and Laura Loesch
Hypothetically, representations of people – videos and pictures - elicit a different neural response than actual
people. In our experiment, we test such differences for live social gaze by using real people as stimuli. The
experimental design was a 2 (between-subject: ASD, matched neurotypical controls) by 2 (social realness: video or
real person) by 2 (gaze: direct or averted) factorial design with blocked trials of direct, averted, and closed gaze.
Several additional measures were collected during the functional magnetic resonance imaging (fMRI) experiment:
eye tracking, respiration, pulse oximetry and skin conductance response (SCR). This project investigates
differences in specific SCRs, a measure of autonomic arousal to gaze events, between the live and video conditions.
We hypothesize that SCRs evoked by real faces will be greater than those to videos, especially for open>closed
gaze trials. This analysis of SCR will subsequently give insight into correlated emotional reactivity to brain
responses in the different conditions. With time, the other measures of autonomic arousal available – heart rate,
respiration rate, and Pupil Dilation response – will be analysed for subsequent inclusion in the fMRI analysis. This
study is the first to examine how people neurally respond to other real people and how this might differ in
individuals with autism.
Inhibition of Joint Inflammation to Alter Progression of Posttraumatic Arthritis Following
Intra-Articular Fracture
Karsyn N. Bailey
Mentors: Steven Olson, Bridgette Furman, and Joel Burdick
Post-traumatic arthritis (PTA) is an accelerated form of arthritis that most commonly develops following fracture of
the articular surface of a joint. Following articular fracture, C57BL/6 mice showed significant signs of PTA, whereas
a different strain of mice, MRL/MpJ mice did not exhibit these signs, suggesting that pro-inflammatory cytokines
such as interleukin-1 (IL-1) and tumor necrosis factor-α (TNF-α) play a role in the pathogenesis of PTA. In this
study, male C57BL/6 mice were subjected to a closed intra-articular fracture of the tibial plateau and treated with
either IL-1 receptor antagonist (IL-1Ra) or soluble TNF receptor II (sTNFRII) via articular injection or systemic
injection. Mice that received a single articular injection of IL-1Ra demonstrated reduced cartilage degeneration
when compared to all other treatment groups except non-fractured controls. Paradoxically, systemic administration
of IL-1Ra or sTNFRII resulted in severe development of PTA. The reduction of arthritic changes in mice that were
locally administered IL-1Ra immediately following fracture suggests a critical role of intra-articular and synovial
inflammation in the development of PTA.
4
Automating Classification of CRTS Transients in Real Time Using Sparse Datasets
Alexander J. Ball
Mentors: S.G. Djorgovski and A.A. Mahabal
The recent growth in and future plans for time-domain astronomy—looking at celestial bodies that suddenly change
brightness—necessitates the development of systems that can automatically classify tens of objects a night now
and tens of thousands in the near future using sparse data. They also need to update this classification when
additional evidence is gathered. Using Catalina Real-Time Transient Survey and associated follow-up and archival
data, we have developed such a system. It combines a Bayesian classifier and a small decision tree to classify
objects currently into 12 types, including supernovae, cataclysmic variables, blazars, and active galactic nuclei. We
hope to incorporate this into the existing time-domain astronomy infrastructure and create a follow-up advising
system with which astronomers can more efficiently convert sparse data into knowledge about objects of interest.
Science Coverage Analysis of Small Orbiting Bodies
Susan M. Ballentine
Mentor: Bill Taber
Orbiting a small body is a challenging task for missing design and navigation teams. When designing a spacecraft
trajectory, an analyst needs to know if coverage meets science requirements. The goal of this project was to
develop a coverage analysis algorithm to be used in the next generation mission design and navigation software.
The first step was to uniformly distribute points on an ellipsoid, and then determine what types of measurements
are needed, how many times a site on a body will be in view, and what the probability is that a particular point or
set of points will be viewed under conditions of interest to scientists (e.g. illumination angles within some bounds,
suitable for stereographic use, etc).
Volatile Transport on Pluto
Sophianna Banholzer
Mentor: Bonnie Burrati
Previous measurements of Pluto’s lightcurve have given evidence of volatile transport of the dwarf planet’s
atmosphere. As the New Horizons Mission nears the date of closest approach, the need for accurate measurements
increases. Changes in the amplitude of the lightcurve and the color of Pluto indicate changes in the albedo and are
evidence for seasonal volatile transport. This project utilized data taken from several nights of observations over
the course of July and August 2012 on the 0.6 m telescope at Table Mountain Observatory and previous
measurements taken Dr. Michael Hicks in order to generate a lightcurve. The images were reduced using IRAF
software in order to calculate the magnitude for Pluto in the B, V, and R bands. These images were also used to
calculate the color of Pluto. While a lightcurve has not yet been calculated from the most recent observations,
based on previous data and the model of viewing geometry, a decrease in the amplitude of the lightcurve should
be visible.
Identification of Novae Events Within Messier 31 Through the Palomar Transient Factory Survey
William Bao
Mentors: Shri Kulkarni and Yi Cao
Classical novae events, known as CNe, are nuclear runaway on the surface of white dwarfs. They are triggered by
the accretion of material from companions in binary systems. The resulting explosions are transients that brighten
and fade in a timescale of days to months. Given the fact that novae are about 10,000 times fainter than
supernovae, we expect to see these events in very nearby galaxies. It is estimated that roughly 60 CNe happen
within the Andromeda Galaxy, known as Messier 31 (M31) each year but only a fraction of these are discovered
and recorded. Utilizing subtraction images of the night sky from the Palomar Transient Factory survey in
combination with Source Extractor, an astronomical image analysis tool, catalogs of possible variables in M31 were
compiled. Through a brute force approach, these generated catalogs will be compared with each other and other
known catalogs of M31 in order to minimize the number of false positives, such as variable stars and cosmic rays
as well as bad subtraction residues. The end result will be a catalog of possible candidates for undiscovered CNe.
The motivation is that with systematical search for CNe in M31, a more complete sample can be obtained, which
enables us to study their physics statistically.
Quantum Universal Solutions to the Yang-Baxter Equation
Aniruddha Bapat
Mentors: John Preskill and Gorjan Alagic
The Quantum Yang-Baxter Equation (QYBE) is the algebraic version of the Yang-Baxter relation, one of the
generating relations of the Braid Group. The aim of this project is to study unitary solutions to the constant QYBE
that are also universal as quantum gates. The braiding nature of these gates could allow for useful properties such
as circuit obfuscation. Two main directions were explored in this project: a search for unitary solutions to the QYBE
and, determining whether any known solutions are universal as quantum gates. Since braid representations are
5
naturally solutions to the QYBE, certain special representations such as the Fibonacci representation were also
investigated. An existing proof that the 4-by-4 solutions to the QYBE are not universal was generalized, when the
matrix in consideration is a permutation matrix with arbitrary phase factors. It was also shown that unitary
diagonal matrices are always solutions to the QYBE.
CHP to Verilog Conversion
Alex Barreiro
Mentor: Alain Martin
To describe circuits and chips, sometimes hardware description languages are used. This way you can send your
design to someone else easily and precisely. Caltech has made its own, CHP, and my research entitles making a
converter that will take in CHP code and convert it to a more well-known language, Verilog. CHP has some
advantages and disadvantages over Verilog, so this is reason to have both. CHP allows for higher level definitions
of circuits, it allows for abstractions that don’t have a physical equivalent. This can make some things much easier,
but CHP is not very widely used. Verilog, on the other hand is known very well.
Investigation of the Mechanism of Soot Deposition From Gaseous Polycyclic Aromatic Hydrocarbons
Andrew Bartlett
Mentor: Guillaume Blanquart
This investigation develops a thermodynamically consistent model that explains the deposition of solid soot
particles from the gaseous byproducts of combustive processes. Using the computational program Gaussian, we
have been able to determine the energy gap between the ground state and first excited state for a number of
aromatic hydrocarbons of varying conformations. This energy difference decreases with molecular mass for linear
polycyclic hydrocarbons; non-linear polycyclic aromatics exhibit the same general trend, but molecular
conformation appears to play a significant role in determining the energy barrier between the ground state and
excited state for these compounds. Further research will use this information to develop a model that accurately
describes soot formation from polycyclic aromatic hydrocarbons.
Secondary Eclipse Photometry of WASP-5b With Warm Spitzer
Nathaniel Baskin
Mentor: Heather Knutson
We present the photometry of the extrasolar planet WASP-5b at the 3.6 and 4.5 µm bands taken with the Spitzer
Space Telescope’s Infrared Array Camera as part of the extended warm mission. We measure secondary eclipse
depths of 0.273% ± 0.0278% and 0.240% ± 0.0241% in the first and second wavelengths, respectively, which is
best matched by the atmospheric models containing no temperature inversion. By comparing the observations to
such models, we gain insight into the planet’s atmospheric composition, as well as how well the planet redistributes
heat from its dayside to its nightside. Between the two wavelengths, we observed a mean offset from the predicted
center of eclipse of 0.100 ± 0.0298 hours, translating to an ecos value of 0.00402 ± 0.00120. A timing offset
greater than 3 could indicate a marginal orbital eccentricity, but it is difficult to draw a definitive conclusion with
the values obtained in this paper, so additional observations will be necessary.
Developing an Android Virtual Response Box
Jonathan Bayless
Mentors: Christof Koch, Uri Maoz, and Liad Mudrik
Response boxes are currently physical objects, made up of buttons, slides, pedals, etc., and thus fixed in their
functionality during an experiment. This is of particular burden when investigating the sense of agency in decisionmaking, where one could highly benefit from modifying the experimental environment online and in real time. I am
developing a virtual response box application for Android tablet devices, which will serve as a universal response
box. I have focused on determining how to program the device, using Java in Eclipse, to allow a simple, userfriendly way to construct a virtual response box or alter an existing one to conduct a new experiment. The
response box allows for practically any desired input from the participant, including a vast array of responses to the
subject in real time (e.g., buttons may appear and disappear, change their shape or form, appear pressed or
depressed). Besides integrating with the Koch lab real-time decision-prediction system, it will also enable new
types of experiments, currently impossible with real-world response boxes.
B-Stars Lonely No More: Conducting at Serendipitous Radial Velocity Survey of B-Stars With
Keck/HIRES
Juliette Becker
Mentor: John Johnson
Studies of the binary rate of stars (binarity) provide valuable information about the star formation process as well
as direct measurements of the physical properties of stars. For stars less massive or as massive as the Sun
(spectral types F through M), this binarity rate has been studied extensively, but this is not true for larger stars.
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Particularly, the binarity rate of B-type stars is currently largely unknown. Over the past fifteen years, B-type stars
have been used as calibrators for the California Planet Survey at Keck Observatory, their spectra being used for
calibration and then saved, unanalyzed. We are using these spectra to conduct a serendipitous radial velocity
survey of stars with spectral types ranging from A1 to B0. We will present our method of determining the precise
Doppler shifts of these rapidly rotating, massive stars and show some of our preliminary radial velocity time series.
Enumerative Properties of the G-Equivariant Hilbert Schemes of Points on Surface Quotient
Singularities
Dori Bejleri
Mentor: Tom Graber
We study the topological invariants of the G-equivariant Hilbert schemes of r points, Xr = Hilbr[ 2/G], on the
quotient of the plane by a cyclic group G of order n acting by the matrix diag(ζ,ζk) where ζ is an nth root of unity.
We define bi(r,k,n) to be the ith Betti number of Xr. We interpret the Betti numbers as certain partitions of rn with a
balanced condition and use the combinatorics of these partitions to prove several results about the topological
properties. The main result is that bi(r,k,n) is periodic in n with period k for large enough n. In particular, this
shows that the classes of these varieties in the Grothendieck ring of varieties are periodic in n for large enough n,
which was conjectured in a recent paper of Gusein-Zade, Luengo and Melle-Hernandez. We conjecture that
analogous statements should be true in higher dimensions and that this is a special case of some more general
periodicity phenomena in the Grothendieck ring.
Analysis of Amyloid Mechanical Properties via Ultrafast Electron Microscopy
Francesco Belfiore
Mentors: Ahmed Zewail and Anthony Fitzpatrick
Amyloid is a polypeptide structure formed as a result of protein misfolding and associated with several human
diseases, including Alzheimer’s and Parkinson’s. Its pathogenic mechanism is still not known, but is likely to be
related to its stiffness, considered to be higher than most other biological macromolecular assemblies. The Young’s
modulus of amyloid was calculated here using dynamical measurements in Ultrafast Electron Microscopy. Amyloidlike microcrystals have been imaged in transmission at nanosecond intervals after laser excitation. Plot of a stressstrain curve confirmed that the material was probed in the elastic linear regime. Scanning Electron Micrographs
were used to calculate the crystal dimensions. The Young’s modulus was inferred from the fundamental frequency
of oscillation and the calculated value (16GPa) agrees with previous experimental and theoretical work setting the
Young’s modulus of amyloid in the GPa range.
Studies of the Tribochemical Formation of Complex Organic Molecules by Aeolian Transport and
Electrification of Organic Particles in Contact With Water Ice in Titan's Dunes
Kerry Betz
Mentors: J.L. Beauchamp and Daniel Thomas
Titan is one of the few planetary bodies besides Earth that is known to exhibit rich organic chemistry, despite its
cold temperature of 98 K and its long distance from the sun. In Titan's longitudinal dune region, high winds are
hypothesized to carry grains of organic molecules, which undergo charging due to collisions with other particles.
Spark discharges can then initiate reactions that could potentially result in biologically important molecules.
Incorporation of oxygen from water ice known to be present on Titan is of particular interest. A quantitative
method of measuring the spark discharges in a system of windblown organic particles has been developed and
refined in order to characterize particle charging in the Titan environment. The effects of temperature and pressure
on detected spark discharges were determined. Using mass spectrometry, possible products of cold-temperature
reactions due to spark discharges were determined and analyzed.
Multi-Ligand, Multi-Receptor Signal Integration in Signaling Pathways
Bogdan Bintu
Mentors: Michael Elowitz and Yaron Antebi
Signal transduction pathways often use multiple types of ligands and receptors to activate the same downstream
signaling protein. Here, we systematically explore such networks and study new signaling mechanisms that cannot
be achieved by using only one ligand. First, we develop mathematical models for a system with two ligands and
one receptor, in which the ligands can have different biochemical properties such as affinity and efficiency. We find
that this system can generate a non-monotonic response function, which can be used in a context of two diffusible
ligands to generate a response in a distant ring around the source of the ligands. This result might have relevant
applications for cell patterning during development. In addition, we show how cells can employ this two-ligand
network to reduce the noise over a range of signal values.
Further extending our mathematical model to a system with two ligands and two receptors, we explain how
apparent synergetic or antagonistic outputs can appear, depending on the concentrations of the ligands, their
strength of interactions with the receptors, and the efficiency of signal transduction. We compare the predictions of
7
these theoretical models with experimental data from two specific signaling pathways in embryonic stem cells: the
interleukin-6 (IL-6) super-family and the bone morphogenetic protein (BMP) pathways. The interleukin pathway is
well described by a model with multiple ligands (CT-1 and LIF) and one receptor (LIFR), while the bone
morphogenetic protein pathway requires the more complex model with two ligands (BMP2 and BMP4) and two
receptors (BMPR1A and ACVR1A).
Molecular Pathways of Brain Irradiation Injury
Michelle E. Bobrow
Mentors: Robert J. Brown and Marianne Bronner
There are currently no available means of treating or preventing the long-term effects of therapeutic brain
irradiation, and the molecular mechanisms of such damage are not well characterized. This study determined the
effects of radiation on gene expression levels in the brain, in order to identify markers of irradiation injury. Fourweek-old mice were exposed to different levels of fractionated or single-dose cranial X-ray irradiation. At several
post-irradiation time points, slices of brain tissue containing the hippocampus were harvested from irradiated mice
and from age-matched, non-irradiated controls for extraction of total RNA. Reverse transcription of mRNA followed
by quantitative, real-time PCR with TaqMan probes was used to analyze the expression of 93 inflammation-related
genes, including VEGF, Tnf, Il-10, Il-9, and Il-9R. At 6 months following a single, 16-Gy dose of irradiation, there
was no change in VEGF expression as compared to controls, whereas Il-9 was upregulated. Interestingly, the proinflammatory cytokine Tnf and the anti-inflammatory cytokine Il-10 were both upregulated. This may indicate that
the balance of pro- and anti-inflammatory molecules in the brain shifts upward following irradiation.
Populating and Exploiting a Young Star Database
Ronnel Boettcher
Mentors: Lynne Hillenbrand and Nairn Baliber
Young stellar objects are stars in the early stages of their evolution. The study of these objects is important for
understanding the early stages of star formation, circumstellar disk evolution, as well as planet formation. Over the
years, ground and space-based telescopes such as the Spitzer Space Telescope, and the Siding Spring Observatory
(SSO) have provided surveys of young stellar objects and star-forming regions. Data from these surveys are
available in vast quantities online through sources like the SAO/NASA Astrophysics Data System (ADS), and the
NASA/IPAC Infrared Science Archive (IRSA). Astronomical data are presented in tables in data catalogues, and
embedded in scientific literature. While data in this form are publicly available online, searches of any particular
young stellar object or star-forming region requires exhaustive searches of multiple sources, hindering the
development of important discoveries. My mentors, Professor Lynne Hillenbrand and Postdoctoral Scholar Nairn
Baliber have created a relational database which will contain data from all nearby star-forming regions. My SURF
project this summer is to assist my mentors in populating the database with relevant young star data, performing
literature searches and cross-correlating those results with large surveys (2MASS and WISE).
Modeling Sub-Filter Scalar Variance in Variable Density Turbulence
Ethan Boroson
Mentor: Guillaume Blanquart
Variable density flows are crucial to increasing efficiency of combustion reactions. This project is focused chiefly on
simulating variable density turbulent flows and comparing to already established constant density turbulent
equations. This is performed through the use of spectra which relate the turbulent length scales to other values
such as velocity, dissipation rate, or the amount of scalar mixing. The main technique used is direct numerical
simulation, which solves the Navier-Stokes equations numerically based on inputs by the user. The project also
requires programs for the creation of spectra and flow visualization. The result of these simulations is a valid
method for analyzing variable density turbulent flows, namely using a forced scalar value and an equation for the
density of the fluid where density is inversely proportional to the sum of the scalar mixing quantity and the position
in the x-direction.
Analysis of Jupiter's Thermal Emissions
Kimberly A. Boydstun
Mentor: Glenn Orton
Over the last few years, substantial changes were observed in Jupiter's axisymmetric regions, such as the
emergence of hotspots at a wavelength sensitive to the depths of cloud tops. In order to understand these
changes, an understanding of all physical processes capable of underlying these transformations must be
developed. This is enabled by mid-infrared imaging of Jupiter from the past two decades at wavelengths sensitive
to temperatures, clouds and abundances of minor constituent gases. After undergoing absolute flux calibration,
images are analyzed using the NEMESIS algorithm [1] to retrieve atmospheric properties, which are then graphed
by adapted IDL programs. The time-variability deviates only slightly from results generated by NEMESIS for zonal
(longitudinal)-mean properties, bolstering confidence in the NEMESIS outputs. These results show the influence on
seasonal dependence of upper-tropospheric temperatures near the poles, despite Jupiter's very low axial tilt.
8
Although further work is needed to ensure the accuracy of the calibrated data, there exist variations of
temperature in time that are potentially correlated with changes in Jupiter's axisymmetric bands. Ultimately these
results will be added to an earlier study of the time variability of tropospheric temperatures [2] and the variability
of cloud and trace gases determined.
[1] Irwin et al. 2008. The NEMESIS planetary atmosphere radiative transfer and retrieval tool. J. Quant. Spectr.
Radiative Transf. 109, 1136.
[2] Orton et al. 1996. 1994. Thermal maps of Jupiter: Spatial organization and time dependence of tropospheric
temperatures, 1980 - 1993. Science 265, 625.
Making Flat Si Surfaces at the Tops of VLS-Grown Si Microwires for Enhanced Electronic Properties and
Monolithic Tandem Structure
Reuben Britto
Mentors: Nate Lewis and Shu Hu
Silicon microwires, grown from SiCl4 through the vapor-liquid-solid (VLS) process, have been shown to possess
high material quality, which enables solar cells to reach efficiencies that rival many wafer-based crystalline Si
technologies. The VLS growth process requires annealing copper catalysts patterned on silicon wafers at 1000 C
before introducing the Si precursor. Copper has a high diffusion coefficient even at room temperature, and it
readily mixes with silicon at this high temperature, forming a Si-Cu transition region at the top of the wire after
VLS-growth. This hundreds-of-nm, Si-Cu intermetallic region is difficult to remove with standard Si processing
techniques like RCA2 etches. This region may hinder wire performance by providing recombination sites for charge
carriers and thereby lowering carrier lifetimes and Internal Quantum Efficiencies (IQEs) of the wires. Here, we
examine a Reactive Ion Etching technique with the goal of fabricating a flat Si surface at the top of the wires. A flat
Si, Cu-free, surface would improve the material and therefore electronic properties of these wires as well as
provide epitaxial sites which open up the possibility of fabricating a monolithic tandem microwire structure.
Isolation of Organisms to Degrade Biopolymers
Julia Brown
Mentors: Richard Murray, Nate Glasser, Emzo de los Santos, and Gita Abadi
Biopolymers such as lignin, alginate, and polystyrene are ubiquitous, difficult to degrade, and a potential source of
biofuel production if a mechanism for efficient degradation can be established. The Caltech iGEM team is
developing a system, housed in E. coli, that is capable of degrading one or more of these compounds and
converting them into more useful products, such as substrates for biofuel synthesis. Using water samples from the
Caltech ponds as a source, we attempt to isolate a bacterium capable of degrading our compounds and determine
the gene(s) responsible for degradation. We hope to express this gene in E. coli in conjunction with
proteorhodopsin and an ethanol production pathway in order to form a biological circuit capable of efficiently
converting a persistent biopolymer into a more useful compound.
Dinickel Bisphenoxyiminato Complexes for the Study of Bimetallic Effects on Polymerization Activity
Aya Buckley
Mentors: Theodor Agapie and Madalyn Radlauer
The syn atropiosomer of previously reported dinickel catalysts with a p-terphenyl framework exhibited resistance to
the inhibiting effects of polar additives, which would poison most polymerization catalysts. Analogous complexes
with an m-terphenyl framework have been synthesized to study the effects of metal-metal distance and orientation
on polymerization behavior. The m-substituted terphenyl backbone was synthesized via Negishi coupling of
2-bromo-4-tert-butylmethoxymethylphenol and 1,3-dibromomesitylene, followed by orthoformylation, deprotection
of the phenol moieties, and imine condensation using 2,6-diisopropylaniline. The syn and anti atropisomers were
separated by flash column chromatography following the Negishi coupling. Deprotonation of the phenol moieties
and addition of two equivalents of NiClMe(PMe3)2 resulted in the desired bimetallic phenoxyiminato complexes. The
polymerization behavior of these complexes will be investigated and compared with those of the p-substituted
analogues.
Morphological Study of Ice Crystal Growth Dynamics
Nina Budaeva
Mentor: Kenneth Libbrecht
The morphologies and growth rates of ice crystals have been observed and documented using a novel experiment,
with the goal of investigating the overarching principles of the molecular dynamics of ice crystal growth. The
experimental set-up consists of two side-by-side temperature-regulated diffusion chambers. Thin ice needles, up to
several millimeters in length and a few microns in diameter, are grown in the first chamber off of a metal wire
through nucleation caused by the application of a high voltage. These “electric” needles are then transferred to the
second chamber with a controllable internal water vapor supersaturation level, and subsequent growth of the ice
9
crystals is observed. The crystal morphology is captured digitally via optical microscopy and is analyzed in the form
of time-stamped images. Varying the supersaturation and overall temperature affects the crystal morphology as
well as growth rate and yields insights into the basic physical principles governing crystal growth.
Synthesis of a More Sterically Stabilized Cyclodextrin Based Polymer to Increase the Efficacy of
Targeted, Systemically Administered siRNA Therapeutics via Cyclodextrin Based Polymer
Nanoparticles
Pallavi Bugga
Mentors: David Baltimore and Devdoot Majumdar
RNAi based therapeutics are an emerging and promising advancement in drug discovery and development, and
show greater capability and applicability in treating diseases that arise from all classes of molecular targets, for
which current conventional therapy agents are insufficient. A major challenge, however, of siRNA therapeutic
mechanisms, is their systemic administration to specific organs in which the target gene is expressed. A previous
finding in our lab showed that the targeted, systemic administration of siRNAs could be made possible by the use
of targeting ligands on a cyclodextrin polymer (CDP)-based nanoparticle system. This system has been thus far
successfully utilized for the treatment of solid tumors in phase II clinical trials, via RRM2 targeting siRNA and
human transferrin targeting ligands. However, we believe the efficacy of this system can be greatly improved by
increasing the mean elimination half life of the nanoparticles. In this proposed study, our primary goal was to
synthesize a more sterically stabilized cyclodextrin polymer-based nanoparticle, thus allowing for an increased
mean elimination half life, and prolonged administration of therapy in the body. To sterically stabilize CDP, we
copolymerized CDP with SPA (Succinimidyl Propionic Acid)-PEG-SPA, via amidification. When complexed with
RRM2 targeting siRNA, we found that our co-polymer did in fact show increased stability than the original polymer.
X-Ray Signatures of Low Frequency Disk Oscillation Around Black Holes
Iryna Butsky
Mentor: Dave Tsang
In this project, we explore different perturbations in accretion disks around black holes. We consider the effects of
different spins as well as different angles of observation. Using ray-tracing code, we create images of the disks as
well as their intensity plots and observe their dependence on the phase of a perturbation. As we perturb the disk,
we hope to detect a relationship between a corrugation mode and its respective intensity profile.
Detecting Primary piRNA Precursors in Mutant Drosophila Lines
Yi Cai
Mentors: Alexei Aravin and Evelyn Stuwe
Genomic information in the germline must be tightly regulated for accurate transmission to the next generation.
Piwi-interacting RNA (piRNA), a class of 23-30 nucleotide small RNA, function in germline cells through RNA
interference to silence retroelement activity and maintain genome integrity. Primary piRNAs are produced from
specific genomic loci, piRNA clusters, and are further amplified in a secondary amplification loop. The primary
piRNA production pathway is not yet clearly understood. Mature piRNAs have 5’-phosphate ends, which are likely
produced by an unknown nuclease. To investigate the molecular components of processing, the abundances of
partially processed piRNA transcripts in flies with mutations in known piRNA processing machinery were examined.
A 5’RACE PCR assay has been developed to identify cluster transcripts with 5’-phosphate ends, indicating partial
processing. This assay has been extended to create libraries of all piRNA precursor transcripts with 5’-phosphate
ends. Deep sequencing of libraries has been performed to determine cleavage sites of primary piRNA processing
and differences in processing between mutant and wild-type flies. This analysis will elucidate protein components
involved in 5’ processing of piRNAs, leading to an increased understanding of the hierarchical involvement of
factors involved in piRNA biogenesis.
Yaw Joint Analysis and Central Module Docking Design for the DuAxel Rover
Juan Diego Caporale
Mentors: Joel Burdick and Melissa Tanner
As more rovers are sent into space to land on planets, moons, and asteroids, we must continue to design new and
different technologies to achieve goals that are currently outside our reach. Many scientifically interesting locations
on the faces of Mars or some moons lie on steep or challenging terrain, and so extreme terrain rovers like Axel and
DuAxel have been developed get to and experiment on such locations. In this paper, we will examine ideas that
would increase the mobility and efficiency of DuAxel by introducing and testing several new mechanical systems
that would in turn increase the flight readiness level of the rover as a whole. More specifically, we will experiment
with a yaw joint test-bed design that allows for easy customizability, so that we may test different parameters of
its performance. Also, we have worked on designing and testing a docking mechanism that would allow both rovers
to dock and undock from the central module while carrying the weight of the central module and allowing for a roll
joint.
10
Discovering Analogues for Solar System Ices: Physical and Numerical Modeling of Highly Porous
Sintered Soda-Lime Glass Powder
Juan Cardenas
Mentors: José Andrade and Julie Castillo-Rogez
Ice agglomerates constitute a significant amount of the small bodies in our Solar System. We seek to understand
the behavior of these icy materials at a multi-scale spectrum to aid in the development of advanced sampling
methods for future in situ exploration of icy bodies, of particular interest are those in the region between the orbits
of Saturn and Jupiter. Ice is currently being developed and tested for these purposes, but it is expensive to
produce and test. This project seeks to find an inexpensive, high-fidelity ice simulant and utilize it for modeling
large-scale motion and mechanical properties. Soda-lime glass beads of 100-190 μm in diameter were sintered on
two different heating schedules and tested for bulk uniaxial compressive strength, wall friction, fatigue life. The
results were examined to develop a physical model for high porosity (~44%) sintered glass powder and the
resultant model was used to develop a discrete element method (DEM) simulation of the material. Sintered glass
powder exhibited several key properties of laboratory synthesized ice. Future investigation will be performed to
assess in greater detail the fidelity of the material as a simulant.
Methane Oxidation on a bis-bipyridine Ruthenium Complex for Commercial Fuel Cell Applications:
A Computational Electrochemical Study
Kurtis M. Carsch
Mentors: William A. Goddard III and Robert J. Nielsen
Efficient alkane oxidation in proton exchange membrane or alkaline fuel cells promises significant importance in a
global market in terms of resource utilization, petroleum independence, and environmentally benign technology.
Despite this strong motivation, precedent literature fails to identify an organometallic catalyst that overcomes the
challenges of C-H activation, CO bond formation, CO2 product formation, and the release of protons and electrons
at a single operating potential and pH with thermally accessible barriers. Density functional theory (B3LYP//M06)
was used to search for such an organometallic catalyst of the form Ru* ≡ (bpy)2Ru(Y)(L) [bpy = bidentate 2,2'bipyridine; (Y) ≡ =O, -OH, -OH2; (L) ≡ carbonyl, alkane derivatives (=CH2, -COH, …)] for complete methane
oxidation. Through a comprehensive analysis of various elementary sub-reactions, the controlled released of eight
electrons and protons via the lowest-free energy route from CH4 to CO2 is traced. These calculations incorporate
Poisson-Boltzmann continuum solvation to obtain the oxidation potentials and pKa’s of intermediates as well as
activation barriers for the liberation of incompletely oxidized products under alkaline reaction conditions. We find
an interesting C-H activation barrier of ~32 kcal/mol (under the current standard of ~35 kcal/mol), yet we similarly
find high-energy intermediate states that impede overall efficiency.
A MicroCT Analysis of Megaladapis edwardsi: A Giant Subfossil Lemur
Jen Caseres
Mentors: John Allman and Soyoung Park
The island of Madagascar provides a large isolated environment for organisms to evolve in, and many organisms
with novel adaptations arise there. This project focuses on the recently extinct Megaladapis edwardsi. Megaladapis
is interesting because it is exceptionally large (over 100 kilograms) and its development can be studied by
comparisons between well-preserved juvenile and adult specimens. The lifestyle and development of Megaladapis
can be examined through microCT scans. The paranasal sinuses are examined to determine whether Megaladapis
was aquatic or arboreal. The inner ear and cranial endocast will be reconstructed from the microCT scans. The
semicircular canals of the inner ear will be measured and compared to known measurements from other primates
to determine agility. The cranial endocast and the nerves visible on the endocast will be examined to determine
olfaction and visual acuity. The teeth of the juvenile will be examined to determine age by dental eruption. All
structur es examined will be compared between the adult and juvenile to study the development of Megaladapis as
compared with other primate species. 11
Synthesis and Reactivity Studies of Ni-Fe Models of CODH
Chung Sun Chan
Mentors: Theodor Agapie and Sibo Lin
The reduction of CO2 is of interest for solar fuel generation. Reversible interconversion between CO and CO2 is
catalysed by a metalloenzyme, carbon monoxide dehydrogenase (CODH), that displays an Fe-Ni active site. This
project aims to synthesize a well-defined organometallic complex that models the reactivity of CODH, by arranging
Ni and Fe centers in close proximity with a disphosphine-catechol pincer ligand to allow for cooperative activation
of CO2. Ni(COD)2 and[Fe(MeCN)3(Me3-TACN)]X2 (X = BPh4 or O3SCF3) were used as metallation reagents.
Characterization of these metallations by NMR, ESI-MS and UV-vis will be presented. Reactions of the resulting
complexes with H2O, CO and CO2 will be discussed.
The Differential Effects of Paracrine IL-2 Delivery by Artificial Antigen Presenting Cells (aAPCs) on
Naïve Versus Activated T Cells
Doreen C. Chan
Mentors: Tarek Fahmy, Fiona Sharp, and David Tirrell
T cells are critical for the clearance of pathogens in the human body, and stimulating the activation of a therapeutic
number of T cells can help treat diseases, such as cancer and HIV. A novel method for the generation of high
numbers of T cells is the use of artificial antigen presenting cells (aAPCs). Our aAPC system consists of a
biodegradable microparticle, which can encapsulate proteins and also present proteins on its surface. This allows us
to incorporate all three signals required for efficient T cell stimulation, which are: antigen presentation (Signal 1),
co-stimulatory molecules (Signal 2), and cytokine delivery (Signal 3). We focused on encapsulating interleukin-2
(IL-2), which is a canonical T cell growth factor, as Signal 3. The aAPC delivers IL-2 to T cells in a paracrine
manner, similar to how T cells are exposed to IL-2 in vivo. We initially sought to investigate the effects of the
paracrine delivery of IL-2 on naïve versus activated T cells. Our results show that naïve T cells proliferate more
robustly then activated cells when incubated with IL-2 encapsulating aAPC. However, both naïve and activated cells
secrete comparable levels of IFN-ϒ. As our aAPC degrades, it releases an initial burst of IL-2 within 24 hours before
it releases a slow steady amount of IL-2. We examined the importance of this burst on both naïve and activated
cells. These studies showed that the initial burst of IL-2 released by aAPCs is not essential for the proliferation and
activation of naïve or activated cells. Overall, our results demonstrate that naïve and activated cells respond
differently to paracrine delivery of IL-2.
Optimization of the Ultrasonic Vocalization Classifier to Analyze Mouse Vocalizations
Tracey Chan
Mentors: Paul H. Patterson and Natalia Malkova
Mice communicate using ultrasonic vocalizations (USVs), sounds with high frequencies that are inaudible to
humans, as pups during isolation from the mother, and as adults during social interactions with other adults.
Mouse USVs can be separated into ten distinct syllable types by time duration and frequency changes. We are
developing a Matlab-based program, USV Classifier, to efficiently classify syllables and analyze syllable sequences
of USV samples. This software will allow for greater understanding of mouse communication, especially syllable
preferences and syllable combinations in relation to age and various social settings. To validate the accuracy of
USV Classifier, I am comparing syllable distributions resulting from classifications done manually and automatically,
by USV Classifier, for five pup USV samples. Software performance is being improved by modifying source code
and user-set parameters. Certain syllable-detecting code functions are changed to reduce overall average
classification error to 18% and missed detection to 4% for the five samples analyzed. The optimal software will be
used to analyze USVs from male pups and adults in various social circumstances in order to study the role of USVs
in mouse communication in an autism mouse model that involves activation of the maternal immune system.
Improving the Electric Field Penetration and Focality of Spinal Cord Electrode Arrays via Manipulation
of Electrode Geometry and Configuration: A Modeling Study
Sevan Chanakian
Mentors: Joel W. Burdick and Jeffrey A. Edlund
It has been shown that people with spinal cord injury related paralysis can be treated with electric field stimulation
to the T11 to L1 region of their spinal cord, which controls primitive movements in the lower body, to allow mobility
in their previously immobile limbs. Currently, an electrode array developed by Medtronic for pain suppression is
used in human patients and an array composed of Parylene C and platinum developed by UCLA is used for rats. We
hope to use the voltage configuration and geometry of the platinum electrodes to improve the stimulation focality
of the arrays. Optimizing our ability to focus the electric field produced by the array would allow us to target
specific regions in the spinal cord and ultimately give the patient their lower body back. Using SolidWorks, six
models were developed for testing purposes. The effects of the electrode geometry and voltage configurations
where then simulated using a combination of COMSOL Multiphysics and Matlab. Preliminary examination of the
simulation data suggests that the electrode voltage configuration play a more curtail role in the focality of the array
than does the electrode geometry.
12
Inversion of Physical Model for Vegetation Remote Sensing
Krishnan Chander
Mentor: Marco Lavalle
The Unmanned Airborne Vehicle Synthetic Aperture Radar (UAVSAR) is an airborne radar developed at Jet
Propulsion Laboratory (JPL) that uses polarimetry and interferometry to make complex correlation measurements
of vegetation on the surface of Earth. Such measurements carry information about vegetation structure and
dynamic changes occurred in the time between the radar acquisitions. A physical model has been developed for the
complex correlation, and it has dependence on six parameters central to the vegetation. The model accounts for
two types of decorrelation: temporal, which is caused by changes over time, and volumetric, which depends on
spatial characteristics of the vegetation. The values of the model parameters are estimated from UAVSAR
correlation images through an inversion algorithm. We have tested different algorithms for the inversion that utilize
the gradient and the Hessian matrix of the cost function over numerical simulations. As we are interested primarily
in estimating the canopy height, we examine the results of the canopy height estimated with different methods
compared with the actual canopy height used to generate the numerical simulations.
Kinetics Studies of Thioester Hydrolysis to Guide the Development of a Reversible Binding System
Christine Chang
Mentors: Harry Gray and Paul Bracher
This project focuses on the measurement of rates of thioester hydrolysis catalyzed by various water-soluble metal
salts using 1H-NMR spectroscopy. We previously studied the exchange reaction of thioesters with thiols in the
context of a reversible covalent binding system. One method of cleaving bound molecules is the irreversible
hydrolysis of the thioester. S-methyl thioacetate, the model thioester selected for study, was observed to hydrolyze
in 30 mM lead acetate with pseudo-first-order kinetics (R2 = 0.95). An effective procedure for the removal of
paramagnetic metals from reaction solutions is under development to facilitate further NMR studies with Mn2+ and
other paramagnetic species. Additionally, the rate of thiol–thioester exchange for various thiols onto a thioesterfunctionalized surface will be quantified by measuring the displacement of fluorescent dye from the binding
substrate.
Mobility Simulation Software for Mars Science Laboratory Mission
Solomon Chang
Mentors: Jeng Yen and Brian Cooper
The Mars Science Laboratory (MSL) is a current robotic exploration rover being deployed to assess Mars
habitability. The Rover Sequencing and Visualization Program (RSVP) is an integral surface operations tool for MSL
that allows rover planners the unique ability of simultaneous visualization and sequencing of a command execution
list. The contribution of this project is a general framework in RSVP to support visual simulation of robotic
commands of current and future extra-planetary robotic missions. This framework enables the design and
evaluation of new robotics missions using a realistic simulation environment with a minimum development cycle.
One area of specific interest in this project is producing a high fidelity slip simulation model for the propagation of
the rover across arbitrary terrain specifications. A secondary area of concern is the development of an expeditious
mobility simulation model for significant mobility commands. As a result of these implementations, RSVP can now
be used as an end-to-end tool for supporting design, development, and operation of a surface vehicle in robotic
exploration missions.
Simulation and Design of the Dispersion-Engineered Traveling-Wave Kinetic Inductance Amplifier
Saptarshi Chaudhuri
Mentors: Kent Irwin, Jiansong Gao, and Jonas Zmuidzinas
Recently, Eom et al.1 demonstrated a new concept for a low-noise cryogenic amplifier known as a DispersionEngineered Traveling-Wave Kinetic Inductance (DTWKI) amplifier. This device makes use of the nonlinear kinetic
inductance of superconducting titanium nitride to achieve high gain bandwidth, excellent dynamic range, and
quantum-limited noise. However, because of the nonlinear origin of the device, the standard linear circuit theory
does not apply. In this work, we develop numerical tools based on finite-difference time-domain (FDTD) and
perturbative methods to solve the nonlinear circuit. We verify our numerical code on a few analytically-solvable
cases, such as shock wave formation on a uniform nonlinear transmission line and a linear transmission line with a
periodic perturbation in impedance. We use this tool to optimize amplifier design. Currently, a DTWKI device is
being fabricated; we will carry out measurements on this device.
1. Eom et al. A wideband, low-noise superconducting amplifier with high dynamic range. Nature Physics 8,
623-627 (2012).
13
Optimizing Cu2O-MgxZn1-xO Heterojunction Solar Cells
Jianchi Chen
Mentors: Harry Atwater and Samantha Wilson
In the photovoltaic (PV) industry, a less costly alternative photovoltaic material is needed for the further progress
of PV industry. Cu2O is a non-toxic, earth abundant material with a 2.1eV direct band gap and is well known as a
suitable photovoltaic material. Recent researches have implicated that ZnO-Cu2O devices is capable of efficiencyimprovement by tuning the electron affinity with different Mg composition. In this research we explore the optical
and electric characteristics of different ZnMgO thin films made by radio-frequency sputtering on fused silica
substrates based on the work in ZnMgO co-sputtering of Kang and Kim (2007). After learning enough about the
characteristics of the thin films, we made photovoltaic devices by sputtering ZnMgO alloy thin films onto Cu2O
substrates grown by tube furnace and explored their characteristics.
Nubots: A Study of Motion in Computation
Moya Chen
Mentors: Erik Winfree and Damien Woods
Over the past few years, DNA has shown itself to be an increasingly viable medium for modeling computation. In
the laboratory, researchers have already implemented instances of model of computation that are ultimately
capable of universal computation, with self-assembling DNA.
However, while previous forms of research have exploited the parallelizability of DNA, few have exploited DNA’s
ability to move, or reconfigure, as a way of manipulating information. In this project, we investigate the properties
of a particular model of computation, the Nubots model, which includes molecular motion as part of its
fundamental toolset. By using a computation complexity based approach, we analyze the power of Nubots
compared to more traditional, but also more stationary, models of computation like Boolean circuits and Turing
Machines.
While this project is entirely theory-based, future directions include implementing the Nubots model in DNA or
other molecules. Further research could also be done to investigate how the power of the model changes when we
restrict the model.
Alkylation of a Ligand to Enable Attachment to an Electrode Surface by “Click” Chemistry
Wen Min Chen
Mentors: Jonas Peters and Joseph Rheinhardt
Electrocatalysis is a promising method for hydrogen evolution. One family of cobalt-containing complexes shows
good catalytic activity in acidic water; however, the mechanism of H2 evolution of is unknown as diffusion allows
only bulk data gathering. A method of eliminating diffusion is to attach the complex to a non-reactive, wellcharacterized surface. Azide-alkyne Huisgen cycloaddition was chosen as the attachment method as it is
irreversible and quantitative. Consequently, our approach requires that the ligand be modified with an alkyne
group, and that the electrode surface be modified with azide-containing compounds. The propane bridge of the
ligand was chosen as the ligand modification site due to symmetry considerations (Fig. 1). Presently, an alkyne
group has been successfully attached to the ligand precursor, but the reaction is low-yielding. Optimization of the
alkylation reaction needs to be done to increase the yield of the ligand precursor in order for the synthesis of the
complex to proceed. Once this has been done, the mechanism of electrocatalytic activity of the complex can be
fully characterized, and the alkylation method can be applied to a series of related complexes.
Me
N
Me
OH2
N
2 ClO4-
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Molybdenum Complexes Supported by a Terphenyl Diphosphine Pincer Ligand
Christine Cheng
Mentors: Theodor Agapie and Emily Tsui
Molybdenum complexes have been known to catalyze the generation of H2 from water as well as the formation of
ammonia from dinitrogen. In this project, the coordination chemistry of molybdenum complexes supported by a
diphosphine p-terphenyl ligand is explored. Different molybdenum-arene binding modes were observed depending
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on metal oxidation state. A molybdenum(II)-acetonitrile species has been utilized as a precursor for the generation
of species displaying molybdenum-element multiple bonds. Reactions with azides and hydrides will be discussed.
The prepared complexes were characterized by a variety of techniques and their reactivity was investigated.
Developing Techniques to Search for Radio Emission From Hot Jupiter Planets
Lin Cheng
Mentors: Gregg Hallinan and Jake Hartman
The detection of radio emission from exoplanets will provide insights into the composition of planetary interior,
orbital parameters, and possibility of magetospheric shields for biosphere on the planets. However, no confirmed
detection has been reported in literature. Hot Jupiters are the ideal objects to search for radio emission due to their
Jovian mass and close proximity towards parent stars. We analyze data taken at Long Wavelength Array station 1
for Hot Jupiter Detection Experiment with 10-75MHz frequency coverage. We aim to increase sensitivity to 10 mJy
level, which is unprecedented at these frequencies. In particular, this project involves pipeline development for
radio frequency interference excision, bandpass calibration and deep integration to lower the noise level. As data
are continuously being taken at Long Wavelength Array, we expect to see emission signals from Hot Jupiter
HD189733b or at least derive model-constraining upper limits.
Investigating the Fiber-Resin Interface of Carbon-Fiber-Reinforced Polymer Composites With
Nanoscale Analysis
Puikei Cheng
Mentors: Julia Greer, Lucas Meza, Sid Pathak, and Karthik Ramachandran
A composite is a material composed of two or more distinct substances, designed to take advantage of the
properties of its constituents. In carbon-fiber-reinforced polymers, the fiber provides high stiffness and tensile
strength while the polymer provides flexibility and a stabilizing matrix. However, this valued combination of
properties occurs only when both substances behave as one—the bulk material should undergo cohesive failure
when strained. Failure by fiber-polymer interface debonding, or adhesive failure, greatly reduces strength.
Therefore, characterizing and improving adhesion between components is crucial. Theoretically, the extent of
bonding at the fiber-polymer interface can be estimated by determining the transition of material properties, such
as modulus and hardness, across the boundary. Previous work suggests that the more gradual the transition, the
better the bond. Nanoindentation, a method of calculating material properties from small indentations, allows for
determining those property changes across small distances. After polishing the fiber-polymer surface to a local RMS
roughness of <20nm, nanoindentation was performed on isolated carbon-fibers embedded in polymers epoxy and
PDCPD (provided by Materia Inc.). Furthermore, SEM images were used to distinguish between adhesive and
cohesive failure in bulk samples fractured in tension. Through nanoindentation, a zone of polymer hardening and
stiffening was found to extend roughly 1um from the fiber boundary in both samples. From SEM analysis, evidence
of adhesive failure was stronger in PDCPD than epoxy samples, though both modes of failure were detected.
Structural Studies of Mitotic Protein Complexes Using Electron Cryo-Tomography
Sarah Cheng
Mentors: Grant Jensen and Cora Woodward
The endosomal sorting complex required for transport (ESCRT-III) is a collection of proteins that facilitate
membrane remodeling events including abscission, the final membrane scission event of cytokinesis. In the
absence of ESCRT-III function, cytokinesis fails and mitotic abnormalities arise. ESCRT-III subunits are
biochemically and structurally well characterized, but the combined higher order complexes they form in vivo are
still undetermined. To advance our understanding of ESCRT-III macromolecular structures, we will use electron
cryo-tomography (ECT) to characterize ESCRT-III assemblies that form during cytokinesis. ECT is an imaging
technique that can provide 3D structural information for large macromolecular complexes captured in a near-native
frozen-hydrated state.
Synchronized cell cultures of Jurkat cells, an immortal human T-lymphoblastoid cell line have been produced. We
confirmed a ten-fold increase in the percentage of cells undergoing mitosis using flow cytometry and used
immunofluorescence to confirm the presence of mitotic structures. Cells have been cryo-preserved by highpressure freezing and will be cryo-sectioned for imaging by ECT. Our results may improve our understanding of
normal cell function and defective cell cycles in cancer or in neurodegenerative diseases.
The ulp-4 Gene Plays a Role in the Aging, Development, and Bioenergetics of Caenorhabditis elegans
Kaitlin Ching
Mentors: Paul Sternberg and Amir Sapir
Mitochondria play an essential role as the main energy source for a majority of cellular functions. As a result,
changes in mitochondrial proteins often create drastic changes in an organism’s overall health. These include
variation in activity level, recovery from stress conditions, development, and lifespan. Mitochondria produce ATP by
utilizing an electrochemical gradient across the inner membrane. The exact function of the mitochondrial protein
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ubiquitin-like protease 4 (ULP-4) is not understood, but expression of the ulp-4 gene is known to increase with age.
Here we show that depletion ulp-4 expression increases C. elegans lifespan. We also found that elevated
expression decreases lifespan, indicating that this is a biologically relevant correlation. A closer look indicated that
this may be due to how ULP-4 regulates mitochondrial membrane potential. Experiments testing other aspects of
mitochondrial function like oxygen consumption and ATP production were also initiated. These results support the
notion that mitochondria impact aging and suggest that ULP-4 affects lifespan due to its role in mitochondrial
function. Understanding the impacts of changing ulp-4 expression could help us figure out how ULP-4 behaves on a
molecular level. This, in turn could provide greater insight into the molecular regulation of the mitochondrial proton
gradient.
Synthetic Inspirations From Cancer-Curing Molecules: A Quest for a Disilylation Reaction and Building
Natural Product Analogs
Linda Chio
Mentors: Brian Stoltz, Jonathan Gordon, Doug Duquette, and Hosea Nelson
There are many examples in literature of both catalytic and enantioselective hydrosilylation reactions adding
silanes to unsaturated bonds. However, there are only a handful of disilylation reactions found in literature that
directly adds a disilane across an unsaturated bond, and all are inefficient or use hazardous reagents. The carbonsilicon bond formed by disilylation is difficult to make and very valuable for chemical syntheses. This project begins
an investigation for an enantioselective catalytic disilylation reaction using transition metal catalysis. The
inspiration for this project was a completed natural product synthesis by the Stoltz group that would be made more
efficient with the discovery of a selective disilylation reaction. Alongside this project, we have been building a
library of analogs of an anti-austerity molecule, (+)-Grandifloracin, that inhibits the growth of cancer cells in
nutrient poor conditions. Using periodate oxidation, a variety of starting substrates, and epoxide opening methods
we hope to make many analogs of this natural product for biological evaluation. From cancer-curing molecules, we
have obtained inspiration to create methods and products that could become useful in chemistry, biology, and
medicine.
Adhesion Measurement of Vesicles by Aspiration
Rohit Chouksey
Mentors: Guruswami Ravichandran and Jacob Notbohm
In biology, cell adhesion is related to processes such as growth, migration, and wound healing. Vesicles, composed
of lipid bilayers, serve as a nice model for the study of cell adhesion. The objectives of this work were to
understand the vesicle adhesion mechanics, specifically how different energies play a role in vesicle adhesion.
Vesicles were formed by the electro-formation method and they were aspirated into the micropipette by varying
the pressure. Vesicle adhesion was studied by aspirating them into a glass micropipette. The projected length of
the vesicles inside the micropipette was found to increase when pressure was increased. When the pressure was
increased further, the projection length decreased. Also, the area of vesicle increased initially then it decreased
which was not expected according to a recently developed theory. It can be concluded that the suction length may
increase/decrease depending upon the interaction of the stretching energy, surface energy, adhesion energy and
pressure potential.
Characterization of Thermal Oscillations in Saturn’s Atmosphere
John R. Christian
Mentor: Glenn Orton
Ground-based images of thermal emission on Saturn are useful in examining the response of the atmosphere to
external radiative effects. Variations in emission at different wavelengths ranging from 4.9 to 24.5 microns are
used to track periodic effects in stratospheric and tropospheric oscillations. Two forms of periodic behavior have
been characterized in Saturn’s atmosphere. The average temperature at each latitude and wavelength undergoes a
sinusoidal oscillation over time. At each wavelength, the peak oscillation amplitude was 5-9 Kelvins, occurring at
planetographic latitudes south of 60° S. All oscillations shared a period of 15 years, roughly half of Saturn’s orbital
period, and were out of phase by less than 3 years. The average values of each oscillation peaked at 20° S, with a
significant drop in the northern hemisphere, which was in the shadow of Saturn’s rings during the study period. A
second form of periodic behavior is a periodic change in temperature with respect to longitude at a single latitude
on the planet at a single epoch. These periodic effects were studied to determine how their amplitude, period, and
phase change in time. Changes in these properties may be related to seasonal effects or be caused by orbital
eccentricities.
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Search for R-Parity Violation Phenomenon at the Large Hadron Collider Using Razor Variables at
√
Sung Bong Chun
Mentor: Maria Spiropulu
R is an additive quantum number, whose parity is odd for supersymmetric (SUSY) particles and is even for
Standard Model (SM) particles. R-parity conserved SUSY thus stabilizes the Lightest Supersymmetric Particle (LSP),
but adding a small R-Parity Violation (RPV) term to SUSY Lagrangian also respects the observed phenomenology in
the Minimum Supersymmetric Standard Model (MSSM). In this project, the third generation RPV decay of the LSP
respecting Minimum Flavor Violation (MFV) SUSY is studied at the Large Hadron Collider (LHC) at CERN, which is
now operating at the unprecedentedly high energy level of √s 8TeV. One possible such decay includes four b(anti)quarks, two leptons, and two neutrinos in its final state. Due to the two neutrinos which are invisible in the
detector, the Razor variables were used to estimate the mass scale of the LSP. SM Monte Carlo data samples were
used to optimize a set of event selection criteria, which were then applied to the real data at √s 8TeV. In search
of a signal, the signal region (at least two loose b-tags in the event) distribution was template fitted using the
shape of the control region (only one loose b-tag in the event) distribution.
Developing an Immersive 3D Data Visualization Engine
Alexandru Cioc
Mentor: George Djorgovski
As both data and ideas become increasingly complex, they become more difficult to represent. As a result, the field
of data visualization is ever evolving. The scope of this project is to devise a new multi-user immersive world using
the popular Unity 3D Game Engine that can be used to visualize data in a simple, intuitive, manner given a data
set with a number of parameters. By learning C#, Java, and the Unity Scripting Language, a working application
was devised. Rather than merely plotting points, the application creates objects of various shapes, colors, sizes,
and also contains a parameter for more information on the point (an interactive link which creates a web browser
within the 3D world). Evolving from a simple plotter to a complex application that features such abilities as rapidly
hiding points of a specific parameter for better viewing, loading multiple CSV files, and interacting with data in
immersive ways, the application has been a success. It can be concluded that the Unity Engine is worthwhile in the
development of data visualization software and is capable of handing hundreds of thousands of data points with
ease. Further work can be done to improve the current application and more efficient programming methods could
be implemented should they be found necessary.
Global Analysis of Neutrino Results Sensitive to θ13, δ, and the Mass Hierarchy
Benjamin Clark
Mentor: Ryan Patterson
I detail the progress made in building a computational framework to combine the results from multiple neutrino
experiments in order to produce confidence intervals based upon all of the available data. At present, I have
modeled the RENO, Daya Bay, DCHOOZ, and MINOS experiments and am able to both generate simulated data
and calculate the χ2 function. I present these intermediate results at this time. I also suggest how this work can be
continued in the future taking into account the recent accurate measurements of θ13.
Optimizing Thermoelectric Efficiency of La3-xTe4 With Barium Substitution
Samantha M. Clarke
Mentors: Sabah K. Bux, Jean-Pierre Fleurial, James M. Ma, Richard B. Kaner, C.-K. Huang, Paul von Allmen, and
Trinh Vo
La3-xTe4 is a high temperature n-type thermoelectric material with maximum zT~1.4 at 1273 K. This system is a
defect structure and the number of La vacancies can vary between 1/3≥x≥0. Previously the carrier concentration
had been optimized through controlling the Te:La ratio. Efforts in the past have shown that controllable doping can
be also be achieve through non-isoelectronic substitutions of the La atoms with rare earth X2+ metals.
Computational modeling suggests the La atoms play a crucial role in defining the density of states for La3-xTe4 and
substitutions could play a crucial role in increasing the power factor of this material. The effects of doping with
barium metal, vacancy versus fully filled structures, and varying carrier concentration are explored. High purity,
oxygen-free samples are produced by ball milling and spark plasma sintering. Powder XRD and electron microprobe
analysis are used to characterize the material. High temperature thermoelectric properties are reported and
compared with baseline La3-xTe4 compositions.
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Passivation of III-V Based High Efficiency Solar Cells Using Trioctylphosphine Sulfide and Related
Surfactants
Bridget Connor
Mentors: Harry Atwater and Carissa Eisler
Small, high efficiency solar cells have the potential to increase the influence and flexibility of solar energy, but one
remaining challenge lies in preventing excited carriers from recombining at surface defects on the edges of the cell.
Passivation techniques for these sidewall facets have been explored very little, since the sidewalls are an
insignificant fraction of the total surface area in larger cells. This study explored Trioctlyphosphine Sulfide (TOP:S)
and Trioctlyphosphine Selenide (TOP:Se) as passivants of GaAs and other III-V semiconductors used in high
efficiency solar cells. The III-V semiconductors were treated in TOP:S or TOP:Se and then characterized using
photoluminescence, x-ray photoelectron spectroscopy, and dark and light IV curves generated on a solar simulator.
While TOP:Se improves the performance of small GaAs cells, the data suggest that its passivating properties are
inferior to those of TOP:S since it does not interact as strongly with the surface. It is expected that the superior
passivation of TOP:S relative to TOP:Se will also be observed in other Gallium containing III-V materials.
Using the Contemporary Model Bacterium Rhodopseudomonas palustris to Gain New Insights Into the
Evolution of Biological Membranes
Elise S. Cowley
Mentors: Dianne K. Newman and Cajetan Neubauer
The Earth’s rock record shows traces of ancient life from as far back as 3.8 billion years in the form of molecular
fossils. Lipids are the most stable of the molecular fossils and can be found throughout the geological record.
Among lipid biomarkers, eukaryotic sterols and their bacterial counterparts, hopanoids, have been used to
reconstruct critical events in Earth’s history. Whether these interpretations are accurate stands to question. Here
we use the metabolically versatile bacterium Rhodopseudomonas palustris to explore the biological function of
hopanoids. Hopanoids are beneficial to R. palustris, but not essential to the membrane allowing mutants to survive.
This permitted systematic analysis of the overall lipid composition of two hopanoid mutants. As a complementary
approach to gain insight into the physiological role of hopanoids, we constructed a genomic library with the aim of
identifying genes in R. palustris that compensate for the lack of specific hopanoids. In my talk, I will discuss how
these approaches are helping us understand modern hopanoid functions and how this understanding can refine our
interpretation of their fossil relatives.
Conditions on the Development of an Equilibrium Solution to a Two Body Mutualistic System: An
Analytic Approach
Oliver Curtiss
Mentors: Josh Tasoff and Colin Camerer
Interspecies mutualism, the way two organisms of different species biologically interact in a relationship in which
each individual derives a fitness benefit, is an important problem in economics and evolution. In attempting to
understand mutualistic relationships, a wide variety of models have been applied: game theoretic, populationdynamics, and biological market models. In this project, we hope to find solutions to the conditions which allow for
the development of interspecies mutualisms in spatially separated ecosystems. By analyzing theoretical
descriptions of the dynamics of mutualisms, a steady state equilibrium solution can be found and then analyzed to
find conditions on the parameters governing the interspecies interactions. These constraints will allow for
experiments to be designed using appropriate biologically engineered bacteria to further study mutualism in a
market model.
The History and Philosophy of Exoplanetary Science
Lorinda Dajose
Mentors: John Johnson and Jon Swift
The existence of other worlds has been postulated for centuries, from the time of the Greeks, through the Scientific
Revolution, and into the modern era in which these speculations have been verified as fact by the discovery of
hundreds of exoplanets. This project traces the evolving visions of prominent scientists and philosophers
throughout the development of exoplanetary science with a narrative based on biographical introspects, revealing
broader societal impacts. In addition to this philosophical examination, we map out the physics, observational
challenges, and historical origins of current exoplanet detection techniques, creating a historical timeline of this
field. In order to come to a deeper understanding of scientific progress, we uncover the origins of the seminal ideas
that catalyzed our modern philosophies on the universe through the stories of visionaries.
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Correlation of Blazar Variability at Optical, Radio, and Gamma-Ray Wavelengths
Radmila Dančíková
Mentors: Tony Readhead and Talvikki Hovatta
Blazars are active galactic nuclei whose relativistic jets are pointed in the direction of the Earth. There are still
many open questions about the internal structure of the jets and how the emission regions at different wavelengths
are connected. Using data from the 40-meter telescope at the Owens Valley Radio Observatory (OVRO) and the
Palomar Transient Factory (PTF) survey, observations of a large number of blazars at radio and optical wavelengths
were correlated, to determine if and how the relationship between radio and optical data for a source differed
across the 601 blazars studied. While individual blazars have previously been studied and compared at different
wavelengths, the surveys carried out by both the 40-meter and the PTF have provided observations at both
frequencies for a larger number of blazars. The modulation indices of the corresponding OVRO and PTF sources
were compared. These results will be used to further study differences between gamma-ray bright and faint
sources, as well as other differing classes of blazars.
The Effects of Phylogenetic Diversity on Temporal Stability of Community Biomass
Poonim Daya
Mentors: Lin Jiang and Victoria Orphan
Much work has been done to answer the question of biodiversity’s effect on the functionality of an ecosystem. The
objective of this study is to investigate whether phylogenetic diversity has an effect on overall community stability,
using bacterivorous protists as model organisms. To this end, I constructed 2- or 3-species protist communities
that differed in phylogenetic diversity, subjected them to a short-term disturbance of high temperature stress at
weekly intervals, and followed community dynamics over time. There have been indications of some trend between
phylogenetic diversity and community biomass temporal stability, but none that are statistically significant.
Significant differences in temporal stability occurred at the population level. These results suggest that there may
be other factors, such as community assembly history and predator-prey interactions, that affect the stability of a
community.
Examining the Energy Absorbance of Cosmic Rays of the SPIDER Bolometers Using Sulfur-35
Maxwell G. De Jong
Mentors: James Bock and Jeff Filippini
The Planck spiderweb bolometer arrays absorbed more energy from cosmic rays than expected from pre-flight
models, resulting in significant data loss due to glitch rate. This research is the first investigation into the effects of
cosmic rays on the antenna-coupled TES (Transition Edge Sensor) bolometer arrays and SQUID multiplexer
summing architecture employed by SPIDER, a balloon-borne CMB polarimeter. Energy deposition from cosmic rays
was simulated with beta particles emitted from sulfur-35. Computer simulations run with different geometries and
activities allowed optimization of the experimental parameters. The energy spikes from beta particles hitting
bolometer islands and their subsequent decays were measured during the experiment. Further data analysis will
allow a better understanding of the decay constant inherent in the electronics and the cross-talk interference
between channels in the SQUID multiplexer. A nanopositioning mechanical scanner was also developed to precisely
characterize different particle channels in a later test.
Gene Circuit Interference in Multiple Plasmid Layouts
Paulo Roberto de Souza Motta
Mentors: Richard M. Murray and Enoch Yeung
The development of increasingly complex artificial gene networks is parallel to the advancement of our
understanding of gene regulatory mechanisms. On one hand, there is an obvious need for predictive models to aid
in network design; on the other, exploring synthetic gene circuits can lead us to recognize our incomplete
knowledge about specific features and to develop both theoretical models and experimental approaches to fill those
gaps. This project focus on interference arising in plasmids due to different combinations of relative gene
orientation and gene location for two genes coding fluorescent reporter proteins, aiming at the quantification of
gene expression distributions for each design. For this goal, 9 different plasmids were designed, representing all
combinations of the three possible gene relative orientations, convergent, divergent or tandem, and three different
possible spacing sequences in between. Subsequent investigations include mathematical modeling of those circuits,
having the potential to generate applications in automatic gene annotation and computer aided gene circuit design.
Concurrently, those models might point out limitations in widely used modeling assumptions that ignore diffusion
times, cell structure and DNA topology.
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Inducing 3D Parallax Vision Using the Microsoft Kinect
Connor DeFanti
Mentors: Mathieu Desbrun and Paul Upchurch
The Microsoft Kinect is a camera that uses a combination of color maps and infrared depth maps to generate 3D
data of its environment. This data leads to useful tools such as facetracking and skeletal tracking algorithms. We
can use these algorithms to predict and estimate the user's head position, and modify the projection matrix of a 3D
scene to reproduce the user’s field of view. We further increase the accuracy of the program by using smoothing
algorithms like Burg’s Algorithm to reduce noise. With accurate enough estimations, the program can induce
parallax vision for the user, effectively allowing the user to perceive 3D without use of specialized screens or
glasses.
Spectroscopic Analysis of Young Stars in the Sigma and Lambda Ori Clusters Observed With the
Palomar Double Spectrograph
Daniel DeFelippis
Mentor: Lynne Hillenbrand
Studying circumstellar disks is essential in comprehending planet formation. However, disk evolution is not very
well understood because previous sky surveys including Spitzer have primarily studied accreting stars found in
molecular clouds, and these stars are almost all less than three million years old. The 2009 WISE explorer mission
has helped by using four infrared filters to map the entire sky, whereas Spitzer had a narrow field of view,
providing many more potential accreting stars to study. Two particular regions of interest mapped by WISE are σ
and λ Ori, star clusters several degrees in diameter that are between three and eight million years old, a rare age
for such clusters. By using both WISE and 2MASS data, stars in these clusters were identified as having an infrared
excess, indicating circumstellar gas and dust, and then observed in December 2011 with the Palomar double
spectrograph. This summer, the images were reduced using the computer program IRAF which performed bias
subtraction, flatfield division, spectra extraction, and wavelength and flux calibration, resulting in one-dimensional
spectra for all identified objects. By measuring emission and absorption lines and comparing each spectrum with
other standards, the objects were verified as young stars and then classified.
The Dyson-Schwinger Equations in the Theory of Computation
Colleen Delaney
Mentor: Matilde Marcolli
The Hopf algebra that gives an elegant structure to the renormalization methods of quantum field theory can also
be used to formulate the Dyson-Schwinger equations, the quantum equations of motion. In recent work by Manin,
a similar Hopf-algebraic renormalization scheme was applied to the theory of computation in order to approach the
halting problem of computer science. Using the computation Hopf algebra of flowcharts, we have investigated the
Dyson-Schwinger equation and its solutions, providing an interpretation of its role in the theory of computation.
Understanding the algebraic and categorical connections between physics and computation may have applications
to subjects such as quantum gravity and quantum computation.
Modeling Scalar Variance in Turbulent Mixing Layers
Charles Demay
Mentor: Guillaume Blanquart
The scalar variance plays a crucial role in predicting turbulent combustion. An effective method to simulate those
turbulent flows is given by Large Eddy Simulation (LES) which requires the subfilter scalar variance to be modeled.
Models have been tested for simple, isotropic, homogeneous turbulence but that is not the type of flows we find in
turbulent jet flames. A more relevant, realistic flow is the turbulent mixing layer (or shear layer). In contrary to
isotropic turbulence, it is characterized by a mean scalar gradient. At this point, it is unclear if models developed
for isotropic turbulence remain valid for mixing layers. Using data from a Direct Numerical Simulation (DNS), these
models have been tested in the present study. This a-priori analysis has been performed in Fourier space to ensure
accurate evaluation of all derivatives and sub-filtered quantities. Finally, a methodology to account for the mean
scalar gradient is proposed for the simulation of mixing layers.
The Role of FGF Signaling on Cell Adhesion During Migration of Caudal Visceral Mesoderm in Drosophila
Development
Neal Desai
Mentors: Angelike Stathopoulos and Snehalata Kadam
Cell migration plays a crucial role during embryonic development of Drosophila required for organ formation. We
hypothesize that the FGF signaling pathway guides caudal visceral mesoderm (CVM) cell migration in the embryo
by regulating cells’ adhesivity. CVM cell migration is required for specification of longitudinal visceral muscles that
ensheath the gut. CVM cell migration is also the longest in all of Drosophila embryogenesis, and yet little
information is known about how cells accomplish their migration. Preliminary studies in the lab have suggested that
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the level of FGF signaling dictates whether the signaling pathway activation supports changes in cell adhesion
(when levels are greater) or chemoattraction (when levels are weaker). Fluorescent in situ hybridization using
riboprobes to detect transcripts and antibody stainings to detect protein localization were performed in various
mutant backgrounds. Genes of study were selected based on previous data suggesting a role in FGF signaling
and/or cell adhesion. The localization of transcripts/proteins in FGF mutant backgrounds will be examined, with the
aim that this study will provide insight into how specific genes of interest interact in this pathway to regulate CVM
migration. By studying spatio-temporal expression of genes of interest in CVM cells during the course of migration,
one can observe to what extent differential gene expression is an important factor for cell migration during
development.
Centralized and Decentralized Markets: An Experimental Study of Endogenous Market Choices
Wesley DeVoll
Mentor: John Ledyard
Many commodities are traded through auctions, ranging from simple consumer goods traded in online
marketplaces like eBay or Amazon to fishing permits in areas controlled by Cap and Trade programs. We
considered the performance of “centralized” markets operating simultaneously with a private market, in order to
analyze subjects’ choices of trading institutions when two competing exchange mechanisms exist. We considered
two centralized market designs: a continuous double auction and a sealed-bid call market. The data shows that
traders overwhelmingly chose the continuous double auction over private markets, but conversely preferred just as
strongly the private markets to the sealed-bid call market, despite the fact that call markets and private markets
displayed comparable efficiency.
Determining Seismic Properties of Iron Oxide at High-Pressures: Implications for Earth’s Core-Mantle
Boundary
Matthew Diamond
Mentors: Jennifer Jackson and June Ki Wicks
Previous research has indicated iron-rich (Mg,Fe)O may be present near the base of Earth’s mantle. This section of
the mantle, called D’’, is the lowest most 350 kilometers of the mantle above the liquid outer core, where the
pressure and temperature correspond to 115-135 GPa and approximately 3300-4300 K. The core mantle boundary
features several mineral phases, mainly silicate perovskite, postperovskite, and (Mg,Fe)O. Recent studies have
shown that iron will preferentially partition into (Mg,Fe)O in the presence of perovskite and posperovskite. The fact
that (Mg,Fe)O has enhanced stability and a high density also indicate the likelihood of its existence near Earth’s
core-mantle boundary. The first goal of this project is to construct an accurate equation of state for the Fe end
member of (Fe,Mg)O, namely wüstite or FeO, up to 90 GPa. We are interpreting data from powder x-ray diffraction
(XRD) experiments that were conducted using a diamond-anvil cell at the Advanced Light Source at Lawrence
Berkeley National Laboratory, California. The sample was loaded with neon as a pressure medium and ruby as a
pressure marker. By observing the 2-theta values of the x-ray reflections of the FeO sample, we can derive the
volume of the sample for each pressure. Precise pressures have been determined by analyzing ruby fluorescence
and in-situ neon volumes. We will use the relation between pressure, volume, and temperature to determine the
actual density of this material at core-mantle boundary conditions. From our equation of state we will determine
the bulk seimic velocity of FeO. Our results will be critical for understanding bulk seismic velocity determinations at
the core-mantle boundary region.
The Development of Matlab Algorithms to Segment and Analyze Fluorescent and NanoSIMS Images and
the Spatial Localization of Bacteria in CF Sputum and Lung Samples Using FISH
Michael Dieterle
Mentors: Dianne K. Newman, David M. Doughty, and Sebastian Kopf
I. Matlab – Hopanoid Project
Hopanoids are triterpenoid lipids that are structurally very similar to sterols, their proposed eukaryotic
counterparts. Fossils of triterpenoid lipids called hopanes are preserved in ancient rocks, some of which are as old
as 2.7 billion years. Hopanoids are produced by both aerobic and anaerobic bacteria, such as Rhodopseudomonas
palustris, and are incorporated into the outer membrane of the cells. While the role of these lipids is not fully
understood, there are indications that they may play a role in asymmetrical cell division, membrane permeability
and stability, and protection of the cells under stress. The intercellular localization of hopanoids was explored by
detecting the localization of deuterium labeled hopanoids by Nano-scale Secondary Ion Mass Spectrometry
(NanoSIMS). In order to process the large amount of information obtained using this technique, a Matlab program
with a graphic user interface was created to identify individual cells, segment them, and compress the information
of the deuterium labeled hopanoids into a usable and robust statistical measurement. The successful results from
preliminary testing indicate that analysis of localization information utilizing this program will permit statistically
accurate localization of deuterium labeled hopanoids in R. palustris to potentially the nanometer scale, which will
significantly improve understanding of the layout and function of hopanoids in the cell membrane.
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II. FISH – CF Project
Cystic Fibrosis (CF) patients are susceptible to lung infections caused by a variety of pathogenic bacteria, such as
Pseudomonas aeruginosa. CF patients can become infected with multiple bacteria at the same time, resulting in
diverse microbial communities inside of the lungs. Little is known about the localization of the different bacteria in
these communities and the relative metabolic activity of bacteria in parts of the communities. The main limitation
in identifying and analyzing the location of different microbes in CF patients’ sputum and lung samples is that
current techniques require the disruption of the 3D structure of the samples. In order to reconstruct the 3D
structure of the specimens during the process of identifying microbes in the samples, Fluorescence In Situ
Hybridization (FISH) probes were used to identify the different microbes in cryo thin sections of the sputum
samples collected from CF patients at the Children's Hospital Los Angeles (CHLA). Probes were designed for
Pseudomonas aeruginosa, Staphylococcus aureus and Stenotrophomonas maltophilia, each with a different and
unique combination of fluorophores that allow the probes to be used simultaneously. If sequential thin sections can
be analyzed using probes that identify multiple bacteria species, then the structure and location of each individual
microbe species can be reconstructed into a 3D model of the sputum or lung sample. Ideally, the same sections
can then be analyzed using the Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) that will indicate the
relative metabolic activity of each microbe in the sample. This information can then be represented in the 3D model
of the sample to identify each microbe type and the microbe’s relative activity in the specimen. This model may
allow the identification of significant metabolic activity rates that depend on the interactions of particular microbes
in close proximity. These techniques will be used to analyze and ultimately generate a 3D model of the bacterial
communities in actual lung samples of CF patients obtained from CHLA.
Conservation of Craniofacial Patterning in Lampreys
Monisha Dilip
Mentors: Marianne Bronner and Stephen Green
Comparisons between the jawless vertebrates, such as the sea lamprey (Petromyzon marinus), and jawed
vertebrates can infer when particular evolutionary traits were gained. In this project, we wanted to determine when
certain aspects of craniofacial patterning, such as blood, ganglion, and immune system development, arose in
vertebrate evolution. In order to determine when blood specification occurs, we performed whole mount in situ
hybridization for blood and immune system genes, including Scl, FoxN, and FLK. Similar to development in frog,
results suggest that lampreys have a primitive wave of blood formation after gastrulation, with the expression of
FLK, followed by a definitive wave of blood formation characterized by Scl expression. Additionally, FoxN is
expressed at later stages in the notochord and the typhlosole, suggesting a role in development of the immune
system. Phox2b is another gene that plays a large role in the craniofacial development of the lamprey. We injected
a conserved regulatory element for the chicken transcription factor Phox2b and saw that regulatory element drove
GFP expression in the cranial nerves IX and X, suggesting that Phox2b regulation is conserved across vertebrates.
These data suggest that much of vertebrate patterning is conserved across jawless and jawed vertebrates.
Single Cell Functional Proteomics Analysis of Effector Immune Cells for Understanding Mechanisms
Involved in Inflammatory Bowel Disease and Stem Cell Biology
Race DiLoreto
Mentors: James R. Heath and Chao Ma
In response to infection or tissue dysfunction, immune cells develop into highly hterogenous populations with
diverse functions. Identifying these functions requires analysis of many effector proteins from single cells. We used
a single-cell functional proteomic microchip platform and a multiplexed ELISA assay to investigate two systems of
immune development. (1) Natural Killer (NK) cells can play a protective role in chronic inflammation, regulating
disease-contributing tissue and protecting host tissues. The Killer Immunoglobulin-like Receptor (KIR) expressed
by some NK cells has been identified as a risk factor for Inflammatory Bowel Disease (IBD), suggesting malfunction
of the NK cells. We compared the functional behavior of NK cell populations from patients from diverse KIR genetic
backgrounds. We observed that NK cells expressing a specific KIR secreted many effector cytokines, correlating to
IBD suceptibility.(2) Hematopoietic Stem Cells (HSCs) are the progenitors of immune cells and are thought to have
no functional capacity against pathogens. Recent studies have identified Toll-like Receptors (TLRs) on HSCs, so we
studied the functional capacity of HSCs upon TLR activation. The HSCs produced an array of cytokines upon
bacterial stimulation, indicating functional capacity for an immune response.
Coding for Decentralized Control System
Yishun Dong
Mentor: Tracey Ho
We study error correcting codes for decentralized control systems. Unlike existing work which considers coding for
control of an unstable plant, we consider coding for cost minimization in networks of stable interacting plants and
find that different codes are needed. We consider a two-player model where each player has a plant and a
controller. The dynamics of each plant affects the other plant in D time steps, which is termed the “dynamics
delay” of the system. In addition, the players communicate their states to the other player’s controller after a d
steps communication delay. The optimal control problem has been solved when the communication is assumed to
22
be lossless and one step delayed. In our work, we model that communication link between the two players to be
packet erasure link. It is found that for systems with one step dynamics delay, coding seems unnecessary.
Whereas, in general if there is a D (>1) steps dynamics delay between the two plants, the success transmission of
the state x(t-D+1) to the other player’s controller is critical for ensuring a near-optimal performance of the overall
system. This motivates the employment of some kind of deadline-driven real time streaming code in such systems.
The performances of uniform spreading streaming codes, limited convolutional codes and tree codes are examined
and compared in this framework.
Automation of a qPCR Diagnostics Device
Demetris Drakos
Mentors: Axel Scherer, Erika Garcia, and Imran Malik
The overall objective of this project is to program a microcontroller to handle all the processes required to perform
sample prep, qPCR and analysis when prompted to do so by the user.
The microcontroller used was NXP1768, which is based on the ARM Cortex M3 architecture, and it was programmed
through Keil’s μVision Integrated Development Environment (IDE).
A flag and interrupt-based approach was used, with interrupts being triggered by the user giving commands,
timers expiring, and error flags being raised. The user’s commands were received through Universal Asynchronous
Receiver/Transmitter (UART) ports, parsed by the microcontroller, and the appropriate action was then taken.
After the microcontroller is given logic to understand the user’s commands, it must then be programmed to control
the motors, heaters, and sensors involved in every step of the diagnostic procedure.
Screening Metal Sulfides as Photocatalysts for the Reduction of Carbon Dioxide
Claire Drolen
Mentors: Jay Winkler and Paul Bracher
We describe a system for screening the activity of metal sulfide compounds in the photocatalytic reduction of
carbon dioxide. The abundance and low cost of CO2 and other C(IV) species make them attractive feedstocks for
the production of solar fuels, but the reduction of carbon dioxide is hindered by the molecule’s thermodynamic and
kinetic stability. Certain known semiconducting materials, most notably sulfide compounds, have ideally situated
band edges that make them capable of facilitating this reaction. We pursued chronoamperometry—which measures
the current drawn (vs. time) by an electrochemical system at constant potential—as a tool to screen the activity of
various sulfide photocatalysts deposited onto a working electrode. In this electrochemical setup, spikes in current
observed to coincide with periods of illumination are assumed to be indicative of functional catalysts. Our initial
focus has been on mixtures of Mn(II) and Zn(II) sulfides, which are known to effect CO2 reduction upon irradiation,
and thus, are logical species to use as starting points for refining our method. Pure MnS and Zn-doped MnS have
displayed the highest catalytic activity, producing photocurrent spikes of approximately 1.5-2 µA when illuminated
with a 405 nm laser.
Light Curve Clustering Through the Use of Unsupervised Machine Learning
Victor Duan
Mentors: George Djorgovski, Matthew Graham, and Ciro Donalek
The time domain is a new and emerging branch of astronomy. With today’s large synoptic sky surveys, large parts
of the sky are being observed and studied, and more and more variable stars are being fond every day. The
amount of data is increasing exponentially, and there is a rising need to automate star classification methods. The
goal of this project was to use statistical and data mining methods to develop an algorithm to quickly and
efficiently determine what type of star a given light curve represents. Two different projects were considered:
separating RR Lyrae and eclipsing binaries in the skew-kurtosis plane and unsupervised clustering using selforganizing maps.
Two of the most common variable stars are RR Lyrae and eclipsing binaries, and it is important to be able to
distinguish between them because RR Lyrae can be used as tracers of galactic structure. Thus, the first part of this
project focused on separating RR Lyrae and eclipsing binaries using the skew-kurtosis plane.
Other common techniques for characterizing light curves are data mining techniques such as Bayesian networks,
k-means, and self-organizing maps. This project will also work on using unsupervised clustering techniques such as
self-organizing maps to try and characterize light curves from the CRTS database.
23
Designing a Custom Liquid Deposition System for the Spotting of Metal–Nitrate Solutions
Walker L. Dula
Mentor: Jay R. Winkler
This project focused on designing, testing, and implementing a custom liquid deposition system to aid in the Solar
Materials Discovery Program. The SMD program is a Caltech project that attempts to facilitate the photoelectrolysis
of water into hydrogen and oxygen using metal–oxide catalysts. Ideally, this would offer a simple means of storing
solar energy in a chemical form as hydrogen gas without the need for batteries. However, there are millions of
possible metal oxide combinations, and the project must screen all of them to find the best catalyst. This SURF
project seeks to expedite the testing process by reproducibly depositing strictly uniform amounts of solution in an
eight-by-eight grid onto a conductive glass plate, where these different solutions will be scanned for photoactivity.
Current methods for spotting solutions are time consuming and lack reproducibility, while this new system is
automatic and amenable to scale-up. While the final prototype has not yet been finished, the first iteration of the
device has been completed and tested. Currently, it is capable of depositing drops of 50 microliters, and the
software designed to drive it allows the user to import grids of solution ratios from Microsoft Excel to the system.
Achieving Extreme Mechanical Behavior Through Negative Stiffness: An Experimental Study
Monica Enlow
Mentors: Dennis Kochmann and Stan Wojnar
Solid materials possess a distinct property called their elastic stiffness, which characterizes the way they react to
applied forces and deformations. In composite materials, the counterintuitive phenomenon of negative stiffness has
attracted significant attention, which refers to a state in which the body’s reaction force no longer opposes the
deformation applied to the system, but instead is directed in the same direction as the applied deformation. Since
the negative-stiffness effect in composites is not well understood, we aimed to analyze this effect in a structural
system comprised of nine springs and two masses. Negative stiffness raises questions of stability, and in most
instances it is unstable. Previously it was believed that for reasons of stability negative stiffness was not allowed in
one of the composite phases, and so its effects were not analyzed. Recent experiments have shown that negative
stiffness is allowed in composites, and this in turn has shown that one can reach new overall properties because
new component properties can be considered. Analyzing the spring system, which is a model consisting of elastic
springs and a support structure to demonstrate the negative-stiffness effect as a consequence of a snapping
instability, in addition to oscillating the system at varying frequencies, which measures the dynamic stiffness of the
scenario, we were able to look at the different projected instances of negative stiffness. By looking at how the
system reaches extreme mechanical properties, we can better understand the mechanics behind what gives
composite materials superior qualities than its constituents.
The Neutron Electric Dipole Moment Experiment
Joshua Escribano-Fontanet
Mentors: Brad Filippone and Ruediger Picker
The report will summarize the work on the optimization of the half scale magnet package: it is a prototype magnet
for a new search of the electric dipole moment of the neutron (EDM) to be carried out at Oak Ridge National
Laboratory. The magnet package will provide the stable magnetic fields for the experiment. To achieve the desired
stability of the magnetic field, two tasks were employed. First, an ultra-low noise current supply was built and
tested that could power the Cos(θ) coil, which generates the main field in the EDM experiment. Second,
superconducting switches were made and tested to eventually run the coil in persistent mode. We present the
results of these studies as well as improvements on the cryogenic system for the half scale magnet package.
Calibration of the NuSTAR Telescope Using Markarian 421, Cygnus X-1, and GRANAT Source 1915 +105
Erin Evans
Mentors: Fiona Harrison and Kristin Madsen
We use two observations of Markarian 421 with the XMM-Newton telescope to create a power law with a
Tuebingen-Boulder absorption model using similar annular regions for both observations to correct for pile-up
errors. We find a model for NuSTAR’s observations of Markarian 421 with similar photon indeces and neutral
hydrogen parameters. We use previous models of the x-ray spectrum of Cygnus X-1 to create a fit of NuSTAR’s
observations of the source, settling upon a model using the Tuebingen-Boulden absorption model, a Gaussian iron
line, and the Xspec model “pexriv”. We also study the spectra of GRANAT Source 1915 +105 and verify that a
model can be found for this spectrum that is similar to those found in other studies of its X-ray spectrum.
24
The Home Hazard Weather Station: Home Sensor Platforms for Environmental Hazard Detection and
Response
Sandra Fang
Mentor: Julian Bunn
Environmental hazard detection (such as detection of fires, earthquakes, floods, and radiation leaks) is increasingly
aided by computer sensors that transmit data to Software-as-a-Service Cloud computing systems in order to
monitor conditions over large areas. However, precise sensors are expensive and few in number, making them
incapable of producing detailed maps of conditions for large communities. By using a large number of relatively
cheap and inaccurate sensors, coupled with a few precise sensors, the accuracy of sensor data is greatly improved
and thus can provide users with a reliable hazard detection system. For this project, a prototype “Home Hazard
Weather Station” comprising of twelve different sensors was constructed, and a program was written to display the
data to a computer terminal. The prototype is one of the many units that will eventually work with the Android
interface and relay its data to a Cloud to generate a map of various environmental conditions. The current setup is
a starting point for more performing complex operations in the future. It is recommended that further studies also
include testing and refinement of the system's sensitivity, as well as creative analysis of multiple types of
environmental data.
Development of Efficient Reduction and Archiving of Planetary Astronomical Data
Greg R. Farquhar
Mentor: Glenn Orton
Observations of astronomical objects in the outer solar system made using ground-based infrared telescopes have
collected large amounts of imaging data. Significant data reduction must be carried out to prepare the images for
analysis. A key data-reduction task is the assignment of planetary geometry, which is necessary to construct
calibrated map projections of the data. This task had been poorly automated, requiring time-consuming and
irreproducible manual fitting. An hill-climbing algorithm coded in the Interactive Data Language (IDL) was
developed to routinely locate the true position of the planet with sub-pixel precision. The algorithm uses a
planetary ephemeris to predict the object's size and shape, employs adaptive preprocessing, and intelligently uses
or blocks out Saturn's rings to improve accuracy. Additionally, the data must be archived with NASA's Planetary
Data System (PDS). To this end, routines were created to search the local file system, identify all relevant files, and
transfer them to a PDS-compliant archival volume. PDS-required ancillary files are automatically produced with
metadata extracted from the images' FITS headers.
Precision Astrometry With ROBO-AO
Dan M. Filler
Mentors: Richard Dekany and Carl Grillmair
We present the astrometric error calculations for images collected at the Palomar 60 inch telescope using the
robotically operated adaptive optics system, ROBO-AO. The precision capability of the instrument is 226.7 as over
15.3 minutes, for two objects located 4 apart. The precision capabilities of the ROBO-AO instrument, will allow us
to tune the Galactic Potential by integrating stellar orbits and comparing with observed data points. We will present
results from tuning the Galactic potential with simulated data from the ROBO-AO instrument and its conceptual
Antarctic counterpart SPRITE.
Optimization of a Citrate Sol-Gel Protocol for the Synthesis of Y2O3 and Other Luminescent
Nanocrystalline Materials
Katherine J. Fisher
Mentors: Michael J. Therien, Joshua T. Stecher, and Harry Gray
We report the successful optimization of a citrate sol-gel method for the preparation of sub-20 nm Y2O3:Eu3+/Li+.
Optimization of this sol-gel protocol permitted increased dopant loading and variability without increases in
polydispersity and crystal size. Particle nucleation and calcination was allowed to occur at a slow temperature ramp
of 2°C per minute to a soak temperature of 800°C, allowing us to obtain nanocrystals of uniform cubic phase.
Varying citrate concentration, oven ramp rate, and soak time ultimately led to an optimized protocol, determined
by Transmission Electron Microscopy (TEM) and X-ray Powder Diffraction (XRD) analysis. Nanoparticle samples
were solubilized through surface attachment of stabilizing ligands, allowing for solution phase spectroscopic
analysis of their emission. Y2O3 was also doped with other di- and trivalent metal ions, such as Bi3+ and Mg2+. The
flexibility of our optimized citrate sol-gel protocol was used to synthesize scintillators with different oxide host
lattices, such as ZnO and ZnMoO4. These small and generally monodisperse nanoparticles are suitable for use in
biomedical applications, such as cancer imaging and stem-cell tracking.
25
Scalable and Reproducible Filters for Minimizing Quasiparticle Generation in Superconducting Quantum
Circuits
Cedric W. Flamant
Mentors: Jonas Zmuidzinas and Christopher McKenney
Next generation far-infrared (FIR) astronomical measurements require large arrays of detectors (> 105) with noiseequivalent powers (NEP) approaching 10-19 W/Hz1/2 Superconducting microresonators using Kinetic Inductance
Detectors (KIDs) are a promising candidate to meet these requirements. These resonators are read out at radiofrequencies (RF) and are inherently multiplexible; however their ultimate sensitivity can be degraded by the
absorption of unwanted radiation. High frequency radiation can couple to the devices via the RF transmission lines.
Historically powder filters (metal powder embedded in epoxy) were developed for low frequency measurements; at
high frequencies the metal powder becomes lossy due to the reduced skin depth. We present a novel design which
is compatible with RF measurements at cryogenic temperatures. Our filter uses a lithographically defined
meandered microstrip line produced using commercially available copper traces on thin Kapton films. The
meandered geometry allows very long wire lengths in small physical geometries, while the thin Kapton film ensures
the bulk of the electric field is in the lossy metal-epoxy mixture. Lithographic control of the geometry allows a
design which is compatible with RF measurements. We have designed and built a first generation device and shown
reasonable matching between simulations and measurements.
Vacuum Enhancements to a Trapped Ion Frequency Standard in Support of NASA’s Space Atomic Clocks
Kyle Flanagan
Mentors: E.A. Burt and R.L. Tjoelker
Requirements for operation of atomic clocks in space will include high stability and long lifetime without scheduled
maintenance. An existing linear ion trap frequency standard (LITS-4) using 199Hg+ [1] is currently receiving vacuum
system updates in support of NASA's Deep Space Atomic Clock (DSAC) project. The turbo-pumped flow-through
vacuum system in LITS-4 is being replaced with one that uses a sealed-vacuum getter-pump [2] simulating the
type used for DSAC. The completed apparatus will serve as a reference in JPL’s Frequency Standards Test
Laboratory and test bed for vacuum technologies that will be used in DSAC flight clocks. Arrangement of
components on the vacuum manifold will more closely match the flight clock paradigm while also improving LITS-4
performance beyond previous achievements [3].
The trapped ion clocks developed at the Jet Propulsion Laboratory use a background “buffer” gas to cool ions to
near room temperature. Previously the buffer gas used in LITS-4 was helium introduced through a heated quartz
leak. Since the collision shift in Hg+ is smaller for neon than for helium [4], LITS-4 is being converted to use neon.
The neon will be supplied using a one-time charge from behind a valve before beginning operation, rather than
from a continuous leak, thereby further improving the stability of the frequency shift due to background neon gas.
References
[1] R. L. Tjoelker, C. Bricker, W. Diener, R. L. Hamell, A. Kirk, P. Kuhnle, L. Maleki, J. D. Prestage, D. Santiago, D.
Seidel, D. A. Stowers, R. L. Sydnor, T. Tucker, “A Mercury Ion Frequency Standard Engineering Prototype for the
NASA Deep Space Network”, IEEE International Frequency Control Symposium, pp. 1073-81, 1996.
[2] E. A. Burt, R. L. Tjoelker, “Prospects for Ultra-Stable Timekeeping with Sealed Vacuum Operation in Multi-Pole
Linear Ion Trap Standards”, 39th Annual Precise Time and Time Interval Meeting, pp. 309-16, 2007.
[3] R. L. Tjoelker, J. D. Prestage, G. J. Dick, L. Maleki, “Recent Stability Comparisons with the JPL Linear Trapped
Ion Frequency Standards”, IEEE International Frequency Control Symposium, pp. 739-43, 1994.
[4] L. Yi, S. Taghavi-Larigani, E. A. Burt, R.L. Tjoelker, “Progress Towards a Dual-Isotope Trapped Mercury Ion
Atomic Clock: Further Studies of Background Gas Collision Shifts”, IEEE International Frequency Control
Symposium, to be published 2012.
Development of a Novel Small Molecule Inhibitor of Plasmodium falciparum Chitinase
David T. Flicker
Mentors: Michael Gilson and Douglas Rees
Plasmodium is a eukaryotic parasite that causes malaria with Plasmodium falciparum the most deadly. Previous
experiments have shown that the Plasmodium falciparum chitinase (PfCHT1), which breaks down the walls
enclosing the mosquito’s blood meal, is essential for parasite transmission through the mosquito. However, the
only known molecular inhibitor of this chitinase is a large, expensive natural product, and so is unsuitable as a
drug. To discover a novel inhibitor more amenable to drug development, 17,000 compounds were screened at The
Scripps Research Institute and one hit was found with an IC50 of 10 µM. To further characterize the hit and its
ability to broadly inhibit GH18 family chitinases, the hit was tested against O. volvus, B. malagi, and H. sapiens
chitinases. We also show whether the hit prevents malaria transmission through the mosquito.
26
An Information-Theoretic Measure of Causality
Suzannah A. Fraker
Mentors: Christof Koch and Virgil Griffith
The Integrated Information Theory (IIT) posits that consciousness is integrated information that is both highly
differentiated and highly unified. This information is generated only when a mechanism’s present state has both
specific past causes and specific future effects within the system in question, so that it generates “cause-effect
information”. However, despite the causal language in which the theory is framed, integrated information (φ) has
previously been calculated using statistical measures that do not always accurately capture causal, as opposed to
informational, relationships. Here we present a counterfactual-based measure that more accurately quantifies the
strength of causal interactions and characterizes “differences that make a difference” using the tightest possible
bounds on the probability of necessity and sufficiency. In addition to its applications to IIT, this measure has
relevance for analyzing arbitrary dynamical systems.
BioSleeve Hardware Design and Development
Josh Fromm
Mentors: Michael Wolf and Chris Assad
As robotic technology becomes more advanced, the demand for seamless robotic integration into everyday life will
increase. However, the current paradigm of robotic control, button and keyboard based interfaces, is neither
intuitive nor portable enough to facilitate many of the potential uses of newer robots. This study examines and
develops the hardware of a next-generation robotic control system, called the BioSleeve, which uses gesture based
commands to control one or more robots. Three distinct BioSleeve hardware systems were developed, each with
unique pros and cons. The first uses a commercial EMG electrode array and has the benefit of low noise and dry
contact electrodes (which allow better packaging and durability than wet electrodes); the downside of this
commercial system is its extremely limited portability and customizability. The second implementation of the
BioSleeve uses two Arduino microprocessor boards to read and relay EMG data wirelessly to a computer. The
Arduino system is much more portable than the commercial system but requires a wet electrode array and nonideal WiFi hardware. The final BioSleeve system developed is a Texas Instruments MSP430 processor based system
that was designed and constructed specifically for the BioSleeve. The MSP system benefits from extreme portability
and ideal hardware but uses a wet electrode array and is very difficult to implement in software and hardware.
Reduction of Noise in CIBER 2 Detector Arrays
Neelay Fruitwala
Mentors: James Bock and Michael Zemcov
In this project, we will study the noise properties of the Teledyne H2RG IR detector array that will be used on
CIBER 2 (Cosmic Infrared Background ExpeRiment). CIBER 2 is a sounding rocket payload that will measure
anistropy in the IR background, which can help improve our understanding of the epoch of reionization. Since the
detector’s pixels are read sequentially, the noise due to detector read out will be correlated between pixels, so it
can be reduced using a reference sampling scheme. We will conduct dark testing of the detector to study the
properties of this correlated noise. To this point in the project, we have successfully assembled the test cryostat
and verified its ability to hold vacuum, keep its contents at the detector’s operating temperature of 77 Kelvin for
long periods of time, and ensure that the detector does not cool down too quickly. We have also completed a
mounting assembly to house the detector inside the cryostat and a warm electronics board to interface with the
detector. A few things need to be completed before testing can begin: the cryostat is still being prepared to house
the detector and interface it to the warm electronics, and the data acquisition system is being worked on as well.
Flow Around Counter-Rotating Vertical Axis Turbines in Steady Flow
Matthew Fu
Mentor: John Dabiri
Counter-rotating vertical axis turbines (VATs) have been shown to yield increased power density in wind farms as
compared to typical horizontal axis wind turbine (HAWT) farms. However, the governing physical mechanisms
remain poorly understood. Scale model experiments in a free-surface water tunnel were conducted to characterize
the effect of parameters such as turbine separation, tip speed ratio, and flow speed on the downstream flow field
and the resulting vortex shedding from VATs. The flow field was visualized using particle image velocimetry (PIV)
and planar laser induced fluorescence. The results are compared and contrasted with recent studies of counterrotating circular cylinders to determine if suppression of vortex shedding plays a similarly important role in
dictating the overall wake dynamics.
27
On-Orbit Vicarious Calibration of GOSAT Satellite
Victor E. Gandarillas
Mentor: Carol J. Bruegge
NASA and other space agencies take measurements from space for earth science. The Greenhouse Gases
Observing Satellite (GOSAT) is one such earth science mission launched in January of 2009 by the Japanese
Aerospace Exploration Agency (JAXA). This sensor measures the amount of carbon dioxide and methane in the
atmosphere in order to improve our understanding of global warming.
All on-orbit sensors degrade with time, meaning the signal from the sensors is lower with time for a constant
amount of light hitting them. On-orbit calibration accounts for this degradation and allows scientific products to be
returned without loss of accuracy, correcting for this change in time.
From June 25-July 2, 2012, the on-orbit calibration of GOSAT was conducted at Railroad Valley, NV. As part of this
campaign, atmospheric and surface measurements were made in order to compute the radiance hitting the GOSAT
sensor. The surface measurements included reflectance measurements at one of six 500x500 m test sites. Ideally,
these measurements would be made to characterize the 10 km GOSAT footprint. As this is not possible, we instead
used the MODerate Resolution Imaging Spectroradiometer (MODIS) instrument, on the EOS/ AQUA platform, to
provide scaling between the actual measurements and the desired GOSAT footprint.
This paper will discuss the desert playa radiance measurement techniques and image processing of MODIS data
discussed above as part of the new calibration of GOSAT. A summary of the 2012 Railroad Valley data sets,
analysis flow, and results are also presented. Currently the calibration is believed to be accurate to within 5%
uncertainty.
High-Order Fourier Continuation Solvers for Maxwell's Equations With Discontinuous Permittivity
Emmanuel Garza Gonzalez
Mentors: Oscar Bruno and Adityavikram Viswanathan
Numerical methods for solving Maxwell's equations are fundamental to modeling complicated electromagnetic
phenomena. In many situations, numerical simulations involve the presence of different dielectric materials in the
domain. At the interface of any two materials, there exists a discontinuity in the permittivity function, which
reduces the spatial accuracy of the numerical method to first order. In this work, we implemented time domain
numerical solvers for Maxwell's equations in one and two dimensions for constant and discontinuous permittivity
problems. High order Fourier Continuation (FC) spatial approximations were employed in conjunction with CrankNicolson time stepping. In order to improve the order of accuracy when several dielectric materials are present,
smoothing techniques for the permittivity function were utilized. Fourier smoothing and local subpixel smoothing
methods were implemented, by which second order accuracy was achieved. In one dimension, we were able to
obtain fifth order accuracy using FC by directly imposing the physical boundary conditions between the dielectric
materials. We also studied the implementation of this method for the two dimensional TM mode. Representative
simulations showing the application of these techniques to the modeling of photonic waveguides and cavities were
also performed.
Sensitivity Analysis for Atmospheric Infrared Sounder (AIRS) CO2 Retrieval
Ilana B. Gat
Mentors: Zhijin Li and Paul Dimotakis
The Atmospheric Infrared Sounder (AIRS) is the first thermal infrared sensor able to retrieve the daily atmospheric
state globally for clear as well as partially cloudy field-of-views. The AIRS spectrometer has 2378 channels sensing
from 15.4 µm to 4.3 µm, of which a small subset in the 15 µm region has been hand selected, to date, for CO2
retrieval. To increase the accuracy of retrievals, we developed a channel ranking system using a mathematical
formalism to rapidly process and assess the retrieval potential of large numbers of channels. Implementing this
system, we identified a larger optimized subset of AIRS channels that can decrease retrieval errors and minimize
the overall sensitivity to other irradiance contributors, such as water vapor, ozone, and atmospheric temperature.
This methodology selects channels globally by accounting for the latitudinal, longitudinal, and seasonal
dependencies of the channel optimal subset. The new methodology is not only expected to increase accuracy in
AIRS CO2 as well as other retrievals, but also enables the extension of retrieved CO2 vertical profiles to altitudes
ranging from the lower troposphere to upper stratosphere. This project aims to demonstrate the beneficial impact
of this new methodology for channel selection on CO2 retrieval using AIRS data.
28
Determining the Mechanism for Mixed Hydrosilylation and Methylation of the Silicon(III) Surface
Rachel Gates
Mentors: Harry Gray and Judy Lattimer
This research explores the photoelectrochemical properties of Vinyl Ferrocene (vFc) covalently bonded to n-type
Si(111) surfaces with various vFc coverage and Si doping densities. Si wafers with resistivity from 0.019 to 34
Ohm-cm were used, and vFc concentrations from 0 to 8% of a monolayer were synthesized and tested. Due to
time constraints for summer research, neither a maximum nor ideal concentration of vFc on the Si surface was
obtainable. Si with resistivity in the range of 1-10 Ohm-cm was observed to have the largest potential shift from
dark to light, with a maximum photovoltage of around 550mV. Surface coverage did not appear to correlate to
potential shift, though other interesting correlations were observed.
3D Dynamic Deformation Measurements Using Digital Image Correlation
Alexandra Gdoutou
Mentors: Guruswami Ravichandran and Mike Rauls
In the present work a new and novel digital image correlation (DIC) technique developed by Xia et al (Xia, S.,
Gdoutou, A. and Ravichandran, G., “A Novel Method for Determination of Three-Dimensional Deformation at Small
Length Scales,” Experimental Mechanics, to appear) will be used for studying dynamic problems. The method
utilizes a diffraction grating placed between the specimen and the camera, resulting in multiple images which are
then used to obtain apparent in-plane displacements using a 2D - DIC algorithm. The true in-plane and out-ofplane displacements of the specimen are obtained from the apparent in-plane displacements and the diffraction
angle of the grating. The validity of the newly developed method was demonstrated through 3D deformation
measurement of a small thin inflated membrane. The pressure chamber for performing the inflation of the
membrane was designed and fabricated and the experimental setup was assembled on an optical table. In the
present work, dynamic membrane inflation experiments were performed and the digital images were acquired
using a high – speed camera. The acquired digital images were analyzed using 2D-DIC software (VIC-2D,
Correlated Solutions, Inc.) to obtain the 3-D displacement data.
Domain-Swapped TCRs to Prevent TCR Mispairing in an Immune-Based Therapy
Marvin H. Gee
Mentors: David Baltimore and Michael Bethune
Anti-tumor immunity can be engineered in cancer patients by transducing autologous T cells with tumor-specific
T cell receptor (TCR) α and β chain genes. However, therapeutic α/β TCR chains can mispair with endogenous α/β
TCR chains, resulting in reduced expression of tumor-specific TCRs and potential autoimmunity by mispaired TCRs.
The α/β TCR must recruit CD3 chains through extracellular and transmembrane interactions to enable surface
expression and signaling. We exploited this necessity to prevent mispairing by swapping domains between the α
and β chains. Correctly paired domain-swapped (ds)TCRs retain all domains necessary to recruit CD3 components,
express on the cell surface, and signal in response to tumor epitopes. By contrast, mispaired TCRs comprising one
domain-swapped and one wild-type chain are unable to recruit CD3, express on the cell surface, or signal due to
lack of domains. Jurkat cells infected with dsTCRs exhibited dsTCR surface expression (reduced 5-fold relative to
wild-type), cognate peptide-MHC specificity, and secretion of IL-2 upon coincubation with cognate antigenpresenting cells. By contrast, surface expression, cognate dextramer staining, and antigen-induced IL-2 release
were undetectable for Jurkats transduced with mispaired TCRs. Flexible linkers improved dsTCR expression to wildtype levels, but ablated function, revealing a disconnect between expression and signaling.
Axel Scoop Sampling Device
Nikola Georgiev
Mentors: Joel Burdick and Melissa Tanner
The Axel rover is a lightweight two-wheeled vehicle that is supported by a host platform through a tether. It can be
detached from the host in order to explore extreme extra-planetary terrain that is characterized by steep craters,
overhangs, loose soil and layered stratigraphy. It potentially provides robust and flexible access to sites of scientific
interest that are inaccessible to current rovers. The goal of this project is to design and build a prototype of a
sampling device for the Axel rover that can efficiently sample loose soils at states ranging from dry to wet and
sticky or even icy state, take multiple samples and store them in the Axel’s instrument bay. The proposed device is
a four-degree-of-freedom mechanism that can efficiently manipulate specifically designed containers to acquire and
store sealed soil samples that may contain unstable substances without any Earth contamination or crosscontamination.
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Understanding the Paleoproterozoic Atmosphere Through Detrital Pyrite
Aya Gerpheide
Mentors: Woodward W. Fischer and Jena E. Johnson
Detrital pyrite located in 2.415 Ga sedimentary rocks from South Africa provides evidence for an anoxic
atmosphere that continued into the early Paleoproterozoic. Timing the rise of atmospheric oxygen is import for
understanding the conditions that cultivated the earliest forms of life and the biogeochemical cycles involved. In
the presence of atmospheric oxygen, pyrite is oxidized readily and rarely survives as a detrital component of
conglomerates. Using a combination of visual and electron microscopy, and using secondary ion mass
spectrometry, detrital grains found within siliciclastic sediments provide a proxy for the presence of atmospheric
oxygen. Detrital grains were visually distinct from later overgrowths by being rounded by mechanical abrasion and
surface textures unaffected by oxygen-induced chemical weathering or hydrothermal alteration. Sulfur isotope
analysis reveals a fractionation in 33S and 36S values including near zero and negative 33S values. Rounded
pyrite with variable isotopic signatures suggests multiple placer origins and detrital grains that underwent several
episodes of erosion and transportation before its final deposition. The results suggest paleoenvironments with little
atmospheric oxygen. Future work will aim to constrain the paleo-oxygen levels via quantitative modeling of the
oxygen-induced chemical weathering during transport.
The Use of Surface Traction to Approximate the Effects of Topography on Earth’s Elastic Deformation
Udaya Ghai
Mentors: Jean-Philippe Avouac and Sylvain Barbot
We provide an approximate solution in the Fourier domain for an elastic deformation in a semi-infinite solid with
arbitrary surface tractions, body forces and topography. The boundary conditions on a surface were approximated
with effective surface tractions for the inhomogeneous Navier’s equation on a flat surface. Correctional factors were
approximated with a Taylor approximation of the normal component of stress on a smoothly varying surface. We
used the perturbation method with correctional factors as arbitrary surface tractions with the elastic Green’s
function to approximate our solution. A successive approximation method that creates effective surface tractions
was used to correct displacement values. Some of the approach is already implemented in FORTRAN in parallel.
This introduction of topography could be particularly useful in the study of earthquake and volcano deformation and
could be potentially expanded to account for the sphericity of the earth for larger spanning earthquakes.
Biomolecular Rate-Regulation Circuits
Giulia Giordano
Mentors: Richard M. Murray and Elisa Franco
Binding of proteins and RNA underlies cell metabolism, gene expression and self-assembly phenomena. Often such
binding has to occur with specific stoichiometric ratios: therefore flux control is important to regulate production
rate and concentration of biochemical species. Flux control loops for two binding species forming an output product
have been implemented with in vitro artificial gene circuits. This research project aimed at generalizing flux
regulation architectures to an arbitrary number of species.
Feedback loops were designed based on negative auto-regulation (which can minimize the potentially harmful
amount of molecules not used to form the product), cross-activation (which can maximize the overall output flux)
and both. It was shown that transcription rate matching can be achieved through proper feedback constants;
negative feedback is faster and maintains stability. The performances of feedback generated with mass action
kinetics and feedback described by Hill functions were compared; stoichiometric negative feedback keeps
concentrations at a lower level. We also studied a possible experimental implementation of a three gene network
for flux matching based on negative feedback.
Chemical Analysis of the Air-Water Interface With Bursting Bubbles: Application to Environmental
Chemistry
Byoungsook Goh
Mentors: J.L. Beauchamp and Daniel Thomas
The process of bubble bursting can lead to charge separation at the air-water interface and subsequent ejection of
charged micro-droplets from this region. The ions released in this process can be monitored to study the surface
composition as well as complex chemical reactions occurring at the air-water interface. In this research, the ions
present in this interfacial region were studied by the detection of ion species from bubble bursting. A Linear Trap
Quadrupole (LTQ) mass spectrometer was used to analyze ion species from bubble bursting with surface active
species such as phospholipids. Results from these experiments were compared with the surface specific sampling
technique Field Induced Droplet Ionization mass spectrometry (FIDI-MS). The phospholipid 1-myristol-2-palmitoylsn-glycero-3-phosphocholine (MPPC) was analyzed, and the result showed the base peak at 728.45 m/z which was
assigned to be the sodium ion adduct of MPPC. Substances such as oleic acid and other environmental samples
such as halide ions are currently under investigation. In conclusion, detection of ions generated by bubble bursting
represents a useful method to probe the chemical composition of the air-water interface.
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Thermal Energy Storage in Phase Change Materials for Solar Decathlon House
Harry Golash
Mentor: Melany Hunt
The U.S. Department of Energy Solar Decathlon is an inter-collegiate competition held every two years in which
participating teams build solar-powered homes to showcase the best strategies for achieving energy efficiency in
residential living. For the 2013 Solar Decathlon, to be held in Irvine, California, the engineers at Caltech have
teamed-up with the architects at SCI-Arc to build a net-zero-energy home (a home that generates all the electricity
it consumes). This year, the home will use a number of passive systems for ventilation, heating, and cooling so as
to lower its overall energy consumption. One way of implementing such as passive system would be to use the
thermal storage capacity of phase change materials. Since phase change materials undergo liquid-solid and solidliquid phase changes, they can store a large amount of latent heat energy, as compared to non-phase-changing
thermal masses, such as water, which only store sensible heat energy. Moreover, since the temperature of a phase
change material remains constant during the phase change, they are useful in regulating the temperature of the
space in which they are stored. By using phase change materials in the walls and in a solar hot water system, the
house will be quite cost and energy efficient.
Inhibition of Convection by Condensation in the Ice Giants: The Role of Double-Diffusive Convection
Erica Gonzales
Mentors: A. James Friedson and Glenn Orton
The planets of our solar system are believed to have evolved from a protoplanetary disk around the Sun. The
intrinsic heat from this formation is found in all planets. Uranus emits much less intrinsic heat than the other outer
planets. We examine what conditions would inhibit the radial heat flow in an atmosphere modeled after Uranus's
atmosphere. Guillot (1995) first showed that condensation of high molecular weight species could inhibit ordinary
convection in hydrogen atmospheres. When a gradient in the mean molecular weight is induced by the saturation
of the vapor, this molecular gradient acts as a stabilizing factor to overcome the destabilizing thermal gradient. We
first confirm the conditions necessary for ordinary convection to be inhibited. We then find the conditions necessary
for double-diffusive convection to be inhibited. Our findings may determine that even layered diffusive convection is
inhibited and thus the saturated layer acts as an insulator that leaves only radiation as a means of heat transfer.
Our findings could explain the low intrinsic heat flow of Uranus and also contribute new factors to consider when
studying the thermal evolution of Uranus and Neptune.
Elucidation of the Mechanism for Palladium Catalyzed Asymmetric Conjugate Addition
Emmett Goodman
Mentors: Brian Stoltz and Jeffrey Holder
Recently the Stoltz lab has pioneered a method of asymmetric conjugate addition of boronic acids using a Pd/tBuPyOx catalytic system. This system has been found to create quaternary stereocenters in high yield and
enantiomeric excess. However, the exact mechanism through which the boronic acid is added is still unclear. As
chromone has an oxocarbenium resonance structure, we think that our conjugate addition may proceed through
such an intermediate. In order to test this hypothesis, we will generate such an intermediate in situ and subject
this intermediate to our conjugate addition conditions. We first synthesized a methyl acetal which we hypothesized
would be in equilibrium with its relative oxocarbenium ion. However, under our conjugate addition conditions, we
observed no conjugate addition product. We then synthesized two more acetals, triflouroethyl and phenyl, which
we believed would be more likely to give way to an oxocarbenium intermediate. Subjecting these to our conjugate
addition conditions, we have thus far found no conjugate addition product. However, we found substantial amounts
of the hemiacetals we used to create these acetals, as well as starting material. These hemiacetals would be
generated in the presence of water; thus we now plan to run our conjugate additions in the presence of phenol and
triflouoroethanol respectively, instead of water. We observed these compounds to be sensitive to air, and believe
that these compounds were in equilibrium with their respective oxocarbenium intermediates.
Robustness in Xenopus laevis
Avion Goordeen
Mentor: Lea Goentoro
According to oral tradition, when a developing Xenopus laevis embryo is exposed to two discrete temperatures
along their anterior-dorsal axis, the cells’ specialization reverse with respect to their location on the axis resulting
in a fully developed wild-type tadpole. To test this possibility, peltier modules were utilized to produce
temperatures on opposing sides of an embryo and a thin insulating sheet between the modules kept the
temperatures exposed to the embryo to remain discrete. The overall results from this experiment have been
inconclusive due to the lack of a sufficient sample size of data. The design and production of a housing device that
holds discrete temperatures across a single embryo holds some progress to understanding why these embryonic
cells exhibit such a robust quality.
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Quantum Statistical Mechanical Systems Associated to Riemann Surfaces
Mark Greenfield
Mentor: Matilde Marcolli
Given a compact hyperbolic Riemann surface, we construct a quantum statistical mechanical system that encodes
its conformal isomorphism class. Building from the spectral triple construction of Cornelissen and Marcolli (J. Geom.
Phys. 58, no. 5, pp. 619-632, 2008), the C*-dynamical system is defined using a crossed-product algebra of the
Riemann surface’s uniformizing Schottky group and the set of continuous functions on the limit set of its action,
along with a time evolution generated by a Hamiltonian constructed from the Dirac operator of the spectral triple.
States of this system are found to be equivalent to zeta functions of the spectral triple, and again from the results
of Cornelissen and Marcolli, characterization of conformal isomorphism class is established.
Electrospray Deposition of Anode Films for High Power Solid Oxide Fuel Cells
Kevin L. Gu
Mentors: Sossina M. Haile and Robert Usiskin
Solid oxide fuel cells (SOFCs) are electrochemical devices that efficiently convert chemical energy to electricity, and
are therefore potential replacements for conventional combustion engines. High performance SOFCs require an
anode with high surface area that is catalytically active. To deposit highly porous films of ceria, a well-known SOFC
anode material, we use electrospray deposition which converts a precursor solution directly into a porous film. An
attractive feature of the electrospray method is that it is an inexpensive and easily scalable, single-step process.
Here we report the deposition of high-performance ceria thin film anodes onto conducting and insulating substrates
by electrospray deposition. Results of anode electrochemical performance by impedance spectroscopy are
presented.
Testing and Improving Theories of Radiative Transfer for Determining the Mineralogy of Planetary
Surfaces
Eyjolfur Gudmundsson
Mentor: Bethany L. Ehlmann
Two radiative transfer theories, the Hapke and Shkuratov models, have been used to estimate the mineralogic
composition of laboratory mixtures of anhydrous mafic minerals from reflected light, accurately modeling
abundances to within 10%. For this project, we tested the efficacy of the Hapke model for determining the
composition of mixtures (modal abundance, particle size) with hydrous minerals, including phyllosilicates. We
examined how the modeled endmember weight fractions and particle sizes affected the shape of the model’s error
function and found that model minima were sensitive to grain size and relatively insensitive to endmember weight
fraction. Extraction of the endmembers’ k optical constant spectra using the Hapke model showed differences with
the Shkuratov-derived optical constants originally used. A sensitivity analysis of selected input and model
parameters was performed. Our findings suggest that the optical constants used significantly affect the accuracy of
model predictions. Further studies will investigate the effect of hydration, permitted variability in particle size,
assumed photometric functions and use of different wavelength ranges on model results.
Characterization of Self-Associating and Complementary Polymers Used to Control Fuel Misting
Ashley Guo
Mentors: Julia A. Kornfield and Jeremy Wei
Airplane crashes can become extremely deadly due to explosions from the fine, highly combustible mist formed by
fuel upon impact. The danger of post-crash explosions can be reduced by adding specially designed polymers into
the fuel which increase droplet size such that fuel mist is significantly less combustible and may even extinguish
fires. This project focuses on characterizing polymer chains that associate end-to-end into large supramolecules,
via both self-associating ends and complementary “donor/acceptor” ends, and determining their effects on mistcontrol properties and fuel behavior. Using 1H-NMR and rheology, we will determine if the polymer chains associate
as predicted and have the desired effect on the fuel’s overall viscosity. Shear degradation tests were used to
demonstrate if polymer solutions experience any loss of viscosity after being circulated through a fuel pump. Spray
tests were performed in order to provide and assess visual evidence of mist control. The polymer-fuel mixture was
also run through a small model diesel engine in order to compare the performance of the doped fuel to the original
jet fuel. Our results lead to future projects that will focus on synthesizing viable polymers for commercial
production.
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Constructing a Non-Magnetic XY-Stage to Search for Lightning Strikes on Earth and Mars
Garima Gupta
Mentor: Joseph L. Kirschvink
The existence of life beyond Earth has been the underlying theme connecting all of the missions to Mars thus far.
Most of these missions have focused on the existence of water on the planet. One indication of a wet, conductive
surface is cloud-to-ground lightning. To prove that there was once lightning, and thus water, on the Martian
surface, we must examine Martian rocks for Isothermal Remanent Magnetization (IRM), which is the alignment of
the magnetic vectors in a material due to an external magnetic field. We can do this by placing a fluxgate
magnetometer at the end of a rover’s instrument arm. This concept was explored through the design and
construction of a non-magnetic XY-stage. The stage is able to move in two dimensions (X, Y) through motor control
and the third dimension (Z) through manual control. Due to differences in shape and size of possible rock samples,
the stage also has the ability to tilt and stabilize. The stage’s movement was programmed and combined with the
magnetometer’s data collection abilities. The magnetometer was then calibrated and tested using actual rock
samples. The stage will be used over the year to search for lightning strikes in rocks found on Earth.
Single Unit Analysis of Gaze Direction in the Human Amygdala
Vaibhav Gupta
Mentors: Ralph Adolphs and Oana Tudusciuc
Social cognition refers to the brain processes involved in interpreting all components of social life. A key aspect of
social cognition is the ability to infer the relevance of facial features in others. The amygdala, a brain region in the
depth of the temporal lobe, has been shown to be key in deciphering emotions such as fear. The exact mechanisms
by which the amygdala processes facial features such as emotion, identity, gaze direction, has not yet been fully
understood. In order to test the role of the amygdala in processing gaze direction, we employed a 1-back task. It
displayed a series of photographs and computer generated images of human faces, each with the gaze directed at
either one of eight equidistant points or directly ahead. Intracranial, high impedance electrodes gathered electrical
signals in the patient's amygdala bilaterally through a Digital Lynx System (Neuralync, Inc.). The raw signals were
filtered, and then sorted into waveforms using Osort and then carefully merged and defined based on the signal to
noise ratio. Through analyzing the differences in firing rates between different types of stimuli, we have come to a
preliminary conclusion that the amygdala does respond to gaze direction. In the three patients analyzed we found
6 statistically significant ( p < 0.05) neurons that showed inhibitory responses. We will continue to collect more
data in order to confirm the results and also to determine any potential relationships between the neurons and
their stimuli.
Visible and Near-Infrared (VNIR) Spectroscopy of Altered Basalts With Application to the ChemCam
Library for Mars Science Laboratory
Bryné Hadnott
Mentor: Bethany Ehlmann
The discovery of Fe, Mg, and Al clays on Mars using VNIR spectroscopy from orbit indicates past low
temperature/pressure hydrothermal and pedogenic environments. In-depth laboratory analysis of Mars-analog
rocks from these settings on Earth was used to build the ChemCam sample library for Mars Science Laboratory,
permitting for more accurate compositional analysis of Martian samples, improved linkages between VNIR’s
mineralogic and ChemCam’s elemental data, and improved recognition of different environmental settings for
aqueous alteration. VNIR spectroscopy was used to analyze 4 suites of altered basaltic rocks—one from San Carlos,
AZ and three from various locations in Iceland. Continuum shape and absorption features were found to vary,
depending on the alteration environment and extent of alteration. Relatively unaltered rocks had electronic
absorptions related to iron. The strength of the 1.9-micron absorption correlated, to first order, with the degree of
weathering and aqueous alteration. Samples with strong 1.9-micron absorptions often exhibited absorption bands
at 1.4, 2.2, and 2.3 microns indicating the presence of clays and/or features between 0.6 to 0.8 microns indicative
of ferric iron oxides. Diagnostic absorption features and continuum slopes have been used to identify a
representative subset of rocks from each suite for further analysis for the ChemCam library.
Laser Desorption-Infrared Spectroscopy for Icy Planetary Bodies
Benjamin Hall
Mentor: Luther W. Beegle
This project is a proof of concept to determine if laser desorption infrared (LD-IR) spectroscopy is a method that
can successfully detect astrobiologically significant compounds in a water ice matrix on icy body surfaces. The goal
is to prove that this cost-effective method can successfully perform in situ observations of icy mixtures. A tunable
IR laser was fired at ice samples and the resulting plume was observed with a photoconductive detector. Many
pieces of equipment have broken down, and the observation process is ongoing.
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Fabrication of Regioregular Poly(3-alkylthiophene) Sorted Semiconducting Single-Walled Carbon
Nanotube Transistors on Flexible Substrates
Jeff Han
Mentors: Zhenan Bao, Evan Wang, and Julia Greer
Single-walled carbon nanotubes (SWNTs) are well-known for their extraordinary mechanical and electrical
properties and possible applications in flexible electrical systems. A method of highly selective dispersion of
semiconducting (sc-) SWNTs from metallic (met-) SWNTs has been found using regioregular poly(3alkylthiophene)s (rr-P3ATs). These sorted SWNTs have been used to fabricate high-performance SWNT transistors
on silicon substrates. Thin-film back-gate transistors on a flexible polyimide substrate with a double dielectric layer
comprised of Al2O3 and poly-4-vinylphenol (PVP) were fabricated with the polymer sorted SWNTs. These devices
were measured to have on/off ratio of >103 and mobility of up to 0.37 cm2/Vs. These flexible transistors will be
doped and used to fabricate CMOS inverters to demonstrate their viability in future flexible integrated circuits.
Categorization of Spitzer Produced Light Curves
Ali Harb
Mentors: George Helou and Mansi Kasliwal
A project undertaken by Caltech’s Infrared Processing and Analysis Center, the Spitzer Space Telescope (SST) has
used light in the infra-red portion of the electromagnetic spectrum to survey the sky, and has provided extensive
digital libraries of image data of outer space. We present the initial results of a manual categorization of light
curves produced by Spitzer by repeatedly observing the galaxies NGC6822, PGC143, PGC2004, PGC2329,
PGC3238, and PGC3844 at the wavelengths of 3.6 µm and 4.5 µm. This initial categorization was based on the
graph’s gradients. It was found that most light curves were varying in gradient, and a code was written to permit a
run through of such a large body of data to categorize them systematically. This code can be altered in the future
so as to permit a more thorough categorization of the light curves, based on different factors (amplitude, rate of
change of gradient…)
Percussive Scoop Sampling in Extreme Terrain
Hima J. Hassenruck-Gudipati
Mentors: Joel Burdick and Melissa Tanner
Axel is a cliff climbing rover that uses simplicity as its main principle to explore extreme terrains for use on moon,
Mars, and beyond. To increase the technology readiness and scientific usability of Axel, a sampling system needs to
be designed and build for sampling different rock composition. To decrease the amount of force required to sample
clumpy and possibly icy science targets, a percussive scoop could be used. A percussive scoop uses repeated
impact force to dig into samples and a rotary actuation to collect the samples. Percussive scooping can reduce the
amount of downward force required by about two to four times depending on the cohesion of the soil and the depth
of the sampling tool. The goal for this summer is to build a working prototype of a percussive scoop for Axel.
Automated Image-Based Change Detection for Instrument Planning
Bryan D. He
Mentor: Kiri Wagstaff
Planetary exploration orbiters are currently sending back large volumes of images from Mars. To process these
images, an automated method of detecting landmarks, classifying the detected landmarks, and detecting changes
between two images of the same location at different times is necessary. Landmarks are detected by using a
salience map, which measures the contrast of each pixel with its neighbors, to identify areas of high contrast,
which represent landmarks. Landmarks are classified by calculating a feature space representation of each
landmark that consists of the mean intensity of the pixels, the standard deviation of the pixels, the area of the
landmark, the perimeter of the landmark, and attributes from an ellipse-fit. The feature space from a manually
classified training set is then used to train a statistical model, which can then be used to classify other landmarks.
Changes are detected by creating a matching between landmarks in two images. The matching is created by trying
to minimize a similarity function that is dependent on the feature space. Recent improvements to the system
include decreases in runtime and memory usage, the support of more image formats, using an affine transform
between images to increase the accuracy of the matching created by the change detection process, and the
addition of several statistical models for classification. The results from the automated system focus the attention
of experts on regions of scientific interest and allow planetary exploration orbiters to target regions of high
importance.
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Technical Notes on the MINERVA Project Sites
Monica He
Mentors: John A. Johnson and Dan McKenna
We report the estimated seeing in the optical band as a function of height at a proposed MINERVA site adjacent to the
48’’ dome at Palomar Observatory. These results are based on the microthermal measurements from an 8m mast
located at the site. We assessed the ground layer seeing contribution to the total seeing using the Kolmogorov theory
of turbulence and Gladstone’s formula. The most significant seeing is found in the lowest 1.5m of atmosphere with
large variations in the height distribution.
Validation of a PCC Anchor Ligand Against the Cancer-Associated E17K Mutation in the Pleckstrin
Homology Domain (PHD) of Akt1
Ying Qiao Hee
Mentors: James R. Heath and Kaycie M. Deyle
Cancer proteins often show mutations indicative of a cell shifting to a malignant state, thus providing diagnostic
value. The E17K mutation is a single amino acid point mutation in the Akt1 PHD binding pocket that is an
interesting cancer biomarker, owing to its manifestation in breast, ovarian and colorectal cancers. yleaf, a 5-mer Damino acid sequence of length 5, has been found to possess a selective binding affinity to the mutated Akt1
binding site with little to no affinity for the non-mutated wild-type site. The aim of this project is to evaluate the
feasibility of using yleaf as an anchor ligand by quantifying its binding affinity for the mutated Akt1 binding site,
using High Performance Liquid Chromatography (HPLC) to detect for the presence of the Akt1 binding site bound to
the anchor ligand. It was found that while it was possible to validate yleaf as an anchor ligand against the Akt1
binding site, minimization of background signal in this detection would be required to accurately quantify the
binding affinity of yleaf for the Akt1 binding site. Validation of this anchor ligand would then allow for a biligand or
triligand to be developed against the Akt1 binding site in order to achieve higher binding affinity and specificity.
Geographical Load Balancing Visualized
Michael Hirshleifer
Mentor: Adam Wierman
We explore how geographical load balancing can improve the efficiency of renewable energy use in data centers.
The model incorporates varying cooling efficiency (considering weather conditions) and electricity prices over time
at each data center. We run a convex optimization using as input real workload, temperature, solar, and wind
traces. We find that using geographical load balancing lets data centers more effectively use locally available
renewable energy, thereby substantially reducing their usage of grid electricity. This conclusion holds across
seasons. We develop a visualization that displays the demand from each of the 48 contiguous U.S. states and the
energy usage, grid energy usage, and renewable energy generation at each of 10 data centers, animated over time
according to the input data and the optimization output. The resulting software can be used to test effectiveness of
and refine routing algorithms.
High Precision Photoacoustic Spectroscopy and Frequency Stabilized Cavity Ringdown Spectroscopy to
Support Remote Sensing
Daniel Hogan
Mentors: Mitchio Okumura and Milinda Rupasinghe
Based on earlier designs of photoacousic spectroscopy (PAS) and frequency stabilized cavity ringdown spectroscopy
(FS-CRDS), highly accurate PAS and FS-CRDS instruments are constructed. The PAS apparatus is designed to
operate near 770 nm, near the A-band of molecular oxygen. The FS-CRDS apparatus is designed to produce
spectra around 2060 nm, near carbon dioxide transitions. The spectra collected by the FS-CRDS instrument are
sufficiently precise to calculate line shape parameters, and the PAS instrument is used to investigate the effects of
pressure on line mixing. The spectra collected by both instruments will be used as reference data for remote
sensing projects, such as NASA's Orbiting Carbon Observatory.
RNA-Seq Analysis in Individuals With Autism and Controls in Fronto-Insular Cortex and Purkinje and
Granule Neurons in the Cerebellum
Nerissa Hoglen
Mentors: John Allman and Nicole Tetreault
The genetic mechanisms of autism are complex and incompletely documented. The goal of this project is to identify
genes expressed in cells found in fronto-insular cortex (FI) and cerebellum that may be involved in causing autistic
phenotypes. Specifically, we are analyzing quantifications of gene expression made using RNA-Seq performed on
Purkinje cells (found in the cerebellum) and bulk dissections of FI tissue. Our principal statistical tool is hierarchical
clustering, an unsupervised method of assessing the similarity of the samples. Hierarchical clustering analysis has
separated the autistic sample group from the control group in both experiments, revealing genes expressed
differently in the autistic cases than in the control cases. Particularly, in FI, we identified a group of genes that
35
work together to regulate synapse spine development that are expressed more highly in the autistic cases than in
the controls, suggesting that abnormal spine development may be a feature of autism. Synaptic spines are
responsible or receiving most of the information passed through excitatory synapses. As more data become
available from cerebellar microdissections, we will also look in Purkinje cells for a pattern of abnormal expression of
spine-related genes.
Visualization of Gene Expression Domains in S. purp Embryos
Laurits Juulskov Holm
Mentors: Eric Davidson and Julius Barsi
Gene regulation is controlled by interactions between trans-regulatory factors and cis-regulatory sequences. These
interactions, organized into regulatory networks, control the changes in gene expression that drive cell
differentiation and ultimately drive development. I have visualized some of these gene expression domains on the
sea urchin S.purp embryos using fluorescent in situ hybridization. This technique uses chemically labeled RNA
probes which bind to the mRNA in the embryo. These probes are then made fluorescent using chemically linked
antibodies which, when excited, reveal the gene expression domains. Performing this at different time points in
development allows us to visualize the changes in gene expression. This knowledge can later be used to examine
the developmental gene regulatory networks by allowing us to look for changes to the wild type expressions
domains when we change the expression of a transcription factor. Together, these results help provide us with a
better understanding of the different events that ultimately change a fertilized egg into an adult animal.
Soil Sampling on Extreme Terrain: A Pneumatic Device
Kristen Holtz
Mentors: Joel Burdick and Melissa Tanner
A key problem in rover exploration missions is that many of the scientifically interesting areas to investigate are
extremely difficult to access given typical flat-topography rovers. The Axel rover was designed to rappel down
steep cliffs using a tether held securely at the top. It is very important that this rover is capable of taking and
analyzing samples of soil on Mars. Goals for such a sampling mechanism are to collect a sample of at least 2 grams
and store it, and to repeat this. The system developed here is a preliminary system that takes one sample and
stores it using a pneumatic device. A pneumatic approach was chosen due to its simplicity, as minimal actuation
will be needed to move soil. This design can be easily integrated with a multi-sample system later on. Tests to
maximize soil collection were done to choose a design for the system, and this design will be implemented on Axel
soon to test its effectiveness. This work was done in conjunction with another SURF student.
Search for Dark Matter and R-Parity Violating SUSY in Razor Variables With CLs at CMS
Max Horton
Mentors: Maria Spiropulu, Maurizio Pierini, Chris Rogan, and Javier Duarte
In the CMS Razor analysis, the "Razor Variables" R2 and MR are used to reduce the presence of Standard Model
background events and characterize potential new physics signals. This makes the Razor variables a powerful tool
for distinguishing whether a signal indicative of Dark Matter events or R-Parity Violating Supersymmetry (RPV
SUSY) events is present in data recorded by the CMS detector at the Large Hadron Collider (LHC). In the search for
Dark Matter and RPV SUSY, we will examine large regions of data rapidly, searching for potential signals. To
determine which potential signal models we can exclude at 95% confidence level, we perform a hypothesis test
based on the CLs test statistic. The purpose of this project is to develop an automated tool to perform this CLs
analysis.
Determining the Interaction Law for 1D Micrometer-Scale Granular Crystals
Gladia Hotan
Mentors: Chiara Daraio and Wei-Hsun Lin
While interactions between spherical particles on the centimeter scale are well-described by the Hertzian force law,
little is known about the interaction law at the micrometer scale, where dissipative effects from electrostatic and
hydrodynamic forces are no longer negligible. The goal of this project is to determine this interaction law by
1) running numerical simulations on hypothesized force laws to find suitable observables, then 2) experimentally
measuring these observables in a micrometer-scale granular crystal and adjusting the parameters of our
interaction law accordingly. Collisions between an SS440C stainless steel sphere and chains of stationary spheres
between one and five spheres in length in a groove on a silicon wafer were captured in real-time using a Phantom
v12.1 high-speed camera. The velocities of the spheres before and after the collisions were extracted via image
processing. Conservation of momentum and energy were demonstrated reliably in the results.
36
The Effect of Market Designs on Efficiency of Fishing
Lin Hou
Mentor: John Ledyard
Tradable fishing quota markets have been suggested as a method to prevent over-fishing. Revenue neutral
auctions and capacity buy-back auctions can make such policies politically viable. We study three market designs—
a continuous double auction, sealed bid auction and a boat buyback auction—in a laboratory setting to compare
their performance and their effect on the efficiency of fishing.
Autonomous Texture Analysis Under Variable Illumination
Daniel C. Howarth
Mentors: David R. Thompson and Dmitriy Bekker
The Texturecam project is constructing a “smart camera” that can analyze surface images to autonomously identify
scientifically interesting targets and direct narrow field-of-view instruments. The approach, based on a machine
learning strategy, trains a statistical model to recognize different geologic surface types and then classifies every
pixel in a new scene according to these categories. However, it is necessary to assure Texturecam’s performance
across lighting conditions because the statistics of an image is highly dependent on the lighting conditions on the
object being imaged. This work seeks to both expand the Texturecam algorithm to perform robust texture
classification across a wide range of lighting conditions and characterize the limitations of this expansion. An image
dataset was collected which consisted of various rock types imaged under numerous lighting conditions. A
performance analysis demonstrates the utility of different input data representations. We characterize the range of
illuminations under which reliable performance can be achieved.
Investigating the Ability of the Commensal Bacterium B. fragilis to Treat Autism-Like Symptoms in Mice
Sophia Hsien
Mentors: Paul H. Patterson and Elaine Y. Hsiao
It is currently reported that 1 in 88 US children are diagnosed with an Autism Spectrum Disorder. Several studies
show a striking deficit in gastrointestinal (GI) barrier function in autistic children, which has led to the leaky gut
hypothesis: leakage of harmful metabolites in the bloodstream can initiate antibody responses or even directly
affect the CNS, ultimately leading to abnormal behavior. Currently, one of the most widely used mouse models for
autism is the maternal immune activation (MIA) model, in which the injection of viral mimic, poly(I:C), in a
pregnant female yields offspring with the core symptoms of autism: deficits in communication, increased repetitive
behavior, and impaired social interactions. Our laboratory has shown that these poly(I:C) offspring also exhibit a
leaky gut. A metabolite screen of adult MIA offspring serum revealed a 40-fold increase in the putative uremic
toxin 4-ethylphenylsulfate (4EPS). I am investigating whether this abnormal metabolite level is sufficient to induce
autism-like symptoms in otherwise normal mice. Daily injections of 4EPS beginning at 3 weeks of age and
behavioral testing at 6 weeks reveals a numerical deficit in sensory gating that does not reach statistical
significance, as well as a significant increase in startle response, enhanced anxiety, and hyperactivity in 4EPStreated mice, with evidence of a gender difference. Our laboratory has also shown that treatment of leaky gut
using probiotic B. fragilis is able to restore normal behavior. I am interested in how other models of autism will
respond to B. fragilis, particularly the Geschwind CNTNAP2 KO genetic model. Following daily oral gavage of B.
fragilis, CNTNAP2 WT and KO mice were tested for autism-like behaviors. Results show no change in hyperactivity
or self-grooming but a potential normalization of ultrasonic vocalization (communication).
Understanding the Role of Nanoscale Metallic Patterns in Surface Enhanced Raman Scattering (SERS)
Daniel Hsu
Mentor: Hyuck Choo
Surface Enhanced Raman Scattering is a highly useful technique that increases the weak Raman effects of
traditional Raman spectroscopy by orders of magnitude through placing analytes on roughened metal substrates. It
has been reported that the technique allows the detection of the presence of single molecules. This study focused
on identifying nanoscale structures on substrates that are responsible for the Raman enhancement, which would
enable us to fabricate substrates with much stronger, more uniform Raman enhancement. On surface-roughened
silicon chips coated with 150-nm layer of gold and a monolayer of BPE molecules, we made atomic force
microscopy and Raman measurements in the same area. The Raman measurement provided us with the locations
of Raman hotspots while the atomic force microscopy revealed the nanoscale topography within the hotspots. We
then superimposed the two measurements together to match the Raman hotspots with corresponding
nanostructures. This allowed us to make statistical analysis and understand which structures and organizations of
geometries occurred most frequently in hotspots: more frequently seen traits are more likely to be responsible for
the SERS enhancement. Further work will include fabrication and experimental verification of the identified SERShotspot nanostructures.
37
Developing Anti-HIV Antibody Fab Capture Agents via In Situ Click Chemistry for Use in HIV
Diagnostics
Connie Hsueh
Mentors: Jim Heath and Jessica Pfeilsticker
As global HIV incidence remains staggeringly high, there persists the need for inexpensive and accessible point-ofcare HIV diagnostic tools, particularly for use in the developing world. Traditional methods identify anti-HIV
antibodies in patients by using enzyme-linked, commercial anti-human antibody capture agents; but these are
costly and unstable toward dehydration and pH or thermal variation. We developed a peptide capture agent that
binds to anti-HIV IgG Fab with similar affinity and selectivity as commercially raised monoclonal antibodies.
Moreover, they are cheap to produce in bulk quantities and stable enough for easy storage and transportation. We
built upon previously discovered anchor peptides, 4B3 and 3D6, and designed ligands by target-catalyzed click
formation. By incubating the target antibody and anchor peptide with a randomized library of pentapeptides, we
selected for ligands with the desired binding properties, as only ligands with structures complementing the anchor
and antibody region will click by azide-alkyne Huisgen cycloaddition. We then characterized the resulting peptide
products by affinity and selectivity assays to determine their efficacy as drop-in antibody substitutes.
Experimentally Validating and Optimizing Rate Constants in a Model of Activation of Camkii Catalytic
Subunits by Ca2+/Cam
Rebecca Hu
Mentor: Mary Kennedy
One major goal in neuroscience is to understand the underlying biological mechanisms that allow for memories to
be stored in the brain. An influx of calcium ions into neurons ultimately results in changes in synaptic “strength”,
which is believed to be an important mechanism by which memories are encoded at synapses. An important early
target for the influx of calcium is Ca2+/calmodulin(CaM)-dependent protein kinase II (CaMKII). CaMKII is an
abundant component of the postsynaptic density (PSD), a scaffold of signaling proteins that adheres to the inner
surface of the postsynaptic membrane. It is activated when the Ca2+-binding protein calmodulin (CaM) binds to its
subunits and is regulated by autophosphorylation, which is critical for its role in regulation of neuronal properties.
Previously, the Kennedy lab used Mathematica to construct a model of the autophosphorylation of monomeric
CaMKII subunits. We carried out kinase assays varying time and Ca2+, CaM, and CaMKII concentrations over the
most sensitive ranges to validate the model and refine its kinetic parameters. From this ongoing research, we have
narrowed down the value for the dissociation constant, KD, between CaMKII monomers from between 1.3 and 45
µM to between 8 and 12 µM.
Geobiological Approaches to Understanding Pulmonary Infections In Situ: Determining Isotopic
Incorporation Rates for Growth Rate Measurements of Cystic Fibrosis Pathogens
Yang Hu
Mentors: Dianne Newman and Sebastian Kopf
Recent efforts in the Newman lab have focused on the application of geomicrobiological approaches to the in situ
study of the microbial community in CF patients’ lungs. Part of this effort is the development of a stable isotope
labeling technique to measure the incorporation of 2H (deuterium) from H2O into fatty acid side chains of
membrane lipids as a proxy for microbial growth. In order to quantify growth rates from deuterium incorporation
for a given microorganism, the rate of hydrogen incorporation from water into lipids (the water incorporation
factor) must be determined. Using a synthetic cystic fibrosis growth medium and gas chromatography + isotope
ratio mass spectrometry, I determined the lipid profiles and water incorporation factors of three major pathogens
found in pulmonary infections of cystic fibrosis patients. These results were compared with previously obtained
data from Escherichia coli, revealing a noticeable difference between the two constant factors.
Pneumatic Sampling in Extreme Terrain With the Axel Rover
Yifei Huang
Mentors: Joel Burdick and Melissa Tanner
Some of the most interesting regions of study in our solar system lie inside craters, canyons, and cryovolcanoes,
but current state-of-the-art rovers are incapable of accessing and traversing these regions. Axel is a minimalistic
rover designed for extreme terrains, and two Axels with a central mother system form a four-wheeled rover to
efficiently traverse flat ground. Upon approaching the edge of a crater, Axel detaches from the mother system and
travels down the cliff guided by the unwinding tether. However, scientific study of extraplanetary terrains requires
instrumentation inside the Axel rover. We aim to develop a simple and reliable sample acquisition and caching
system that could retrieve multiple samples from various sites before returning them to the mother system where
more sophisticated instruments could perform further analysis. For simplicity and robustness, we propose a
pneumatic sampling system which uses compressed air, guided with a nozzle, to blow soil into a sample canister.
Numerous types of nozzles were designed, built, and tested. Different designs for nozzle deployment, sample
caching, and pressure containment were considered. Finally, a prototype of the entire sampling system was built
and evaluated for performance and feasibility. This work was performed in conjunction with another SURF student.
38
Distribution of Hydrogen Fluoride Towards SgrB2 Complex
Madiha Hussain
Mentors: Thomas G. Phillips and Raquel Monje
The study of diffuse interstellar gas provides a deeper understanding of the properties of the molecular gas in the
early epoch of the galaxy formation and the fundamental constraints in galactic evolution. Light hydrides are
particularly important as they are thought to be at the root of reaction chains that have been theorized to form gas
phase molecules. The spectra produced by these molecules lie at sub-mm wavelengths which are blocked by the
Earth’s atmosphere. Therefore, these molecules are more easily observed using space observatories like Herschel.
We present HIFI/Herschel observations of HF J= 1 – 0 transition towards the bright continuum source Sagittarius
B2. As this source is at the Galactic center, the line-of-sight towards it passes through the spiral arms of the
Galaxy, enabling the sampling of different cloud classes simultaneously. In this paper, the HF observations at
different offsets about SgrB2 (M) are used to determine the HF distribution along these clouds. We observe a
complex variation of column density which suggests that these clouds have an internal structure. We deduce the
physical and chemical properties of the clouds that could have produced the observed distribution.
Nonlinear Dynamic Behavior of Periodic Structures Based on Carbon Nanotube Arrays
Alina T. Hwang
Mentors: Chiara Daraio and Namiko Yamamoto
Carbon nanotubes (CNTs) are highly potential energy dampers because CNTs have a nonlinear, hysteretic response
during compression. The periodic structure consisting of CNTs and rigid interlayers is anticipated to be an effective
damping structural layer, applicable in impact damping or continuous vibration damping. Previous impact testing
on the periodic structure consisting of stainless steel and CNTs has shown the unique trend of decreasing wave
velocity with increasing dynamic force. The origin of such a trend is still unknown and needs to be studied. In this
work, we evaluate the effect of two potential factors on this trend: interface and CNT microstructure. In evaluating
the interface effect, the surface roughness of the rigid interlayer was considered to be low if the roughness was
smaller than 600 nm. We were able to eliminate the interface effect in this study by improving the surface
roughness of the rigid interlayer. As for the CNT microstructure effect, multiple CNT samples with different
densities are being tested, without the interface effect, in comparison with conventional damping foams. This work
is critical in order to understand the mechanisms behind this unique trend and to effectively tailor the periodic
structure for various damping applications.
Modeling the Kinetic Activation of CaMKII in the Postsynaptic Density
Ariella Iancu
Mentor: Mary Kennedy
The creation or deletion of a memory occurs with the strengthening or weakening of the connections between
neurons that form a network. This process is initiated in a highly organized protein complex found in postsynaptic
spines of excitatory synapses—known as the postsynaptic density (PSD). When glutamate receptors and ion
channels open in the PSD, Ca2+ flows into the spine and activates a series of enzymes, including
Calcium/calmodulin-dependent protein kinase II (CaMKII). CaMKII initiates regulation of synaptic connections by
changing the activity of other proteins, as well as its own individual subunits, through catalyzing their
phosporylation by ATP. To understand the highly tuned regulation by calcium ion, the Kennedy lab has begun
creating a kinetic model of activation of CaMKII that will eventually be used in a realistic model of calcium influx
into spines. They created a kinetic model in Mathematica to describe the dynamic relationship between Ca2+,
Calmodulin and catalytic subunits of CaMKII. We have used purified reagents to test and constrain the parameters
of the model by comparing predictions of the model to the results of biochemical assays of activation and
autophosphorylation of CaMKII monomers. We have provided new constraints on two important parameters of the
model: the affinity of two activated CaMKII monomers for each other (monomer KD) and the affinity of activated
calmodulin for individual CaMKII monomers (KACT).
Investigating the Role of Dopamine Receptor 1 in Predicting the Timing of Reward in Mice on Circadian
Time Scales
Jonathan Ikpeazu
Mentor: Andrew D. Steele
It is known that circadian schedules of both vertebrates and invertebrates are influenced by oscillators such as
light. The rising and setting of the sun dictates the behavioral rhythm of nearly all mammals on earth due to the
entrainment of a region within the hypothalamus called the suprachiasmatic nucleus (SCN). In rodents, it has been
found that there is also a food-entrainable oscillator in the brain capable of dictating metabolism and producing
arousal before meals. The neural substrate for this entrainment is yet unknown, but lesion experiments place the
area outside of the SCN. Mice “predict” meals by showing an increase in activity about 2 hours before mealtime.
One mutant, the dopamine receptor 1 knockout (D1R KO), does not seem to predict meals in such a way however.
In this study, we use more potent rewards to investigate entrainment in the D1R KO brain. In the first experiment,
39
we test whether WT and D1R KO mice can be trained to predict timed daily sexual activity of male mice. This
experiment asks about reward that is unrelated to food. In the second experiment, we test whether the daily
feeding of a more palatable meal will result in entrainment of the D1R-KO brain. A preliminary view of the evidence
shows it is likely that the D1R KO brain is not capable of predicting these more palatable meals. The sex interaction
experiment is so far inconclusive.
Comparing Depth of Information Processing Across Visual Masking Techniques
Gregory Izatt
Mentors: Christof Koch, Julien Dubois, and Nathan Faivre
Psychophysicists have developed a multitude of techniques in order to prevent stimuli from reaching visual
awareness. Though each of these techniques establishes subjective invisibility, it is possible that they each stop the
processing of visual information at different stages. Such differences are important to understand in order to make
sense of presently discrepant findings in the unconscious processing literature. To that end, we developed an
experimental paradigm in which we could mask faces with either “backward masking” or “continuous flash
suppression” such that the subject was not aware which technique was being used. In a famous/non-famous
categorization task, the magnitude of priming effects were compared across both masking techniques, and across
different hierarchical levels of prime-target relationships; this comparison allowed us to infer the depth of
information processing allowed by each technique.
Toward Photocatalytic Carbon-Chlorine Bond Formation by Binuclear Palladium(II) Complexes
Megan Jackson
Mentors: Harry Gray, Maraia Ener, and Jeff Warren
A great many Pd complexes can perform regioselective C-H functionalizations, which are essential in the synthesis
of pharmaceuticals and agrochemicals. Our research seeks to improve these catalysts by replacing harsh chemical
oxidants with electricity or light and inert salts. We can chlorinate a variety of aryl compounds including
benzo[h]quinoline and 2-phenylpyridine using bulk electrolysis. Our current efforts focus on performing the same
reactions photochemically. Fluoroborated tetrakis(μ-pyrophosphito)diplatinate(II) (Pt(pop-BF2)), is a potential
photosensitizer in this system because of its long-lived electronically excited state that undergoes facile electron
transfer reactions. Cyclic voltammetry was used to determine the PtII-II/PtI-PtII reduction potential (-1.3 V vs. SCE).
We used this value and fluorescence data to calculate the reduction potential of the electronically excited state
(E°(*PtIIPtII/PtIIPtI) = 1.4 V vs. SCE). Fluorimetry and laser quenching experiments were conducted to probe the
photochemical properties of this molecule.
Evolving the Community Seismic Network
Satyendra Jadaun and Jainil Parekh
Mentors: K. Mani Chandy and Julian J. Bunn
Community Seismic Network is an ongoing project at Caltech. It has already shown a few successes and holds the
promise of being a critical part of emergency response in case of earthquakes due to the early warning and the
spatial intensity estimation (shake maps) it can generate. However, the most critical need for such a system is in
developing countries like India where the existing episensor networks are poor. The project aims at designing a
sensor platform (hardware and software) optimally suitable for deployment in such a situation. It would solve the
problems faced by the current design like network constraints and computer issues, while aiming for a lower cost
per system.
Currently the CSN server back-end only considers warnings (or ‘picks’) from sensors in a predetermined South
California region. But the system can be easily generalized to accept warning from a sensor in any location,
demarcated via a geographic bound that is algorithmically generated, called geocell. The system can then
determine the probability of an earthquake event in the geocell given sufficient number of sensors, and thus work
for serving early warning in every part of the world. Investigations through trial runs on a development system
show promising results for such a structure and mean that the CSN can be a truly global event detection
framework.
Applying a General Principle of Cofactor Switching to Ketol-Acid Reductoisomerases (KARIs)
Ruchi Jahagirdar
Mentors: Frances Arnold, Jackson Cahn, and Sabine Brinkmann-Chen
We aim to switch the dependence on the native cofactor of Alicylobacillus acidocaldarius, a ketol-acid
reductorisomerase (2227 KARI), from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide
adenine dinucleotide (NADH), as NADH is a more industrially favorable. Most NAD(P)H-dependent enzymes share a
characteristic structural element, the Rossmann fold. The A-β2 loop of this fold directly interacts with the side of
the ribose of the cofactor that is phosphorylated in NADPH. Analyzing the cofactor binding loop of the 2227 KARI
structure, we selected amino acid residues situated within 4Å of the 2’ phosphate of NADPH and thus conceivably
interact with the cofactor, for mutation. We designed a library that mutated serine 52 to either aspartate or
40
glutamate and randomized arginine 48. Screening of this library yielded hits with a beneficial NADH/NADPH ratio.
Sequencing five of these hits resulted in a S52D mutation with three having an additional R48K mutation. In the
rescreen, we identified additional hits carrying R48A/C mutations. Based on these results, we designed a library
coding for R, K, C, and A at residue R48 with an S52D mutation and randomizing G50. By repeating this process of
beneficial mutations, we hope to design a fully cofactor switched 2227 KARI mutant.
Effect of the Electrostatic Response of a Polymer Backbone on a Charged Globule
Shruti Jain
Mentors: Zhen-Gang Wang and Issei Nakamura
Polyelectrolytes are polymers whose repeating units have ionic groups. Their thermodynamic properties combine
those of both electrolytes and polymers. The conformation of polymers affects many bulk properties like viscosity
and turbidity. Polyelectrolyte conformations are in turn affected by factors such as polymer architecture, solvent
affinity and charge. Existing models of such systems assume spatially uniform dielectric constant of the solution
equal to that of the solvent. However, the dielectric constants between solvent molecule and polymer backbone are
generally different. In this study, the significance of this effect was investigated at a single molecule level, taking a
salt-free charged globule as a simplest example. Monte-Carlo simulations based on Bond Fluctuation Model were
used to study the variations in solvent distribution and counter-ion distribution in the solution with changes in
dielectric constant of the polymer and solvent. Asphericity, acylindricity and relative shape anisotropy were
obtained to quantify conformational dissimilarity among the different polyelectrolyte systems. The results show
that the conformation of a polyelectrolyte is significantly dependent on the dielectric constant between the polymer
backbone and the solvent.
Retinal Prosthesis System for Vision Restoration
Julie Jester
Mentors: Azita Emami-Neyestanak and Manuel Monge
Patients with conditions such as Age Related Macular Degeneration and Retinal Pigmentosa suffer vision loss and
blindness due to deterioration of photoreceptors in the eye. Previous research has shown that vision can be
restored via electrical stimulation of the retinal using an implanted electrode array. A prosthesis system has been
designed to take an input signal from a camera mounted near the patient’s eye, transmit the processed image
wirelessly to the implant and stimulate the retinal cells. The external image processing system is designed and
prototyped using an FPGA. A monitor is attached to the development board to display the output signal.
Extracting HIV-Neutralizing Antibodies From the Female Genital Tract of South African Patients
Siduo Jiang
Mentors: Douglas Kwon, Melis Anahtar, and Pamela Bjorkman
The HIV pandemic continues to burden more than 30 million individuals worldwide despite over 30 years of
intensive research. Globally, over 90% of HIV transmission occurs during heterosexual intercourse, and most new
cases arise in women between ages 14-24. As a result, the mucosal, or immune, surfaces of the female genital
tract (FGT) acts as a key target for vaccine design as it is the primary site of HIV infection and the female’s first
line of defense against the virus. The CAPRISA 004 trial, conducted at the CAPRISA site in Durban, South Africa,
tested the efficacy of a tenofovir gel, a reverse transcriptase (key HIV enzyme) inhibitor, applied to the FGT before
and after intercourse. It was found that individuals with adherence to the gel demonstrated a nearly 30% reduction
in new HIV infection. However, the mechanism of this control is not yet understood, particularly the interaction
between the tenofovir drug and local FGT mucosal immune system. In order to better understand the machinery of
this vaccine to further improve its reliability and safety, cytobrush samples from the cervix were collected from the
trial patients in South Africa, and shipped to the U.S. to be analyzed using a cutting-edge single-cell analysis
technology developed recently at MIT. We have collected multidimensional immunological data from the very
limited numbers of cells from these cytobrush samples. Particularly with patients who remained HIV negative, the
belief is that the antibody response may play an important role in prolonging HIV control. This new technology
incorporates a process known as microengraving which enables the identification of antibody-secreting cells, and
the recovery of these cells for sequence retrieval and analysis and antibody cloning and expression. I have isolated
several antibody sequences to date, and these antibodies will shortly be tested for HIV neutralization potency.
Additionally, this project has also sought to investigate the antibody and other immune responses of elite
controllers (individuals who are able to maintain their viral load) with the hopes of identifying new and potent HIV
neutralizing antibodies and unraveling new clues for future vaccine design.
Generalizations of Helly’s Theorem
Zhaorong Jin
Mentor: Leonard Schulman
In combinatorial geometry, Helly’s Theorem is a classical result which states “for any collection of compact convex
sets in R with empty intersection, there is a sub-collection of cardinality at most d  1 that also has empty
intersection”. Well understood as the original theorem is, little is known for its generalizations which are of
d
41
particular interest. Two possible ways of generalizing the theorem are dropping the convexity condition to some
extent and allowing the entire collection to have nonempty intersection. We find a counter example to the following
conjecture “if S
 {Ci } where each Ci is the union of at most k compact convex sets in R d then there exists a
subset S’ of S whose size depends only on k, d and  such that
 C    C  B( ) (here  is an arbitrary

CS '
CS
 ) is the open ball of radius  ,the addition denotes the Minkowski sum,
S (C ) denotes the  -contraction of the set C, and Su (C ) is the closed u-slab of minimal width
positive real number, B (
C



uS d 1

u
containing C )”, and prove a special case in
R 2 where each Ci is the union of at most k “strips”(2-dimensional
slabs) with the same width.
Functional Characterization of a Candidate Myod1-Associated Long Non-Coding RNA in Muscle
Differentiation
Robert F. Johnson
Mentor: Barbara J. Wold
In muscle differentiation, MyoD is a master regulator protein which is responsible for differentiation of
multipotential precursor cells to myoblasts, cells committed to the muscle cell lineage. Recent studies have shown
multiple instances in which long intergenic non-coding RNA (lincRNA) are transcribed in mouse and human
genomes and play an important role in regulatory processes in the cell. Previous observations in the Wold lab
identified an evolutionarily conserved candidate lincRNA upstream of the MyoD gene and found that it is expressed
specifically in C2C12 myoblast cells. We set out to determine whether this lincRNA is involved in myogenesis by
loss-of-function and gain-of-function assays on the lincRNA locus in C2C12 cells. In the loss-of-function assays we
planned to delete the lincRNA locus in C2C12 cells using Transcription Activator-like Effector Nucleases (TALENs)
and observe its effects on myogenesis. To this effect, using various computational tools we identified sites for
deletion and designed multiple target sequences. We are presently in the process of validating and constructing the
TALEN target sites and performing the loss-of-function assays. These studies will advance our knowledge of the
regulation of muscle differentiation as well as our understanding of the roles lncRNAs can play in biological
systems.
Multivariate Quadratic Cryptography
Timothy Johnson
Mentor: Leonard Schulman
As quantum computers come closer to reality, various public-key cryptosystems currently in use become
dangerously insecure. It is believed, however, that quantum computers provide no significant advantage against
the class of Multivariate Quadratic (MQ) cryptosystems. In this project, a new form of MQ cryptosystem was
implemented efficiently in Python using the Sage library. Then the time and space complexity of using this system
were estimated theoretically, and tested for various values of our system’s parameters. Next, two of the primary
attacks against MQ systems were studied, and the performance of these attacks was analyzed theoretically. These
attacks were then also implemented using Sage and tested experimentally, to see what values of our parameters
are required for our system to be secure.
Currently the main drawback of our system, as for most MQ systems, is the size of the public key. For the largest
vallues of our parameters, a few hundred MB memory are required. Further work may be done to implement a
variant of our system with conserable lower space requirements, and to analyze its security.
Human Magnetoreception
Kristján Jónsson
Mentors: Joseph Kirschvink and Shinsuke Shimojo
Many organisms are influenced by earth's magnetic field, ranging from fish, birds and mammals to bacteria and
bees. They use magnetic cues to orient themselves and navigate. This means that they have some kind of
specialized organs/organelles that can transduce the weak energy present in an earth-strength magnetic field into
a coded stream of neural action potentials providing information to the brain. There is some suggestive, yet not
firmly-established, evidence pointing to humans possessing a similar mechanism, albeit unconscious. By placing a
human subject into a three dimensional Merritt et al. 4-square coil system and exposing him to a carefully
controlled dynamic and static magnetic field, we aim to to see if this vestigial sense can be brought into
consciousness. However, this experiment will be a stepping stone for a more elaborate one using EEG equipment to
monitor brain activity and using both psychophysical and neural feedback procedures to train the human
magnetosense into consciousness.
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Designing a New Instrumental Conditioning Paradigm for Spatial Learning
Rebecca Jordan
Mentors: Thanos Siapas and Maria Papadopoulou
We are developing an instrumental conditioning paradigm to study hippocampal-dependent spatial learning.
Electrophysiological recordings in the hippocampus have demonstrated the existence of place cells, the firing of
which is dependent on the animal's location within the environment. The route a rat follows when traversing an
environment dictates the order in which place cells are activated. With our assay we aim to bias the trajectories the
animal will take through space. We use different auditory cues to indicate distinct spatial locations within an open
field arena, at which a reward is provided. By combining the tones in a particular sequence we aim to train rats to
visit the associated locations in the designated order, thereby forcing them to follow a particular trajectory so as to
maximize reward. During this project, we have set up the arena, programmed the aforementioned tasks and we
are currently in the process of evaluating how well the animals can learn the tasks. We are using different
individual rats to measure learning rates and within-group variability. These tasks will be combined in future
experiments with electrophysiological recordings in freely behaving rats to study how activity in the hippocampus
evolves during spatial learning.
On-the-Fly Task-Level Plan Correction for Planar Mobile Robots in Unknown Environments
Alex B. Jose
Mentors: Richard M. Murray, Scott C. Livingston, and Pavithra Prabhakar
Recent work in robotics has made use of formal methods for automatically synthesizing reactive controllers based
on high-level task specifications. However, recent work on formal methods in robotics make limited or no use of
new information as it becomes available online. In this project we analyze potential solutions to this limitation
through use of an incremental plan generation (“patching”) algorithm, wherein a plan to perform a task is
improved online as new sensor data becomes available. The patching algorithm takes advantage of a notion of
nearness in space, thus allowing plans to be partially resynthesized in response to local environmental changes. We
apply this algorithm to the problem of simultaneous localization and mapping (SLAM) in robotics. Specifically, we
implement a patching algorithm in simulation and on the LANdroid robotic platform. This work extends previous
implementations to environments, represented by variable-coarseness occupancy maps, which change in time
through the insertion, translation, and removal of obstacles and goals. We demonstrate the effectiveness of the
algorithm on a dynamic mock office environment.
Measuring the Viscosity of Novel-Metallic Glasses at Elevated Temperatures With Parallel Plate
Rheometry
David Joseph
Mentors: William Johnson and Georg Kaltenboeck
Amorphous metals (metallic glasses) offer much promise over their crystalline cousins with superior strength,
elastic energy storage and corrosion resistance. However, there are several key challenges that must be overcome
before their widespread commercial application. These centre on cost and manufacturing techniques. To compete
with more traditional materials, metallic glasses must be made with less noble elements and ideally should be
processed with one step manufacturing techniques. A promising approach is injection moulding of the metals, but
to achieve this it is necessary for the glasses to have sufficiently low viscosities for the timescale of the processing.
This requires elevated temperatures above the glass transition; however, crystallisation must be avoided. Hence, it
is necessary to characterise new glasses (made from cheaper metals) to determine their viscosity behaviour as a
function of temperature and investigate if while avoiding crystallisation the viscosity is low enough. The objectives
of this SURF have been to set up the experiments capable of measuring the viscosity over the elevated
temperatures and timescales required, repeating measurements on well-studied glasses to ensure the setup is
correct before characterising new Fe-based glasses. It is anticipated that by the end of the placement several novel
glasses will have been characterised.
Hallucinogenic Brain Activity in a Mouse Model of Schizophrenia Using MEMRI
Devashish Joshi
Mentor: Paul Patterson and Natalia Malkova
Maternal infection during pregnancy is a major contributor to schizophrenia in offspring. A key symptom of
schizophrenia is hallucinations, occurring in 50-70% of all people diagnosed. Hallucinations can be induced in mice
using the hallucinogenic drug, 2,5-dimethoxy-4-iodoamphetamine (DOI). Our group used Manganese Enhanced
Magnetic Resonance Imaging (MEMRI) to show that DOI specifically stimulates accumulation of manganese in the
frontal cortex an hour after injection. However, MEMRI of longer-term DOI effects on brain activity have not been
studied. Twenty-four hours after injecting manganese, baseline images are collected followed by double injections
of DOI/saline in intervals of one hour. The mice are imaged again eight hours after the baseline. Masks of the brain
images will be made through skull stripping and the saline and DOI groups will then be co-registered to find
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regions of activity. The results will be analyzed for statistical significance, potentially locating new regions of
activity. In addition, we are assessing techniques to increase the permeability of the blood brain barrier (BBB) to
manganese.
Direct Evolution of Terpene Synthases for Non-Natural C15 Substrates
Karolina Kalbarczyk
Mentors: Frances H. Arnold and Ryan Lauchli
Terpenes represent about half of known natural products, catalyzing reactions which increase the complexity of
substrates and generate cyclizations of the linear diphosphate substrates, therefore forming rings and
stereocenters. With their diverse functionality, terpenes have the potential to be highly evolvable, with the ability
to accept a wide range of non-natural compounds and with rather high product selectivity. Directed evolution of
terpene synthases can be used to increase activity of the synthase on a specific substrate. Using 19B7, a mutated
terpene synthase that has been evolved for thermostability, we have done directed evolution to select for increased
activity on the unnatural substrate referred to as Surrogate 2, shown in Figure 1. We introduced mutations for this
evolution using random mutagenesis, through error prone polymerase chain reactions, and through site specific
saturation mutagenesis, where an NNK library is designed with a specific active site amino acid targeted for
mutation. The mutant enzymes were then screened and selected for enhancement of the desired functionality, and
subsequent rounds of directed evolution will follow. For evolution of terpene synthases on an unnatural substrate,
site directed mutagenesis has proved the more successful and efficient route, by altering key positions within the
active site.
Figure 1 Surrogate 2 and Product
Regulation of an in vitro Transcriptional Network With Target Molecules: A Modular Approach
Shaunak Kar
Mentors: Richard Murray and Jongmin Kim
In vitro transcriptional circuits enable synthetic biologists to construct biochemical circuits with rich dynamical
behavior in a simple, programmable and modular fashion. Such circuits have also been shown to control nanoscale
devices. To make these circuits functionally more versatile, it is important that the basic functions of inhibition and
activation can be regulated not only by nucleic acid molecules (DNA or RNA) but also by biologically relevant nonnucleic acid molecules namely, proteins and metabolites. Here we engineered a modular interface for these
switches, using aptamers to sense non-nucleic acid signals coupled with toehold-mediated strand displacement to
generate the appropriate inhibitory/activation single stranded DNA signal to regulate the in vitro transcription
switches. In this case we were able to sense the enzyme thrombin which served as the non-nucleic signal for our
proposed design. Binding of thrombin to its aptamer successfully induced a conformational change to allow the
subsequent strand displacement to occur. The sensing event was then fluorescently read out by the state change
of the in vitro transcription switches in an environment favourable for transcription. The current circuit design
allowed a sensitive detection of Thrombin at nanomolar scales. Further, a straightforward redesign can be applied
to sense other molecules by using the appropriate aptamer sequence with little extra design complexity. We hope
to scale up this system using the enzymes T7 RNA Polymerase and RNase to achieve rich dynamical behavior.
Production of Cryogenic Reference Spectra for the Characterization of Icy Planets
Maro J. Kariya
Mentors: James Bradley Dalton III and Corey Jamieson
The bulk of our knowledge of surface deposition is derived from remote sensing. In particular, visible and nearinfrared (VNIR) observations provide unique identification of surface materials. Characterizing the surface deposits
of icy planets is our most direct way to constrain their interior compositions, which in turn can help identify planets
capable of harboring life. For example, Europa may contain a liquid water layer beneath its icy crust. Aqueous
chemistry within this ocean has been predicted to produce sulfate salts. On Earth, there are microorganisms that
thrive in sulfate salts. Characterizing surface deposits using remote sensing measurements depends upon available
laboratory reference spectra. Most mixture modeling analyses use reference spectra that has been taken under
standard temperature and pressure conditions using only one grain size fraction. Under extreme temperatures and
pressure, as well as for different grain sizes, absorption bands of water in substances change significantly in the
VNIR region of the electromagnetic spectrum. Thus, it’s imperative to produce reference spectra taken at
temperatures appropriate to icy satellite surfaces (~50-150 K), of relevant grain sizes (≥10-20 µm thick), and at
wavelengths (0.3-5.5 µm) corresponding to observations taken by Galileo and Cassini in order to accurately
characterize surfaces of icy planets. This work provides reference spectra for magnesium sulfate hydrates of
various grain sizes under conditions appropriate to icy planet surfaces.
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Reactivity of Low Oxidation State Molybdenum Complexes Supported by an m-Terphenyl Diphosphine
Ligand
Jennifer Karolewski
Mentors: Theodor Agapie and Guy Edouard
Conversion of dinitrogen to ammonia (N2 + 3H2  2NH3) is an important industrial process, as ammonia is a
primary ingredient in fertilizer. However, the currently employed Haber-Bosch process is extremely energy
intensive, utilizing approximately 1% of the world’s energy consumption per annum. Based on the precedent of a
Mo-PNP pincer type catalyst, an organic ligand framework was employed to target a structurally similar POP pincer
complex. The ligand was then metallated with molybdenum precursors to form a Mo0(CO)3 species. Efforts were
then made to displace the carbonyl ligands by oxidation and ultraviolet (UV) radiation, in an attempt to bind
dinitrogen. The prepared compounds were characterized using 1H and 31P{1H} nuclear magnetic resonance (NMR)
spectroscopy, infrared (IR) spectroscopy, gas chromatography mass spectroscopy (GC-MS), electrospray ionization
mass spectroscopy (ESI-MS), and single crystal X-ray diffraction (XRD).
Understanding the Effects of Ultraviolet and Green Light in the Dusk Sky on Mouse Cone Cells
Raj Katti
Mentors: Christof Koch and Stefan Mihalas
Mice are widely used as model organisms for understanding brain activity. However, to date, there is not a reliable
model of the mouse visual system. We seek to model the first processing layer in the mouse visual system, make
video recordings of natural scenes from a mouse’s typical environment, and understand the link between the model
and the scenes based on the mouse’s specific ecological niche. The model must address peculiarities of the mouse
visual system including two types of opsins– 'S' opsin with peak sensitivity to ultraviolet light, and 'M' opsin with
peak sensitivity to green light—in mouse cone cells and the distribution of cone cells on the retina with 'S'dominant cells in the ventral region (upper visual field) and 'M'-dominant cells in the dorsal region (lower visual
field). Since mice are primarily nocturnal/crepuscular animals needing to avoid predators and possessing a large
visual field but lacking significant eye mobility, it seems evolutionarily advantageous to put UV-sensitive cones in
the upper visual field, which mainly sees the sky, and green-light sensitive cones in the lower visual field, which
mainly sees the ground. This is consistent with estimates of peak frequency shifts resulting from multiple Rayleigh
scatterings and with the video recordings of the sky at dusk made with ultraviolet- and green-sensitive cameras.
The recordings will allow future work on our model to estimate optimal opsin coexpression patterns.
Observation of Sound Bullets Generated by a Non-Linear Acoustic Lens
Thomas Anderson Keller
Mentors: Chiara Daraio and Carly Donahue
Acoustic fields are used to probe opaque media, to image the interior of the human body and to evaluate materials
and structures non-destructively. Current methods of acoustic imaging use actuators that cannot generate nonoscillatory, high-amplitude signals. In this work, we assemble and test a nonlinear acoustic lens that can focus
solitary waves. Solitary waves are compact stress pulses that can achieve large amplitudes and travel at a tunable
velocity. We use granular chains as nonlinear wave-guides to generate and transmit solitary waves. The objective
is to transmit these solitary waves from the chain to an adjacent linear medium, i.e., water. Using an array of
multiple granular chains we can focus the solitary waves, allowing for the creation of localized, high-energy
acoustic excitations deemed “sound bullets.” The granular chains in the array are separated from the water using
baffles, the choice of which influences the transmission of the acoustic signal. Through experimentation, we find
that the most effective baffles are rigid and flexible. These acoustic excitations transmitted from the granular
chains to the water are observed via the use of a robotically positioned hydrophone. Preliminary results using well
performing baffles and only three chains demonstrate a central focused area of pressure.
Immunoassay Development for Frequency-Shift Based Magnetic Bio-Sensor
Aroutin Khachaturian
Mentors: Ali Hajimiri and Alex Pai
Current molecular level diagnosis is performed in stationary, high-cost facilities with extreme complexity. The CHIC
lab has developed a frequency-shift based CMOS magnetic bio-sensor that can detect 1-µm magnetic beads on
handheld PCB platform. A method for detecting DNA strands in an array format on the magnetic bio-sensor has
been developed and tested. An alternative method, based on Enyzme-Linked Immunosorbent assays, has been
developed for detection of proteins. The resulting device can substitute high-cost facilities and be operates by the
end user in point-of-care diagnostics.
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Optimizing a Heterologous Benzylisoquinoline Alkaloid Biosynthetic Pathway in Saccharomyces
cerevisiae
Sohini Khan
Mentors: Christina Smolke and André Hoelz
Benzylisoquinoline alkaloids (BIAs) are medically important plant natural products. Heterologous construction of
BIA biosynthetic pathways in the yeast Saccharomyces cerevisiae is being explored as a cost-effective, sustainable
source for BIAs, reducing dependence on agricultural sources. The cytochrome P450 oxidoreductases (P450)
salutaridine synthase (SalSyn) and canadine synthase (CAS) are limiting to the heterologous pathway, possibly due
to non-ideal NADPH-cytochrome P450 oxidoreductase (CPR) partnering. The goal of this project is to examine how
mutant and novel CPRs affect activity of P450s in the morphine and berberine biosynthetic pathways. Three
mutants of Eschscholzia californica CPR (EcCPR) and two Aradopsis thaliana CPRs (ATR1 and ATR2) were
characterized by Western blot analysis to determine full-length expression levels, confocal microscopy to observe
localization of GFP-tagged CPRs, and in vivo substrate feeding assays analyzed with LC-MS to measure
accumulation of BIA products. ATR2 was expressed at a higher level but less well localized than ATR1, and only
ATR1 resulted in higher activity of P450s in both berberine and morphine biosynthetic pathways. The three mutants
of EcCPR displayed varying expression and localization profiles, but none resulted in higher CAS activity relative to
the no CPR controls. Further experiments will determine whether ATR2 activity can be improved by lowering its
expression level.
Analysis and Design of Novel in vitro Bistable Toggle Switches
Ishan Khetarpal
Mentors: Richard M. Murray and Dan Siegal-Gaskins
Bistability is a mathematical property observed in many systems, including biocircuits with a great array of
applications. A recent analytical paper predicts several biocircuits which theoretically should exhibit bistability.
These predictions include the Gardner toggle switch and a derivative of it with only one multimeric inhibitor protein.
This study explored the parameter space of the Gardner toggle switch computationally, and recreated it
experimentally under various conditions to verify the analysis. Further, through protein engineering, a monomeric
inhibitor protein was designed for use in the design of the one-arm toggle switch. The properties of this inhibitor
were characterized.
Noncommutative Geometry in Random Surfaces
Justin Khim
Mentor: Matilde Marcolli
Noncommutative tori are well-studied algebras that arise in a number of settings, particularly in mathematical
physics. Another area to which they have been applied is the theory of random surfaces, but at the moment, the
extent of this analysis is somewhat limited. Thus, we further examine random surfaces as they relate to
noncommutative tori.
Electrochemically Coated Ceria Layer for Solid Oxide Fuel Cell Anode
Chang Sub Kim
Mentors: Sossina M. Haile and WooChul Jung
State-of-the-art Solid Oxide Fuel Cell (SOFC) anodes are composed of nickel, an electrocatalyst as well as an
electronic conductor, and yttria-stabilized zirconia (YSZ), an ionic conductor. Such anodes suffer from carbon
coking due to catalytic deposition of carbon on the nickel surface in the SOFC operating environment – high
temperatures (650°C or higher) and hydrocarbon fuel atmosphere. Two principal goals of this project are (1) to
cover the anode with a dense, gas-impermeable layer of ceria to improve long-term thermal and chemical
stabilities in SOFC operating conditions, and (2) to coat a high surface area ceria structure on top of the dense
layer of ceria to increase overall reaction rate in the anode. Cathodic Electrochemical Deposition (CELD) is
employed as a coating method for both dense and porous ceria structures. Physical attributes of each coating are
characterized by scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), and x-ray diffraction
(XRD). Performance analyses of symmetric cells (anode-electrolyte-anode) with and without ceria coatings,
conducted by AC impedance spectroscopy, are presented.
Thermal Management of Monocrystalline Photovoltaic Panels
Do Hee Kim
Mentors: Melany Hunt and Andrew Gong
The Solar Decathlon competition, organised by the US Department of Energy, encourages students to design, build,
and operate an energy efficient and solar-powered residential house. One of the main challenges that must be
addressed is the effect of the Southern Californian climate, the venue of the 2013 competition, on the energy
production. Southern California’s climate in September and October generally has high temperature and low
humidity. The increase in temperature of the solar cells will have a significantly negative impact on the photovoltaic
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panel’s performance. This scientific investigation attempts to calculate the effects of high ambient temperature on
the energy production of the monocrystalline photovoltaic panels, to explore different solutions to cooling the
panels that comply within the competition rules, and to determine how much the panel array size can be reduced
with temperature control.
BiVO4 Photoanodes in Combination With Heterogeneous Oxygen Evolution Catalysts for Solar
Water-Splitting
Laura Kim
Mentors: Nate Lewis and Josh Spurgeon
There is an increasing effort in the semiconductor photocatalysis field to store solar energy by efficiently splitting
water into oxygen and hydrogen fuel using sunlight. However, no semiconductor material that clearly meets all the
criteria for an effective photoanode has yet been discovered. BiVO4 is a promising candidate for the photoanode
because it is an n-type semiconductor that has a good valence band edge alignment for water oxidation and a
relatively low band gap of 2.4 eV. It is oxidatively stable, and is composed of earth-abundant elements. Due to the
poor catalytic ability of BiVO4, a sacrificial reagent or a catalyst is required to oxidize water. We seek to improve
the current-voltage performance and faradaic efficiency of oxygen production of BiVO4 by using various methods to
incorporate oxygen evolution catalysts. We will also investigate an optimal thickness of the material that maximizes
the photoelectrochemical properties under front-side illumination for application as the top cell in a tandem
configuration.
Progress Toward the Cycloisomerization of Alkynal
Seohyun (Chris) Kim
Mentors: Sarah Reisman and Haoxuon Wang
Various oxygen-containing heterocyclic compounds manifest in natural products, most of which draw our interests
for their potentially useful biological activities. Hence, studies in heterocyclizations and cycloisomerizations have
attracted attention, since development of effective preparations can help syntheses of these natural heterocyclic
compounds. However, effective strategies of preparation of seven-membered dihydrooxepines have not been
sufficiently studied, despite the numerous intriguing and potentially beneficial products possessing seven
membered dihydrooxepine rings, such as acetylaranotin or MPC1001B.
The objective of this project is to study metal vinylidene cycloisomerization of alkynal to prepare seven-membered
oxepines. In order to obtain the cycloisomerization product, different reaction conditions, including catalysts,
ligands, additives, and solvents, will be screened, with the goal of discovering a more efficient synthesis than that
previously reported.
Currently, two model alkynal substrates are prepared. Various metals will be investigated to study the reaction.
Optimizing Microfluidic ELISA Tests for Measuring Secreted Proteins From T Cells
Soyoung Kim
Mentors: James R. Heath and Alex Sutherland
Enzyme-linked immunosorbent assays (ELISA) are the most common and sensitive methods to detect protein
levels, but are not easily adapted to measure multiple protein levels from small samples, such as a single cell. In
order to solve this problem, microfluidics-devices have been developed for measuring protein levels in single T
Cells. The goal of this research was to optimize the steps in creating these microfluidics devices by improving the
patterning of biological materials onto a substrate for their use in a single cell ELISA. This was accomplished by
optimizing the protocol to make the microfluidics-device, as well as the patterning of biological materials to be used
in the single cell ELISA. After analyzing the amount of DNA on the surface using a GenePix fluorescence scanner,
the results show the necessary loading of DNA was achieved, ELISAs. Therefore, it is considered that this
microfluidic-device can improve the efficiency to measuring protein levels of T Cells successfully.
Modeling the Appearance of Transitional Disks With Gaps Opened by Forming Planets
Stacy Kim
Mentors: Neal Turner and Andrea Isella
When a protostar is born from a swirling, contracting cloud of dense gas, it emerges with a rotating dusty and
gaseous disk, produced by accretion of the surrounding interstellar material and the demands of angular
momentum conservation. A portion of these disks has an observed deficit of infrared (IR) flux, which can be
explained by a gap that has been observed to stretch across tens of sun-earth distances. Hydrodynamic models
have demonstrated that such large gaps can be produced by the formation of Jupiter-mass planets. The gap alone
fails to reproduce the observed IR fluxes. Filtration of large grains coupled with grain growth within the gap has
been shown to be a promising mechanism for reproducing low IR fluxes. To further investigate this mechanism,
Monte Carlo radiative transfer models combining a planet-induced gap with dust filtration or grain growth have
47
been calculated, from which synthetic observations can be generated. Comparisons with actual observations allow
us to analyze the dust filtration and grain growth hypothesis. We can also predict how effectively disk observations
with the new radio telescope ALMA can constrain this hypothesis.
Using Bioinformatic Analyses to Discover Novel Putative G-Protein Coupled Receptors in the Parasitic
Nematode Trichinella spiralis
Young Min Kim
Mentor: Paul Sternberg
The nematode Trichinella spiralis is an infamous parasitic organism that is well known for causing trichinellosis, a
disease that may result in fever, nausea, diarrhea, and even death, in humans that consume undercooked meat. In
2000, it was estimated that almost 11 million people worldwide were infected by T.spiralis, making the worm one
of the most important helminths to be studied. More than 40-50% of all present drugs target G-Protein Coupled
Receptors (GPCRs), proteins that play a central role in signal transduction. GPCRs have also been extensively
studied in nematodes, since it is through those proteins that the worms receive environmental chemical cues and
act accordingly. Due to such biological and clinical significance, I have decided to analyze novel putative GPCRs in
T. spiralis in an attempt to uncover useful facts about the worm, potentially aiding future studies on the prevention
of T. spiralis infection. In this study, various bioinformatic tools and programs, including 7TMRmine, InterProScan,
Blast2Go, Pfam, NCBI BLAST, SMART, and orthology analysis, were used to identify putative novel GPCRs in T.
spiralis. Specifically, I have focused on the detection of 7 transmembrane domains, the most prominent
characteristic of GPCRs, in T. spiralis genes. By accumulating a comprehensive list of putative GPCRs, it will be
possible to study new potential drug targets and a better understanding of the biology of T. spiralis.
Self-Anchoring Handheld Coring Drill for Use by Astronauts in Microgravity Conditions
Jonathan King
Mentor: Aaron Parness
The objective of future NASA exploration missions is manned in situ sampling and analysis of various astronomical
bodies in the solar system (including Asteroids, Comets and Mars), and the return of samples to Earth for further
study. Conventional drills require a relatively high axial preload or weight-on-bit, which limits their use in
microgravity and on inverted surfaces. To resist these large reaction forces during drilling, a robotic anchoring
mechanism that effectively grips to rough and rocky surfaces has been integrated with a coring drill. The system
consists of a compact rotary-percussive drill with a custom coring bit, a linear translation mechanism and spring
system that will maintain preload and weight-on-bit, and a custom planetary ball screw actuated compliant
anchoring mechanism that employs an omni-directional array of micro-spines that cling to a surface by
opportunistically catching on surface asperities. A prototype based on this design work is currently in fabrication
complete with onboard power and controls, to be followed by testing and data collection.
Optimizing Kinetic Parameters of Terpene Synthase via Directed Evolution
Rebekah Kitto
Mentors: Frances Arnold and Ryan Lauchli
Terpenes are natural products that have many applications as flavors, fragrances, and essential oils. However,
aside from these common uses, terpenes have considerable potential as advanced biofuel precursors. The biofuel
capabilities of terpenes have prompted research into the improving the efficiency and thermostability of terpene
synthases in order to improve production on an industrial scale. This project focuses on the use of directed
evolution to engineer a terpene synthase mutant with improved kinetic activity. This particular project focuses on
the evolution of the Cop2 enzyme, which is known to react with the natural substrate, Farnesyl Diphosphate (FPP).
Substitution of FPP with a slightly modified surrogate substrate, dubbed Surrogate 1, allows the reaction to produce
methanol as a side product. This methanol can be measured using an AOX-Purpald screen and will serve as an
indicator of the amount of product present, thereby measuring the overall activity of the mutant enzyme. As of
right now, we have evolved the Cop2 parent enzyme through random mutagenesis to produce more active mutant
terpene synthases. The T50 of Cop2 was also measured and found to be 37ºC, a temperature that we hope to
improve through later evolution.
Products expected from the natural substrate
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Increasing Ethanol Yield in E. coli and Z. mobilis
Kathryn B. Knister
Mentors: Richard Murray, Emzo de los Santos, Nate Glasser, and Gita Abadi
The 2012 Caltech iGEM (international Genetically Engineered Machine) team, competing against over 100 other
universities, is genetically modifying Escherichia coli and Zymomonas mobilis cells to increase yield of ethanol and
other biofuels. During anaerobic respiration, when no oxygen is present, the fermentation pathway may produce
biofuel as a byproduct. The team will increase ethanol yield by knocking out other fermentation pathways and
increasing the concentration of the reducing agent NADH available for biofuel synthesis. One step toward increasing
yield is detecting changes in ethanol production. The team developed an MTT formazan color change assay to
detect ethanol concentrations from liquid cultures of both E. coli and Z. mobilis. The more ethanol present, the
more yellow MTT will be converted to purple MTT formazan. The level of change is detectable by a 570nm
colorimetric plate reader. Additionally, the team developed transformation protocol for Z. mobilis, a bacterium
which naturally produces more ethanol during respiration, but is not as commonly used in lab as E. coli.
Implementation and Characterization of a New Torque Measurement Scheme for Robotic Actuators
Justin R. Koch
Mentors: John Leichty and Matthew Frost
As robotic actuators and control schemes become increasingly complex such systems require accurate force torque
measurements at individual joints. While sensors exist that measure these forces this new torque measurement
scheme presents a method that utilizes sensors already built in to most actuators. Through the use of encoders,
the torque on a joint can be calculated based on the windup in the gearbox. This allows robotic actuators the
benefits of force torque information without the additional mass and volume of dedicated sensors. Such benefits
include the ability to dynamically adjust rigidness of the actuator or to measure external forces acting on the
system.
In order to run the experiments necessary to characterize this scheme, a device was constructed that allowed fine
control of the actuator, as well as the capturing of sensor data. This device utilizes an Elmo Whistle motor
controller and an Arduino Mega microcontroller to process data and control the user interface via an LCD screen.
Powering the system is a power supply with an emergency stop button for quick power-off. The device can also be
used in other applications for debugging or calibrating actuators in use on robotic systems.
Design and Fabrication of Digital Electronics for Next-Generation Integrated Camera
Chris Kolner
Mentor: Colin McKinney
Engineering-grade cameras on past space missions, such as the highly successful MER CCD cameras, have been
hampered by their limited ability to function in harsh environments. This has required the cameras to include bulky
and power-inefficient environmental support systems to ensure proper operation in their target environment. The
Next-Generation Integrated Camera (NIC) prototype aims to provide a low-power, wide-temperature, engineeringgrade camera which can be developed and deployed on future space missions without the need of environmental
support electronics.Part of the camera design includes digital control electronics for interfacing the camera with
host systems and reading out pixel data from the camera. These controls are designed and implemented first on a
development board to be used with a smaller version of the camera which will be fabricated for testing and
diagnostics. The digital control electronics scan the pixel array and are responsible for managing the analog-todigital conversion (ADC) of the data, as well as generating clock and control logic, and a video stream output which
conforms to the CameraLink standard. Ultimately, the digital design will be included in the final camera chip which
will be fabricated after full testing has been completed on the smaller model. This will allow for a single chip to
perform all of the necessary camera functions.
Effects of Recent Perceptual History on Valence and Attention
Swadhruth Komanduri
Mentor: Árni Kristjánsson
The human mind is quite heavily influenced by its perceptions of the world. To understand exactly how this
mechanism operates, experimental research has focused on the effects of short-term perceptual history. Recent
work using eye-tracking equipment shows that short-term visual history affects the allocation of visual attention.
Furthermore, other work shows that perceptual history also affects valence of the items that were recently seen.
To further understand the influence of short-term perceptual history on visual attention and cognitive behavior,
we have designed two experiments. In the first experiment, we measure the impact of recent auditory signals on
visual perception. Subjects hear one of three tones before being presented with a simple visual task. Unknown to
them, two of the tones have probabilistic associations with particular locations on the screen. We examine how
the auditory cues affect response times in the search task. In the second experiment, we look at evaluative
conditioning effects of visual history on the items that are seen. The observers are presented with a reward--‐
incentivized search task and are told that based on the time it takes for them to complete the task, they will either
49
be rewarded or punished (increments or decrements of money earned). If they succeed, they are presented
with one set of images, and if they fail, they are presented with a different set. We then measure any
changes in valence of the images that are presented.
QuakeSim Project Networking
Daniel L. Kong
Mentors: Andrea Donnellan and Marlon Pierce
QuakeSim is an online computational framework focused on using remotely sensed geodetic imaging data to model
earthquakes. With the rise in online social networking over the last decade, many tools and concepts have been
developed that are useful to research groups. In particular, QuakeSim is interested in the ability for researchers to
post, share, and annotate files generated by modeling tools in order to facilitate collaboration. To accomplish this,
features were added to the preexisting QuakeSim site that include single sign-on, automated saving of output from
modeling tools, and a personal user space to manage sharing permissions on these saved files. These features
implement OpenID and Lightweight Data Access Protocol (LDAP) technologies to manage files across several
different servers, including a web server running Drupal and other servers hosting the computational tools
themselves.
Refining Electrohydrodynamic Deposition (Electrospray) Techniques for Use in Synthesizing Solid Acid
Compounds
Jeffrey Kowalski
Mentors: Sossina Haile, Chatr Panithipongwut, and Rob Usiskin
Solid acids are promising electrolyte materials for intermediate temperature fuel cells to address the decreasing
supplies of fossil fuels and their environmental effects. The problem examined in this project is the reproducible
synthesis of solid acids by electrospray deposition, specifically the solid acids in the cesium hydrogen sulfate—
cesium dihydrogen phosphate (CsHSO4—CsH2PO4) family and the solid solutions of tricesium rubidium hydrogen
diselenate ((CsxRb1-x)3H(SeO4)2). Different concentrations of solutions as well as stoichiometric and nonstoichiometric solutions were electrosprayed in the cone jet mode on a boron doped silicon wafer. The voltage, fluid
flow rate, inlet gas flow rate and temperature, and substrate temperature were varied in order to achieve a stable
Taylor cone. The resulting deposits were then examined using X-ray diffraction (XRD), scanning electron
microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDS) analysis in order to establish the nature of the
product.
Synthesis of New Chelating NHCs for Application to Ruthenium-Catalyzed (Z)-Selective Metathesis
Reactions
Lilja Kristinsdóttir
Mentors: Robert H. Grubbs and Vanessa Marx
Olefin metathesis is used in the making of C-C double bonds which is important in many fields, including polymer
chemistry, organic synthesis, biochemistry and materials chemistry. Ru-catalyzed metathesis generally leads to the
more stable (E)-isomer, but recently, chelating catalysts were synthesized in the Grubbs group that turned out to
be (Z)-selective. To date the best catalyst system is the adamantyl-chelated catalyst bearing a nitrate ligand which
in most cases gives more than 90% conversion with high (Z)-selectivity. The group has explored replacing the
nitrate ligand, backbone substitution on the NHC and changing the N-substituents on the NHC. The effects of
altering the chelating atom have still not been studied so we are synthesizing catalysts which have nitrogen- and
sulfur-based chelating groups. The majority of this presentation will focus on the synthesis of these new bidentate
chelating NHCs and their subsequent attachment to ruthenium. These catalysts will be examined for improved
performance and stability in (Z)-selective metathesis.
Perturbing Embryonic Stem Cell States by Inducible Expression of Pluripotent Transcription Factors
Jennifer Ky
Mentors: Michael B. Elowitz and John Yong
Embryonic stem (ES) cells are pluripotent, meaning each cell has the potential to differentiate into any adult cell.
A fundamental theme of stem cell research is investigating how ES cells make cell fate decisions at the single cell
level. Recent findings suggest that ES cells exist in at least two coherent cell states, each characterized by
combinations of high or low levels of expression of bimodal genes. These cell states may bias differentiation to
result in lineage priming. To investigate the dynamics of cell state switches, the bimodal genes Nanog, Rex1, Cdx2,
Klf4, Lifr, and Trim 28 will each be transfected into reporter cell lines and overexpressed to gauge if such
perturbation is sufficient for cell state switches. Their effects will be monitored through flow cytometry which
measures the reporter fluorescence of each individual cell, indicating a high or low state. These genes are in the
process of being cloned into inducible constructs and the transfections experiments will be carried out as soon as
the constructs are ready.
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Cobalt Catalyzed Hydrogen Evolution
Stephanie M. Laga
Mentors: Harry B. Gray and Smaranda Marinescu
Hydrogenase enzymes that contain iron and nickel cofactors catalytically evolve dihydrogen, a clean and renewable
fuel, from water. However, the large size and relative instability of these enzymes under aerobic conditions has led
to the search for well-defined molecular catalysts that can produce dihydrogen in a non-biological system.
Synthetic cobalt complexes are being developed and tested as electrocatalysts for the production of hydrogen.
These complexes have a tri-phosphorus ligand framework with aryl groups that have been substituted with electron
donors (-CH3 and -OCH3). Because the ligand is not commercially available, several synthesis pathways, adapted
from literature procedures, have been investigated. The necessary phosphine was synthesized from inexpensive
starting materials and reagents. This phosphine was used in reactions with KOtBu or Ni(PPh3)2Cl2 to form the
desired triphos ligand. 1H and 31P NMR revealed that the former method yielded the desired ligand with the highest
purity (>90%). Cobalt (II) iodide was combined with one equivalent of the triphos ligand, yielding the cobalt (II)
complex as reddish purple crystals, whose structure was confirmed by NMR and X-ray crystallography. Cyclic
voltammetry showed that the CoI/II reduction potential of the complex had shifted down 500 mV in comparison to
the unsubstituted triphos system that had been previously investigated by the Gray group.
Developing an Improved Method for the Extraction of Fossils From Asphalt
Katherine Q. Lai
Mentor: Alex Sessions
Located near Los Angeles, Rancho La Brea is home to asphaltic deposits that have accumulated literally millions of
fossil bones over the past ~40ka. While bones from macrofauna can be excavated with hand tools, microfossils
must be isolated by dissolving and sieving the asphaltic matrix. Currently this is done using solvents that are either
environmentally unfriendly or too expensive. The scale of the task is also daunting, with several cubic meters of
excavated asphalt waiting to be processed. The purpose of this SURF project was thus to develop an improved
methodology for dissolving asphalt to recover microfossils, with the three goals of minimizing its environmental
impact, lowering its cost, and increasing throughput. Based on extensive laboratory tests, we have settled on
biodiesel as an optimal solution. Although it is a relatively poor solvent at room temperature, its efficacy improves
dramatically with temperature, completely dissolving asphalt in as little as 10 minutes at 80ºC, and dissolving up to
~50% asphalt by weight. Rates of dissolution are primarily a function of temperature, solvent/asphalt mass ratio,
and matrix composition. Surface area/mass ratios were found to have relatively little influence on rate. Biodiesel
also provides several other benefits, including low cost, low volatility, low toxicity, and easy disposal. A minor
drawback of biodiesel is that it leaves an oily residue on samples, and does not air-dry. We tested a number of
drying strategies for samples, and found 95% ethanol at room temperature to be optimal. Based on these findings,
we present a model system for recovering microfossils from asphalt that provides high throughput and minimal
handling.
Measurement of the CMS ECAL Performance With Z Dielectron Decay Events in 2012 Data
Valère R. Lambert
Mentors: Maria Spiropulu and Adolf Bornheim
The detection and measurements of the decay mode of the Higgs boson into two photons for the Compact Muon
Solenoid experiment (CMS) is crucially dependent on the energy resolution of the Electromagnetic Calorimeter
(ECAL) as the energy resolution of the detector dominates the mass resolution of the decay channel. The mass
resolution of the ECAL detector is measured by reconstructing the Z peak from its decay channel into two electrons
with an optimization of electron ID selections and measuring the width of the peak by fitting it with a convolution of
BreitWigner and CrystalBall functions. We measure the mass resolution of the CMS ECAL with Z dielectron decays
in 2012 Data and Monte Carlo and discuss potential reasons for discrepancies between Data and Monte Carlo
performance, such as regression corrections, MC shower simulation, detector calibration, laser correction from the
detector monitoring system and increased pile up.
SpectroPolarimetric Aerosol Retrieval System Development
Ryan Langman
Mentors: Olga Kalashnikova and Michael Garay
Aerosols, small particles suspended in the atmosphere, currently present one of the largest uncertainties in climate
prediction. To better understand how aerosols affect climate forcing, it is necessary to have a reliable means of
measuring aerosol microphysical and optical properties on a global scale. The Multiangle SpectroPolarimetric
Imager (MSPI) is a remote sensing instrument with the ability to measure polarization more accurately and in a
broader spectral range than any current satellite-based instrument, which should allow for significantly more
accurate retrievals of aerosol properties. But before polarimetric measurements can be utilized for aerosol
characterization, a good understanding of how aerosol microphysical properties relate to polarization is required. In
order to explore these relationships, we used Mie theory and a Dynamic Light Scattering code to simulate spherical
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and non-spherical particles, respectively. The results were used to examine correlations between aerosol shape,
size, and composition, degree of linear polarization, and single scattering albedo. We then used these studies to
begin developing an aerosol retrieval system for MSPI.
Controllable Fabrication of Nanoelectronic Devices
Pawel Latawiec
Mentors: Axel Scherer and Sameer Walavalkar
Recent advances in silicon etching techniques have opened up new avenues for basic research as well as device
engineering. Beginning with a flat substrate, intricate three-dimensional geometries can be developed. Upon
further processing, device dimensions can be pushed to the nanoscale, where quantum effects become important
in determining behavior. This project investigates electrical transport in silicon nanowire transistors and the optical
properties of silicon quantum dot emitters coupled to gold surface plasmons. These devices are fabricated by a
scalloped sidewall etch which introduces profile variation. After a terminal oxidation step, silicon volumes are
brought into the mesoscopic regime. Transistors are contacted via a self-aligned nickel silicide. Initial results reveal
consistencies with tight-binding simulations as well as confirm the ambipolar nature of the device. Silicon quantum
dots are fabricated in a similar process. After gold deposition and reflow, the emitters couple with the surface
plasmon modes. Luminescence of gold nanoparticle mats and coupled emitters is measured and compared against
bare emitters. Technologies like three-dimensional etching pave a clear path in pushing novel physics experiments
toward reproducible device reality.
Support Vector Machines for Seabed Scallop Detection
Michael Lauria
Mentor: Thomas Runarsson
In this paper the problem of detecting Icelandic scallops in noisy images of seabed is considered. In previous work
a support vector machine (SVM) was trained on manually curated data, achieving 80% accuracy on a test set of
positive instances. The introduction of Bayesian estimation denoising, a locality-improved kernel, and new feature
selection methods resulted in improved accuracies. A comparison of combinations of these methods showed that
denoising in conjunction with a feature selection of the center of the image and a locality-improved kernel yielded
the best results. This method, with kernel parameters set by cross-validation, resulted in an accuracy of 96.33%
on a larger test set which included both positive and negative instances, however, it resulted in only 73.18% on
the previous test set. Removing the denoising step actually improved this result to 74.53%.
Controlled Phase Object for Calibration of Schlieren Imaging in T5 Hypervelocity Shock Tunnel
Albert K. Lavin
Mentors: Joseph Shepherd and Nicholaus Parziale
The T5 Hypervelocity Shock Tunnel uses the Schlieren imaging method to visualize changes in density of flows in
the test chamber. While this method provides a clear qualitative image of the test results, it does not provide
precise numerical data describing the aforementioned density gradients. In order to provide a numerical
comparison to these images, a controlled phase object can be introduced into the Schlieren system to gather
images of known density gradients and ambient conditions. This controlled phase object uses a controlled
temperature difference across a gas gap to create a known density gradient in the gas. When imaged, the
controlled phase object successfully produced and showed a known engineered density gradient. In practice, this
device can be used to ensure successful imaging results for upcoming experiments as well as provide information
on the internal conditions of the test chamber during a test.
Creating Tools in Virtual World, vCaltech, for Scientific Data Visualization
Elizabeth Lawler
Mentor: George Djorgovski
With data sets in multiple scientific fields becoming increasingly complex a need for a way to better visualize
complex data has arisen. Data visualization in immersive virtual realities answers this need by allowing data to be
plotted with multiple attributes, such as size, shape, color, position, etc. An immersive world also lets researchers
move through and around their data creating greater comprehension of the data set. OpenSim is an open-source
version of SecondLife and is a virtual world server that provides a 3D immersive experience. Working in Caltech’s
own virtual world, vCaltech, and using C#, Linden Scripting Language, OpenSim Scripting Language, and
OpenSim’s modules, a 3D plotter and other visualization tools will be developed. This project seeks to improve
virtual worlds as a tool for scientific research and education by expanding on and creating new tools for
visualization that will allow researchers to quickly graph large magnitude data sets, efficiently update data sets,
select points with similar characteristics for further examination, and other applications of visualization.
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ISS EarthKAM Image Geo-Correction Interface Using the Google Earth API
Dennis Lazar
Mentor: Paul Andres
EarthKAM is an educational program funded by the National Aeronautics and Space Administration. The program
aims to provide the public the ability to picture Earth from the perspective of the International Space Station (ISS).
A controllable camera is mounted on the ISS in a nadir pointing window however, timing limitations in the system
cause inaccurate positional metadata. Manually correcting images within an orbit allows the positional metadata to
be improved using mathematical regressions. The manual correction process is time consuming and thus,
unfeasible for a large number of images. In the previous interface the metadata is downloaded, edited through the
Google Earth application, and uploaded back to the server. Our web interface uses the Google Earth JavaScript API
along with PHP-PostgreSQL to present the user the same interface capabilities without leaving the web. The simpler
graphical user interface will allow the public to participate directly and meaningfully with EarthKAM. Our knowledge
may also be applied to imagery from the Mars Exploration Rover (MER) and Mars Science Laboratory (MSL). We
are exploring the use of similar techniques to place ground based observations in a Google Mars environment
allowing the MSL Science Team a means to visualize the rover and its environment.
Textual Topic Modeling With Applications to Political Science
Jetson Leder-Luis
Mentors: Dustin Tingley, Arthur Spirling, and Jean Ensminger
Topic modeling is an important tool for computational analysis of text. In order to gain insight into the content of
documents without direct human processing, topic modelling code is used to fit distributions of topics, which are
words with various weights, to documents and corpora. In this project, we develop modified versions of the
Correlated Topic Model software to incorporate new statistical approximations, document-level metadata, and
corresponding metrics and visualizations to the new models. Results on sample datasets are discussed.
Impact of a Single Edge on the Network Capacity
EunJee Lee
Mentors: Michelle Effros and Michael Langberg
Finding the capacity region of a general multi-source multi-demand network is often a hard problem.
Understanding how much difference a single edge can make in the capacity of a large network is important for
developing systematic tools for bounding the capacities of such networks. In this study, we investigate the impact
of a single edge connected to a terminal edge. Also, we found the multiplicative change, as opposed to the additive
impact, of removing a single edge on network capacity by using equivalence between upper and lower bound
network topologies. Further, we can extend the result to find a new family of networks having consistent impact of
removing a single edge on network capacity.
Investigation of Room Temperature CVD-Grown Graphene Using Plasma-Etching Technique on Copper
Substrates
Jong Yeon Lee
Mentor: Nai-Chang Yeh
Graphene has remarkable electronic and physical properties, such as the massless relativistic dispersion relation
near its Dirac points at the edges of the Brillouin zone, and the presence of inequivalent valleys that allows charge
carriers to travel without back scattering, which results in high electronic mobility. However, current fabrication
processes such as chemical vapor deposition cause strain and distortion, so that strain-induced effects such as local
pseudo magnetic field and charging arise. To decrease these mobility-lowering effects due to strain and distortion,
plasma-etching technique was introduced to treat the surface of transition metal substrates, followed by CVDgrowth of graphene at room temperature. These room temperature grown graphene samples were mainly
examined through Raman Spectroscopy because Raman spectral shifts of the G and 2D bands can provide
information about the average biaxial strain on the graphene. Conductance measurement and Scanning Tunneling
Microscopy/Spectroscopy were also performed for detail investigation. Moreover, to investigate substrate
dependence in CVD method, single crystalline copper substrates with (111) and (100) crystalline orientations were
used for comparison with graphene grown on polycrystalline copper foils. Experimental results allow comparison
between high-temperature (~ 1000C) CVDgrown graphene and room temperature grown graphene, showing
significantly reduced strain in graphene sample fabricated by our new method.
Partial Polarization Transfer for Rapid and Sensitive Nuclear Magnetic Resonance
Juhee Lee
Mentor: Daniel P. Weitekamp
Nuclear magnetic resonance is a very powerful method to noninvasively obtain chemically-specific spectra and
images revealing molecular transport and reactions. A current challenge is to maximize the information available
from coupled spin systems comprised of a slowly relaxing isotope S and a more sensitive, but rapidly relaxing,
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isotope I. The HINDER (hyperpolarized insensitive nucleus delivers enhancement repeatedly) strategy (V.A. Norton
and D.P. Weitekamp, J. Chem. Phys. 2011) employs efficient partial polarization transfer from S to I in order to
obtain multiple points of a kinetic time series from a single reservoir of initial spin order. Example pulse sequences
were derived analytically for the InS system, but numerical simulations are needed to optimize pulse and timing
parameters and to include the effects of spin relaxation. Software has been developed for this purpose and is being
applied to design experiments for small molecules suitable for metabolic imaging with stable isotope spin labels.
Study of the HCAL Fit-Based Noise Filters in 2012 Data
Lisa M. Lee
Mentors: Maria Spiropulu, Artur Apresyan, and Yi Chen
Performance of the fit-based filters for anomalous background signals for the 2012 collision data needs to be
studied and validated. These filters typically use the pulse shape to separate signal from anomalous signals. The
higher pileup conditions at the Large Hadron Collider in 2012 require that the filter performance be reevaluated
since the signal shape can be influenced by in-time and out-of-time pileup. Using 2012 data, we examine various
noise discriminants, specifically pulse-shape discriminants (isolated, flat, spike, and triangle pulse-shape), the
isolation-based R45 filter, as well as the Χ2-based Λ statistics, for the Hadronic Calorimeter (HCAL) barrel and
endcap anomalous signals. Using these, we determine which areas of the detector are persistently noisy, as well as
the performance of the algorithms on 2012 data. Overall, read-out-box 8 is particularly noisy this year, and the
endcap regions have an unusual number of channels flagging as noise, but these channels are contributing low
energy so the current algorithms are still acceptable. I have also proposed a new configuration of the algorithms to
remove over-tagging of the channels.
Understanding the Molecular Mechanisms That Regulate Nicotine Response in C. elegans
Michelle Lee
Mentors: Paul Sternberg and Meenakshi Doma
C. elegans exhibit a behavioral response to nicotine that parallels those seen in mammals such as acute response,
tolerance, withdrawal, and sensitization. Systematic laser ablation of command interneurons showed that the AVA
interneuron is essential for the behavioral response to nicotine. Accumulating evidence suggests that epigenetic
and transcriptional processes play an important role in addiction. Strains mutant in specific genes involved in
epigenetic and transcriptional regulation processes were analyzed using a population assay that tracks multiple
worms at the same time to quantify their locomotory responses to acute or chronic nicotine. MATLAB software was
then used to extract the weighted mean speed, track distribution, distribution of track means, and mean speed for
each worm population. Mutant genotypes that show altered behavior from the control group indicate that they play
a role in nicotine response.
Rising Hope for Rising Up: Constructing Stand Frame for People With Spinal Cord Injury
Seoungjun Lee
Mentor: Joel Burdick
Seeking a possible medical solution to epidural spinal cord injury, SCI scientists have developed the study of
electrical stimulation to provide a better understanding of nervous systems. In particular, a team of researchers
from Caltech, UCLA, and the University of Louisville has utilized a stimulating electrode array to assist a man who
had paraplegia as a result of a motor vehicle accident in July 2006. After training sessions over 26 months, the first
patient, Rob, was able to achieve full weight-bearing standing with supportive stand frame during electrical
stimulation, and he also recovered voluntary movement over his limbs after seven months of epidural stimulation.
This paper specifically discusses the key design features and adjustments of a stand frame that patients may utilize
at home to enable post-clinic training sessions under the influence of epidural stimulation. This project, focusing on
designing and constructing a new stand frame for SCI patients, develops the configuration of a balance board and
analyzes the functions of T-slotted framing structure known as 80/20. Preparing for the third patient, various
support mechanisms including straps and heel cups are improved to accommodate patients of different physique.
The future design development focuses on safety issue and relatively more practical and inexpensive construction
of the frame.
Do Mechanosensitive Channels Have Help When Bacteria Are Osmotically Shocked?
Sojung Lee
Mentors: Rob Phillips, Heun Jin Lee, and Maja Bialecka-Fornal
Mechanosensitive channels (MSCs) are channels that protect bacteria during sudden decreases of aqueous
environment osmolarity, so called downshocks. During a downshock, MSCs are opened, allowing a net influx of
water and outflux of various solutes (osmolytes). This process protects bacteria from membrane rupture included
by osmotic stress. When there is no shock, there are some proteins such as porins and transporters which are
related to the routine maintenance and/or transport of water and osmolytes. It is unclear if these proteins provide
osmotic protection on their own or in conjunction with MSC’s when a shock occurs. In this study, we made single
deletions of a selection of porins, transporters and associated osmo-regulatory genes in Escherichia coli strains that
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have various MSC’s deleted. By examining how the survival rates of these mutants depend on the osmotic shock
conditions (e.g. magnitude and speed of change), we can see if MSC’s receive help from other osmotically-related
genes.
Half-Integral Finite Surgeries on Knots in S3
Eileen Li
Mentor: Yi Ni
Suppose that a hyperbolic knot in S3 admits a finite surgery. Boyer and Zhang proved that the surgery slope must
be either integral or half-integral, and they conjectured that the latter case does not happen. We use the correction
terms in Heegaard Floer homology to prove that if a hyperbolic knot in S3 admits a half-integral finite surgery, then
the knot must have the same knot Floer homology as one of the six cable knots that are known to admit such
surgeries. Since the knot Floer homology contains a lot of information about the knot itself, this result gives strong
evidence in favor of Boyer and Zhang’s conjecture.
A Fundamental Study of Electron Hopping in Engineered Cytochrome c552
Fanfei (Faustine) Li
Mentors: Harry B. Gray and Oliver Shafaat
Many important biological processes involve long distance electron transfer processes, which must occur on short
timescales to be biologically relevant. Traditional electron tunneling theory estimates timescale much longer have
been observed. One possibility is that the electron hops through an intermediate before reaching the acceptor. This
project aims to study electron transfer reactions through amino acid intermediates, using cytochrome c522 as a
scaffold. Various c552 mutants, with different intermediates were engineered. One plasmid, with G41C Y45W
mutations, will serves as a control, while a second mutant, G41C Y45W M69A, is engineered to more readily exhibit
electron hopping. Cytochrome c552 mutant plasmids were expressed in E. coli, and purified using column
chromatography. Purified mutants were then labeled at the mutant cysteine with a ruthenium photosensitizer, and
repurified. A nanosecond laser pulse excites the photosensitizer, which is oxidized by an external quencher. An
electron is then pulled from the intermediate, which subsequently oxidizes the iron heme from FeIII to FeIV. The
electron transfer events were monitored using transient-absorption spectroscopy, observing the change in oxidized
heme soret. Using transient absorption spectroscopy we hope to observe electron hopping events in c552, allowing a
systematic study of long-range electron transfer.
Measuring Neutrino Mass Through Tritium Decay: Project 8
Jarvis Li
Mentors: Joseph Formaggio, Noah Oblath, and Ryan Patterson
Currently, neutrinos are known to have mass, as is evident from the non-zero Δm2 values. However the absolute
masses and the mass hierarchy of the three neutrinos are not yet known. Knowledge of the neutrino’s mass is an
important component of the standard model. Recent experiments using tritium beta-decay have placed an upper
limit of the electron neutrino mass of approximately 2.3 eV. More precise experiments are needed to actually
measure the mass. Project 8 is a new collaboration that aims to measure the electron neutrino mass also through
tritium beta decay. In this experiment, we place tritium gas inside a magnetic field, causing the decay electrons to
undergo cyclotron motion. We will then measure the cyclotron emission from the electrons, which is inversely
proportional to the electron’s kinetic energy. With Project 8 we hope improve the energy resolution by using a
differential approach to measuring the electron energies. Currently the Project 8 experiment is still in the prototype
phase. Magnetic field measurements, RF cavity design, construction of the amplification chain, and development of
the data acquisition system are underway.
Investigating the Impact of Topography on the North American Monsoon
Jingyuan Li
Mentors: Simona Bordoni and Hyo-Seok Park
Although monsoons are some of the most prominent features of large-scale summertime circulation in the world,
the fundamental mechanisms responsible for them are poorly understood. Recent studies suggest that topography
may play a larger role in the monsoon system than previously believed. Mountains can impact the circulation by
both thermal (atmosphere over elevated topography are heated to higher temperatures) and mechanical forcing
(mountains can serve as a mechanical obstacle to flow and thus precipitation). In this study, we analyzed the
effects of topography on the North American monsoon. Several different GCMs (General Circulation Models) were
run, both with the topography intact and with the removal of the Rocky mountains region. Results, especially
precipitation, winds, and moisture transport, were analyzed to give provide insight into how topography affects this
monsoon. In addition, comparison with observed data allowed us to compare the different models and their
accuracy.
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Studying the Thermodynamics of Glass-Forming Metals Using Ohmic Heating
Nannan Li
Mentors: William L. Johnson and Georg Kaltenboeck
Capacitive discharge heating was used to heat metallic glasses at rates of 105 -106 K/s; avoiding crystallization and
allowing measurement of liquid properties at temperatures previously inaccessible. By simultaneously measuring
the current, voltage drop, and temperature of a material during the discharge process, dynamic enthalpy and
temperature measurements were acquired for Zr46.25Ti8.25Cu7.5Ni10Be27.5 (Vitreloy 4). The effect of this rapid heating
rate upon relaxation processes occurring during the glass transition was studied. The effects of thermal history on
glass transition temperature and enthalpy recovery were studied by annealing samples at various temperatures
near Tg before using this high-speed calorimetric technique.
A High-Throughput Screen to Identify Small Molecules That Affect Circadian Rhythms in Larval
Zebrafish
Suna Li
Mentors: David Prober and Eric Mosser
The circadian clock, driven by a cyclic negative feedback loop of gene expression, is an attractive target for sleep
disorder research because of its role in regulating the sleep/wake cycle and other physiological processes. We
performed a novel in vivo high-throughput chemical screen using transgenic per3-luc larval zebrafish, in which the
circadian period3 (per3) promoter rhythmically drives expression of the firefly luciferase (luc) gene. By measuring
bioluminescence over time and determining the parameters of the oscillations, we were able to identify small
molecules that modulate the circadian clock in larval zebrafish among available drug libraries. Preliminary
clustering analysis revealed overlapping molecular and functional profiles among small molecules with similar
phenotypes. We further characterized select small molecules with a locomotor assay to determine their behavioral
effects on wild-type (TLAB) larval zebrafish. We will continue screening small molecule libraries, and will also begin
in situ experiments in order to visualize the neural pathways affected by circadian rhythm modulators. We expect
future clustering analyses to shed light on the mechanisms of poorly understood compounds and on the pathways
involved in regulating the circadian clock.
Fabrication and Analysis of Silicon-Germanium Microwire Arrays: Toward an Efficient, Economical
Multijunction Solar Device
Ben Lieber
Mentors: Harry Atwater, Hal Emmer, and Dan Turner-Evans
Multiple band gap, multijunction photovoltaics are of interest as these structures allow for more efficient solar
spectrum absorption as compared to single junction devices. While single junction microwire array photovoltaics
have demonstrated promising optical and photovoltaic performance, little attention to date has been devoted to
multijunction microwire array photovoltaic devices. An outstanding goal of the Atwater group and collaborators is
to fabricate a III-V on Si1-xGex architecture microwire array photovoltaic device. The scope of my project involved
growing the Si1-xGex microwire arrays via chemical vapor deposition (CVD) using the vapor-liquid-solid (VLS)
method. During growth, microwires were subject to p-type (Boron) diffusion under varying growth conditions
including time, grading, and spacing to optimize growth rate and fidelity, as well as Ge to Si precursor
concentrations in an effort to control the composition of the microwires themselves. Microwire array characteristics
including fidelity, conductivity, doping density, and elemental composition will be presented, as well as efforts
toward making pn junction SiGe devices.
Nanoindentation Modeling of Viscoplastic Solids
Ee Jane Lim
Mentors: Julia R. Greer, Siddhartha Pathak, and Nisha Mohan
We consider an isotropic, three-dimensional continuum mechanics-based model to describe the dynamic, finite
deformation of elastic-viscoplastic solids in response to nanoindentation, a continuation of the analysis of the twodimensional uniaxial compression model recently developed and understood in Hutchens et. al. (2011). In this
indentation model, we study a compressible elastic-viscoplastic constitutive relation with piecewise, linear
hardening-softening-hardening flow strength. Besides one-element manual verification, the validity of the model in
describing the deformation mechanism of viscoplastic solids is further verified from two other tests, i.e. by
comparing the results of non-normality condition at one of its possible states of normality and stress invariant
analysis. Using the verified model, we explore the effects of varying hardening-softening-hardening flow strength
parameters on the radius and depth of the plastic zone propagation in the material as a result of nanoindentation.
Unlike in monolithic materials, we observe linearly increasing radius and depth of the plastic zone with increasing
strains at low initial hardening-softening transition flow strengths and strains, which conforms to non-linearity at
higher softening-hardening transition flow strengths and strains. The effect of indentation on the total energy and
kinetic energy of the material confirms the quasi-static analysis on the model.
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Phospholipids as Potential LOX-1 Inhibitors
Haebin Lim
Mentor: Douglas Rees
Lectin-type oxidized LDL receptor 1 (LOX-1) is an endothelial receptor protein that mediates the transfer of oxLDL,
the main component of plaque, from the lumen to the foam cell. Previous studies have shown its inhibition to be
significant in limiting plaque formation and certain variations of phospholipids may inhibit the attachment of oxLDL
to LOX-1. The carboxyl group on one of the carbon chains of 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine
(PAzPC), a commercially available version of the phospholipid, is expected to bind to the nitrogen of lysine (171) on
LOX-1 while the other carbon chain is expected to enter the hydrophobic tunnel. In order to test the binding of
PAzPC to LOX-1, the LOX-1 protein was expressed on Origami B cells and crystallized with and without PAzPC. The
phospholipid was further modified by attaching polyethylene glycol (PEG) for solubility in blood-like conditions and
amine for selectivity. The amine is expected to attach to the serine (170) on LOX-1. Modifications were tested via
Biacore experiments.
iGEM 2012: Increasing Ethanol Yields by Integrating Proteorhodopsin in Bacterial ATP Production
Pathways
Daisy Lin
Mentors: Richard Murray, Emzo de los Santos, Nate Glasser, and Gita Mahmoudabadi
NADH is an important reducing agent in the biofuel synthesis pathway within bacteria such as Escherichia coli and
Zymomonas mobilis. However, bacteria also require lots of NADH in cellular respiration. Bacteria convert NADH to
NAD+ with NADH dehydrogenases in order to generate the proton gradient that drives ATP synthase to produce
ATP. To reduce competition for NADH, proteorhodopsin, a light-driven proton pump, and a pathway for producing
retinal, a required co-factor, will be transformed into strains of E. coli and Z. mobilis in which the genes for NADH
dehydrogenases have been removed. These cells should demonstrate increased biofuel production in comparison
with wild-type bacteria.
Development of a Functional Measure of Barrage Activities and Investigation of Its Nonlinear Effects
Upon a Single Realistic Neuron
Randall Lin
Mentors: Christof Koch and Erik Schomburg
Dendritic properties and specific spatiotemporal configurations of synaptic input are essential to somatic spiking.
Little work has been done to formally quantize the amount of information transferred to the soma that these
nonlinear effects are responsible for. There has been previous work regarding the information theoretic effects of
single synapse to somatic spiking. Extending this measure to barrage-like events of specific spatiotemporal
synaptic events can fully explore the nonlinearities present in the dendritic tree.
Perfluoroalkyl-Poly(Ethylene Glycol)-Poly(Acrylic Acid) Triblock Copolymers for Mucoadhesive Drug
Delivery
Yulan Lin
Mentors: Julie Kornfield, Yong Ba, and Jeremy Wei
Hydrophobic drugs can be loaded into the core of polymeric micelles, which form from diblock or triblock
amphipathic polymers. Poly(ethylene glycol) based copolymers are of interest because PEG is nontoxic and
nonimmunogenic, and fluoroalkyl ended PEG (Rf-PEG) has been shown to form a gel in aqueous solution. However,
previously synthesized Rf-PEGs have not shown mucoadhesive properties. The desired mucoadhesive properties
could potentially be conferred by adding poly(acrylic acid) (PAA), since polyelectrolytes tend to stick to mucus. To
synthesize this new material, heterobifunctional PEG with a hydroxyl at one end and an amine at the other will be
used: first, an Rf group is attached using a Mitsunobu reaction to the hydroxyl end, then the amine end is modified
with a RAFT agent through EDC/DMAP coupling. The poly(tert-butyl acrylate) will be polymerized on the end of the
Rf-PEG, and then converted to poly(acrylic acid). The resulting material will be characterized by gel permeation
chromatography, NMR spectroscopy, a mucoadhesiveness test, and rheology. These tests will allow for the
hydration kinetics, mucoadhesiveness, and rheological properties to be studied. Further tests will be run to
determine its usability in targeted, controlled, drug delivery systems.
Measuring and Modeling the Vapor Pressure Isotope Effect in Ethane
Chloe Ling
Mentors: John Eiler, Matthieu Clog, and Nami Kitchen
The Caltech laboratories for stable isotope geochemistry installed a novel high resolution, multi-collector mass
spectrometer. This prototype is capable of achieving mass resolution up to 27,000 (M/ΔM), while maintaining the
high precision and accuracy of dual inlet gas source mass spectrometry, allowing for differentiation between
molecules with identical cardinal weights (e.g., 13CH4 and CDH3 of mass 17). I am using this instrument to make
precise (±1/10,000) measurements of the vapor pressure isotope effect (VPIE) of liquid ethane (C2H6) for 3
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isotopologues: C2H5D, 13CCH6, and 13C2H6. These data will be compared with prior, lower precision experiments on
C2H5D to establish the accuracy of our measurements. Our addition of previously unanalyzed species, 13CCH6 and
13
C2H6, will eventually be used to refine first-principles models of VPIE’s. The experiments I conducted were
designed to achieve liquid-vapor isotopic equilibrium, demonstrated through bracketing, where the starting
materials were chosen with contrasting differences in isotopic composition and shown to converge in composition
towards equilibrium. Equilibrium experiments were then conducted between -140°C and -95°C and showed small
variations in isotopic composition. This method of measuring the VPIE was viable in a lab, and may be widely used
in the future to study complex organic molecules with the prototype.
ALD Ohmic Contacting Layers for Semiconductor Tandem Water Splitting Devices
Anna Liu
Mentors: Nathan Lewis, George L. Argyros, and Robert Coridan
In the rapidly expanding world of alternative energy, great emphasis has been placed on abundance, renewability,
and impact on the environment, which is why solar water-splitting devices have been receiving a great amount of
attention. The Lewis Group has been exploring the use of separate materials for the photocathode and the
photoanode so that both the hydrogen and oxygen gas evolution reactions can take place in the solar device
simultaneously. However, direct contact between suitable cathode and anode materials yields weak photocurrent
between the two components. Thus we hope that the use of atomic layer deposition (ALD) will provide a conducting
intermediate layer that will promote sufficient photocurrent to split water. Thus far, we have used ALD to deposit
9TiO2:1NbO2 in varying thicknesses onto silicon photocathode substrates and then electrodeposited WO3 as a
photoanode. Current/cm2 was found to be very weak in samples with only a 2nm intermediate layer thickness.
However, current/cm2 evolved in the 130nm 9TiO2:1NbO2 ALD samples were comparable to that of the 130nm
sputtered ITO samples. These observations suggest that a 2nm intermediate layer is too thin to serve as a suitable
current-promoting layer and that Nb-doped TiO2 rivals ITO in its effectiveness as an intermediate layer material.
Interaction Between Membrane Proteins Derlin and US11
Audrey Liu
Mentors: Youngsoo Jun, Bo-Young Kim, and Yun-Kyung Choi
Human cytomegalovirus (HCMV) employs various strategies to disrupt the MHC class I-mediated antigen
presentation pathway for immune evasion. The HCMV gene product US11 induces degradation of MHC-I molecules
via an evolutionarily conserved process termed ER-associated protein degradation (ERAD). HCMV US11 captures
MHC class I molecules in the ER, where they acquire antigenic peptides, and brings them to Derlin, which may
function as a protein-conducting channel dislocating MHC class I molecules into the cytosol. Once in the cytosol,
MHC class I molecules are eventually degraded by the proteasome. US11 has only one transmembrane domain and
when a certain amino acid in this domain is changed such that US11 cannot interact with Derlin, US11 can no
longer translocate MHC class I molecules. Therefore, they are likely to interact through their transmembrane
domains. However, which Derlin transmembrane domain interacts with US11 remains unknown. Using coimmunoprecipitation and Western blotting analyses, we set out to determine this. Identification of the Derlin
transmembrane domain interacting with US11 will provide insight into how the two proteins cooperate to degrade
MHC class I molecules for immune evasion. Understanding more about this evasion mechanism could elucidate
methods to combat HCMV.
Improving Insar Deformation Measurements Over Slowly Deforming Regions: Assessing the Quality of
Atmospheric Noise Predictions From Global Atmospheric Models
Cong Liu
Mentors: Romain Jolivet and Piyush Shanker Agram
Using Interferometric Synthetic Aperture Radar (hereafter referred to as InSAR) to estimate low tectonic strain
rates is challenging because of atmospheric delays. The atmospheric delay consists in two contributions: the
turbulent delay, random in space and time, and the stratified tropospheric delay, which is correlated with the
topography. Different prediction methods can be used to estimate the stratified delay, but they rely on external
datasets, which are not always available. Empirical methods exist as well but need to be used carefully when
tectonic deformation correlates with the topography. Recently, Jolivet et al. 2011 have shown the benefits of the
use of Global Atmospheric Models (hereafter GAMs) to predict the stratified tropospheric delays on interferograms,
all over the world at any time. However, such corrections show variable efficiency over different areas.
In this research, we calculate InSAR delay maps prediction with data from three different climate models, ERA,
NARR and MERRA for interferograms covering the long valley area from 1992 to 2008, the Kunlun fault zone from
2003 to 2009 and the Parkfield segment. We compare the delay predictions from different models and assess for
the quality of each correction. We show estimates of the noise level as a function of the Global Atmospheric Model,
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the season the SAR images where acquired and the time. Our primary results show very few differences between
Global Atmospheric Models. Finally, we test the importance of atmospheric correction in a time series analysis to
improve the overall signal to noise ratio.
Reference:
Jolivet, R. et al., 2011. Systematic InSAR tropospheric phase delay corrections from global meteorological
reanalysis data. Geophysical Research Letters, 38(17).
Engineering Protein-Based Viscoelastic Hydrogels
Erik Liu
Mentors: David. A. Tirrell and Maren E. Buck
The development of new biomaterials is important for tissue engineering and cell-based therapies. In this project,
recombinant DNA was used to generate artificial extracellular matrix (aECM) protein. Multidomain aECM proteins
were composed of elastin and fibronectin domains flanked by pentameric zippers. Expression of these proteins
yields over 50mg/L. Mixing of the tri-block protein with 100mM sodium phosphate pH 7.5 permits formation of
hydrogels. The gel is homogenized by heating in boiling water and cooling on ice. Injectability and rheology of the
hydrogel were studied, showing that the gel is injectable through a needle. Current efforts focus on stabilizing
cross-linking the polyhistidine tags and creating higher-order structures using Cu2+. Initial studies indicate that
these gels are more viscous and hold shape better while remaining injectable. These observations will be quantified
using rheology.
Box Office Prophecy
Hui Liu
Mentor: Charles R. Plott
Motion picture revenues are extremely uncertain. The research is motivated by experimental evidence that a
properly designed information aggregation mechanism (IAM) can collect information that is dispersed across
individuals. The research question is whether accurate information about motion picture revenues is dispersed as
intuitions. Basically, can we gather the wisdom of the crowd. We implemented the Box Office Prophecy market for
movies opening the following week for ten weeks. Typically ten to fifteen people participated in each session. Each
session was composed of (1) box office guessing for two long range movies designed to extract the information in
a time frame in which accuracy of box office results cannot be used as an incentive and (2) a pari-mutuel betting
system for two short range movies. The data demonstrates that information aggregation is occurring in the parimutuel betting system and the prediction we get with IAM is a more reliable possibility distribution rather than a
single source. Moreover, there is evidence that participants generally are affected by the public information
exposed to them before their bidding.
Observation of Cellular Self-Assembly Through Bright-Field Microscopy
Ashley Lo
Mentors: Chin-Lin Guo and Jordan Maslov
Cells have an extracellular matrix (ECM) on their exterior surface, which regulates processes such as growth,
reparation, intercellular communication, and self-organization. When the ECM’s of each cell “detects” the presence
of other cells within their vicinity (~600 μm), these ECM’s will extensively branch out and connect to those of
neighboring cells.
Although it is widely known that the ECM plays a critical role in the ability of cells to self-organize and form
functional structures (organs, ligaments, fibrils, tendons, nerves, blood vessels, etc.), most research is focused on
the beginning (random, scattered cells) and end stages (tissues and organs). Less is known about the intermediate
steps of cellular self-organization. Our research goal is to observe how cells interact and assemble in the early
stages of structure formation. MDCK and MCF-10A cells were cultivated in a cell culture, and seeded into circular
wells 0.5-1.0 mm in diameter and roughly 1 mm deep, containing a medium solution and 2.5% dissolved collagen,
in attempt to stimulate the in vitro formation of ECM and epithelial (cellular) structures such as tubules and lumens
respectively, which are almost ubiquitously found in multicellular organisms.
Waterfall Plunge Pools Evolution Under Constant Forcing: A Study Using Low Temperature
Polyurethane Foam
Daniel Y. Lo
Mentors: Michael P. Lamb and Joel S. Scheingross
Waterfalls are common features in mountain river systems and their locally high erosion rates may set the pace of
landscape evolution through waterfall retreat. The rate of this retreat is thought to be governed by vertical bedrock
incision and undercutting in plunge pools that develop at the base of these waterfalls, but experimental and field
studies examining this relationship have been lacking. Here we attempt the first step in determining the controls on
the erosion rate by examining plunge pool evolution under constant forcing in controlled laboratory conditions.
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Through a series of abrasion mill experiments, we show that erosion of commercially obtained polyurethane foam
scales with tensile strength following the same relation as concrete and a range of rock types, thus showing that
foam is a viable bedrock simulant without traditional concrete inconsistencies. Flume experiments with constant
sediment and water discharge saw the plunge pool evolving following the conceptual model we develop. The plunge
pool first deepens, then widens as sediment deposition due to the greater depth hinders vertical incision but not
lateral erosion. These results show that the “tools” and “cover” effects developed and tested in low-gradient river
channels can be extended to understand waterfall plunge pools evolution.
Predicting the Blazar Anisotropy Energy Spectrum of the Gamma-Ray Background
Cassandra D. Lochhaas
Mentor: Jennifer Siegal-Gaskins
The gamma-ray background is created by many objects and processes that emit light at high energies, including
blazars, star-forming galaxies, and possibly dark matter annihilation. I predict the contribution of unresolved
blazars to the gamma-ray background by creating a mock catalog of blazars and creating sky maps at different
energies from the catalog. The simulated catalog is detailed and includes an energy spectrum for each blazar
varied to match the observed differences in blazar spectra, a random angular position and redshift for each blazar,
and observed flux accounting for the attenuation of high-energy photons due to the extragalactic background light.
From the sky maps, I calculate the angular power spectrum, which gives a measure of blazars' contribution to the
gamma-ray anisotropy. I compare our simulated measure to actual gamma-ray background anisotropy
measurements to determine the blazar contribution to the anisotropy energy spectrum. By understanding the
blazar contribution to the gamma-ray background, we can constrain the contributions of other known and proposed
gamma-ray sources, including dark matter.
Graphene Plasmonic Devices
Josue J. Lopez
Mentors: Harry A. Atwater and Victor Brar
Recent experiments have demonstrated that graphene, a single-layer of carbon atoms arranged in a honeycomb
structure, can support highly confined surface plasmons in the infrared energy range. The energy and dispersion
length of these plasmons have been predicted and demonstrated to be tunable via electrostatic and chemically
induced doping of graphene. The control over the plasmon dispersion is a unique characteristic of graphene and
allows the exploration of a new regime of plasmonics that cannot be accessed in plasmonically active noble metal
structures. To use graphene as a platform for plasmonics, it is crucial to integrate scalable techniques for the
growth of graphene and subsequent fabrication of nanostructures. Herein, we present graphene nanoribbon and
nanohole arrays fabricated via electron and focused ion beam lithography using chemical vapor deposition grown
mono-layer graphene. The graphene was transferred and patterned on Si3N4 surfaces that reduce surface charge
traps and help maintain the atomic smoothness of graphene. Moreover, we transfer graphene onto hexagonal
boron nitride, a substrate that has been shown to increase the electron mobility of graphene and can lead to
improved performance of graphene-plasmonic devices operating in the infrared regime. Our fabrication scheme
now enables the investigation of gate-tunable plasmons in graphene.
Template-Assisted Electroplating of Nanocrystalline Pt Nanostructures
Colleen Loynachan
Mentors: Julia R. Greer and Xun (Wendy) Gu
The influence of reduced external sample size on the mechanical behavior of nanoscale metallic materials with
complex microstructures is not yet well understood. We use template-assisted electroplating techniques to
fabricate platinum nanostructures of controllable geometries. Elucidating the deformation mechanisms of
nanocrystalline platinum is important because of its widespread use in MEMS/NEMS devices. This project
investigates the emergence of novel mechanical properties when extrinsic and intrinsic size effects are combined at
the nanometer scale by investigating the compressive strength of 50 nm diameter nanocrystalline Pt nanopillars.
The nanofabrication methodology used for synthesizing these nanostructures was potentiostatic pulsed
electrodeposition into an electron-beam lithography patterned PMMA template. Electroplating parameters such as
voltage, pulse time, and electrolyte bath conditions were optimized to produce 50 nm pillars and thin films
structures. Compression tests were performed on the 50 nm pillars using the SEMentor (an in situ SEM +
nanoindenter) to determine yield strength and stress-strain behavior. We compared this result to strengths of
pillars with diameters varying from 100 nm to 1 micron with a fixed grain size of 12 nm to determine if there is an
external sample size effect in Pt nanostructures.
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Effects of Varied Stimulus Attribute Processing on Consumer Choice
Tong Lu
Mentors: Antonio Rangel and Cendri Hutcherson
A widely-accepted theory in neuroeconomics is that the brain makes simple choices by assigning values to all
options under consideration and then compares these values to make a decision. During the time course of a
decision, different attributes of the choices at hand are considered at varying times, which can be simulated with
the drift diffusion model. In our studies we show that people are able to significantly alter their food choices when
presented with exogenous cues. Analysis of decision reaction times and mouse tracking data confirms that people
take into account health and taste attributes of foods at different times during the decision making process.
Hand-Off Between Plasmonic Nano-Tweezers in a Nano-Optical Conveyor Belt
Tsung-Ju Jeff Lu
Mentors: Lambertus Hesselink, Jason Ryan, and Yuxin Zheng
Conventional optical tweezers are used to physically hold and transport microscopic dielectric objects. However, the
diffraction limit hinders optical tweezers from manipulating particles below 1 micron. Instead, near-field optics can
be used for trapping particles smaller than 1 micron. Near-field optics can overcome the diffraction limit by taking
advantage of deeply subwavelength field distributions near structured metal-dielectric interfaces. Hence, we sought
to design and fabricate a nano-optical conveyor belt utilizing near-field optics. Specifically, we used gold nano-pillar
plasmonic nano-tweezers for optical trapping. For a nano-optical conveyor belt, we would need to place multiple
nano-pillars close together in a linear array. By rotating the polarization of the nano-pillars back and forth by 90
degrees, we can transport nano-sized particles with dimensions smaller than 100nm in a peristaltic manner. The
basis for the peristaltic movement would be to achieve hand-off between two neighboring plasmonic nanotweezers. The fabrication of the nano-pillars was done using template stripping, which resulted in smooth surfaces
for our devices. Then, we used an optical set-up capable of delivering a controllable laser source to test our devices
for trapping and hand-off capabilities. For future work, we would also like to create a nano-optical conveyor belt
using C-apertures.
Aerial Survey Data Pipeline for Use With Consumer-Level UAV Electronics: Automatic Image
Processing, Mapping, and Surface Analysis
Archan Luhar
Mentor: John Leichty
Imaging with an unmanned aerial vehicle (UAV) is a powerful way to survey an area because it can quickly show a
visual overview perspective. Recently, these drones have become popular in the hobbyist community with cheap
and easy flight control systems available such as ArduPilotMega. Attaching a camera and this system to an airplane
or quadcopter body creates a powerful surveillance machine. Of specific interest to this project is processing the
raw data collected from the UAV to create and analyze a map automatically. There do exist online services to
create maps given this data, but they are not desktop-based, free, or open source. Methods were researched and
implemented to extract and synchronize video frames with positional and orientation sensor data, accurately and
precisely correct fish eye distortion, orthogonalize images taken at an angle, overlay the images to create a
mosaicked map, and analyze the images for certain features such as lakes. Such an all-in-one system and analysis
could be useful to quickly survey partially frozen Alaskan lakes to predict methane seep levels from the areas of
high-contrast unfrozen sections. More generally, with more work on expanding vision capabilities, such a system
could be used to quickly scout an area and identify features such as pools, buildings, and any other type of
discretely defined visual object.
Reverse Engineering of Cell Function
Patrik S. Lundin
Mentors: Richard M. Murray and Jongmin Kim
As the area of synthetic biology develops the need for effective troubleshooting is growing. This project aims to
address this by implementing a genetic circuit, consisting of short (<100 base pairs) double stranded DNA
genelets, in a translation/transcription system. The initial approach was to utilize an Escherichia coli lysate for
closest resemblance to the living cell. The results show a rapid degradation of DNA in this system. Several schemes
to evade this were evaluated; phosphorothioate bonds, lambda phage protein gamS, specific competitive inhibition
and steric streptavidin block. Only the competitive inhibition of exonucleases facilitated a slightly slower, although
not sufficiently, rate of degradation. In light of these issues we advice continuing the implementation of small
genelet circuits in a nuclease free system, i. e. the PURExpress kit.
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Probing the Environment and Dynamics of Modified Cytochrome P450 Electron Transfer Systems With
Time Resolved Fluorescence Techniques
Katja E. Luxem
Mentors: Martin Hof, Honza Sykora, and Harry Gray
Fluorescent probes are frequently used to study protein properties and dynamics. In a previous research project,
we studied electron transfer from the heme to a ruthenium photosensitizer in a modified cytochrome P450 system.
In this project, observed electron transfer was correlated with BADAN fluorescence decay in four cytochrome
mutants. The four mutants exhibited different degrees of BADAN quenching by energy transfer, solvent relaxation,
and photoinduced electron transfer. These changes are reflected in the time resolved emission spectra of BADAN.
Photoinduced electron transfer between tryptophan and BADAN was further characterized. This research elucidates
the relationship between protein structure and observed electron transfer in our model system, and provides
interesting methodological considerations when using the BADAN fluorophore.
Phase Behavior of Side-Group Liquid Crystal Polymers and Small Molecule Liquid Crystal Mixtures as a
Function of Side-Group Alkyl Spacer Length
Nikolaus Mackay
Mentors: Julie Kornfield and Zuleikha Kurji
Liquid Crystals (LCs) are molecules that exhibit phase behavior that is intermediate between that of solids and
liquids, that is, they flow like liquids, but also retain the orientational order that is characteristic of crystalline
solids. Polymers that are functionalized with liquid crystal side-groups, known as side-group liquid crystals
polymers (SGLCPs), can be dissolved in LC solvent adopting an anisotropic conformation upon dissolution due to
the nematic interactions between the solvent and polymer side-groups. These materials have shown promising
applications in non-linear optics, data storage, and display materials. A fundamental question that arises concerns
the role of SGLCP molecular structure in nematic-isotropic transition temperatures (Tni). Mixtures of SGLCP and
small molecule LCs typically show an increasing Tni with increasing polymer concentration, with the maximum Tni
occurring at 100% polymer. Recently, however, the Kornfield group has discovered that at certain concentrations
of SGLCP in LC solvent there is a Tni elevation of 15ºC above both the Tni of pure SGLCP and that of the pure LC
solvent. Decoding this high temperature nematic phase involves investigating the relationship between SGLCP
structural parameters, and their respective phase diagrams. To that end, I have synthesized mesogenic sidegroups with 3,4,5,6,7 carbon spacers for the functionalization of 1,2-polybutadiene. The resulting SGLCPs will be
dissolved in small molecule liquid crystal solvent and a phase diagram of concentration vs temperature will be
mapped out for each SGLCP. The Tni will be determined using differential scanning calorimetry and polarized
optical microscopy.
Superresolution Imaging and Analysis of Telomeric Proteins in Hela Cells
Shalini Majumdar
Mentors: Jigar Bandaria and Melany Hunt
The linear arrangement of eukaryotic chromosomes makes the chromosome ends (telomeres) prone to enzymatic
attack or being misrecognized as DNA damage sites. This could lead to activation of DNA repair machinery and stop
the cell cycle. In mammals, telomeres involve a six-protein complex (shelterin) that protects and regulates
telomere length and sequesters the telomeric termini. Electron micrographs have shown that telomeres end in a
large duplex loop, in which the telomeric terminus is protected in a large displacement loop. However, human
telomeres consist of 2000 - 30000 base pairs of double stranded DNA and recruit thousands of shelterin proteins.
The role of telomere length and abundance of sheleterin in telomere protection remain unclear. We hypothesize
that TRF1 and TRF2 components of shelterin pair and loop telomeric DNA by forming oligomers and the long
telomeric DNA is compacted into a small cluster for efficient telomere protection. To test this hypothesis, we use
superresolution imaging techniques, namely photoactivated localization microscopy (PALM), to image the telomeres
in mammalian cells. mEOS2 tagged TRF1 and TRF2 proteins show that telomeres exist in very tight clusters inside
of the cell. I am testing how disrupting the dimerization domains of TRF1 and TRF2 affect the cluster size.
Characterizing and Classifying the Variability of Transient Objects
Allison Maker
Mentors: George Djorgovski, Ciro Donalek, Matthew Graham, Ashish Mahabal, and Mike Yang
The Catalina Real-time Transient Survey (CRTS) provides us with a catalog of millions of variable stars—stars that
experience a periodic change in luminosity over time. The data for each star includes images and light curves,
which help to determine which type of variable star the object is, or whether the object is not a variable star at all,
but the result of data or recording errors. Most of these objects have already been classified, many by hand.
Methods exist to automate classification, but these are inefficient. The goal of this project is to use data mining
techniques to help find better methods for computerized classification. Important subprojects included going
through 15,500 pre-categorized light curves to aid in figuring out which period-finding algorithms functioned the
best, finding the best statistical parameters of the light curves to best aid in classification, and using Hidden
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Markov Models (HMMs) to map the light curves to find whether distinct models can be used to represent different
classes. This research has made it possible to more efficiently automatically classify variable stars using data that
can be drawn from their light curves.
Southern California Seismic Network (SCSN) Seismometer Orientation Campaign: An Analysis of Field
Data and Vault Conditions
Galina Malakhova
Mentors: Egill Hauksson and Valerie Thomas
The Southern California Seismic Network is comprised of approximately 262 broadband seismic stations that
include three-component seismometers, strong motion sensors, and dataloggers. The orientation of the network’s
horizontal sensors is important for analyses such as locating earthquakes and studying the polarization of body and
surface waves to determine the structure of the earth. Two methods were used to determine the orientation of the
horizontal sensors in the field. Originally, a field technician would determine the direction of “north” using a
compass. Recently, an Octans precision orientation device was used to re-measure the original reading, and to
determine true “north”. In this study, we compare these two readings for each site. We investigated what
conditions are most likely to cause errors in the compass reading, and thus result in an incorrect orientation of the
sensor. The compass readings and the Octan measurements were compiled and analyzed. The conditions causing
the greatest error are being located in a ground level, indoor vault; a floor sensor installation; a north line marking
on the floor rather than on the sensor container; and the sensor having a North marking arrow on its carrying
handle. The individual sensor misorientation was then compared to calculated estimates from an independent
study. A strong correlation supports the validity of both methods.
Applications of Randomized Matrix Solvers
Michael Malek
Mentor: Alan Barr
Data intractability is a problem in virtually every technical field. Inherent limits on computational ability as well as
simple time and budgetary constraints often make direct use of large data sets difficult, if not impossible. Though
classical solutions do exist for this problem of matrix decomposition, many are simply too slow when confronted
with large data sets. In this paper, we examine a new breed of algorithm that exploits randomness to quickly
compute approximate matrix decompositions (we refer specifically to those outlined in “Finding structure with
randomness: Probabilistic algorithms for constructing approximate matrix decompositions”1) and apply these
algorithms to linear systems that arise in a method for physical modeling proposed by Ronen Barzel and Alan Barr2.
1.
N. Halko, P.G. Martinsson, and J.A. Tropp, Finding structure with randomness: Probabilistic algorithms for
constructing approximate matrix decompositions, 2011; available online from
http://authors.library.caltech.edu/27399/1/Halko2011p16112SIAM_Review.pdf
2.
Ronen Barzel, Alan Barr, A Modeling System Based On Dynamic Constraints, 1988; available online from
http://authors.library.caltech.edu/27399/1/Halko2011p16112SIAM_Review.pdf
Modelling the Influence of Sea Ice on Ocean Microseism
Jay Man
Mentor: Victor Tsai
It has been shown that the main source of background seismic noise (microseism) comes from ocean waves. There
exist quantitative models for the transfer of wave energy to the ground, although their validity is still unclear and
the subject of ongoing research. We assume that processes which affect waves will also affect microseism,
therefore the attenuation of ocean waves by sea ice should have a quantifiable effect on microseism in ice-bound
areas. By considering ongoing research into the many variables which govern the interaction of ocean waves with
sea ice, we attempt to determine the relative sensitivity of microseism to these variables. The model will present
potential ways of quantifying sea ice properties to which it is sensitive through the use of microseism data. This
could provide a way to test the validity of the models for the generation of microseism by ocean waves. In addition,
it could be used to quantify the properties of sea ice from the archived seismic record before satellites were in use.
Predicting Therapeutic Response and Resistance of Glioblastoma Multiforme Cancers
Janani Mandayam Comar
Mentors: Jim Heath and Nataly Kravchenko-Balasha
Glioblastoma multiforme (GBM) tumors are the most aggressive primary brain tumors in adult humans. We are
characterizing the thermodynamic states of GBM cells through the measurements of chemical potential of
functional proteins and calculations of energy barriers between the states in order to build a predictive model that
describes the process of cellular transformation and development of therapeutic resistance. In order to construct a
complete picture, we aim to measure the metabolic flux of the cells by determining the ATP levels, glycosylation
rates, and O2 consumption levels. Phosphoprotein concentration of GBM (U87-derived) cells treated with the drug
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Erlotinib (an inhibitor of the epidermal growth factor receptor, EGFR), the phosphotase PTEN (a tumor suppressor
that inhibits the AKT pathway), and a cancerous, mutated form of EGFR, called EGFR vIII was determined using an
ELISA. The analysis has shown that Erlotinib-treated cells experienced an overall decrease in phosphoprotein
concentration. We intend to measure phosphoprotein concentrations of GBM39 cancer, resistant and drug removed
GBM resistant cells. Furthermore we will measure the ATP concentration in each of the experimental groups to see
how phosphoprotein levels correlate with ATP levels in order to assist us in building a free energy map. Investigation of Optical Coupling in 1d Fabry-Perot Nano-Resonators for Solar Cell Applications
Prateek Mantri
Mentors: Harry Atwater, Dennis Callahan, and Jonathan Grandidier
Integral components in nano-optics, optical resonators are already becoming an increasingly important component
in light trapping for thin film solar cells. Depending on a resonator’s material, geometry, and environment it will
trap light at a given frequency, potentially enhancing the absorption in a solar cell active layer at that frequency.
Solar cells, however, often require absorption enhancement over a broad range of frequencies. One way to
increase the bandwidth covered by an optical resonator is to couple it to other resonators, hybridizing their
resonances. In this study we investigate the effect of optical coupling in 1D nano-resonators. Various new designs
have been analysed and optimized for enhancing solar cell absorption. This study could be extended to study
coupling between layers of multi-junction solar cells and can also be combined with other 2D and 3D light trapping
strategies for thin film solar cells.
Synthesis and NMR Studies of Complex Solid Acids
Mary Anne Manumpil
Mentors: Sossina M. Haile and Chatr Panithipongwut
Solid acids are promising candidates for the electrolyte portion of a fuel cell due to their high proton conductivity.
Ball milling was used as a new approach to develop reproducible syntheses of the specific solid acids
Cs3(HSO4)2(H2PO4) and Cs6(H2SO4)3(H1.5PO4)4. The relationships between chemical shift(s) of 1H nuclei, O-H-O bond
lengths between adjacent tetrahedra, and temperature were investigated using solid state-nuclear magnetic
resonance (NMR) and high temperature X-ray diffraction (HT-XRD) to gain a better understanding of proton
movement within the crystalline structure of the solid acid. For Cs6(H2SO4)3(H1.5PO4)4, the changes in proton
chemical shifts and O-H-O distances with temperature are consistent with changes in the structure. Lastly, shorter
O-H-O distances correspond to larger chemical shift(s) while longer O-H-O distances give smaller chemical shift(s).
The Mechanical Behavior and Microstructure of Helium Implanted, FIB-Less Metallic Nanopillars
Jacqueline Masehi-Lano
Mentors: Julia Greer and Peri Landau
Uniaxial compression experiments reveal the effects of helium implantation on the mechanical properties of 100
nm-diameter, monolithic, metallic nanopillars and 100 nm-diameter, interface-containing nanopillars in order to
shed light on the physical mechanisms radiation induces on mechanical properties, and to provide insight for the
controlled design of robust, radiation-tolerant, metal-matrix systems of nuclear reactors. Arrays of nanocompression specimens of single crystalline Cu, single crystalline Fe, and interface-containing Cu/Fe nanopillars
comprised of a single Cu grain on the bottom half and a single Fe grain on top, were fabricated by templated
electron-beam lithography and electrodeposition. Helium was implanted at various energies to produce a uniform
concentration of 0.35at% across the pillar height. Microstructural characterization using scanning electron
microscopy and transmission electron microscopy reveals that implantation does not alter the pillar surface and
that the pillars contain a uniform distribution of helium bubbles across their height. Compression tests on
monolithic Cu and monolithic Fe, both as-fabricated and implanted, nanopillars were performed using a HysitronTM
nano-indenter in a load-controlled modulus for the monolithic pillars, and a displacement-controlled modulus for
the interface-containing pillars. True stress-strain curves show that the uniform implantation leads to significant
increases in flow stresses for the monolithic Cu and Fe pillars compared to their as-fabricated counterparts. The
increase in strength is attributed to helium bubbles acting as obstacles for glide dislocations. Interface-containing
Cu/Fe nanopillars do not show an increase in strength. This is caused by misalignment between the uneven pillar
top and flat-punch indenter tip, which leads to the pillar buckling or collapsing under the applied load.
Exploring the GET Pathway for Tail-Anchored Proteins Through Protein Crystallization and Isothermal
Calorimetry
Jacqueline Maslyn
Mentors: Bil Clemons and Harry Gristick
The GET pathway, found in almost all eukaryotic organisms, functions in the targeting of tail-anchored membrane
proteins to the Endoplasmic Reticulum (ER). Tail-anchored proteins function in several key processes in the cell;
including apoptosis, protein translocation, and membrane fusion. The central component of the pathway, Get3,
functions in binding the tail-anchored protein and targeting it to the ER membrane. Upstream of Get3, the Get4/5
complex functions in bridging Get3 and Sgt2 so that tail-anchored protein handoff can occur properly. Recently, the
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Clemons lab solved a crystal structure of a truncated Get3/4/5 complex. We are now in the process of validating
the structure and biochemically characterizing the interaction using ITC and pull-down assays. Our work also
involves the human homologue of Get3, Trc40. While over twenty different structures of Get3 have been published
in the last three years, they are all from fungal species and very little is known about the human GET pathway. We
are attempting to solve the structure of Trc40 by itself and in complex with its ER receptor WRB, the human
homologue of Get1.
Improving the InSAR Scientific Computing Environment (ISCE)
Sei Masuoka
Mentor: Marco Lavalle
The InSAR Scientific Computing Environment (ISCE) is a new software tool developed recently by the Jet
Propulsion Library (JPL) and the Stanford University. The ISCE development team at JPL is currently working on the
implementation of a new module, the polarimetric-interferometric module. The polarimetric-interferometric module
exploits the InSAR correlation measured between two radar images acquired with different combinations of
receive/transmit wave polarization to extract information about the structure and the temporal evolution of forests.
While working at JPL, I helped the ISCE team develop the polarimetric-interferometric module. I have implemented
a routine that generates the second-order polarimetric-interferometric descriptor (i.e., the coherency matrix). I
have used C code with an efficient management of memory in order to handle multiple data files. I have also
helped implement a polarimetric change detector, which uses the coherent changes between two polarimetric data
rather than the amplitude only. We use a change detector relying on the amplitude and phase of the radar data to
detect changes in scattering mechanisms, which can have anthropogenic or natural origin. I test the new algorithm
using UAVSAR and ALOS/PALSAR data and compare the result with previous approaches.
The Effect of Surface Morphology on the Catalytic Activity of Copper Electrodes for the Electrochemical
Reduction of CO2
Austin P. Mayron
Mentors: Nathan Lewis and Jacob Good
Making the anthropogenic carbon cycle renewable will require a detailed knowledge of the mechanism of catalysis
of CO2 into fuel. One of the most promising candidates for this process is polycrystalline copper, as it is an efficient
catalyst capable of producing hydrocarbons. The exact surface chemistry of this reaction is unknown so, to improve
the efficiency of CO2 reduction, this chemistry needs to be elucidated. Copper electrodes were mechanically
polished with fine emery papers and electrically polished in 85% by weight H3PO4 to create flat, unoxidized
electrodes. From there, the electrodes were subjected to a variety of conditions that selectively roughened and
oxidized the surface. Going forward, these electrodes will be used to reduce CO2 in a custom electrochemistry cell
which allows in-situ measurements of liquid and gas phase products with a mass spectrometer. The electrodes will
then be characterized with Atomic Force Microscopy (AFM) and X-Ray Photoelectron Spectroscopy (XPS). This will
hopefully provide a better understanding of the specific effects of electrode surface features in the electrochemical
reduction of CO2.
Online Real-Time Prediction of Action Timing Using EEG and Intracortical Recordings in Humans
Naomi A. McArthur
Mentors: Christof Koch, Uri Maoz, and Liad Mudrik
Neuroscientific research of free will research over the last 30 years has revealed that binary motor decisions might
be predicted well in advance of a person’s conscious intention to move. However, such research was never
conducted in a live setting—online and in realtime—with a patient before. The goal of this project was to gather
data from both subjects with EEG caps and patients implanted with intracortical electrodes as they press a button
to advance through a series of video clips, and then incorporate the data gathered into a learning model that would
predict the timing of the button press. This learning model will be used in real time to predict the movement of the
patient before movement occurs. During the course of the project, new data was collected, the parameters of the
patient’s task were changed, and the learning model was tested against available data. Future directions would
involve incorporating eyetracking data to improve accuracy, refining the learning model further, testing in real time
with new patients, and observing the effects on the patient’s agency and decision-making when they realize that
their movements are being predicted.
Optimization of Chromatin Immunoprecipitation and Data Analysis for the Exploration of E Protein
Binding Patterns and Their Role in T-Cell Differentiation
Kayla McCue
Mentors: Ellen Rothenberg and Sagar Damle
Certain E proteins, transcription factors that tend to bind to the genomic sequence known as the E-box, are known
to be involved in the specification and differentiation of T-cells. This project sought to deepen the understanding of
what role they play. To get a genome wide picture of the binding sites of these E proteins, a procedure known as
chromatin immunoprecipitation (ChIP) sequencing can be used. Using an early T-cell line and a pre-B-cell line for
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mice, conditions for ChIP were tested for optimization for different antibodies. A GATA3 ChIP that was run provided
data used to test standard analysis as well as a morphological analysis in production during this project. Once the
conditions for the different transcription factors are optimized using the cell lines, the procedure can used to find
binding patterns of additional E proteins in primary cultured mouse T-lymphocytes. By comparing these datasets,
regulatory patterns could be discovered and linked to nearby genes to give an indication of how these E proteins
regulate T-cell differentiation.
Epidural Spinal Stimulation: Modeling of the LumboSacral Spinal Cord in Order to Investigate Improved
Microelectrode Array Designs
Carson McNeil
Mentor: Joel Burdick
Epidural Spinal Stimulation, a promising therapy used to help paraplegics is being pursued by a collaboration
between researchers at Caltech, UCLA, and the University of Louisville. This therapy involves the implantation of a
flexible, biocompatible, electrode array in the epidural space of the lumbrosacral spinal cord of an SCI patient. In
order to evaluate which arrays and stimulus patterns are the most successful in assisting the patients, a simulation
pipeline has been created. The geometry of the lumbosacral cord is modeled as a mesh, and the electric field
penetration is found by solving Maxwell’s equations on the mesh. After this, a model of the neurons in the cord are
put into the field, and the way that action potentials propagate down the neurons is investigated. These results can
be used to create better general stimulation electrode array designs and potentially a greater understanding of the
stimulation process.
Extraterrestrial Chemistry With a Focus on Icy Satellites: A Review
Elaine McVay
Mentor: James (Brad) Dalton
Remote sensing data, computer models, and laboratory simulations have all provided valuable insight into the
chemistry of numerous outer space environments, including icy satellite surfaces and the interstellar medium.
Extraterrestrial compounds identified so far range from volatile ices and inorganic salts to organic molecules as
complex as the sugar glycoaldehyde and the amino acid alanine. Models of chemical reactions and laboratory
simulations are particularly useful in analyzing chemical processes themselves and determining mechanisms
through which compounds are formed in a certain environment. Simulations can determine the stability of a
compound in a particular environment as well as the direction of a chemical reaction. These two methods of
research also provide clues as to what to look for when analyzing remote sensing data.
Remote sensing data has been collected by spacecraft such as Voyager I and II, Galileo, and Cassini, as well as
with ground based telescopes. Imaging spectrometers are particularly useful for collecting reflectance spectra of icy
satellites in the near infrared wavelengths, while visible imaging systems collect wavelengths between 0.35-0.7
microns. This information is highlighted on the Solar System Spectral Database in Dalton 2010. Laboratory
reflectance spectra of pure compounds that cover these two ranges are particularly useful in modeling the
composition of icy satellites.
This paper will review recent work that relates to the chemistry of space, with a particular focus on the
characterization of the surface chemistry of icy satellites in our solar system. It will also highlight the work that
needs to be completed with regards to reference laboratory spectra required to create accurate models of icy
satellite chemical composition.
Physically integrated Ag films as ohmic contacts to the emitter layer of core shell radial pn junction Si microwire
array photovoltaics hold potential for cost-effective, large-area devices. State-of-the-art Si microwire photovoltaics
use a transparent conducting oxide top contact, which involves intensive processing.1 Furthermore, indium tin
oxide contacts cannot be used in a flexible polymer embedded device due to mechanical fracturing when the device
is peeled from the substrate. It has been demonstrated that a thin metal film can be integrated into a Si microwire
array without electrical shorting.2 Employing evaporated films of Al2O3 as electrical insulation layers, Ag films were
deposited to provide wrap-around contacts to only the emitter shells of silicon microwires. These Ag films also
served as a back reflectors redirecting light to the solar cells. Prior to Ag film integration, pn junction devices were
tested electrochemically in 100 mM / 0.4 mM dimethylferrocene (Me2Fc+/0) redox couple in methanol to verify the
solar energy conversion properties and to check for macroscopic electrical shorting. Open circuit voltage of 340 mV
and short circuit current density of 4.4 mA cm-2 were observed. Enhanced light absorption in wrap-around contact
devices are expected increase the short circuit current density compared to conventional pn junction Si microwire
devices, leading to higher device efficiencies.
1.
M.C. Putnam, S.W. Boettcher, M.D. Kelzenberg, D.B. Turner-Evans, J.M. Spurgeon, E.L. Warren, R.M.
Briggs, N.S. Lewis, H.A. Atwater. Energy Environ. Sci., 2010, 3, 1037–1041.
2.
C. Xiang‡, A.C. Meng‡, N.S. Lewis. Proc. Natl. Acad. Sci. USA, 2012.
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Testing the Hypothesis of Late Cretaceous True Polar Wobble (TPw)
Harrison Miller
Mentor: Joe Kirschvink
It has been believed that True Polar Wander (TPW) is responsible for slight variations in seafloor magnetic
patterns. However, preliminary data from Italy and South Dakota suggests that the small variations are too quick
to be TPW. Rather, a different movement is responsible, True Polar Wobble (TPw). The goal of this research is to
capture higher-resolution data for the time period between Chrons 33n and 34n that will hopefully help create a
better understanding of how the pole behaves. Data from Italy has yet to be fully analyzed, but Magnetic
Susceptibility readings seem to show the said wobbling as well as exhibiting a correlation with Milankovitch Cycles.
Data from Australia’s Canning Basin also seems to show us similar wobbles.
Use of Osmium (Iii) Complexes to Determine Influence of Base Mismatches on Oxidative DNA-Protein
Crosslinking
Kelsey Miller
Mentor: Eric Stemp
8-oxoguanine is a common oxidation product in DNA and can lead to mutation. The metallointercalator
Ru(phen)2dppz2+ is a useful luminescent probe for DNA that has also found use as a guanine-selective oxidizing
agent via the flash-quench technique. Here, we use its osmium analogue as a selective way to oxidize 8oxoguanine in double-stranded DNA, as visualized by oxidative DNA-protein crosslinking. With the 3+/2+ couple at
1.15 V for Os(phen)2dppz2+, this metallointercalator should be able to oxidize 8-oxo-G (~0.7 V) without oxidizing
guanine (~1.3V). MALDI mass spectrometry data confirms that oxidizing guanine using Ru(NH3)63+ and
Ru(phen)2dppz2+ produces 8-oxoguanine. In plasmid DNA where 8-oxo-G has been incorporated, flash-quench
treatment with Os(phen)2dppz2+ and Co(NH3)5Cl2+ leads to crosslinking with histone. Furthermore, in gel shift
experiments with a duplex of the oligonucleotide 5’-ATATGATAT8GATATGATAT-3’ (8 = 8-oxo-G) and its
complement, flash-quench treatment with Ru(phen)2dppz2+ in the presence of histone leads to a band of
intermediate mobility (presumably 1:1 crosslink) and to a band of well-shifted material. In contrast, analogous
treatment with Os(phen)2dppz2+ produces only the band of intermediate mobility, consistent with the presence of a
single site that is oxidizable by the osmium complex.
Analysis of Conformer Populations and Dihedral Angles From NMR Coupling Data
Suraj Mirpuri
Mentors: John D. Roberts, Bill Carroll, and Bright Emenike
In computational chemistry, the problem of identifying the dihedral angle around a “CH2CH2” fragment of ethane
systems has many issues such as the dependence on various minimization schemes and the lack of accounting for
solvent effects, making solutions unreliable and unable to handle flexible molecules. Of specific interest to this
project is to write a program that will, given dipolar and vicinal coupling constants from NMR, be able to fit a
dihedral angle for the gauche conformer, trans conformer, and their relative proliferation in solution holistically.
The program obtains structural data from the user, narrows down a list of dipolar couplings using singular value
decomposition, and then superimposes structures to find a fraction gauche with best fit. The program then uses
this value for the gauche fraction in the Haasnoot-Altona relation to back calculate a dihedral angle for the gauche
conformer. This method is both chemically intuitive and mathematically sound, and therefore provides an easy way
to reliably determine dihedral angles despite conformational averaging in solution.
The Fly Puffer: Investigating Escape Mediated by the Mechanosensory System of Drosophila
Neeli Mishra
Mentor: Gwyneth Card
We are interested in studying escape behavior of animals for many reasons: it is necessary for their survival, it is
robust and it is innate. Previous research has shown that Drosophila perform a special set of escape maneuvers
when they are presented with a looming stimulus. This behavior is known to be coordinated by the giant fiber
pathway. The giant fibers are large, descending command-like interneurons that cross the cervical connective. It
has been shown that the giant fibers arborize in regions of the brain that are responsible for visual processing.
However, the giant fibers also innervate the antennal mechanosensory motor center (AMMC), which is responsible
for mechanosensory input. This aspect has not yet been studied. Therefore, some of the important issues we have
been investigating are whether mechanosensory stimuli can elicit escape (wind) and if flies perform multisensory
integration (vision and wind). We have designed a device to address these questions and have performed initial
tests on wild-type and mutant (AMMC-suppressed) flies.
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X-Ray Computed Microtomography: Application of GPU Computing for Faster Image Processing
Abel Misrak
Mentors: Youngjoo Chung and Hyoungyu Kim
Developments in X-ray computed microtomography have wide ranges of applications ranging from biology to
aerospace. Current improvements in technology make it possible to obtain large amount of tomographic data in a
few minutes. However, fast processing of such large amount of data is still difficult. New solutions are mandatory in
order to fully exploit the advantages provided by the high acquisition speed. Currently, there are two beamlines
dedicated for X-ray imaging at the Pohang Accelerator of Postech. At these beamlines, a commercial software,
Octopus, is used to reconstruct two-dimensional cross-sectional images of various samples. However, Octopus is
slow, and is not customizable. In this project, a Mathematica program was developed that has functionalities
similar to that of Octopus but allows customization. Using the built-in InverseRadon function of Mathematica did
not optimize the speed of image reconstruction. Thus, the next step of the research involves using CUDA parallel
computing architecture on Graphic Processing Units for faster image processing.
Implementation and Characterization of the Digitizer and Filterbank for the Large-Aperture Experiment
to Detect the Dark Ages
Jama Mohamed
Mentors: Anthony Readhead and Glenn Jones
I am working on a subset of the equipment to detect hydrogen emissions with LEDA. The end goal is a VHDL
interface to the ADC using the CASPER tools (yellow block). This type of CASPER block allows specification of
various parameters that can be modified such as digital clock manager configurations. Following this, a VHDL
wrapper for the ADC interface will have been specified and further testing will take place to ensure that the output
data is time aligned.
The ADCs are Analog to Digital Converters which are capable of transforming a continuous analog signal into a
discrete digital one at high sampling rates. In this project, the boards will be taking the signals from the 512 dipole
antennae and converting them into digital which can then be processed by the rest of the system. To take
advantage of the processing power of the ROACH II Virtex 6 FPGAs that are being used, it is necessary to route 32
antennas worth of data into a single board. In addition to utilizing the capabilities of the boards, this also lets us
use only 16 boards and greatly reduces the hardware needed to process the data.
Three-Dimensional Imaging of Cellular Shape Changes in the Developing Zebrafish Heart
Arman Mohsen Nia
Mentors: Scott E. Fraser and Vikas Trivedi
Morphogenesis creates complex biological forms out of simpler structures, each step of which is driven by
considerable changes in gene expression. The heart is the earliest functioning organ, required soon after
gastrulation, early in its own morphogenesis. Its function must change as its morphology changes i.e. the form and
function are tightly coupled together, and being a highly dynamic structure, with its contractions, it generates
multiple types of forces at different scales. The vertebrate heart is built up through a series of steps taking two flat
layers of cells to a hollow tube to a multi-layered, multi-chambered, chirally twisted structure of the final functional
organ. Additionally, contractile beating commences early in the developing heart, shortly after the formation of the
heart tube. Previous experimental results show that Zebrafish (Danio rerio) cardiovascular development provides
the accessibility and visibility needed for studies of tissue, as well as a growing body of work demonstrates that the
insights gained from Zebrafish offers important insights into cardiovascular development in higher vertebrates.
Here we present our results on the cell shape changes at different stages in live Zebrafish embryos. Endogenous
fliptrap vectors were used for obtaining Zebrafish embryos with florescent protein expressed in different layers of
the heart, endocardium and myocardium to be used for imaging via high resolution confocal at different stages.
Images thus obtained were then processed using MATLAB and IMARIS to estimate the cell shape changes during
heart development.
A Novel Investigation of Solvent Effects on the Conformational Equilibria of 1,4-Butanedioate in Protic
and Aprotic Solvents
Gregory Malcolm Moore
Mentors: John D. Roberts, Bill Carroll, and Bright Emenike
Scalar J13/J14 vicinal proton couplings of 2,3-13C labeled 1,4-butanedioate have been used to evaluate
conformational equilibria across a broad array of protic and aprotic solvents. The calculated fractions of gauche
conformers in these solvents range from as low as 0.20 to as high as 0.98. This unexpectedly dynamic variation in
conformational preference suggests the presence of an influential solvent effect or effects acting to favor the
gauche conformer. Initial evidence suggests that electrostatic repulsion between solvent lone pairs and 1,4butanedioate’s negatively charged carboxylate substituents may be a factor favoring the gauche conformer. This
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gauche-favoring effect appears to be mitigated by trans-favoring solvent effects such as solvent-solute hydrogen
bonding, solvent-solvent hydrogen bonding-like interactions, solvent-solvent π stacking, and the obfuscation of
solvent lone pairs by solvent substituents.
Adjusting Macromonomer Sizes and Ratios for Improved Photonic Crystals
Melody A. Morris
Mentors: Robert H. Grubbs and Benjamin R. Sveinbjornsson
Compared to traditional block copolymers, brush block copolymers self-assemble much more easily due to less
chain entanglement as the backbone is stretched by the steric effects of the side chains. In earlier studies in the
Grubbs group, it has been found that brush block copolymers will rapidly form nanostructures with photonic
bandgaps, thus reflecting light across the visible spectrum, from the ultraviolet to near infrared. Such structures
are known as photonic crystals. The peak wavelengths were linearly related to the molecular weight of each
segment of the block. In this work, in addition to changing the lengths of the blocks, the size of the
macromonomers that compose each block have been changed to examine the effect of the side chains on selfassembly. In addition, different molecular weights of macromonomer have been examined in each block to look
into how bulkier blocks will affect the formed nanostructures. These polymers could have future uses in coatings
and paints, especially in the near infrared region to minimize the “urban heat island effect” from near infrared
photon thermalization.
A Survey of the Radio Frequency Interference at the Site of the Future Owens Valley LWA
Alexander Mouschovias
Mentors: Tony Readhead, Gregg Hallinan, Oliver King, Glenn Jones, and Jake Hartman
In order to characterize the RFI at the site of the future OVRO LWA station, a survey was conducted of the RF
spectrum up to 200MHz. We use 3 custom cross-dipole antennas, whose signal is broken up into 1024 channels by
a ROACH FPGA correlator. The survey covers several weeks of observation. We have identified several of the
strongest continuous and transient sources of RFI.
Constraining Planetesimal Formation Mechanisms From Planetary Debris Disks
Eric Mukherjee
Mentors: Ruth Murray-Clay, Rebekah Dawson, and Charles Steidel
An understanding question in planet formation is how objects in protoplanetary disks grow from dust to large
bodies of size >1 meter. While bodies much larger than 1 meter can grow through gravitational binding and those
smaller than 1 meter can grow through collisions, experimental results show that at sizes of ~1 meter, high
velocity collisions between particles may result in destruction of bodies rather than accretion. Furthermore, objects
of size ~1 meter have a short timescale for spiraling into the central star through gas drag. Models describing how
planetesimals cross this 1 meter size barrier result in different predicted size distributions, such as the top heavy
distributions described by turbulence-aided gravitational collapse. To distinguish between models for planetesimal
growth, we simulated the evolution of different “planetesimal initial size distributions” using a code we produced.
The code statistically traces the evolution of the sizes and velocities of a predetermined population of
planetesimals, incorporating the evolution rates described by Goldreich et al. (2004), as well as taking into account
the effects of destructive collisions. We will use this code to generate predictions of collisional dust production to
compare with observations of debris disks, allowing us to shed light on the signatures of planetesimal formation
mechanisms revealed by dust in debris disks.
Measuring Mass-Loss Rate as a Function of Fundamental Stellar Properties for Red Giants
Jorge I. Muñoz
Mentor: Raghvendra Sahai
The stage at which substantial mass-loss begins on the red giant branch (RGB) has always been a mystery to
astronomers. It is well known that RGB stars have very low mass-loss rates of about 10-9 Mʘ, while AGB stars have
very high mass-loss rates of about 10-4 Mʘ. However, this relationship results in the question of how the mass-loss
rate changes as stars evolve through the RGB phase to reach the AGB phase. We aim to determine a functional
relationship between the stellar mass-loss rate and fundamental stellar properties (e.g., luminosity, effective
temperature), as stars ascend the RGB and reach its tip.
The spectral energy distributions (SED) of a large sample of red giant stars in the Galactic Bulge have recently
been determined by Uttenthaler et al. 2010. These SEDs utilize mid-infrared data from observations made with
Spitzer and near-infrared data from the 2MASS and DENIS databases. The SED is dominated by the stellar
radiation with a smaller contribution due to thermal emission by dust in the circumstellar envelope resulting from
the mass-loss. We constructed a grid of SED models spanning a range of mass-loss rates and stellar effective
temperatures using the DUSTY radiative-transfer code, where the central star has been modeled by the MARCS
stellar atmospheric models. We are using this grid to measure mass-loss rates for a statistical population of bulge
red giants and thus derive the mass-loss rate as a function of luminosity and effective temperature for these stars.
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Optimal Bacon-Shor Codes
John C. Napp
Mentor: John Preskill
We analyze Bacon-Shor codes, quantum subsystem codes that are well suited for applications to fault-tolerant
quantum computing because error syndrome information can be extracted by measuring only two-qubit operators
that are spatially local if the qubits are arranged in a two-dimensional lattice. We estimate the optimal code block
size and minimum logical error rate assuming perfect syndrome measurements. We extend this analysis to
asymmetric Bacon-Shor codes, which are customized for correcting biased noise (e.g., noise biased towards
dephasing). In addition, we consider the case where the maximum number of physical qubits to be encoded into is
bounded. We also obtain an upper bound on the failure rates for the case of noisy measurements. Finally, we
consider higher-dimensional Bacon-Shor codes.
Modeling of Negative Index Metamaterials Using POV-Ray
Chiraag Nataraj
Mentors: Jaret Riddick, Amy Pancio, and Harry Atwater
The motive of the present research is to investigate the possibility of creating “hide-in-plain-sight” effects using
negative index metamaterials (NIMs). The objective is to determine if and how it is possible to use NIMs in order to
conceal or disguise an object. In order to investigate these questions, POV-Ray, a raytracing software, is used to
model negative index of refraction metamaterials in various configurations. Investigations are conducted based
upon varying geometry and gradients of index of refraction to study the effect on an observer's perception of an
object enclosed in metamaterial. Results indicate that reflectance and transmittance of a given object are the same
whether the index of refraction is positive or negative. Furthermore, using certain combinations of metamaterials
and ordinary materials, a variety of optical effects can be achieved. Finally, at certain viewing angles, NIMs are not
necessary in order to produce “hide-in-plain-sight” effects - positive index of refraction metamaterials would also
work. The present results portend that “hide-in-plain-sight” may not be far off in the future.
Effects of Alkali Metal Chelation on the Conformational Preferences of 2-Alkoxyethanols
Luis A. Navarro
Mentors: John D. Roberts, Bill Carroll, and Bright Emenike
In alkoxides, alkali metals generally act as counterions, but other functional groups in the molecule may introduce
intramolecular interactions with the cation and impact the conformational preferences of the molecule. This study
focuses on the effects of varying the size and nature of the cation on the gauche preferences of 2-alkoxyethanol
systems.
Synthesis of a Cobalt Catalyst for Hydrogen Evolution
Ana M. Neferu
Mentors: Harry B. Gray and Smaranda C. Marinescu
Hydrogen evolution is generally accepted as the most efficient way of storing solar energy. Even though a
significant number of catalysts have been developed for this process, no catalyst suited for widespread use is
available yet. Platinum is an efficient but very expensive catalyst, hydrogenase enzymes are unstable, and
molecular catalysts based on earth-abundant metals lack efficiency as they undergo catalysis at high
overpotentials. The Gray laboratories have recently developed a cobalt(I)-triphos complex
(Co(triphos)(MeCN)[PF6]) as molecular catalyst for proton reduction at only 20 mV overpotential, which is the
lowest overpotential established for any synthetic complex. The current work aims to synthesize and characterize
an analog of this complex with a p-CF3 substituted triphos ligand. Progress has been made toward synthesizing and
characterizing the ligand from commercially available, inexpensive starting materials. Upon synthesis of the cobalt
complex, its electrochemical behavior will be investigated. The reduction potentials are expected to be upshifted as
compared to the already available catalyst, which will allow access to the highly active Co(0) and Co(II)-H species.
Online Domain-Agnostic Video Summarization
Ilya Nepomnyashchiy
Mentors: Pietro Perona and Michael Maire
Summarizing unstructured video is one of many problems in computer vision that requires searching through a
very large space to find rare “events”. We present an online method to locate the more informative portions of a
video and then sample the video in both time and space based on this analysis. This method uses a linear
regression method, taking a feature vector at every sampled frame and producing a sampling rate. We discuss
both the classifier and set of features used. We then demonstrate that our classifier performs well on several
categories of video as determined by both similarity to a groundtruth and human ratings.
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The Role of CIP2A in Neural Crest Development
Pushpa Neppala
Mentors: Marianne Bronner and Laura Kerosuo
The neural crest is a population of pluripotent migratory stem cells derived from the dorsal neural tube during
neurulation. The chicken neural crest provides an excellent nonmalignant in vivo environment to study the
regulatory mechanisms of epithelial to mesenchymal transition (EMT), which is also a hallmark of cancer
metastasis. A complex gene regulatory network, of which so far only a small fraction is known, guides neural crest
development, and the Myc protein family, known also for their oncogenic potential, has been shown to be involved
although their function in the neural crest is not yet known. CIP2A (Cancerous Inhibitor of Protein Phosphotase 2A)
has been identified in cancer cells to be responsible for c-Myc overexpression via a competitive inhibition
mechanism. The goal of this study is to identify CIP2A’s interactions with Myc proteins and other putative targets in
neural crest cells. Through in situ hybridization, it was identified that CIP2A is expressed in the neural folds and
tube during neurulation as well as in the migratory neural crest stream. qPCR was used to determine the relative
expression levels of CIP2A and the Myc family members during neural crest development. Finally, studies to
determine the function of CIP2A by using morpholino knockdown and overexpression are ongoing.
A Natural Isomorphism Between the Cartier Module of the rth Exterior Power of a p-Divisible Group
Scheme of Dimension 1 and the rth Exterior Power of the Cartier Module of a p-Divisible Group Scheme
of Dimension 1
Joshua Nevin
Mentors: Elena Mantovan and Mohammad Hadi Hedayatzadeh
p-divisible Group schemes over arbitrary commutative rings arise in a variety of natural contexts in algebraic
geometry. This project generalizes a known result over perfect fields of finite characteristic. Over a perfect field k
of finite characteristic p, the rth exterior power of the Dieudonné module of a p-divisible group scheme G of
dimension 1 over k (as a W(k)-module) is naturally isomorphic to the Dieudonné module of the rth exterior power
of G. By using a functorial equivalence between p-divisible group schemes over R and p-nilpotent displays over R,
we show a natural isomorphism between the rth exterior power of the Cartier module of a p-divisible group scheme
G (as a W(R)-module) and the Cartier module of the rth exterior power of G . We first establish a lemma that
states that the functor defining a categorical equivalence between p-divisible group schemes over R and p-nilpotent
displays over R commutes with taking exterior powers. Then we explicitly describe the Cartier module of a pdivisible group scheme as a module over the Cartier ring by transferring the problem to the category of 3n-displays
over R.
Cross-Correlation Analysis of Simulated Fermi LAT and Planck Satellite Data to Determine Detectability
of Star-Forming Galaxies
Rok Nezic
Mentors: Jennifer Siegal-Gaskins and Olivier Doré
Star-forming galaxies (SFGs) are a very abundant population, and are important because they give insight into star
formation history and the evolution of the interstellar medium throughout the cosmic time. They are galaxies with
an intense production rate of large and short-lived stars, and are also a major component of the observed all-sky
background radiation in both the infrared and gamma-ray energy bands. Due to their high number density and low
luminosity which create a relatively isotropic emission across the sky, the angular resolution of both the Fermi
Large Area Telescope (LAT; surveying the sky in gamma-ray frequencies) and the Planck satellite (microwave and
infrared) prevents us from detecting the SFGs individually. I focused on using existing models of SFG emission and
distribution to create simulated all-sky maps in gamma-ray and infrared energy bands. I then performed a crosscorrelation analysis on the simulated data, taking into account realistic uncertainties for Fermi LAT and Planck
measurements. The results of this research can be used to determine the feasibility of such a cross-correlation
analysis when Planck data is publicly released, and to assess the extent of obtainable information.
The Consequences of Scintillation Effects on the Measurement of 21-Centimeter Radiation
Chantal Nguyen
Mentor: Christopher Hirata
21-centimeter radiation is electromagnetic radiation in the radio spectrum emitted when hydrogen atoms move
from a higher energy state to a lower energy state. Cosmologists study 21-cm radiation from neutral hydrogen in
the universe, which is measured via massive arrays of radio antennae, in order to probe the "dark ages” when
galaxies first began to form. Two effects that potentially pose problems in the study of 21-cm radiation are
scintillation of synchrotron radiation emitted by active galactic nuclei (AGNs) and scintillation of radiation emitted
by compact sources such as pulsars, since these effects are not easily subtracted from 21-cm spectra. Scintillation
parameters and brightness temperatures were calculated from literature-listed quantities, and source counts were
calculated from a previous theoretical model. Calculating the brightest source per beam will follow. The goal of the
project is to obtain an upper limit to the two scintillation effects, which will provide an answer to how problematic
the effects are.
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Dimensional Collapse in Optimal Uncertainty Quantification
Lan Huong Nguyen
Mentors: H. Owhadi and T. J. Sullivan
In science and engineering, numerical modeling and experimental data help in studying various large-scale
complex systems. Unfortunately, both of these involve uncertainty. In a lot of cases the response function is nondeterministic and the information on inputs and response functions incomplete. For these systems Uncertainty
Quantification (UQ) might seem computationally intractable. Optimal Uncertainty Quantification (OUQ) framework
poses the UQ problems as optimization problems over infinite-dimensional spaces of probability measures on inputs
and response functions. Finite-dimensional reduction theorems of Owhadi et al. show that computing sharp bounds
on output uncertainties is possible. Working within the Mystic computational optimization framework, which
facilitates solving OUQ problems, we exploit the numerical phenomenon of ‘dimensional collapse’, where the
optimization parameters (discrete probability measures) collapse to a lower-dimensional object. ‘Dimensional
collapse’ highly reduces dimension of the search space, and hence decreases the computational burden. We
implement a code for detecting the collapse and applying corresponding changes to the optimizer by having
optimizers generate (a) metadata that describes the collapse phenomena, and (b) ‘live code’ that will alter the
execution of the optimization to reflect the collapse.
Lyophilization: Stabilizing Reagents for qPCR Microfluidic Chips
Loc Nguyen
Mentors: Axel Scherer and Imran Malik
Lyophilization is a promising technique used that freeze-dry chemicals and biochemicals for ambient temperature
storing purposes. In fact, many medical applications that require lyophilized products have been a success in the
industry. However, many lyophilized PCR reagents have been done in PCR tubes and only compatible for advanced
PCR or qPCR systems. In order to make a PCR/qPCR device available to many remote parts of the world for health
care diagnosis purpose, we need to redesign a new PCR machine that is compact and easy-to-use for most
inexperienced people. That requires a new cartridge design which is flat to fit the mobile machine. By controlling
the temperature, pressure and moisture levels in lyohphilization processes, we try to figure out the optimal
protocol to freeze-dry qPCR assays effectively and efficiently on a flat surface. We also characterize the phase
transition profile of water during lyophilization processes. We can now lyophilize some lyophilization-compatible
PCR assays with self-built lyophilizer. However, in 10 weeks, some objectives cannot be completed as expected so
we need more time to investigate the quality of lyophilized products and to optimize lyophilization protocol for time
and energy efficiency.
Diffeomorphism Based Motion Planning for Bootstrapping Vehicles and Robots
Adam Nilsson
Mentors: Richard Murray and Andrea Censi
A major challenge for robots to become a part of people’s everyday life is the complexity of calibrating and
configuration. We are considering a motion planning problem for bootstrapping robots, which are robots that does
not need any initial specifications of its sensors and actuators. Given a initial image and a goal image, we ask for a
sequence of control commands that makes the robot observe the goal image. Using machine learning, the robot
can learn a diffeomorphism model of the relation between its sensor data and commands, by analyzing a large set
of images with commands in between. The only information available to the planner is the learned models and the
sensor images, unlike a standard motion planing problem where the controller knows the robot's dynamics. A
search for the path to the goal image can be done by applying the learned models on the initial image. Such a
search becomes fast very large since the images are large and the possibilities of commands are many. By
composing the learned models for the basic commands, a graph of models for sequences of commands can be
generated once, and later on be used without a high computational cost.
Synthesis and Characterization of Nanoparticles for Hydrogen Evolution on Semiconductor Substrates
Paul Nuñez
Mentors: Harry Gray and James McKone
Titanium dioxide (TiO2) and Niobium doped TiO2 (NDT) has been investigated as a candidate for a passivation layer
as well as creating a junction to increase the barrier height to p-type silicon. By increasing the barrier height to Si,
the open circuit potential (Voc) will in turn increase as well as the overall efficiency of the device. Preliminary results
for photoelectrochemical hydrogen production show that by depositing a thick underdetermined amount of TiO2 and
NDT on p-Si that the Voc increases by a factor of 1.4 to 1.8 relative to bare Si. Although the Voc increases with the
overlayer of TiO2 and NDT, about 16% of light is lost due to absorption and reflective losses from the NDT
overlayers relative to TiO2. The overlayers prove to be beneficial as devices of 1.4% and 2% efficient for TiO2 and
NDT respectively have been fabricated consistently relative to bare p-Si. This is a significant improvement from the
typical efficiency of 1%. This technique has promise for further optimization and applications to other p-type
semiconductors.
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Passive Systems Solar Decathlon
Juan Pablo Ocampo
Mentor: Melany Hunt
My SURF dealt with researching passive systems that can be applied to a house so that the house itself can be
more energy efficient and reduce its carbon footprint. One of the main systems I looked into was a trombe wall,
and different ways to build it and apply it. Using some cubes for testing, I created a Phase Change Material (PCM),
brick and wood south walls with insulation along the other sides of the cubes. In the end, I realized that the PCMs
generally kept the inside of the cube at a slightly cooler temperature during the day, but a slightly warmer
temperature at night. This means that the PCMs are acting as needed and cooling or heating the inside of the cube
as the day goes on.
Thermal Diffusivity Measurements of Materials Showing Negative Thermal Expansion
Abraham Ortega
Mentors: Brent Fultz, Tian Lan, and Hillary Smith
Proposed theories on the source of negative thermal expansion (NTE) point to anharmonic terms in the potential
energy associated with the mean displacement from equilibrium in a lattice. We believe that phonon (collective
excitations in a lattice) anharmonicities that would lead to a thermal expansion anomaly would also hinder thermal
conductivity. Materials demonstrating NTE were chosen in order to study the relationship between mean free path
length and temperature. We will be presenting the thermal diffusivity measurements for our compounds in the
temperature range of 25-800 degrees Celsius.
Traffic Simulation in a Two Way Street
Bertrand Ottino-Loffler
Mentors: Daniel Abrams and John Doyle
This research primarily focuses on optimizing traffic flow in urban settings. Most modern traffic signals maintain a
fixed period of oscillation, but there is no reason to assume that is optimal. We wish to examine how simple cars
react to an optimized system of fixed-period lights or to a signal system with adaptive timing scheme known as a
chimera state. A network of oscillators are said to be in a chimera state if they all maintain the same natural
frequency, but are coupled in such a manner that the population spontaneously splits into synchronized and
desynchronized populations. We approach this problem by creating simulations in Matlab and Netlogo, as well as by
making theoretical predictions when possible. Simulations of a two-way street confirm theoretical predictions under
basic assumptions, showing maximum efficiency for timings that strongly (but not exclusively) favor one direction
over another. Prospective models show that this result holds for low densities of interacting cars, and possibly for
relatively high ones.
Development of a Cryogenic Assembly of a Scanning Tunneling Microscope (STM) and a Scanning
Electron Microscope (SEM) for Studies of High-Temperature Superconductors
Bryance Oyang
Mentors: Nai-Chang Yeh and Marcus Teague
We began the construction of a combined scanning tunneling microscope (STM) and a scanning electron
microscope (SEM) capable of studying samples at liquid helium temperatures of 4.2 K and above. The STM allows
for atomic resolution imaging and spectroscopic studies of samples, while the SEM has a wide field of view capable
of locating features to be studied by the STM. The microscopes will operate in an ultra-high vacuum (UHV)
environment inside a main vacuum chamber. A second preparation chamber connected to the main chamber by a
gate valve will be used for sample preparation or STM tip exchange. Both chambers are mounted on a vibration
isolation table to reduce noise. When completed, the STM/SEM will be used to study high temperature
superconducting cuprates as well as other interesting condensed matter phenomena.
Partial Identification in the Ecological Inference Model
Geunwook Paek
Mentor: Robert Sherman
Combining aggregate and individual-level data arises in many applications. However, it is not easy to draw
inferences about individual behavior when we observe outcomes of interest and covariates in separate datasets.
One example is the classic ecological inference problem from political science: voting outcome across electoral
districts is observed from administrative records, individual demographic data within a district is observed from
survey data and the researchers want to infer voting behavior conditional on districts and demographic attributes.
We study partial identification and inference procedures for counterfactual analysis in such model in which the
outcomes and covariates are only observed in separate datasets. To allow covariates to be either discrete or
continuous, we use the results from Copula theory and treatment effect literatures, and obtain sharp bounds on
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counterfactual outcomes. To present an application, we address the counterfactual question: Fixing the voting
population in 1980, how would the Republican vote share have changed if George W. Bush and Al Gore had run in
1980?
Studying Neuromodulation to Understand Hunger Control in Adult Drosophila
Ketaki Panse
Mentors: David Anderson and Hidehio Inagaki
The brain translates changes in internal metabolic state into changes in feeding behavior to maintain energy
homeostasis, but how the brain does so is not well understood. Understanding this translation can lead to insight
into human diseases such as obesity and cardiovascular disease. We would like to develop a general model for
state-dependent modification of behavior and arousal in Drosophila melanogaster. Specifically, the purpose of this
project is to understand the neural mechanism of hunger control in Drosophila melanogaster. To do so, we look at
feeding behavior in both loss-of-function and gain-of-function mutants of neuropeptides. Neuropeptides—small
molecules that mediate neuronal communication by acting on cell surface receptors—change how neural circuits
process information in different states. Thus, studying neuromodulation is integral to understanding how the brain
functions. Studies have shown that neurons with the neuropeptide AstA have an inhibitory influence on several
feeding behaviors in Drosophila melanogaster, and this influence is observed even in the absence of changes in
metabolism or energy expenditure. Similarly, we hope to determine the influences of neuropeptides NPF, sNPF, and
octopamine. NPF and sNPF are the Drosophila homologue of NPY, known to be responsible for central regulation of
feeding in humans.
Evolving the Community Seismic Network
Jainil Parekh and Satyendra Jadaun
Mentors: K. Mani Chandy and Julian J. Bunn
Community Seismic Network is an ongoing project at Caltech. It has already shown a few successes and holds the
promise of being a critical part of emergency response in case of earthquakes due to the early warning and the
spatial intensity estimation (shake maps) it can generate. However, the most critical need for such a system is in
developing countries like India where the existing episensor networks are poor. The project aims at designing a
sensor platform (hardware and software) optimally suitable for deployment in such a situation. It would solve the
problems faced by the current design like network constraints and computer issues, while aiming for a lower cost
per system.
Currently the CSN server back-end only considers warnings (or ‘picks’) from sensors in a predetermined South
California region. But the system can be easily generalized to accept warning from a sensor in any location,
demarcated via a geographic bound that is algorithmically generated, called geocell. The system can then
determine the probability of an earthquake event in the geocell given sufficient number of sensors, and thus work
for serving early warning in every part of the world. Investigations through trial runs on a development system
show promising results for such a structure and mean that the CSN can be a truly global event detection
framework.
Sample Processing Through Subcritical Hydrolysis of Organics
Sangavi Pari
Mentor: Valerie Scott
Well-characterized and efficient sample processing techniques are important to enable successful in situ chemical
analysis on planetary bodies. The goal this summer is study the Micro-scale Ion Analyzer (MIA), an instrument
designed using the principles of the Sub-Critical Water Extractor. This instrument utilizes water alone to extract a
variety of organics by taking advantage of water’s unique properties under high temperature and pressure. The
objective is to see if MIA can hydrolyze different types of bonds under the various experimental conditions that
may represent those found in larger molecules or those between targets and regolith. MIA will be tested by
exposing different sample stock solutions to different conditions (varying temperature, pressure, and time). The
resulting sample solutions will be collected and analyzed by detection technologies such as the HPLC, GC-MS, or
FID. Under the conditions explored in these experiments, no effect of pressure on hydrolysis was observed. Initial
experiments on soil samples examining the extraction of typical pollutants (polycyclic aromatic hydrocarbons and
polychlorinated biphenyls) have been done.
Phylogeographic Analysis of Phylloscopus ruficapilla in the Eastern Arc Mountains of Tanzania
Alison Parisian
Mentors: Rauri Bowie and Bruce Hay
The Eastern Arc Mountains of Tanzania are a chain of sky islands, mountains separated from one another by terrain
which is uninhabitable to the species which live on the mountains. This system is ideal for phylogeographic studies
of montane bird populations as the population on each mountain is spatially distinct from the others. Phylloscopus
ruficapilla is a species of warbler which occupies these montane habitats. Through genetic analysis of P.ruficapilla
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samples collected from birds in populations across the range and in surrounding areas this study hopes to reveal
information on the genetic structure of these populations and the natural elements which may facilitate or hinder
gene flow. A phylogeographic analysis was conducted using two mitochondrial and five nuclear loci amplified from
samples of nearly one hundred individuals. Preliminary results show distinct population structure within the birds
sampled, with greatest genetic distinction between populations in the Eastern Arc and those from outlying areas
including the Mahale Mountains to the west and Zomba and Rungwe mountains to the south. Within the Eastern
Arc, birds from the northern and southern parts of the range show clear genetic divergence, suggesting that gene
flow is restricted between these two regions by the intervening stretch of uninhabitable arid shrubland.
Numerical Solution of the Linearized Einstein Equation in 3D using the Cactus Toolkit
Cheol Woo Park
Mentors: Christian D. Ott and Roland Haas
Tidal disruptions of stars caused by close encounters with black holes are violent cosmic events that can yield
different radiation patterns depending on the orientation of the orbit. These radiation patterns can provide
information about both the black hole and the internal structure of the disrupted star. This project aims to explore
the regime of ultra-close encounters of a white dwarf (WD) with an intermediate mass black hole (IMBH) by finding
the numerical solution of the linearized Einstein equation in 3D. General relativity is a non-linear field theory in
which few exact solutions are known, so the systems of interest are often described by employing approximation
techniques. In this project, we employ perturbation techniques to solve the Einstein field equation because the
mass of the WD is sufficiently smaller than the IMBH. We split the full metric
into background piece
given
≪
. The Einstein field equation can then be
by the metric of the black hole in isolation and a perturbation
linearized around the exact solution to find a linear wave equation for the trace-reversed perturbation.
Identifying Mechanisms Within CD4+ T Cells of Elite Controllers to Limit HIV-1 Replication
Sungjin Park
Mentors: Xu Yu, Jin Leng, and David Tirrell
While most HIV patients depend on Highly Active Antiretroviral Therapy (HAART) to prevent HIV disease
progression, there are a small number of individuals called elite controllers, who are able to control HIV infection
without treatment. However, many of the mechanisms by which the immune systems of elite controllers are able to
effectively contend with HIV remain unknown. A previous study by the Yu lab has shown that CD4+ T cells of elite
controllers upregulate p21, which impedes transcriptional elongation of HIV-1 mRNA by inhibiting cyclin-dependent
kinase (CDK) 9 and the phosphorylation of RNA polymerase II. In order to assess the importance of CDKs in HIV
replication, a series of CDK inhibitors and CDK-targeting siRNAs were used to treat CD4+ T cells before infection
with VSV-G-pseudotyped HIV. Preliminary results show that one of the CDK inhibitors significantly inhibits HIV
infection and HIV reverse transcription. The significance of reverse transcriptase phosphorylation in HIV replication
was also evaluated by comparing the replication capacity of the wild type HIV to that of a mutant HIV construct,
which encodes phosphorylation-resistant reverse transcriptase.
Development of a Scanning Mass Spectrometry Probe for Chemical Analysis of Submerged Interfaces
Aleena Patel
Mentors: J.L. Beauchamp and Daniel Thomas
A novel electrospray source, the Scanning Mass Spectrometry Probe (SMS Probe), is proposed and a prototype has
been assembled. The SMS Probe relies on capillary action and a negative pressure difference between the spray
chamber and atmospheric pressure to drive the continuous flow of sample through a tapered silica capillary tube.
An electric field generated by high voltage applied between the ion transfer tube and the capillary initiates soft
electrospray ionization of the sample at the tapered tip. Generated ions can then travel through the transfer tube
to the mass spectrometer for analysis. It has been shown ions can travel successfully through the transfer tube.
Using a translation stage the exposed end of the capillary can be positioned to sample selectively from waterorganic interfaces. Further tests of the instrument will be presented.
Vesicle Adhesion Using AFM
Mohak Patel
Mentors: Guruswami Ravichandran and Jacob Notbohm
Vesicle adhesion helps us model cell adhesion, which is associated with many biological processes such as cell
growth and migration. Atomic force microscopy (AFM) has been widely used in image scanning and adhesion
experiments, but adhesion of vesicles using AFM has not yet been studied. In this work, a new experimental
procedure to analyse vesicle adhesion in a force-distance experiment using AFM is outlined. Adhesion experiments
are performed on both layers of vesicles and single vesicles. Both non-specific and specific adhesion are addressed.
The protocols for performing the experiment and functionalizing the AFM tips with avidin are described. The forcedistance curves obtained are analysed to find the strength of adhesion and its dependence on loading rates. The
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force-distance curves for non-specific adhesion are compared with a theoretical model. The peaks obtained with
specific adhesion are analysed and reported. No “snap-off” force is observed in force-distance curves for both
specific and non-specific because of large contact area between the AFM tip and vesicle.
Lateral Connections in the Helmholtz Machine
Evan J. Patterson
Mentors: Christof Koch and Nikhil Joshi
A fundamental goal of unsupervised learning is the discovery of structure in complex and noisy data. Probabilistic
generative models, which learn to generate data from a set of hidden causes, have proven to be an effective
method for discovering this structure. One such model is the Helmholtz machine, a multi-layer probabilistic neural
network trained using a variant of the expectation-maximization (EM) algorithm. A key simplifying assumption in
this model is that each unit in a particular layer is conditionally independent of the others, given the state of the
previous layer. In other words, the network has no lateral connections. In this paper, I explore variants of the
Helmholtz machines which relax this assumption. The investigation is motivated primarily by the possibility of
obtaining sparse representations in the hidden units. In a sparse representation, only a small fraction of the hidden
units are activated at a given time. Sparse representations are interesting for biological reasons. In addition,
sparsity may facilitate the human interpretation of individual hidden units—a task which is often impossible in the
standard Helmholtz machine.
Development of an Assay for Quantitative Evaluation of Mitophagy in Mouse Embryonic Fibroblasts
Justin Paz
Mentors: David Chan and Anna Salazar
Mitophagy is a cellular mechanism involving selective degradation of mitochondria by the autolysosome. Defects in
mitophagy signaling may play a role in the development of neurodegenerative diseases like Parkinson’s; therefore,
knowledge of this process on a cellular level will be important for understanding disease pathogenesis. The
objective of this project is to develop a reliable assay to observe mitophagy in mouse embryonic fibroblasts (MEFs).
The assay will then be used in an siRNA screen to identify unknown mitochondrial proteins involved in mitophagy.
This will help researchers uncover details about when and how mitochondria are selected for degradation.
Mitophagy was induced using hypoxic conditions and observed using matrix targeted green fluorescent protein
(GFP)-Link-monomeric (m)Cherry. During mitophagy, the GFP portion of the fluorescent protein is quenched in the
acidic environment of the autolysosome. The resulting red puncta of mitochondria were used to quantify the level
of mitophagy. After 48 hours at 1.00% O2, 15.33% of cells showed 16+ red puncta/cell, compared to 3.02% in
normoxic conditions. Once RNAi knockdown MEFs are generated, they will be subjected to hypoxic conditions and
will be evaluated based on their deviations in mitophagy from the hypoxic control. Candidate genes displaying
significant changes will be analyzed further.
A Combinatorial Approach to Matrix Multiplication
John Peebles
Mentor: Chris Umans
The problem of how to efficiently multiply two n by n matrices has been studied for over four decades. It seems
that the general consensus is that it can probably be done in time O(n^(2+c)) for any arbitrarily small constant
c>0, but this has not yet been proven. In order to prove this, it is sufficient to construct a conjecturally optimal
version of a certain type of combinatorial object called a strong uniquely solvable puzzle (SUSP). We give an
overview of these objects and some related combinatorial objects and discuss the connections between them,
including a new object we have formulated that is a slight relaxation of an SUSP. The interest in studying the
related objects is that they may yield insights on the construction of SUSPs.
True Polar Wander: What Really Killed the Dinosaurs?
Brian Penserini
Mentor: Joe Kirschvink
True Polar Wander (TPW) is a fundamental physical concept that describes the movement of the solid earth with
respect to the spin axis. Since planets must spin about their maximum principal moment of inertia, alteration of the
mass distribution of a planet will drive the spin axis to regain its orientation of the principal moment.A
paleomagnetic sampling of a ~84 Ma section of the Scaglia Rossa limestone in Italy was conducted in order to
document “wiggles” representative of short-term oscillations in geomagnetic declination and inclination due to TPW
at a higher resolution than previous samplings. Confirmation of such an event would imply that a mass anomaly
occurred during the Late Cretaceous, possibly a result of the waxing and waning of large-scale ice sheets or, more
interestingly, change in heat flow across the core/mantle boundary that could have led to the magnetic reversal
ending the Long Normal Chron as well as a superplume that may have been the eventual kill-mechanism of the
End-Cretaceous mass extinction.
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Stable Maps to Quadric Hypersurfaces
Christopher Perez
Mentors: Tom Graber and Zhiyu Tian
It is not known whether or not the moduli space of stable maps
,
is irreducible when is a general
,
,
is irreducible. Quadric
hypersurface. However, it has been show that when is a homogeneous variety
,
⊂ ℙ are homogeneous varieties under the action of
1 . We attempt to describe the moduli
hypersurfaces
,
and study the cones of effective and ample divisors on these moduli spaces.
spaces
,
The Evolution of Young Stars: Exploring the Properties of Pre-Main-Sequence Stars Through Color-Color
and Color-Magnitude Diagrams
John Pharo
Mentor: Lynne Hillenbrand
There are many theoretical models describing the core evolution and atmosphere of a Pre-Main-Sequence star as
the star contracts and moves onto the Main Sequence. These predict the observed magnitudes of young stars with
various ages and masses for different photometrc systems. It is not known, however, how well each combination of
core and atmospheric models predicts the development of a Pre-Main-Sequence star. The Tool for Astronomical
Data Analysis (TADA), developed by Nicola Da Rio, provides a good way to analyze this problem. Producing colorcolor and color-magnitude diagrams for useful photometric systems, one can see the predictions of model
combinations for specific masses and ages of young stars. By comparing each combination of theoretical models to
data from young star clusters, such as the Pleiades Cluster or the Lambda Ori Cluster, one can evaluate the
efficacy of each combination. One can also see which colors are most useful for future studies of young stellar
populations. This and other results from the TADA analysis could prove helpful in determining the characteristics of
observed young stars, such as age and mass.
Determining the Minimal Recognition Motif of the Light Harvesting Chlorophyll a/b-binding Protein
Samantha Piszkiewicz
Mentors: Shu-ou Shan and Thang Xuan Nguyen
Protein homeostasis is essential for all cells and requires the proper control of the folding, localization, and
interactions of all proteins. The misfolding and aggregation of proteins are detrimental to cells and have been found
to be the root cause of numerous age-related diseases. To study the general mechanism of disaggregase of a
typical hydrophobic membrane protein, we will use the cpSRP pathway as a model system to define the nature of
such aggregates. The Shan Lab has shown the robust disaggregase activity of the 43kDa chloroplast signal
recognition particle (cpSRP43) for the disassembly of aggregates of the family of the multi-transmembrane light
harvesting chlorophyll a/b –binding protein (LHCP), focusing on the binding interactions between cpSRP43 and a
stretch of 18 amino acid residues in LHCP known as the L18 motif. By systematically shortening the length of L18,
we have determined the minimal construct that can support LHCP-cpSRP43 recognition and LHCP aggregate
disassembly. This will allow us to engineer the recognition motif into other aggregate-forming proteins with
minimal disruption to structure and function, which we can then use to probe the capabilities and limitations of
cpSRP43.
Properties of Cuprate Superconductor Ca-YBCO in the Overdoped Limit
Hoi Chun Po
Mentors: Nai-Chang Yeh and Chien-Chang (Kyle) Chen
While YBCO has long attracted much interest as a prototype of high-temperature superconductors, its properties
begin to resemble those of the conventional superconductors, which are better understood, when it reaches the
overdoped limit due to the addition of Ca dopants. Samples of different doping levels were epitaxially grown on a
lattice-matching crystal substrate using a pulsed-laser deposition system. The quality of the samples was
characterized using an X-ray diffractometer and the magnetic properties were studied by performing AC
susceptibility measurements with a homemade Hall probe technique and magnetization measurements with a
SQUID magnetometer (SQUID: Superconducting Quantum Interference Device). The oxygen content, and thereby
the doping level, of the samples was varied by subsequent annealing. The samples characterized in this project can
be further studied through scanning tunneling spectroscopy, which would reveal more physical properties, for
instance the superconducting pairing symmetry and the evolution of a competing order phase coexistent with
superconductivity, as a function of doping levels. Bridging between unconventional and conventional
superconductivity, the study of these overdoped samples would further our understanding of the still mysterious
physics behind the high-temperature superconductors.
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The Role of Histone H3 Lys79 Methylation in Histone Transfer
Alexander Port
Mentors: Mair Churchill, Pamela Bjorkman, and Wallace Liu
Nucleosomes, the primary structural component of chromatin, serve a pivotal role in regulating the transcription,
replication and repair of DNA. Chromatin Assembly Factor 1 (CAF-1) and anti-silencing function 1 (Asf1) are two of
the chaperones involved in nucleosome assembly and disassembly. We used fluorescence resonance energy
transfer to study the “hand-off” of H3/H4 dimers from Asf1 to CAF-1. The H3/H4 with a single residue substitution
of the H3 Cys110 to Glu110, which decreases the stability of the H3/H4 tetramer, has similar FRET signal and
affinity for CAF-1 as the WT H3/H4. These results suggest that CAF-1 binds to a pair of H3/H4 dimers in near
tetrameric form, priming them for deposition onto DNA in the tetramer form. However, our finding that the
wildtype form of the H3/H4 dimer binds with a higher affinity to Asf1 than to CAF-1 is not consistent with the
proposal that of chaperones will guide proteins along thermodynamically favorable pathways, and suggests that
other mechanism are required for Asf1 to hand off H3/H4 to CAF-1. One possible modulator of chaperone binding
affinities is post-translational modification to the histone proteins, in particular H3 Lys79 methylation and H3 Lys56
acetylation.
iGEM: Implementation of Proteorhodopsin in E. coli to Increase Ethanol Production
Ralph Edward Pursifull
Mentors: Richard Murray, Nate Glasser, Emzo de los Santos, and Gita Abadi
The Caltech iGEM (international Genetically Engineered Machines) team will be competing with over 100 teams
from other universities. The Caltech iGEM team’s project features the use of proteorhodopsin to increase ethanol
production in modified E. coli cells. Proteorhodopsin is a light powered proton pump that can be used to
supplement ATP production in bacteria without an adequate proton gradient. By transforming proteorhodopsin into
an E. coli cell that has NADH dehydrogenase knocked out, the cell will be able to survive, despite the disruption in
the cellular respiration pathway. This leads to a buildup of NADH in the cell. NADH can be used as a reducing agent
in the biofuel production pathway. This can lead to an increase in biofuel production.
The Effect of Graphene on the Stability and Photoelectrochemical Properties of Silicon
Suyeon Pyo
Mentors: Nathan Lewis and Adam Nielander
Silicon photoanodes were covered by graphene monolayer or bilayer grown via chemical vapor deposition (CVD).
Graphene layer was shown to prevent oxidation of silicon according to XPS spectrum. The graphene-covered silicon
electrode in contact with an aqueous ferricyanide/ferrocyanide solution began passing cathodic current at a more
oxidizing potential than H-terminated silicon electrode in the dark. Under illumination, the graphene covered silicon
electrode displayed a short-circuit current (Jsc = 1.5 mA cm-2) and open-circuit voltage (Voc = 0.20 V) that were
relatively constant when the electrode potential was swept back and forth between more oxidizing and more
reducing potentials. The values of Jsc and Voc decreased much more rapidly in the bare H-terminated silicon
electrode than in the graphene-covered silicon electrode though the initial values Jsc and Voc of both electrodes
were similar. The reduced rate of anodic oxidation of the silicon covered by graphene contributed to such stability
of the photoanodes.
The Effects of Tcf1 and Fog1 in the Regulation and Maintenance of T-Cell Specification and
Differentiation
Shuyang Qin
Mentors: Ellen V. Rothenberg and Sagar Damle
Several critical transcription factors regulate and sustain T-cell lineage and commitment from multipotent
hematopoietic progenitors in which ETP cells are phenotypically characterized by cKit+/CD25-, DN2 by
cKit+/CD25+, DN3 by cKit-/CD25+, and DN4 by cKit-/CD25-, Two such factors, T-cell factor 1 (Tcf1) and GATA3
are highly expressed within early progenitors. Furthermore, a cofactor of GATA3, friend of GATA (Fog1) is also
largely present. Here, we show that different expression levels of these proteins exert profound effects in the
maintenance of T-cell fate. Specially, we suspect that reduced expressions of Tcf1 in fetal liver hematopoietic
progenitors infected with Tcf1 shRNA downregulates CD25 and upregulates cKit expression, suggesting that T-cell
differentiation may be partially repressed, while reduced Fog1 levels downregulates CD25 and slightly cKit,
producing almost an opposite effect. We aim to show, using quantitive RT-PCR data whether the downregulation of
Tcf1 and Fog1 affect mRNA expression of crucial T-cell specific genes, including GATA3. We conclude that Fog1
plays a role in the regulation of expression of T-cell essential genes and confirm the regulatory effects of Tcf1.
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Studying the Effects of Soiling on Photovoltaic Arrays in Southern California
Brynan Qiu
Mentor: Melany Hunt
In the Solar Decathlon 2013 competition sponsored by National Renewable Energy Laboratory and the US
Department of Energy, students are tasked with designing and constructing a net zero, solar powered house for a
target market. For the Southern California Institute of Architecture/California Institute of Technology team, the
target market is located in Southern California, which experiences the greatest efficiency losses for photovoltaic
solar arrays from soiling due to the dry, arid climate. Hence, reducing the effects of soiling will help in the
engineering competitions and will be an area for potential innovation. Therefore, modeling and physical testing of
soiled solar panels have been conducted to determine efficiency losses, along with steps taken to ensure the
validity of results from modeling software. Potential solutions fit for a residential scale system have also been
discussed.
Maximizing Alcohol Production Using Proteorhodopsin in E. coli
Chenxi Qiu
Mentors: Richard Murray, Nathaniel Glasser, Emmanuel de los Santos, and Gita Mahmoudabadi
Escherichia coli naturally produce ethanol through fermentation. In order to increase ethanol production, we are
knocking out “nuo” and “ndh”, two essential genes that make NADH dehydrogenase. NADH dehydrogenase
converts NADH to NAD+. Without these essential genes, more NADH will be available for biofuel synthesis – NADH
is a reducing agent in the biofuel production pathway. In order to allow the E. coli to grow without either “nuo” or
“ndh”, we are inserting proteorhodopsin into the cell membrane. Proteorhodopsin is a light powered proton pump,
an essential gradient that is used for ATP production. Cells with proteorhodopsin can survive without NADH
dehydrogenase, which will lead to a increase of NADH available and thus more biofuel (alcohol) can be produced.
Retrofit of Cryogenic Testing Apparatus for Microwave Kinetic Inductance Detectors
Matthias Raives
Mentor: Sunil Golwala
The Multicolor Submillimeter Inductance Camera (MUSIC) relies on new Microwave Kinetic Inductance Detectors
(MKIDs) to make millimeter-wave observations. Recently, multi-scale pixel technology was developed that allow
arrays of pixels in MUSICs 576×576 grid to function as a single pixel, increasing the efficiency of the different
bands that MUSIC observes in. The Dewar that will be used to keep the detectors at 0.25K for testing has a large
snout to house the magnetic shielding structure. Replacing the current shielding structure with a more compact one
allows the detectors to see radiation up to 45° off-axis as well as enabling faster cooling of the Dewar, without the
magnetic field attenuation falling below acceptable values. The model of the retrofit Dewar was completed in
SolidWorks. The primary areas of retrofit were the optics assembly and the 0.35K intercooler (IC) and 0.25K
ultracooler (UC) stages. Analysis was also done on a simplified model of the Dewar to ensure that the thermal load
did not exceed the capacity of the cooling systems. The analysis indicated that the Dewar would have operating
temperatures of approximately 0.37K and 0.26K at the IC and UC stages, respectively, indicating that the thermal
load is within operating parameters.
Practical Improvements to the Bus Protocol for Anonymous Communication
Hari Ravi
Mentor: Tracey Ho
In this paper we examine tradeoffs between efficiency and anonymity in the Bus Protocol of Beimel and Dolev. In
particular we address the probabilistic overwriting of messages by other communicating pairs by dividing the
resources amongst multiple buses, each bus traversing a different Hamiltonian cycle through the network, having
each processor send only to the bus that traverses the path in which the distance between the processor and the
destination of its message is minimum. We discovered using more paths largely eliminates this problem of
overwriting, although it weakens the anonymity guarantee. As a result, we quantify anonymity so that a user of
our model can determine appropriate parameters depending on how much they are willing to relax the perfect
anonymity requirement. In the case in which we have an excess of resources, we introduce two additional
strategies, sending multiple copies of a message and a simple coding approach, to further counter this problem of
overwriting while maintaining a high degree of anonymity.
Quantitative Dissection of Genetic Variability
Manuel Razo Mejia
Mentors: Rob Phillips and James Boedicker
Many large scale genomic efforts aim to map genotypic variability among individuals. However, a simple model
system where the link between genetic variability, gene regulation, and function can be studied in detail is missing.
Here we report the use of the theoretical framework that thermodynamical models of gene expression give as a
guide baseline to inquire into the patterns that the evolutionary process has followed. By studying a collection of
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≈1000 E. coli natural isolates from all over the world, as representative examples of genetic variability, we can
explore variations in the regulation of the well known lac operon. We analyzed the changes in the language of
thermodynamic models (i.e. changes in the number of the main molecular players involved in regulation or in the
binding energy associated with these molecules) to gain insight into the sources and patterns of variability among
individuals of the same species. The first part of the project has shown that there is a wide range of regulatory
profiles in the collection, but further studies at the sequence level are needed in order to extract conclusions about
the evolutionary story that the gene expression has followed among these strains.
Seismic Arrays for Nonpoint Source Earthquakes
Jesse Redding
Mentors: Pablo Ampuero and Linseng Meng
Seismological arrays designed for use in earthquake early warning systems have thus far been designed only with
point source earthquakes in mind. This project will try to correct that oversight. It attempts to optimize the
geometry of seismic arrays (the location of seismic stations in an array in relationship to each other) so that they
can quickly and accurately interpret signals from both point source earthquakes and those with non-stationary
fronts. This is being accomplished through the use of existing array data to tune a synthetic data generator, which
will be used to simulate earthquakes so that the effectiveness of various array geometries can be tested.
Design and Implementation of a PCB for Evaluating a Semiconductor Laser Feed-Forward Phase-Noise
Reduction Method
Angad S. Rekhi
Mentors: Ali Hajimiri, Firooz Aflatouni, and Behrooz Abiri
Narrow-linewidth lasers are important in many fields that require very precise characterization of light sources,
including optical tomography, interferometry, and coherent optical communications. Methods to reduce the phase
noise of semiconductor lasers using electrical feedback have been shown to work, but involve a tradeoff between
phase noise reduction and system bandwidth. A feed-forward method that circumvents this tradeoff has been
designed by others and has been shown to work on the benchtop. For this project, a printed circuit board (PCB)
was designed and assembled that will be used to verify the operation of this feed-forward method in silicon.
Experimental Set-Up and Analysis for Measuring Polarizability of the 5d6s3D1 State in Ytterbium
Paul Reshetikhin
Mentors: Dmitry Budker and Alan Weinstein
We finished the experimental setup for measurement of the vector polarizability of the5d6s3D1 state in Ytterbium.
This measurement will be used in future parity violation experiments on this state. The experimental setup consists
of two cavities, and interaction cavity and a reference cavity, and a feedback system that keeps a 408 nm laser
light in resonance with the cavities. With the work done this summer, the optical setup is complete, the feedback
system is operational, and the stability of the cavities has been characterized.
The Cohomology of Hilbert Schemes of Points on K3 Surfaces
Stephanie Reyes
Mentor: Andrei Jorza
We study two combinatorial aspects of a conjecture of Hasset and Tschinkel on Langrangian subspaces of Hilbert
schemes of points on K3 surfaces, via an understanding of the SO(22)-invariant geometrically constructed classes
of the cohomology of the Hilbert schemes. We first attempt to find and prove a general plethysm rule for special
orthogonal groups by studying the cohomology of the Hilbert schemes as representations of SO(22). Secondly, we
study the combinatorics of SO(22)-invariants of the Hilbert schemes in an effort to increase their computability.
Characterization of Multilayered Microparticles Fabricated by Layer-by-Layer Assembly and
MicroContact Printing
Stephanie Reynolds
Mentors: Jingjiao Guan, Jim Heath, and Peipei Zhang
Layer-by-layer (LbL) assembly has recently emerged as a versatile fabrication method to produce micro- and
nanoscale structures with precisely controlled compositions. By allowing for the integration of various biomolecules,
ions, and polyelectrolytes in a well-defined manner, LbL assembly, combined with microcontact printing, can be
used to prepare multilayered micro/nanoparticles with specific shapes and sizes that can be used for various
biomedical applications. We have designed a procedure to incorporate multivalent ions (e.g. Gd3+) into such
particles by placing a micropatterned poly(dimethyl siloxane) (PDMS) stamp in alternating solutions of ions and/or
polyelectrolytes. The presence of ions in the particles has been confirmed using atomic force microscopy and
europium ion phosphorescence visible under a fluorescence microscope. Additional confirmations will be done using
magnetic force microscopy and energy-dispersive X-ray spectroscopy. Particles have been successfully
microcontact printed onto glass slides and poly(vinyl alcohol) films and are geometrically and structurally stable
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when they are released by water vapor. The resultant micro/nanoparticles have the potential to be used as
multifunctional devices for drug and gene delivery, and may also allow in vivo particle tracking by techniques such
as magnetic resonance imaging (MRI).
Applications of Shell-Bound Organic Matter and Its Hydrogen Isotopic Composition to
Paleoceanographic Studies
Addison Rice
Mentors: Peter deMenocal, Pratigya Polissar, and Jess Adkins
The desire to understand our planet’s past has fueled the need for robust paleoclimate proxies. Paleoceanic salinity
is of particular interest because of a calcite precipitation equation, relating temperature, oxygen isotopes of calcite,
and salinity. A reliable proxy has yet to be found, but shell-bound organics may hold the answer. The hydrogen
isotopic composition of the compounds found inside calcite shells may trace the composition of seawater, which is
related to salinity. To test this, foraminifera were rigorously cleaned to remove any non-shell-bound organics, then
dissolved in 5N HCl to release the organic compounds. The resulting solution was extracted with dichloromethane
and put through a silica gel column. From this there was no evidence of alkanes, ketones, or esters in the organic
membrane, but fatty acids with chain length 16 and 18 were found in concentrations an order of magnitude above
what was found in the procedural blanks. To ensure that these compounds are not contamination, the procedure
was closely examined and modified to eliminate these fatty acids. In addition, tests will be completed to determine
whether the size fraction used will alter the results and whether the compounds are coming from outside of the
shell.
Characterization of the Prototype BetaCage: A Device for Low-Level Radiation Screening
Alexander Rider
Mentors: Sunil Golwala and Robert Nelson
Good measurements of rare events are fundamentally limited by background. Studies of solar neutrinos that
advance our understanding of how the sun shines, searches for neutrino-less double beta decay to determine if the
neutrino is its own antiparticle, and the search for the elusive WIMP particle composing the dark matter pervading
the universe, have background contributions from the decays of radio-isotopes. This makes being able to measure,
characterize, and screen for trace radio contamination essential for making these measurements possible.
Screening for low-level radio contamination is complicated by the fact that the detector used as a screener is
limited by its own background. The prototype BetaCage employs a multi-wire gas proportional detector to achieve
a very low background. This type of detector uses gas as a detection medium, which has a very low mass and
therefore an inherently low background. A multi-wire gas proportional detector can also resolve particle
trajectories, allowing us to exclude decays not originating from a sample. I have characterized the performance of
a prototype for a final radio-pure version to be operated underground at the Soudan Mine.
Evolution and Sporulation of Bacillus subtilis in the Presence of Antibiotics
Giulia Ripellino
Mentors: Richard M. Murray and Vanessa D. Jonsson
Sporulation is a defense mechanism that gram-positive bacteria from the firmicute phylum can undergo when the
cell is starved. This project investigates the evolution and sporulation of Bacillus subtilis in the presence of
antibiotics. The study is designed to examine if antibiotics can induce sporulation, if there is a correlation between
antibiotic concentration and sporulation, and if resistance to the antibiotic effects sporulation. A rolling culture of
B. subtilis is kept at constant OD and antibiotic pressure using a turbidostat. Daily measurements monitor the
amount of vegetative cells and spores in the cultures. Results show that sporulation occurs after 48-72 hours and
that sporulation occurs earlier in the lower concentrations of antibiotic as compared to the control culture where no
antibiotic is added.
Remanent Magnetization From Lightning Strikes: Can We Find Paleolightning on Mars?
Andrea (Annie) Ritch
Mentor: Joe Kirschvink
Lightning strikes leave an extraordinary record of their occurrence in ferromagnetic rocks in the form of isothermal
remanent magnetization, which is a permanent remagnetization of the rock as a result of the strong, short-term
exposure to the current carried by lightning. The current of a lightning strike can often exceed 104 amperes,
thereby creating a magnetic field of 10-100 mT within a meter of the point of the strike. By using a fluxgate
magnetometer and a scanning mechanism, the magnetic field surrounding the point of lightning strike can be
analyzed, and that is the scope of this project. After understanding what lightning strikes look like in the eyes of a
fluxgate magnetometer, the ultimate goal is to put a magnetometer on the surface of Mars to find evidence of
paleolightning there, for this could very well be indicative of the presence of a water-containing atmosphere and
moisture on the ground surface, both of which are relevant to the generation of life.
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Aircraft Electric Power System Modeling
Robert Rogersten
Mentors: Richard Murray, Necmiye Özay, Mumu Xu, and Ufuk Topcu
Modern aircraft increasingly relies on electric power for subsystems that traditionally have run on mechanical
power. Therefore, the safety-criticality of aircraft electric power systems has increased rendering the design of
these systems challenging. Of specific interest for this project is the construction of models that ensure safe
distribution of electric power within the aircraft. The models constructed in this project utilize a control logic
synthesized by the Python-based software TuLiP. This control logic is tested in both hardware and software
simulation models for topologies that correspond to synthesized controllers. Each fault in a given topology requires
a sensor to communicate with the system. If any faults are detected, the system responds accordingly. Therefore,
deciding on the characteristics and functionality of the sensors to be employed is an important consideration for
each topology. In this project the models are developed and tested with progressively more sophisticated
controllers.
Development of a Near Infrared Two-Color Pyrometer for Non-Contact Thermometry of Moving Heated
Particles
Sebastián Rojas Mata
Mentors: Joseph Shepherd and Stephanie Coronel
Non-contact thermometry provides an alternative to conventional methods of temperature measurement in
experiments in which the object of study is in motion or unstable in nature. One such experiment involves
determining the parameters (temperature, velocity, size and material) of small hot metal particles that affect the
ignition of flammable mixtures. A two-color optical pyrometer was developed to obtain temperature measurements
of the falling particles prior to ignition. The theory behind two-color pyrometry is presented in order to justify the
design specifications, especially the choice of wavelengths (1705 nm and 1940 nm) and considerations regarding
radiation absorption at those wavelengths by moisture in the air. The device and its components described.
Alignment and calibration processes, involving diffuse light sources and a blackbody source, are explained. Results
from tests involving glow plugs and thin metal strips are presented to quantify the reliability and accuracy of the
pyrometer. Preliminary sphere temperature measurements are also presented. An error analysis is carried out
based both on theory and experimental data.
Observation Planning for the Nuclear Spectroscopic Telescope Array
Kexin Rong
Mentors: Fiona Harrison and Brian Grefenstette
The Nuclear Spectroscopic Telescope Array (NuSTAR) mission deploys the first focusing telescopes to image the
sky in the high energy X-ray (6 – 79 keV) region of the electromagnetic spectrum. During a two-year primary
mission phase, the telescope will map selected regions of the sky in order to hunt for young supernova remnants
as well as hidden black holes. Immediately following NuSTAR’s successful launch and mast deployment, intense
science operations are carried out in Caltech. However, the current observation planning procedures are imperfect
and prone to cause errors when, for example, scientists manually pass data from one place to another. The
objective of this research is to develop tools that calculate important parameters for observations, such as
instrument availability and spacecraft pointing.The tools integrate and modify a number of existing codes based on
understandings of how the telescopes operate in practice. Upon implementation, the tools may improve the
efficiency and accuracy of NuSTAR observation planning. Less experienced scientists will also be able to crosscheck
observing plans.
Functional Study of Protein Interactions in the N-end Rule Pathway
Connor E. Rosen
Mentors: Alexander Varshavsky and Christopher Brower
The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Destabilizing Nterminal residues of protein are recognized by the specific ubiquitin ligases of the N-end rule pathway. A key
component of the N-end rule pathway is the arginyl-tRNA-transferase, or Ate-1, which conjugates the destabilizing
amino acid arginine to N-terminal glutamate, aspartate, or cysteine. We have identified a novel binding partner of
Ate-1 through a yeast two-hybrid assay, and confirmed the interaction through co-immunoprecipitation
experiments. This protein, tentatively named Atl-1 (Ate-1 ligand-1) exhibited isoform specificity in binding to only
two of six known splicing-derived isoforms of Ate-1. Atl-1 inhibited Ate-1-dependent arginylation of E. Coli βGalactosidase in vivo, as shown through co-expression studies in S. Cerevisiae. Consistent with the Atl-1-Ate-1
binding data, this inhibition occurred in an isoform-specific manner, as Atl-1 differentially inhibited each of the four
tested isoforms. These studies suggest a role for Atl-1 in mediating the activity of specific Ate-1 isoforms.
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Ligand Binding Characterization Involving Selective Addition of Different Stoichiometries
Iva Rreza
Mentors: Dennis Dougherty and Christopher Marotta
Neuronal nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels prevalent in the central and
peripheral nervous system. Specifically, the α4β2 receptor, the most abundant of the nAChRs and one of the most
abundant receptors in the brain, is believed to underlie nicotine addiction. Nicotine chemically resembles
acetylcholine, the natural neurotransmitter of the receptor, and binds to α4β2 with high affinity as an agonist of
ACh. Here we present studies done on a previously discovered new agonist of α4β2, Sazetidine-A (Saz-A), by
means of electrophysiology tests on Xenopus oocytes. We confirm the results of Saz-A selecting for one of the α4β2
stoichiometries the (α4)2(β2)3 over (α4)3(β2)2 as a full and partial agonist respectively. We also propose a binding
model for Saz-A and report corresponding relative strengths of each binding interaction.
Investigations of Language Production Mechanisms Using fMRI
Elizabeth Ryan
Mentors: Nancy Kanwisher, Evelina Fedorenko, and Paul Sternberg
The cognitive and neural mechanisms that support language production are not yet fully understood. The goal of
the current project is to examine brain activity during overt description and naming tasks using functional magnetic
resonance imaging (fMRI). A participant is presented with a series of images of objects or simple events and is
asked to name the objects or describe the events. In the control conditions, the participant is asked to read sets of
words or simple sentences. Based on previous work (including work in the Kanwisher lab), language-sensitive brain
regions are predicted to respond more strongly to the event description condition than to condition where
participants name three unrelated objects because the former involves not only accessing the lexico-semantic
representations of three content words but also constructing a larger meaning from those component parts. The
“multiple demand” brain regions are predicted to be more active during the naming/description conditions than
during the control (reading) conditions because the former are more cognitively demanding. Moreover, MD regions
in the left frontal lobe may be especially active during language production tasks because lesions to left frontal lobe
frequently lead to production difficulties. The functional region-of-interest analyses will be complemented by more
traditional whole-brain analysis methods.
Membrane Protein Expression: An Informatics Perspective
Shyam M. Saladi
Mentors: Bil Clemons and Axel Müller
Membrane proteins comprise more than 25% of all proteins, many essential to cellular functions. Despite their
importance and abundance, membrane proteins remain poorly understood. Unlike soluble proteins, their synthesis
does not stop with translation; it also requires translocation and integration into a lipid bilayer. These additional
requirements hamper heterologous membrane protein expression and thus impede the study of membrane
proteins. We aim to overcome this bottleneck by exploring the wealth of sequence information along with
experimentally determined parameters.
We address the interplay between biophysical, genomic, and sequence dependence in membrane protein insertion
into biological membranes. The hydrophobic nature of the lipid bilayer imposes certain constraints onto the
membrane protein sequences while the genome’s GC-content and the protein’s function lead to further constraints.
Data supports subtle overall biophysical differences between genomes and provides additional insight as to possible
sequence dependences in membrane protein integration. These results will form the basis for a membrane protein
structural biology target predictor. Moreover, they will aid in the development of methods to improve expression of
membrane proteins.
Oxidative Stress-Sensitive Crosslinkers for Hydrogel Formation and Photolithography
Stephanie Rae P. Samson
Mentors: David A. Tirrell and Nicholas Ball
Reactive oxygen species (ROS), such as ·O2-, H2O2, and ·OH have the capability to destroy both healthy tissues and
foreign bodies with the human body. When compared to healthy cells, cancerous cells appear to lack the balance
between ROS and antioxidants which allows the radical species to cause irreparable damage to the DNA due to
increased amounts of oxidative stress. Our strategy is to harness the reactivity of these reactive oxygen species to
develop oxidatively-sensitive gels and thin films using elastin proteins based on the extracellular matrix. Organoselenium cross-linkers with N-Hydroxysuccinimide (NHS) or Sulfo-N-Hydroxysuccinimide (Sulfo-NHS) functionality
were synthesized. These cross-linkers are sensitive to β-carbon elimination (Grieco elimination) in the presence of
H2O2 and NaIO4, leading to degradation of our material. These selenium-based cross-linking agents have also be
used in the formation of thin films of cross-linked protein by spin-coating in organic solvents. Difficulties due to the
insolubility of NHS-functionalized cross-linkers at higher concentrations arose, though the use of cross-linkers with
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sulfo-NHS functionality afforded better water solubility and has ameliorated these issues. This should allow for
further exploration of hydrogels and thin films. These thin films will be used for photolithography by exposure of
the film to UV-active photosensitizer for cell patterning.
Client for Community Seismic Network on Android Platform
Pritesh Sankhe
Mentors: Julian J. Bunn and K. Mani Chandy
Community Seismic Network project at Caltech is an earthquake monitoring system based on a dense array of low
cost accelerometer sensors. A framework for reading the sensor data and relaying it to the cloud was developed on
an Android platform. This is a modification over the current CSN-Droid Android application which uses the inbuilt
accelerometers and machine learning algorithms for detection of seismic activity. This new version of the
application interfaces the Phidget sensor and implements the KSigma algorithm for detecting the picks. Picks
indicates abnormal deviation from the steady state acceleration. It then sends the picks to the cloud application
built on the Google App Engine. The probability calculations on this data from all the distributed sensors are carried
out on the cloud to determine any seismic activity. This client was then tested with the official CSN client to see
how both of them performed based on timing synchronization and the sensor acceleration measured. The
developed client is observed to be robust and consistent with the official client.
Gyrokinetic Studies of Plasma Turbulence
Hunter Sceats
Mentors: Frank Jenko and Paul Bellan
Turbulence describes a random distribution of structures in a continuum, occurring across a wide range of length
scales and existing for a range of characteristic times. We consider the evolution of turbulence in strongly
magnetized plasmas by means of simulations using the Gyrokinetic Electromagnetic Numerical Experiment (GENE)
code. We investigate the distribution of energy across different length scales in fully-turbulent plasmas. We
demonstrate a power-law dependence of energy density on wave-number, in agreement with earlier studies by
Tatsuno et al., but demonstrate a continuous dependence of the power-law coefficients on the collisionality of the
plasma. Further studies of turbulent plasmas may be able to explain the discrepancy between the observed and
predicted rates of magnetic reconnection in astrophysical plasmas.
Implementation of DTN Technology on the Android Platform
Brooklyn L. Schlamp
Mentors: Leigh Torgerson and Josh Schoolcraft
The goal of this project was to create an Android port of ION, a delay tolerant networking (DTN) protocol
implementation. This would allow us to send information from an Android tablet computer constantly, without
having to concern ourselves with propagation delays or disruptions in the outgoing link path. If those occur, the
Android DTN software will handle the data appropriately for delivery when the links do become available. In order
to port ION to the Android platform, we developed an interface on the Android tablet to interact with already
written ION code. This works by creating a node which uses a transmission control protocol (TCP) connection to
send data. We have concluded that such a port is possible and with this we can achieve DTN technology on a
variety of Android devices. With further development, we can create many projects to fully utilize this port and
DTN.
Dissecting the Physiology of Anger in Flies
Jonathan Schor
Mentors: David J. Anderson and Brian Duistermars
Subjectively, we are keenly aware of the onset of our own anger and equally familiar with the fact that such a state
can persist long after the initiating stimulus has been removed. In a state of anger, we also may feel a sense of
heightened awareness; we might even go so far as to call ourselves emotionally aroused. However, while our
intuitions regarding the basic qualities of our anger may be sound, our physiological understanding of these
phenomena lacks a general theory. Here, we show that in Drosophila melanogaster, the fruit fly, aggressive
arousal leads to a persistent increase in the propensity to perform aggressive behaviors, where the action itself is a
motion-dependent reflexive response. Following a screen for aggressive phenotypes, a genetically modified fly was
isolated that constitutively displays wing threats towards moving objects. Subsequent experimentation using a
computer-controlled magnet revealed that the increase in wing threat behavior is not only due to aggressionspecific arousal, but is distinct from and opposed to sexual arousal in flies.
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Development of a Wireless Infrared Laser Interface Between Nanoscale Neural Probes and the
Macroscopic World
Elizabeth C. Schroder
Mentors: Axel Scherer and Akram S. Sadek
Over the last decades, much progress has been made on the miniaturization of neural probes in response to the
numerous problems associated with conventional electrodes, including tissue damage, gliosis, and infection. These
problems primarily result from the necessity of a wired connection from the probe to an external data acquisition
system. Several attempts have been made at developing radio-based wireless systems, but none has addressed
the problem of having a wired tether to the probe itself, which causes instability and movement in the neural
tissue. To address this, we propose using the near-infrared window in biological tissue to transmit data wirelessly
through the skull via a high-frequency (1-30MHz) modulated infrared laser. The probe data are encoded in the
infrared beam via orthogonal frequency division multiplexing. Data are recovered by a photodiode connected to a
microprocessor-controlled lock-in amplifier capable of demodulating the signal across multiple carrier frequencies.
The data are then transmitted over Bluetooth to any Bluetooth-enabled device. The use of Bluetooth obviates the
need for a physical connection to the detector and facilitates use of the device in conjunction with existing
technology. Further work could make the detector implantable and adapt the technology for use with other
implantable biomedical sensors.
Simulation, Fabrication, and Optimization of Microelectrodes for Glucose Detection
Mehmet Sencan
Mentors: Axel Scherer and Muhammad Mujeeb-U-Rahman
Diabetes is a significant health problem. Continuous blood glucose monitoring guided treatment has shown
effective in mitigating the symptoms. Current systems for continuous blood glucose monitoring involve centimeterscale implants which tether through the skin to an outside transmitter. It is proposed that a micron-scale,
untethered implant would be more comfortable and effective. An invaluable part of such system is the electrode
assembly. In this research, progress is made towards optimized electrode geometry for a micron-scale system.
Potential electrode geometries are simulated via COMSOL. Selected geometries are fabricated utilizing CMOS
compatible techniques. The fabricated electrodes are functionalized and tested. The results of the tests are fed
back into the simulation to increase accuracy and optimize the next design run.
Oculomotor Behavior in TD and ASD in Infancy or Toddlerhood
Elizabeth Sharer
Mentors: Ralph Adolphs and Jed Elison
Early oculomotor behavior supports the framework for an infant’s engagement with the environment and thus
social perception. Early deficits in processing social information (such as faces) are proposed to severely affect the
later development of various social abilities and account for much of the social dysfunction observed in individuals
with autism. Aberrations in oculomotor behavior may contribute to deficits early in social perception development.
Previous research has demonstrated subtle oculomotor differences between autism spectrum disorder (ASD) and
typically developing (TD) population, but not in infancy. This study characterizes the developmental patterns of
saccade dynamics in low-risk, high-risk with a diagnosis, and high-risk without a diagnosis for autism. Eye-tracking
data was collected as infants, ranging from 6 months to 24 months, watched a dynamic video. Oculomotor metrics
were extracted from raw eye-tracking data. Preliminary results suggest no differences in saccade dynamics
between groups at 24 months. However, the data suggest a trend towards disorder specific effects such that lowrisk and high-risk negative groups show larger average saccade amplitudes at 12 months (m=190, n=53; m=192,
n=33) than those with ASD (m=120, n=10). Further research will attempt to comprehensively characterize the
developmental trajectories of saccade dynamics.
Neurogenetic Control of Lethargus in Caenorhabditis elegans
Jordan A. Shaw
Mentors: Paul W. Sternberg and Julie Cho
We want to know if neurons that respond to different sensory stimuli during lethargus, a sleep-like state in C.
elegans, are modulated and, if so, how. First, soft touch assays tested overall mechanosensory response changes
in lethargus. Because assays in wild-type worms indicated no difference between awake and sleeping response to
soft touch, we looked to see if we could elicit larger responses in less sensitive mec-17 mutants. The force of
stimuli could have made it impossible to observe a difference between the sleep and awake states. To control
stimulus intensity, we used optogenetic assays, which use blue light to depolarize specific neurons using
channelrodopsin, a light-gated cation channel. Activation of the ALM and PLM suggests that mechanosensation is
altered in sleep, but that the threshold is low enough to robustly detect a touch stimulus. We are testing the effect
of an egl-4 mutation that increases neuronal activity. Experiments depolarizing the ASH in egl-4 mutants will
elucidate whether or not increased sensory signaling alleviates the previously found reduction in response to ASH
stimulation in lethargus (Cho, unpublished data). Additionally, optogenetic assays with glr-1 mutants could further
clarify the relationship between the ASH and its interneurons in this model of sleep.
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Investigation of the Mechanism of Propidium Monoazide Exclusion From Dead Cells
Amanda N. Shelton
Mentors: Adrian Ponce and Christina Stam
Propidium monoazide (PMA) is a DNA-intercalating dye that is excluded from viable, membrane-intact cells and,
upon reaction with visible light, PMA crosslinks to DNA, making it unavailable for amplification in quantitative
polymerase chain reaction (qPCR). PMA-qPCR is an emerging method to quickly and specifically determine only the
living fraction of a microbial population, however the mechanism by which PMA is excluded from living cells is not
well understood. We examine the mechanism of PMA exclusion using a gram-negative bacterium, Escherichia coli,
and a gram-positive, Bacillus atrophaeus. We force PMA inside both living cells and membrane-intact, killed cells
using electroporation, which uses a capacitor to create transient pores in the cell membrane, and then observe the
effects using qPCR, colony counts and fluorescence microscopy. We also explore the relationship between PMA
shifts in qPCR Ct values and the temperature and duration at which cells are treated with heat, since at some
temperatures, cell membranes are not damaged by heat even when cells are no longer culturable.
Mean-Field Analysis of d-Wave Superfluidity in Optical Lattices of Ultracold Polar Molecules
Jacob Quinn Shenker
Mentors: John Preskill and Alexey Gorshkov
The slave-boson mean-field technique has been applied fruitfully to the standard t-J model of high-temperature
superconductivity. Previous work has identified a generalization of the t-J model with long-range interactions which
may be realized by an optical lattice of ultracold polar molecules. We apply the slave-boson method to explore the
phase diagram of this system, and in particular to ascertain that exotic d-wave superfluid state that has been found
in the standard t-J model also exists in the generalized model.
Illumination of the Brain With Infrared Light
Jeff Sherman
Mentor: Azita Emami
Victims of Traumatic Brain Injury (TBI) can be saved from permanent damage by immediate treatment. Delivering
the drug quickly after injury remains a problem. In an effort to develop a quick delivery system, the Dougherty
Group has developed a chemical that will help reduce the damaging effects of TBI, if delivered promptly. However,
this chemical is only activated in the presence of infrared light. If a potential TBI victim is injected with the
chemical before the incident, then irradiating his or her brain with infrared light will provide the treatment
necessary to save a person. We seek to design a lightweight, low power optical helmet that will illuminate the
wearer’s brain with infrared light to activate the previously administered chemical. To design the helmet, an optical
simulation program was used to simulate the scattering and absorption effects of hair, scalp, skull, and brain. The
system is designed to evenly apply infrared light throughout the brain without heating up the tissue or the device
more than 1oC. Once the design is complete, fabrication and testing will follow.
Functionalizing and Optimizing Members of the Discoidin Family as Antibody-Mimetic Scaffolds
Kevin Shi
Mentors: Steve Mayo and Gene Kym
Antibodies, the traditional means of protein-based molecular recognition, are burdened by size, fragility,
immunogenicity, and other shortcomings. This has prompted the search for alternative scaffolds. In this work, an
integrated computational, combinatorial, and chemical approach is employed to develop members of the discoidin
family as antibody-mimetic scaffolds. The full discoidin (factor V/VII, C2-like) domain, an 18 kDa β-sandwich with a
number of variable-sequence binding loops, has been incorporated into the homologous family member lactadherin
(MFGE8). The binding interface to the target antigen integrin is rationally designed by incorporating an integrin
binding hotspot in conjunction with an antibody-mimetic degenerate codon library. The highest affinity binders are
screened using yeast surface display (YSD), and the designs are validated.
Protein Dynamic Studies of Cytochrome cb562 Mutants
Dong Woo Shin
Mentors: Harry Gray and Nicole Bouley Ford
Denatured proteins poses serious problems in biological systems, often acting as the pathogen in various diseases
such as the BSE (“mad cow disease”) and CJD (Creutzfeldt–Jakob disease). By observing intermolecular diffusion in
unfolded proteins, properties and characteristics of the denatured proteins can be understood in more detail. Using
cytochrome cb562 mutants with a ruthenium photosensitizer in various locations, the method of contact quenching
was used on proteins to measure the rate of contact formation between the photosensitizer and the iron heme. As
the ruthenium photosensitizer comes into contact with the protein’s iron heme, the quenching of the luminescence
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of the photosensitizer was observed using a nanosecond laser. From this study, the decay rate of the
photosensitizer was observed in varying GuHCl concentrations and distances of the photosensitizer to the heme.
This study will shed light as to the nature of rigidity and the movements of the unfolded protein.
Large-Area Transfer of CVD Graphene to Silicon Substrate and Applications
Corwin Shiu
Mentors: Michael Roukes, Mehmet Selim Hanay, and Peter Hung
Graphene has unique mechanical, electrical and optical properties that make it a very promising material in future
technology. We use chemical vapor deposited (CVD) graphene which can be grown on copper substrates to
arbitrary sizes. We optimized the transfer of graphene from the copper surface to a silicon wafer. By varying the
transfer parameters, we minimize the formation of holes and cracks in our graphene, improving device quality and
yield. We have discovered that the polar/non-polar interactions between the solvent for PMMA and etching solution
play an instrumental role in retaining a planar surface during the transfer process. We report better graphene
contact by functionalizing the substrate to wick away trapped water molecules. We discover graphene is lifted off in
acetone during the PMMA removal step. By optimizing our transfer parameters we have been able to produce 1cm
by 1cm continuous graphene. The improved transfer of graphene has led to higher quality suspended graphene
nanoelectromechanical system (NEMS) and increased yields as evident by electron microscopy images. We have
successfully observed multiple mechanical resonances of our devices through both optical and electrical detection
schemes with capacitive drive.
Identifying FERMI Gamma-Ray Blazars Using Optical Variability
Haran Kumar Shiv Kumar
Mentors: S. George Djorgovski and Ashish Mahabal
The LAT instrument aboard the Fermi Gamma-Ray Space Telescope has discovered a couple of thousand gamma
ray sources. The telescope gives error ellipses in their positions. Among these, 35% are gamma ray sources with
no known associations. Half of these are expected to be Blazars. The project’s aim is to identify these sources by
analyzing data of their variability in the optical regime. The process of obtaining candidates involves characterizing
all CRTS(Catalina Real Time Transient Survey) objects within the error ellipse of each unassociated source and
identifying outliers as Blazar candidates. Since Blazars are highly variable, the characteristics used are
predominantly concerned with variability. The candidates have their light curves plotted and analyzed to further
filter the list. A search for radio sources will be done for the error ellipse and the results cross-matched with the list
of candidates to determine which of them are radio-loud and variable objects. These are the most likely to be
Blazars. The most promising candidates will then have their spectrum taken for final identification.
Verifying the Orbital Period of CR Boo
Gregory Simonian
Mentors: Thomas Prince and David Levitan
I explored a method to determine the orbital periods of a class of rare, highly relativistic, outbursting binary stars
undergoing mass transfer called AM CVns. These objects have the shortest observable periods of all known binary
objects; therefore determining their periods is extremely important. The only currently accepted method for
measuring the period of a noneclipsing AM CVn is by tracing the movement of the hot spot—the location where
material from the donor star hits the accretion disk of the accretor. It has been postulated that the orbital period of
an AM CVn system can also be measured from its brightness variability. I attempted to confirm the 24.513 minute
orbital period of CR Boo, the third brightest known AM CVn, previously estimated from brightness variability by
using a time-series of spectra to monitor the movement of the hot spot. Surprisingly, the hot spot could not be
detected. If confirmed, this result may challenge the assumption that all AM CVns always possess prominent hot
spots.
Synthesizing Stable Grain Boundaries in Metals Through Molecular Dynamics
Kiara Camille Simpao
Mentors: Dennis Kochmann and Gabriela Venturini
Molecular dynamics is a widely-used method for simulating the behavior of materials on an atomistic scale.
Simulations created using this method have been used to study a material’s mechanical properties. Another
method that is being developed is the quasicontinuum (QC) method, which approaches materials from both
continuum and atomistic perspectives. To aid in the development of using the QC method to model plastic
deformation and crystal defects, models for the initial conditions must be constructed using molecular dynamics.
Using LAMMPS, a molecular dynamics simulation program, lattice structures for copper were created by writing
input files that are compatible with the program. The structures were modified to contain various defects, focusing
on various types and degrees of deformations. The minimum energy values of the models at zero temperature and
at finite temperatures were measured to ensure that the structures were stable. Work is ongoing to create grain
boundaries, and when these models are successfully created, they will be adapted for aluminum and vanadium.
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The Formation and Evolution of the Atmosphere of Jupiter: A Study Through Computer Simulation
Timothy Sinclair
Mentor: David Stevenson
The interiors of gas planets, including Jupiter, Saturn, and gas giant exoplanets, are not well understood because
of the lack of direct observation, although they are typically taken to have solid cores surrounded by a
homogenized gaseous atmosphere. The formation of these gas giants is usually taken to be by accretion onto a
solid embryo of gas and incidental solid objects, which undergo ablation to populate the atmosphere with new
material. Computer simulation of the formation and evolution of the atmosphere of Jupiter creates a model for
Jupiter that attempts to explore the interior of Jupiter in order to better understand what the interior of Jupiter may
resemble. This model starts with a rocky inner core roughly the size of Mars with an envelope composed of a
hydrogen/helium mixture in hydrostatic equilibrium. Planetesimals are selected from a likely statistical distribution
of size and their encounter with the growing planet is simulated so that their mass is distributed in various layers of
atmosphere so as to maintain the atmosphere’s stability. A process of hydrogen/helium gas influx is also
simulated. The result is a planet that grows in core mass, atmospheric mass, and atmospheric metal content. The
models suggests that as the body grows beyond about half an earth mass, most incoming planetesimals are broken
up and evaporated well above the core surface, dispersing their high molecular weight material into the growing
atmosphere.
4D Visualization of Building Response to Seismic Ground Motions
Prastuti Singh
Mentor: Monica Kohler
Earthquakes are California's costliest disaster. The major source of this loss is structural damage and disruption to
infrastructure. This damage can be moderated through advance knowledge of how buildings will respond in the
event of an earthquake. The purpose of this project was to develop software packages that output informative 3D
and 4D visualizations of building response during an earthquake given real or scenario seismic data. Both real and
scenario (synthesized based on a basic shear beam model) seismic data were integrated with simple, 3D building
models to create the visualizations. These consisted of peak acceleration, velocity, displacement, and inter-story
drift values for each floor superimposed on the building in separate visualizations. The peak values are an indirect
measure of potential damage. The 4D visualizations comprise movies of building “shaking” that allow the user to
clearly see how the building will respond to an earthquake. These visualizations will further public knowledge of
structural response and lead to new procedures that minimize delays in response time.
Single Cell Analysis of MiR-155 and MiR-146a Regulation of the Macrophage Immune Response Using
In Situ Hybridization Chain Reaction
Nikita Sinha
Mentors: David Baltimore and Arnav Mehta
MicroRNAs play a significant role in the complex gene regulatory network that tightly regulates mammalian
hematopoiesis to ensure balanced and appropriate hematopoietic output. Here we develop a technique to detect
target miRNAs on a single-cell level by in situ hybridization chain reaction (HCR), in which RNA probes
complementary to mRNA targets trigger chain reactions where fluorophore-labeled RNA hairpins self-assemble into
tethered fluorescent amplification polymers. While theoretically identifying and imaging miRNAs by HCR in situ
hybridization should be no different from mRNAs, the short sequence and low endogenous signal intensity of
miRNAs required us to optimize the technique. We found that the protocol for miRNAs is different from that of
mRNAs in that cells need to be treated with proteinase K to make miRNAs available for probe binding, and that
cells need to be fixed with 1- ethyl-3-(3-dimethylaminopropyl)-carbodiimide to prevent leakage of miRNAs out of
the cell during hybridization and amplification steps. Next we aim to understand the fine-tuning of NF-kB signaling
at the single-cell level in the context of miR-155 and miR-146a. This in turn will elucidate how microRNA
expression can confer different functional properties to subsets of macrophages and how this might contribute to
pathological inflammatory responses.
Automated Information Retrieval System (AIRS): An Economical Safeguard Against Data Loss for High
Altitude Balloon Missions
Russell Smith
Mentors: Jeff Booth and Jason Rhodes
Long duration balloon missions such as the High Altitude Lensing Observatory (HALO) acquire such high quantities
of data that they require cost prohibitive downlink bandwidth. AIRS provides a backup data transfer mechanism so
that flight duration is not limited by fear of total data loss. An autonomous glider with GPS and autopilot carries a
solid state hard drive to an approved location near the balloon’s position. For maximum safety, the mass and final
kinetic energy have been minimized. Accurate waypoint targeting both simplifies recovery and further mitigates
risk. A low drag, low aspect ratio wing provides rapid penetration through high crosswinds, yet supports slow
landings at a high angle of attack. The 450g laminated thin wall fiberglass and foam capsule includes a solid state
drive rated to withstand 1500G, more than double the capsule's impact force in an unlikely control system failure.
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A radio signal is broadcast after landing, allowing AIRS to be easily located with a directional receiver. AIRS has
been designed, fabricated, and fitted with an autopilot. We are seeking approval to perform drop tests from
weather balloons in private NASA airspace at Dryden, hopefully demonstrating the feasibility of safe and easy data
retrieval at low cost.
Photoreversible Protein Patterning in Hydrogels Using Bioorthogonal Reactions
Seorim Song
Mentors: David A. Tirrell and Cole A. DeForest
Hydrogels have been proven to be very useful for three-dimensional cell culture due to their many similarities with
native tissue and because their chemical and mechanical properties can be tuned to direct encapsulated cell
function. Existing advanced hydrogel systems enable the introduction of biomolecules such as proteins with spatial
control, but they fail to capture the inherently dynamic nature of protein presentation found in vivo. The goal of
this project is to develop a system that enables proteins to be patterned both in and out of a hydrogel platform
with full spatiotemporal control. A combination of bioorthogonal reactions was used – strain-promoted azide-alkyne
cycloaddition (SPAAC) for hydrogel formation, a photocaged aminooxy-aldehyde reaction to introduce proteins into
the material, and an o-nitrobenzyl ether photodegradation to release pre-patterned proteins from the hydrogel.
The kinetics of photopatterning was examined by nuclear magnetic resonance spectroscopy and fluorescent
microscopy-based assays. Experimentally-obtained protein patterning concentrations were found to be in excellent
agreement with theoretical predictions.
Evaluation and Benchmarking for Robot Motion Planning Problems Using TuLiP
Nick Spooner
Mentors: Richard Murray, Pavithra Prabhakar, Necmiye Özay, and Ufuk Topcu
Model checking is a technique commonly used in the verification of software and hardware. More recently, similar
techniques have been employed to synthesize software that is correct by construction. TuLiP is a toolkit which
interfaces with game solvers and model checkers to achieve this, producing a finite-state automaton representing a
controller that satisfies the supplied specification. For motion planning in particular, a model checker may be
employed in a deterministic (non-adversarial) scenario to produce a path satisfying a specification φ by checking
against its negation ¬φ. If a counterexample is found, it will be a trace which satisfies φ. This was achieved in the
TuLiP framework using the linear temporal logic (LTL) model checkers NuSMV and SPIN. A benchmark scenario
based on a regular grid-world with obstacle and goal regions and reachability properties was devised, and extended
to allow control of various complexity parameters, such as grid size, number of actors, specification type etc.
Different measures of performance were explored, including CPU time, memory usage and path length, and the
behavior of each checker with increasing problem complexity was analyzed using these metrics. The suitability of
each checker for different classes and complexities of motion-planning problem was evaluated.
Uptake of Organosilicates by Soil Microbes
Andrew Stanek
Mentor: Jared Leadbetter
Hundreds of thousands of tons of artificial silicon and organosilicate compounds are released into the environment
every year as components in everything from electronics to pharmaceuticals. It stands to reason that these
compounds are biodegradable. Silicon is chemically similar to carbon, an essential element of all known life, but the
silicon cycle in microbes is not well understood. It stands to reason that bacteria adapted to survival in silicon-rich
environments should be able to metabolize these compounds. Defined media assays and spectrophotometry
indicate that rapidly-growing bacteria capable of using organosilicate compounds as sole carbon sources are
common in ordinary environments. I conclude that organosilicate-metabolizing bacteria likely render artificial
organosilicate compounds biodegradable, but the specifics of the environmental and microbial silicon cycle remain
unclear.
Analysis of Axud1 Expression and Function During Neural Crest Formation
Michael Stone
Mentors: Marianne Bronner and Marcos Simoes-Costa
The neural crest is an embryonic population that gives rise to a variety of derivatives such as the peripheral
nervous system, pigment cells, and bones and cartilage of the head. High throughput RNA sequencing screens
have identified different genes that were previously unknown to be specifically expressed in the developing neural
crest, one such gene being Axud1. In this project I will describe the expression of Axud1 in chicken embryos using
whole mount in situ hybridization and investigate the role of this gene in neural crest formation. Functional analysis
was performed by morpholino mediated knockdown through electroporation of stage HH4 chicken embryos. Axud1
is expressed in the premigratory and migrating neural crest cells, neural folds, somites, genital ridges, and tail bud.
Knockdown of Axud1 causes loss of activity of neural crest specific enhancers. Furthermore, neural crest markers
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such as FoxD3, Sox9, and Sox10 appear downregulated in embryos that have been electroporated with
morpholino. These results suggest that Axud1 has an important role in neural crest development and is required
for the expression of a number of genes that are involved in neural crest specification and migration.
Engineering Escherichia coli to Animate Images in Response to Light
Ashley Su
Mentors: Richard Murray, Nate Glasser, Gita Mahmoudabadi, and Emmanuel de Los Santos
Previous studies have shown that high-definition images can be produced by Escherichia coli using projection of a
pattern of light onto the bacteria. Current objective of researching this bacterial system is to introduce a
degradation tag that will degrade the emission of red fluorescent protein (mCherry) while the image is produced to
create a moving bacterial lawn modeling an animation. This spatial control of gene expression can be used to
model rates of degradation versus rates of synthesis of mCherry and investigate signaling pathways through spatial
and temporal control. We have begun to engineer Escherichia coli to selectively use the lighting portion of the
bacterial system instead of using the regulation in response to osmotic shock. We have created two constructs of
mCherry with separate degradation tags that vary in the final three amino acids (AAV, LVA). We have also begun
to explore varying strengths of osmotic pressure onto our constructs using varying salt concentration in a RFP
assay. These results provide insight into an insufficiently explored collaboration between art and biology and may
prove useful for signaling temporal and spatial applications of bacterial films.
Entrainment of Single Neurons to Extracellular Electric Fields
Chen Sun
Mentors: Christof Koch and Costas Anastassiou
In the past decades studies have shown that extracellular fields feed back and impact the electric potential across
the neuronal membrane which in turn, can affect neuronal activity via purely electrostatic, so-called “ephaptic”
coupling (Arvanitaki, 1942). Because ephaptic effects on neurons are not well understood, this project will start
from the very basics: investigating the effects of simple sinusoidal extracellular fields on individual neurons. The
purpose is to better understand how the observed effects of sinusoidal electric fields on single neurons occur, and
to come up with a more complete formulation for understanding and predicting their spiking output with respect to
the external stimulus. So, first, a theoretical framework and neuronal model, called a “discrete probabilistic model”
(DPM) was developed to allow investigation of this problem. Next, experimental results, especially from
Anastassiou et al 2011, were used to test the model. Finally, some new predictions on the behaviour of neurons in
the presence of sinosoidal ephaptic fields were generated using this model. The DPM predicts that the ability of
extracellular fields to entrain spikes depends both on spike history, as well as the properties of the neuron.
Synthesis and Optimization of a Chelated Ruthenium Catalyst for E-Selective Olefin Metathesis
Benjamin A. Suslick
Mentors: Robert Grubbs and Myles Herbert
Basic organic chemical reactions are essential to many industrial processes, including those used to make
pharmaceutical drugs and petrochemicals. One such reaction, olefin metathesis involves a ruthenium complex that
catalyzes a process that reacts two olefins causing them to “swap” fragments creating a new olefin containing
compound. This reaction, however, produces two different isomers of the final product: E and Z. Since selectivity is
essential for any industrially used process, investigation into preparing enantio-pure products was performed. It
has recently been shown by the Grubbs group that changing the size and shape of the N-heterocyclic carbene
(NHC) ligand attached to the ruthenium catalyst can change the selectivity of metathesis reactions. Herein
attempts to synthesize catalysts for E selective metathesis have been made. The steric properties of the NHC
ligands were changed to favor a geometric conformation in the intermediate that correlates to the E-isomer. NHC
ligands were synthesized using a multistep route starting from N-(2-bromoethyl)phthalimide. The diamine was
created form the starting material via substitution and deprotection, and was then ring closed and substituted with
a range of alkylating groups to allow for control over the final steric properties of the NHC.
Rover Mobility: Understanding and Refining Simulations of Rover Wheel Interactions With Soft Soils
Wesley Swank
Mentors: Brian Trease and José Andrade
Although Mars rovers have been in use for exploratory and scientific purposes since 1997, the methods employed
to simulate and predict their mobility over soft soils largely rely on experimentally derived computation models that
have gone unchanged for decades. As the Mars Exploratory Rover Spirit’s eventual failure due to immobilization in
soft sand indicates, the challenge of maintaining rover mobility across these surfaces is very much relevant to
current endeavors at the Jet Propulsion Laboratory. The aim of this project is twofold: to contribute to existing
quasi-static computation models through dynamic experimentation; and to provide the Computational
Geomechanics Group at Caltech with the background and infrastructure to apply their ongoing work in physicsbased modeling of granular materials to simulations of rover interactions with soft-soil surfaces.
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Creating an Ontology to Define Processes in Ground Systems Group 318
Sam Szuflita
Mentors: Oleg Sindiy, Patricia Lock, and Kathleen Crean
As part of an ongoing effort in the Ground Systems (GS) Engineering section to standardize its practices, process
modeling is being employed to capture the products and procedures used by the section. This work is being done
using the MagicDraw software tool to create models in Systems Modeling Language (SysML) and Business Process
Modeling and Notation (BPMN). In order for these models to be compatible and scalable, it is essential that they
share a well-defined, domain-specific taxonomy. It is also important to define and characterize the allowed
relationships among these terms. My focus has been creating an ontology that rigorously defines these terms via
their properties and allowed relationships. This ontology can then be used to develop a set of common views and
products that can be tailored to address the concerns of specific stakeholders. It is also important for this ontology
to be built on logical quantifiers so it can be queried and checked for soundness.
High Temperature Monitoring of the Height of Condensed Water in Steam Pipes
Nobuyuki Takano
Mentors: Yoseph Bar-Cohen, Xiaoqi Bao, and Shyh-Shiuh Lih
Steam pipe systems are used as a district heating system in various major cities including Manhattan. They provide
steam from central power stations under the streets to support heating, cooling, or power to high rise buildings and
businesses. Excessive rise in the level of water condensation in steam pipe systems is a source of concern due to
the possible excitation of water hammer effects which may lead to serious consequences including damaged vents,
traps, and piping. The use of high temperature ultrasonic transducers in a pulse-echo test configuration provides
the ability to track through steam pipe walls the condensation of water. The primary focus of this SURF internship
has been on getting data to determine the condensation height of water through the steel pipe at temperature as
high as 250ºC. The task involved both experimental studies of various transducers performance, ultrasonic wave
response as well as software development. The results of the experiments are used to establish an in-service
health monitoring breadboard system capable of sustaining temperatures as high as 250ºC and used to measure
the height of condensed water inside steam pipes.
Validation of Procedures Used by CMS in the Characterization of Higgs Candidate Events
Alex Takeda
Mentors: Maria Spiropulu, Si Xie, and Emanuele di Marco
With the recent announcement of the discovery of a new bosonic state at the Large Hadron Collider (LHC),
hypothesized to be the long-sought Higgs boson, the correctness of the procedures used for characterization and
classification of this state has become very relevant. This project worked on a number of different aspects in the
analysis of the HZZ4l decay channel, related especially to lepton detection. Characterization of this channel relies
on the accurate prediction of lepton detection efficiency and resolution, but currently used algorithms for prediction
of these detector effects are computationally demanding. This project developed a validation procedure for a faster
simulation algorithm written by the Caltech group, and showed its adequacy for predicting efficiency and
resolution. Another issue analyzed in lepton detection was the use of multivariate analysis techniques, such as
boosted decision trees, for reconstruction of the actual lepton energies from detected values, in order to discover
whether the current reconstruction algorithms can be improved. Some questions outside of the scope of lepton
detection were also analyzed, such as the distributions of the two intermediate Z in the HZZ4l decay. The official
analysis uses an invariant mass proximity criterion to perform the pairing, but there are other possible pairing
criteria that could be helpful in the detection of new physics. Current data in the signal region is scarce, but the
algorithms developed for this pairing analysis will be available for future, larger datasets.
Genetic Manipulation of Synapse Formation and Synapse Structure
Alison Tan
Mentors: Thomas Südhof, Stephan Maxeiner, and Paul Patterson
The objective of this project is to study novel uncharacterized mutant mouse lines to provide insight into the
function of different synaptic proteins. We analyze a mouse line in which Ribeye is deleted from the retina as well
as the latrophilin-2 conditional knockout mouse line. Ribeye is a special splice form of CtBP2 expressed in retinal
and inner ear ribbon synapses only; the protein has an A-domain by alternative splicing specific for ribbons and a
B-domain that it shares with CtBP2. Through techniques such as PCR genotyping, quantitative RT-PCR,
immunofluorescence analysis and immunoblotting, we are able to verify differences on RNA transcript and protein
level. Immunoblotting of seven different allelic combinations allows us to qualitatively evaluate protein levels using
an antibody against Ribeye and CtBP2 that detects the B-domain and an antibody against GFP that recognizes
GCamP3. The screening of photoreceptor ribbon synaptic complexes for ribbon-associated proteins, such as
Bassoon, in the retinae illustrates the expected horseshoe shape in the OPL (outer plexiform layer). We determine
the lethality of latrophilin-2 conditional knockout mice and aim to understand the cause of lethality through
different embryonic stages. Success of these experiments will be assessed by results of immunofluorescence
analysis and immunoblotting.
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Geobiology of the World's Deepest Hydrothermal Vents: Lipid and Lipid Carbon Stable Isotope
Composition Analysis of Macrofauna Discovered Near the Hydrothermal Vents
Stephanie M. Tan
Mentors: Max Coleman and Sarah Bennett
Deep sea hydrothermal vent ecosystems are primarily sourced by chemosynthetic bacteria and have minimal
photosynthetic influence and thus are possible analogues to systems which may exist under the icy surface of
Europa. Study of macrofauna samples collected from the world’s deepest hydrothermal vents at the Mid-Cayman
Rise, sheds light on organic matter dispersal pattern and its origins, whether being photosynthetic or
chemosynthetic, near the hydrothermal vents. Knowledge of these will play a part in future work of estimating
potential biomass on Europa. We analyzed samples from both a shallow (2300m) vent site named Von Damm and
the deepest (4960m) vent site ever discovered named Piccard. We extracted lipids from samples that are
representative of various trophic levels, including shrimp, squat lobsters, a sea anemone and a flying fish. We
analyzed the samples by Gas Chromatography Mass Spectrometry (GCMS) for lipid compositions and will identify
the carbon isotope composition of the individual lipids using Gas Chromatography Isotope Ratio Mass Spectrometry
(GC-IRMS). We anticipate that the lipid and lipid isotope compositions will characterize lipids as being less
photosynthetically influenced at Piccard than at Von Damm. We have finished the process of lipid extraction and
GCMS analysis. Preliminary data demonstrates noticeable differences between samples from different vent sites.
Further quantification of data enables me to specify the relationship between the origin of lipids present in each
sample. From this information, I can conclude whether or not Piccard is less photosynthetically influenced than Von
Damm.
Iterative in situ Click Chemistry: Developing a Capture Agent for kRas
Grace Y. Tang
Mentors: James R. Heath and Ryan K. Henning
Ras proteins regulate signaling pathways responsible for many cellular responses such as proliferation, survival,
and differentiation. The g12d residue in Ras is susceptible to mutations that are strongly associated with
developmental disorders and cancer; greater than 30% of all human cancers have activating kRas mutations. Ras
is also deemed undruggable, so there are currently no effective methods to treat Ras mutations in cancer patients.
Our aim is to use in situ click chemistry to synthesize a multi-ligand capture agent which differentiates between
wild type and mutant kRas. E. coli cells are modified to synthesize mutant kRas proteins incorporating
Azidohomoalanine (Az2), which allows for click chemistry with peptide strands. Before beginning screening for
potential anchor ligands, SDS-PAGE and Western Blotting can be used to express the proteins and the Az2 click
handle. We successfully expressed two Az2-incorporated mutants and began screening for an anchor ligand.
Further screens are required to develop a multi-ligand capture agent with higher affinity. Negative screens against
the wild type kRas can also lead to a differentiating capture agent.
Data Analysis of Tropical Cyclone Size
Nicholas Tang
Mentor: Hui Su
The geometric size of a tropical cyclone (TC) is directly related to its destructive potential. However, widely used
measures for TC activity and destructive potential, such as the accumulated cyclone energy (ACE) and power
dissipation index (PDI), are based on maximum wind speed, without considering storm size. Our analysis of the
Automated Tropical Cyclone Forecast (ATCF) and Joint Typhoon Warning Center (JWTC) best track data shows that
storm size is positively correlated with TC intensity and translation speed globally. The revised ACE and PDI (RACE
and RPDI) take into account storm size but do not have a significant effect on annual trends for TC activity and
destructive potential. In the Atlantic basin (AL), the RPDI bears a stronger correlation with September sea surface
temperature than the PDI over the past decade, implying a potentially strong linkage between global warming and
the destructiveness of the Atlantic hurricanes. The annual trends of RACE and RPDI over the Western Pacific basin
(WP) exhibit negative correlation with local SST, suggesting the dominant factors in determining TC activity are
different for AL and WP.
Start-Up Dynamics of Vertical Axis Turbines
Katherine Taylor
Mentor: John O. Dabiri
We present an experimental study of the self-starting behavior of vertical axis turbines, in order to guide the
design of systems that operate in unsteady flows. The torque, angular velocity, and power generation of a scale
model turbine were measured in a free surface water tunnel for different starting angles of the rotor blades and for
different flow speeds. The starting behavior of the turbine was found to be sensitively dependent on the initial
angle of the rotor at low flow speeds. A conceptual model was developed in order to explain the observed behavior
in terms of the instantaneous lift and drag on the rotor blades.
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Quantum Statistical Mechanical Systems and Spectral Triples for Multifractals
Nicolas Tedeschi
Mentor: Matilde Marcolli
The study of fractals has led to connections to two seemingly disparate mathematical structures: spectral triples in
noncommutative geometry and operator algebra based quantum statistical mechanical systems. Fractals can be
described in noncommutative geometry through a spectral triple, which consists of an algebra of operators, a
Hilbert space, and a Dirac operator which is self-adjoint with bounded commutators with all operators in the
algebra. This description can be used to encode the geometric properties of a fractal analytically, for example
Hausdorff dimension through the trace of the Dirac operator. Likewise there is a quantum statistical mechanical
system (also involving an algebra of operators, which describes the observables of a system along with a group
homomorphism specifying the system’s time evolution) that can be uniquely assigned to each fractal. This
viewpoint links the thermodynamic properties of the quantum statistical mechanical system to the geometric
properties of the fractal. We study the way that the multifractal decomposition of fractals such as the Cantor set
leads to useful decompositions of the corresponding spectral triples and convert this information into quantum
statistical mechanical systems and subsystems that are similarly related to the fractals.
Conformational Changes in Succinic Acid With Temperature and Metallic Cations Bridging to Form
Analogues of Intramolecular Hydrogen Bonds
Sofia P. Tedesco
Mentors: John D. Roberts, William Carroll, and Bright Emenike
Intramolecular hydrogen bonding is common in biochemical pathways. Succinic acid is a simple organic molecule
which can serve as a model to investigate intramolecular hydrogen bonding as a monoanion in nonpolar, aprotic
solutions. This study focuses on the effect of variable temperature and metallic cation substitution for hydrogen on
the strength of intramolecular bridging. Nuclear magnetic resonance (NMR) is used to determine the fraction
gauche (FG) of the molecule.
Semidefinite Programming for Optimal Power Flow Problem
Thanchanok (Nicky) Teeraratkul
Mentors: Babak Hassibi and Subhonmesh Bose
The optimal power flow (OPF) problem is nonconvex and generally NP-hard. We follow the semidefinite
programming (SDP) optimization, which is the dual of rank relaxation of the OPF problem. A global optimum
solution to the OPF problem can be retrieved from a solution of this dual convex problem when the duality gap is
zero. This condition is satisfied by the standard IEEE benchmark systems with 6, 9, 14, 24, 30, 57, 118 and 300
buses systems, after a small resistance (10-4 per unit) is added to every transformer that originally assumes zero
resistance. Nonzero duality gap occurs when line flow constraints are strict. In this case, we propose the heuristic
approach based on Newton’s step, and stochastic approach to find a feasible solution.
Development of a Novel Solid-Supported Ruthenium Catalyst
Darius Teo
Mentors: Robert H. Grubbs and Raymond Weitekamp
We have demonstrated an efficient synthesis of backbone-substituted imidazolinium salts, which we propose to
employ as N-heterocyclic carbene (NHC) ligands for organometallic catalysts. These functionalized NHCs will be
used to develop solid-supported olefin metathesis catalysts, with the goal of demonstrating a continuous flow
reactor. The efficiency and recyclability will be tested using ring-closing metathesis. The distance between the
heterocycle and surface-tethering group will be varied to explore its effects on catalyst activity and decomposition.
Analysis of the Ratio of Ortho to Para Water Using Fourier Transform Infrared Spectroscopy
Elizabeth Terlinden
Mentor: Geoffrey A. Blake, Daniel Holland, and Sergio Ioppolo
Molecules may be grouped into isomers based on the nuclear spin states of their constituent atoms. Our research
addresses the two spin isomers of water, ortho and para. Ortho water contains two hydrogens whose spin states
are aligned, while para water contains two hydrogens whose spin states are antialigned. Under normal conditions,
the ratio of ortho to para in the atmosphere is about three to one. However, in the 1980s a deviation as large as
ten to one in the presence of adsorbent (material to which water adheres) was reported. Our group thought the
question of sufficient interest to pursue. We used a Fourier Transform Infrared Spectroscope (FTIR) to detect the
spectrum of water in general and the respective spectra of ortho and para water specifically. We will construct
theoretical spectra from known lines and calculate corresponding peak widths from values that differ based on
pressure and frequency. From these, we will determine the relative contributions of the ortho and para spectra and
calculate the ratio.
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A Quaternion Analogue to the Gaussian Moat Problem
Brent Terry-Penak
Mentor: Dinakar Ramakrishnan
The Gaussian moat problem, an unsolved problem in number theory, poses the question of whether it is possible to
walk from zero to infinity on the complex plane with a fixed step size while only stepping on the Gaussian primes.
While significant progress has been made on the problem, its four-dimensional analogue over the quaternion
primes has not previously been considered in detail. The quaternion moat problem was analyzed to determine if
results similar to those found over the Gaussian primes could be proven over the quaternion primes as well. Some
basic results about the quaternion moat problem were proven; these results should provide a basis for any future
studies of the problem and form another step towards a conclusive answer to both the Gaussian and quaternion
moat problems.
Improving ISS EarthKAM Metadata Corrections From the Browser With the Google Earth Plugin
Robert Quin Thames
Mentors: Paul Andres and Barbara McGuffie
The ISS EarthKAM digital camera is periodically mounted in a window on the International Space Station (ISS). As
the ISS orbits the camera takes pictures of the Earth’s surface. These pictures are used by NASA and Sally Ride
Science as an educational outreach tool. Students from around the world can gain a better understanding of the
images by matching them up with their surroundings using Google Earth allowing them to view and study Earth
from the Space Station’s perspective.
The position of the image is initially calculated based on the known location of the Space Station at the time the
picture was taken. However, the camera system’s clock is imprecise and thus positional metadata can be
inaccurate. Previous solutions to this problem involved manually downloading individual KML files, making
adjustments locally using Google Earth and uploading the corrections to the server. The new interface uses the
Javascript Google Earth Plugin and updates the database directly from the browser environment. Furthermore,
after a few corrections are made, mathematical regressions are carried out to automatically correct other images.
A similar interface may be applied to map images from other satellites such as the Mars satellites or surface
images from the Mars rovers.
A Topological Model of Electric-Magnetic Duality
Ryan Thorngren
Mentor: Anton Kapustin
Electric-Magnetic duality was recognized in its classical formulation in the time of Maxwell: if one exchanges electric
and magnetic fields in the absence of matter, the underlying physics is left unchanged. More recently, with the
advent of quantum electrodynamics, the duality has taken on a richer character with many physical and
mathematical applications. An analoguous phenomenon has been conjectured in supersymmetric Yang-Mills theory,
where the exchange swaps a Higgs phase, where the photon has mass, with a confining phase, where charges are
localized. In this project, I examine topological models of these two phases and discuss implications of electricmagnetic duality between them.
Probing the Atmospheric Turbulence at Mount Palomar With the Generalized SCIDAR
Suk Sien Tie
Mentor: Nicholas Konidaris
We present the design and data analysis of an instrument which studies the atmosphere above the Palomar
Observatory. By distorting the phase and amplitude of star light, atmospheric turbulence is a significant limiting
factor on the quality of astronomical data and images. Knowing the atmospheric turbulence profile allows one to
choose an ideal observing site and improves the performance of adaptive optics system. We constructed a
generalized SCIDAR (scintillation, detection, and ranging), adapted to the Palomar 60-inch telescope, which uses
binary star systems to measure atmospheric turbulences at various altitudes. Three binary star systems were
successfully observed on July 26 at the Palomar 60-inch telescope. The data collected will be analyzed through
auto and cross-correlation to retrieve the altitude(s) of the dominant turbulent layer(s) and the wind velocity
profile. The refractive-index structure constant Cn2, from which one can derive various atmospheric parameters, will
be extracted as a function of altitude from the auto-correlation via an integral inversion method.
Analytical Examination of Topological Order of the Ising PEPS
Mohit Tiwari
Mentors: John Preskill and Spyridon Michalakis
The Projected Entangled Pair States (PEPS) framework is a new way of describing quantum states. We investigate
a particular model, the Ising PEPS. The Ising PEPS can be transformed to a version of the 2D classical Ising Model
which was completely solved in the 1960s by Lieb, Schultz, and Mattis. We are interested in using this connection
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to determine whether the local ground states of the Ising PEPS Hamiltonian are unique or indistinguishable under
local measurements. We then investigate generalizations of these techniques to other systems that can be
described in the PEPS paradigm.
Atmospheric Properties of Hot Jupiter HAT-P20
Joshua Tollefson
Mentor: Heather Knutson
Hot Jupiters are exoplanets with masses and radii similar to our own gas giants but with much smaller orbital
periods. Exoplanets HAT-P20 and GJ 436 are one of the few discovered Hot Jupiters with surface temperatures
smaller than 1000K. As in cool stars, the dominant carbon-bearing molecule varies by temperature, with carbonmonoxide prevailing at temperatures over 1200K and methane taking over below this. Curiously, CO is more
abundant in GJ 436, making it important to determine if all planets have similar chemistries or if this planet is
merely an outlier. Raw photometry for HAT-P20 was extracted and reduced using observational data from the
Spitzer Space Telescope at absorption bands for CO and CH4: 3.6 μm and 4.5 μm respectively. Eclipse depths were
fit in both bands, allowing properties of the planet's emission spectra to be obtained. These results will help narrow
down the atmospheric conditions of the planet and provide constraints for its composition, ultimately resolving the
question: does HAT-P20 have a spectrum associated with expected equilibrium chemistry, or is it more akin to that
of GJ 436?
Generation and Reaction of ortho-Quinone Methides Under Mild Basic Conditions
Christopher Tonge
Mentor: Brian Stoltz
The focus of my proposed research through the SURF program this summer is the generation of ortho-quinone
methides under mild basic conditions. Ortho-quinone methides (o-QMs) are a class of reactive molecules that are
prone to dimerization and are often unisolable. They are therefore generated and reacted—typically by conjugate
addition or Diels-Alder reactions—in a single operation, and have been applied in a variety of total syntheses.
Various carbonate substrates are used to demonstrate the scope of the reactivity of mild bases (eg. alcohols,
imines, mild carbon nucleophiles, and amines).
Terrestrial Laser Scanning of Transient River Morphology
Aaron Tran
Mentors: Michael P. Lamb and Phairot E. Chatanantavet
Smaller and more affordable terrestrial laser scanners (TLS) can enable the study of fluvial geomorphology with
fine spatial resolution and accuracy. We use a FARO Focus3D laser scanner to study an evolving sediment bed in
flume experiments that simulate a coastal river exhibiting non-uniform flow (backwater) as it enters a wider ocean
tank and spreads in a plume. We develop and test scripts for TLS self-calibration and a refraction correction for
through-water scanning. Raw and corrected data are compared to experimental calibration data to estimate
systematic errors. Corrected scan data are used to create digital elevation models (DEM) of the sediment bed and
compared to DEMs obtained using a point laser displacement sensor. Additionally, we discuss current research on
the response of the sediment bed to varying flow conditions, which is readily visualized using our TLS scans.
Metabolic Engineering and Construction of Expression Plasmids in Zymomonas mobilis
Huey-Ru (Debra) Tsai
Mentors: Richard Murray, Nate Glasser, Emzo de los Santos, and Gita Abadi
In the search for renewable biofuels, microorganisms are used to produce biofuels. The bacterium Zymomonas
mobilis is an efficient producer of ethanol. Attempts were made to increase the limited substrate range of Z.
mobilis through metabolic engineering. The project plan was to assemble a plasmid carrying an allose degradation
operon and transform it into Z. mobilis. Thus, Z. mobilis would able to ferment allose as a sole source of carbon.
There were also attempts to transform a genomic library into Z. mobilis to express many new metabolic pathways.
There was also work done to develop a new method of gene deletion in Z. mobilis.
High Throughput Screening of Endogenous Small Molecule Metabolites in C. elegans Using Microfluidic
Setups
Anand Upadhyaya
Mentor: Paul Sternberg
The nematode C. elegans secretes small sugar-based molecules called ascarosides that have attractive effects in
the worms’ mating. Combinations of these molecules are important in determining the environment for such
attraction. There are also numerous derivatives of the ascarosides that have similar effects on the nematodes. I
will test combinations of ascarosides and their derivatives to determine the effects on the worms. A microfluidic
chip is being calibrated in order to pass chemical and buffer through a 48 worm environment. The use of this chip
is a significant improvement over the previously standardized attraction assay, which only allowed for data
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collection from ten worms at the most. Natural variation in response to these chemicals is also being measured by
comparing two wild-type isolates and recombinant inbred lines created between these two parent strains. The lab
strain N2 is attracted to the chemical, but the wild strain is not. Attractive responses have also been observed in
two recombinant inbred strains.
Digitizing Plume Height and Motion Using MISR Satellite Images and Comparison of Red/Blue Band
Retrievals
Alexandre Van Anderlecht
Mentors: Veljko Jovanovic and Michael Garay
The Multi-angle Imaging SpectroRadiometer (MISR) is an instrument aboard NASA's Terra Satellite. With nine
cameras, MISR measures atmospheric and surface properties at different angles and four spectral bands (blue,
green, red, and near-infrared). Standard products report both zero-wind and wind-corrected stereo heights. The
MISR INteractive eXplorer (MINX) software computes aerosol heights, wind speeds, albedos, and the power of fires
after manual user digitization. Plumes need to be digitized in order to complete the time series for North America,
and specifically, the plumes from the year 2000 were digitized. Obtaining realistic smoke heights is essential to
accurately model aerosol transport, as these models reflect the impact of fires on the atmospheric composition, air
quality, and reflect the variability of plume heights in different climatic conditions. In addition, a set of plumes from
different years and regions were digitized in the red, blue, and a combination of the red and blue bands to
determine the retrieval effectiveness of each band in relation to the surface brightness and visual density with
respect to the aerosol. Theoretically, the absorption optical depth decreases with increasing wavelength,
approximated by the Absorption Angstrom Exponent (AAE), a power-law wavelength dependence. Due to this
property, more scattering should occur with the blue band, generating more height retrievals and higher heights;
however, initial results show apparent inconsistencies. Determining a relationship between aerosol heights and
wavelength along with an examination of other optical properties will be used to explain the discrepancies in the
observed height retrievals from the two MISR bands.
Improving Radial Velocity Precision for Extra-Solar Planet Surveys
Andrew Vanderburg
Mentors: John Johnson and Phil Muirhead
Measuring precise radial velocities of stars requires exquisite knowledge of the spectrograph's Line Spread Function
(LSF) as both a function of time and position on the detector. Currently, the LSF of the Keck HIRES spectrograph is
modeled by a fifteen parameter function, and fit using a non-linear least squares algorithm. While this technique is
good enough to measure radial velocities with a precision of 1 meter per second, the LSF model is known to be a
major source of systematic error, especially in low signal-to-noise regimes. I perform exploratory data analysis and
use the conclusions to improve the way the LSF fitting routine. I present an improvement in radial velocity
precision of 25 percent on low signal-to-noise observations of a radial velocity standard star. Improved precision in
low signal-to noise situations is of particular importance to radial velocity follow up of stars with Kepler planet
candidates, which are typically much fainter than the stars normally observed in radial velocity planet surveys.
Object Recognition and Localization Using Tactile Sensing
Mariya Vasileva
Mentors: Joel Burdick and Thomas Allen
Tactile sensing is defined as the process of determining physical properties and events through contact with objects
in the surrounding world. As one of the main sensing modalities in human beings, the sense of touch plays a vital
role in effective robotic manipulation. Object recognition and localization is a fundamental problem in intelligent
systems that, if solved, would enable robotic devices to interact autonomously with unstructured environments and
perform sophisticated manipulation tasks in a variety of complex situations without human supervision. The
Defense Advanced Research Projects Agency (DARPA) is sponsoring a two-phase competition to enhance research
into autonomous robotic sensing, grasping and manipulation of objects. JPL/Caltech is one of six teams competing
in this event. My current work as part of the team focuses on the feasibility of using data from a capacitive array
tactile sensor to estimate unfamiliar object position, orientation and geometry. In order for tactile data to be useful
for manipulation, exploration and response applications, several important parameters need to be determined.
Information is required about the location of contact, contact forces, local geometry, and surface roughness.
However, without prior knowledge of the internal mechanisms of the tactile sensor, other parameters are also
needed for calibration, such as active area of the sensor, reaction under different types of loading, and spatial
resolution. This paper presents an experimental method to recover the spatial resolution of the sensor and use it to
construct an algorithm for estimation of the contact force and location within a predefined reference frame. While
the results presented are limited to point and line contact, future work involves developing a method for
recognition and localization of random types of contact, which can be used in building a model of any unknown
object geometry.
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Determination of Device Specific Astrometric Error Sources in Infrared Arrays
Corinne Vassallo
Mentors: Christoph Baranec and Roger Smith
I have developed a tool to characterize and quantify the systematic astrometric error sources within an HgCdTe
Focal Plane Array (Infrared Detector), a device that will be used for a future campaign to search for planets around
nearby M-dwarf stars at Palomar Observatory. Astrometry is the measurement of the positions and movements of
celestial bodies and is useful for both astronomical research and space navigation. However, astrometry is limited
by the precision of the detectors used to make measurements. Therefore, the characterization of the systematic
error sources within detectors is crucial in order to mitigate their effects. I began error characterization with an
experimental setup that uses a mask to project thousands of point sources representing stars onto the infrared
detector. The mask was then moved in a designated way, and I tracked individual simulated stars through the
resulting images. I then calculated each spot’s relative motion to the average motion of all the spots, which gives a
measurement of the intrinsic astrometric error. This procedure will be used to validate future data processing
methods to reduce the intrinsic astrometric error.
Synchronization of Nano-Oscillators
Eugene Vinitsky
Mentor: Michael Cross
The goal of this project is to examine the synchronization properties of a variety of nano-oscillators. The Roukes
group has developed several nano-oscillators, but as a result of difficulties in operating at the nano-scale, they
often exhibit a significant range of frequencies and are easily subject to noise. However, if the oscillators are
synchronized, they operate at a uniform frequency and often have reduced noise. We have examined noise
reduction and synchronization features of phase-shifted feedback oscillators and non-degenerate parametrically
driven oscillators.
Archival and Analysis of Sea Ice Thickness in the Arctic Ocean Based on On-Ice In Situ Historical
Measurements: Understanding the Impact of Seasonality on Ice Thickness Studies
Ratnalekha (Lekha) Viswanadham
Mentor: Benjamin Holt
Arctic sea ice cover has shown changes, including span of cover and average thickness, both of which are related
to changes in climate patterns in the last few decades. Studies of Arctic sea ice cover do not consider the
seasonality of ice thickness (that there exists a natural change in ice thickness throughout the year due to natural
temperature changes from seasons); all studies so far are made from raw data. Data points were corrected to a
sinusoidal regression of ice thickness over time using a script made in MATLAB that parses through the master
database, corrects the dates to fractions after the earliest year, and plots the ice thicknesses. Comparisons were
made between the original data, the given trend, and the newly adjusted data. Future work would include
comparing histograms of the original data to the adjusted data and looking at the change in the ratios between ice
thickness and snow depth. Future work would also include continually adding well-documented datasets into the
database to provide a more complete picture of the Arctic Ocean. Implications of the results would be the nature of
changes in ocean levels and temperature changes in the Arctic Ocean.
Understanding Feedback in Bacterial Toxin-Antitoxin Systems
Vinay Viswanadham
Mentors: Richard Murray and Dan Siegal-Gaskins
Bacterial toxin-antitoxin (TA) systems are operons consisting of two genes, one of which codes for a molecule toxic
to the host and a second that codes for the antidote. Mathematical models of TA system dynamics have the
potential to shed light on bacterial genetic addiction, antibiotic resistance, and bacterial population regulation. The
focus was on generating a deterministic mathematical model of ParD1-ParE1, a stereotypical type-II TA system,
with an emphasis on capturing the negative feedback caused by the binding of either antitoxin or a toxin-antitoxin
heterodimer complex to the system’s promoter. An in vitro cell-free experimental environment was used to
simulate isolated components of the circuit, particularly the activity of the antitoxin, using cell extract from E. coli
to perform transcription and translation. Statistical methods were applied to the model and experimental data in
order to determine physical constants of the circuit.
Building a 3-D Stage for a Magnetometer to Find Lightning Strikes
Christine Viveiros
Mentor: Joseph Kirschvink
One of the most important questions about Mars has been whether the surface has or has ever had water on its
surface. If there was water, this could provide insight into the early stages of life on earth. Water is conductive,
and so lightning would have struck the Martian surface. These lightning strikes would have left a specific magnetic
pattern in the lightning-struck rocks that can be measured by a magnetometer. To simulate this here on Earth, we
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have built a 3-dimensional stage that holds a small magnetometer probe. We programmed it so that it can raster
through a path and build up a magnetic map of the rock it’s probing. This setup serves as a prototype for future
Mars mission that we are pushing for.
Price Discovery in Unstable Trading Environments
Andrew Vollmer
Mentor: John Ledyard
Traditional economic theory suggests that a commodity’s price moves towards equilibrium based on its excess
demand, which is the amount that agents would like to hold at current prices minus the amount that exists in the
market. Earlier work has shown this hypothesis to be insufficient in environments that converge to equilibrium
because of dependence on excess demand for other commodities and the role of quantity adjustment in price
movements. Using experimental data from one of Scarf’s (1960) unstable environments, we explore price
discovery on three levels. First, we study if and how prices respond to excess demand for each commodity.
Second, we test a theory of quantity adjustment that often leads to local equilibria. Finally, we compare differences
in the results caused by the choice between continuous double auction and call market formats.
An Exploration Into Products of Photolysed Diiodomethane in the Presence of Oxygen
Matthew Voss
Mentors: Mitchio Okumura and Leah Dodson
It is necessary to understand the fate of unsaturated volatile organic compounds in the troposphere. Modeling the
oxidation of atmospheric alkenes is essential for the prediction of tropospheric chemistry. In particular, the
ozonolysis of alkenes is an important step in the conversion of pollution to photochemical smog. Rudolf Criegee
proposed of a class of intermediates that form in the ozonolysis of atmospheric alkenes that are 1,3 dipoles, with
the smallest intermediate being formaldehyde oxide (CH2OO). In order to observe this transient species, pulsed
visible laser cavity ringdown spectroscopy was used to probe a flow cell with precise timing. The interrogated
system was photolysed diiodomethane in the presence of oxygen in the low pressure regime. Spectra of the
products were collected in the visible region.
Identifying Candidate Causative Genetic Variants in a Family With Left-Ventricular Non-Compaction
Cardiomyopathy
Allika Walvekar
Mentors: Euan Ashley, Paul Sternberg, and Stephen Pan
With the advent of massively parallel DNA sequencing, the possibility of sequencing an entire human genome as a
diagnostic test is quickly becoming economically feasible. This new technology has already enabled the discovery of
the etiology of many previously unexplained genetic diseases. One such disease is left ventricular non-compaction
(LVNC), a rare form of inherited cardiomyopathy with a heterogeneous genetic etiology. While a few mutations
have been previously described in this disorder, the causative genetic mutations for most cases have not been
identified. We recently applied whole exome and genome sequencing on affected family members from a large
three-generation pedigree with LVNC. Using extensive analyses involving algorithms incorporating co-segregation
as well as linkage analysis, we will show that we can successfully narrow down the list of candidate genes for this
disorder to a select few for further biological testing. Further elucidating the genetic etiologies of inherited
cardiomyopathies such as LVNC will be extremely useful in exploring the mechanism behind these diseases,
developing targeted therapies, and identifying family members at risk. In addition, developing pipelines to
successfully find candidate genetic variants in sequencing data will be an important tool for the future analysis of
genomes for other individuals and families with genetic diseases.
Building an Integrated In-Incubator Microscope to Examine Endothelial Cell Response to Shear Stress
Alex Wang
Mentors: Alex Dunn, Maggie Ostrowski, and David Tirrell
Atherosclerosis, the hardening of the artery wall, is a dangerous condition that can lead to heart attack, stroke, and
death. In the arterial tree, atherosclerosis is most prone at branch points, asperities and other regions where blood
flow is disturbed. Findings show that at these regions of disturbed flow, vascular endothelial cells (ECs) upregulate
genes and proteins that promote atherosclerosis due to reciprocating shear stress. In contrast, in laminar and
steady flow regions shear stress is uniform, and ECs upregulate genes protective against atherosclerosis.
Understanding the effects of disturbed flow on ECs can provide insights into the role of complex flow patterns in the
pathogenesis of vascular disease. In this project, we designed an integrated in-incubator microscope and flowpump system that can expose EC’s to multiple flow conditions and shear stress distributions. Specifically, we
looked at a flow system around an obstruction, modeling an atherosclerotic lesion or stent step that will disturb the
flow. The results show that endothelial cells respond in a significant way to shear stress gradients and this
response is possibly mediated by a mechanosensory complex.
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Analyzing the Ulp-4 Pathway and Its Role in the Mitochondria in the Model Organism C. elegans
Ann Wang
Mentors: Paul Sternberg and Amir Sapir
Stress and aging have been found to regulate mitochondrial activity by affecting protein recruitment. These
processes have been correlated with genetic and protein damage accumulation, but the molecular mechanism
behind this is largely unknown. Here we characterized the activity of Ubiquitin-like Protease-4 (ULP-4), a protein
which is localized to the mitochondria in stress and aging, and its predicted substrate HMGS-1 and regulator
ATFS 1. We have also begun a screen to find the age-dependent transcription factor for ULP-4 and have
investigated more than a hundred genes. Furthermore, 3-hydroxy-3-methylglutaryl CoA Synthase-1 (HMGS-1) was
predicted to interact with ULP-4 from an online yeast hybrid assay. We found it to be expressed in both the
cytoplasm and the mitochondria in normal physiology. In aging and the mitochondrial stress response, we
observed an accumulation in the gut and body wall muscle. In the future, we hope to investigate if hmgs-1 is
regulated by atfs-1, the known regulator of ulp-4 during stress. Our studies lay a strong foundation for further
investigation of these genes’ roles in mitochondrial stress and aging.
Selected Mutations in Capsid (CA) Protein of Moloney Murine Leukemia Virus (MMLV) and the
Integration of Viral Genome
Ben Wang
Mentors: Stephen Goff and Pamela Bjorkman
It has been found that the Gag protein plays a vital role in the viral life cycle of MMLV and that the protein is
eventually cleaved by viral protease into four different proteins, namely 1) the MA membrane protein, 2) a protein
known as p12, 3) the CA capsid, and 4) the NC nucleocapsid. Specifically, it is also known that some mutations in
the CA protein allow for successful reverse transcription (RT) of the viral genome but still result in noninfectious
virus. One possibility is that the mutated CA prevents successful integration of the viral genome into the host
genome. To explore this possibility, appropriate CA mutations were gathered from lab stock or generated from
overlap PCR and site-directed mutagenesis. The mutated viral genomes were then amplified through
transformation of DH5a bacterial cells, isolated through maxiprep, and used to transfect 293T cells. Shortly, the
collected viral particles will be used to infect 3T3 cells, which will then be assayed for protein production, mRNA
formation, and DNA integration. These assays may show that some domains of the CA protein are necessary for
viral genome integration, which has been suggested but has never before been fully explored.
Anonymous Communication Against Active Adversaries
Eric Wang
Mentor: Tracey Ho
We consider anonymous communication in a peer-to-peer (P2P) system in the presence of active adversarial nodes
whose identities are a priori unknown. Existing work has proposed network coding strategies for anonymous
communication over rectangular overlay subgraphs where the adversaries seek to identify source and sink nodes.
In this work we further consider active attacks by adversarial nodes seeking to disrupt communication through the
network. We propose a communication protocol in which subgraphs are periodically changed based on feedback
from the sink as to whether valid or corrupted information is received. The source nodes analyze the network and
deduce adversarial likelihoods for nodes in the network based on previous communication sessions. From this
analysis, effectiveness of attacker nodes is reduced through fewer appearances in future subgraph choices. We
determine a practical approach for network selection based on performance analysis and anonymity considerations.
Protein Expression of the Pglb Gene
Esha Wang
Mentor: Bil Clemons
Protein glycosylation is the most abundant protein modification chain found in nature. The
oligosaccharyltransferase central to this pathway is known to be PglB, which catalyzes that attachment of a
modified heptasaccharide to a lipid carrier for further transport. We attempted to promote protein expression in
three types of vectors: pET33b::Dd pglB, pRSF:: Dd pglB, and pRSF::Dv pglB. When these vectors are transformed
into E. coli competent cells, the pglB gene locus is sufficient in catalyzing the glycosylation of proteins. After
running gels for the first two attempts, it was clear that certain conditions needed to be changed, such as
amplifying the histidine tag in order to obtain a more accurate Western Blot and SDS PAGE gel reading. We are
currently in the process of expressing the proteins using the plasmid pKatN10His, and we hope that this round will
be successful.
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Identification of the Genes Involved in the Maintenance of Stem Cell Populations in Arabidopsis
thaliana Shoot Apical Meristem
Lawrence Wang
Mentors: Elliot Meyerowitz and Yun Zhou
Continuous organogenesis in plants is dependent on the maintenance of stem cell populations. The shoot apical
meristem (SAM) in higher plants consists of three clonal layers: the epidermal L1, the subepidermal L2, and the
corpus L3. Within this framework, SAMs can be divided into three zones: the central zone (CZ), the peripheral zone
(PZ), and the rib meristem (RM). In Arabidopsis thaliana, stem cell populations in the SAM are maintained by a
negative feedback loop involving the WUSCHEL (WUS) and CLAVATA (CLV) signaling pathway. clv mutants (clv1,
clv2, and clv3)result in an enlarged SAM and an over-proliferated stem cell pool, while the wus mutant loses the
ability to maintain the SAM. CLV3 signal restricts the expression domain of WUS, a homeodomain transcription
factor gene expressed only in a few cells within the rib meristem (RM), which is also referred as the stem-cell
organizing center. In turn, WUS activates CLV3 expression in the overlying central zone (CZ). The molecular
mechanism that underlies the CLV–WUS feedback loop in regulation of SAM dynamics is being examined. Several
novel genes in the WUS pathway have been identified and characterized. Their functions in control of stem cell
populations and the involvement of different layers of regulation over CLV3/WUS feed back loop will be examined
through molecular and genetic analyses, which could potentially build up a coherent model of cell-cell
communication in maintenance of the stem cell niche in plant development.
Light Trapping Through Resonant Nanosphere Array and Sol-Gel Antireflection Coating
Max Wang
Mentors: Harry Atwater, Jonathan Grandidier, and Dennis Callahan
Light trapping schemes are extremely important in increasing optical path length to enhance absorption in thin-film
solar cells. Two innovations toward this objective are nanosphere arrays and graded index antireflection coatings.
Nanospheres couple freely propagating sunlight into several resonant modes within the thin-film array. Graded
index antireflection coatings also reduce reflection of light at the air/cell boundary at all wavelengths and incidence
angles. Simulations show that both nanosphere arrays and graded index coatings individually enhance absorption
in solar cells across nearly the entire wavelength range. My project involves experimentally depositing close-packed
titanium dioxide spheres and silica sol-gel coatings with varying refractive indices onto glass substrates. Though
silicon dioxide spheres have already been deposited onto silicon, titanium dioxide spheres have proven more
difficult to use due to their higher density and hydrophilicity. Various sol-gel layer processes have also been
adjusted so that the thicknesses and refractive indices are tunable. The final goal is to be able to deposit a closepacked uniform titanium dioxide nanosphere array and/or a graded index antireflection coating onto any solar cell.
A Mass Spectrometry-Based Approach to Determine Affinities of Ca2+ With DREAM
Melissa L. Wang
Mentors: Michael L. Gross, Henry Rohrs, Jun Zhang, and Jesse Beauchamp
Events leading to pain perception at the molecular level are key areas of research for drug advancement.
Endogenous opioid receptors and ligands modulate pain. Prodynorphin, a basic building block of the opioid
endorphin, is regulated by a downstream regulatory element (DRE). A downstream regulatory element antagonist
modulator (DREAM) binds to the DRE and represses the transcription of prodynorphin. DREAM, expressed in the
brain and spinal cord neurons, has four EF-hand motifs that bind calcium. In the presence of calcium, DREAM does
not bind to DNA. Using the PLIMSTEX (protein ligand interaction by mass spectrometry, titration, and H/D
exchange) strategy, we determined the binding affinities of intact DREAM with Ca2+. The four equilibrium
dissociation constants were K1= 0.68 μM, K2= 0.68 μM, K3= 19 μM, and K4= 0.04 M. A further analysis of the
protein at the peptide level after enzyme digestion could elucidate the binding order of the EF hands. These results
provide additional insight into the conformation and dynamics of DREAM and can potentially further substantiate
the PLIMSTEX approach for determining binding orders of protein-ligand complexes.
The Role of DNA Charge Transport in the Repair Helicase XPD and Its Associated Diseases
Winnie W. Wang
Mentors: Jacqueline K. Barton and Timothy P. Mui
Repair proteins with redox-active [4Fe-4S] clusters are thought to detect genomic damage through the process of
DNA charge transport (CT). In DNA CT, the [Fe-S] clusters are continuously oxidized and reduced by the exchange
of electrons with other DNA-bound proteins down the base stack. The human Xerodoma pigmentosum group D
(XPD) helicase, which contains a [4Fe-4S] cluster and displays DNA-bound electrochemical activity, is thought to
perform its Nucleotide Excision Repair (NER) function by DNA CT. This project explores the possibility of CTdeficiency as a cause of XPD diseases. Specifically, the rationally designed M331A mutation aims to restore
electrochemical signal in the L325V mutant, a known CT-deficient mutant of SaXPD—the thermophilic ortholog of
XPD. Cyclic voltammetry was performed on DNA-bound wild type SaXPD and the mutants: L325V, M331A, and
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L325V/M331A. Further experiments are needed to fix the inconsistent signal ratio between the wild type and the
L325V mutant. Nevertheless, the double mutant’s signal was consistently higher than that of the L325V mutant,
which is promising in terms of the M331A mutation’s ability to rescue CT in the L325V mutant.
Renewable and Cooling Aware Geographical Load Balancing
Yizhen Wang
Mentor: Adam Wierman
This paper explores the benefits of geographical load balancing in terms of efficiently using renewable energy.
Practical concerns on dynamic cooling efficiency and dynamic electricity price are included in the model. The
problem is modeled using a convex optimization based framework parameterized using real workload,
temperature, solar and wind traces. The result suggests that after using geographical load balancing, the
renewable energy usage increases significantly and grid usage decreases significantly. Such result holds across
seasons.
Design and Synthesis of Rhodium Metalloinsertors for Improved Biological Activity
Carla L. Watson
Mentors: Jacqueline K. Barton and Alexis C. Komor
Mismatch repair (MMR) deficient cells are linked to degenerative diseases such as cancer and leukemia and are
resistant to many chemotherapeutics currently in circulation. Preferentially targeting MMR-deficient cells, rhodium
metalloinsertors have been found to bind to base pair mismatches with high affinity. Crystal structures have shown
that these complexes bind via insertion of one of their ligands into the base stack, with ejection of the mismatched
base pairs. Several new rhodium metalloinsertors have been synthesized and characterized. Their binding affinities
have been determined, and their antiproliferative activities towards MMR-deficient and MMR-proficient cells
measured through an Enzyme-Linked Immunosorbent Assay (ELISA). Overall, more lipophilic insertion ligands
contributed to faster and more potent biological activity.
Mapping the Connectivity of von Economo Neurons
Nicholas Weil
Mentors: John Allman and Soyoung Park
The von Economo neurons (VENs) are notable because they are affected in certain neurological diseases, are a
recently evolved phylogenetic specialization, and are hypothesized to have functional roles in adaptive social
behavior. Although VENs appear to be projection neurons, their targets are currently unknown. Recently, diffusion
tensor imaging (DTI) has emerged as a type of magnetic resonance imaging that can be used to perform
probabilistic fiber tractography, a process that produces an image of probable axonal pathways passing through a
point. In this project, tractography was performed on DTI data of post-mortem human brains to map neural
connectivity of the VENs in the frontoinsular cortex (FI). Results indicate significant differences in connectivity
between the medial and lateral FI VEN populations. While our results suggest that the medial VENs in the FI are
not well connected to other parts of the brain, we found connections of the lateral FI VENs with the uncinate
fasciculus, frontal pole, and areas involved in the somatosensory system and visceral motor movement. These
results provide insight on the role of VENs in social emotions and are consistent with some symptoms of patients
with certain neurological disorders.
Sub-Nyquist Sampling of Action Potentials
Alexander S. Wein
Mentors: Lakshminarayan Srinivasan and David Rutledge
Recently, various methods have emerged for sub-Nyquist sampling and reconstruction of signals with finite rate of
innovation (FRI). These methods seek to sample parametric signals at close to their information rate and later
reconstruct the parameters of interest. Some proposed reconstruction algorithms are based on annihilating filters
and root-finding, but these have been shown to fail in the presence of noise. A more robust method is based on the
Markov chain Monte Carlo method called Gibbs sampling, but this approach runs too slowly to be feasible for realtime applications. We present a fast greedy algorithm, IterML, for reconstructing FRI signals from noisy samples.
We show that it outperforms Gibbs sampling both in terms of accuracy and speed.
Comparative Imaging of the Bacterial Type VI Secretion Apparatus
Gregor Weiss
Mentors: Grant J. Jensen and Martin Pilhofer
The bacterial type VI secretion system (T6SS) is known to be involved in diverse processes such as competition,
symbiosis and pathogenicity, but it is still relatively new and unexplored. In the last few years, some proteins and
genes, which are related to this secretion system, were identified. A breakthrough, namely the requirement of a
dynamic phage tail-like structure, was achieved by imaging the T6SS with electron cryotomography (ECT) in Vibrio
cholerae. Furhtermore, genes associated with T6SS are found in 25% of all other gram-negative bacteria. For this
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study, 14 different bacterial strains with T6SS related structures were selected, to be imaged in a near-native
state, which can only be achieved with ECT. This will allow us to identify conserved parts of the apparatus and to
track the evolution of these intriguing nano-machines. For the first time, it was possible to purify T6SS sheaths
from Myxococcus xanthus and subsequently to image them with negative stain electron microscopy. Moreover
phages and also pyocins, which are related to both bacteriophages and T6SS, could be imaged. With regard to
these insights it seems reasonable to assume that the discovered structures really share a common evolutionary
path, which has still to be verified with mass spectroscopy and genomic analyses.
Theory of Mechanical Resonators Coupled Through Optical Channel
Paul Weitekamp
Mentor: Oskar Painter
Recent advances in the theory and fabrication techniques of high Q optomechanical resonators have allowed for
increased control over light-matter interactions and observation of quantum phenomenon. Two mechanical modes
in close proximity can become synchronized and, at low enough temperatures, entangled through a common
hybridized optical mode. Synchronizing multiple mechanical modes can effectively improve the coupling between
optics and mechanics and reduce phase noise by increasing coherence. Entanglement of GHZ mechanical modes
would mark an achievement in applying quantum mechanics to macro-scale objects. Our goal is to design and
fabricate an on-chip device that couples multiple mechanically isolated center of mass oscillators through an optical
input/output channel.
On the Structure of Overgroup Lattices in Exceptional Groups of Type G_2(q)
Jake L. Wellens
Mentor: Michael Aschbacher
We study overgroup lattices in groups of type G_2 over finite fields and reduce Shareshian’s conjecture on D∆lattices in the G_2 case to a smaller question about the number of maximal elements that can be conjugate in such
a lattice. Here we establish that, modulo this smaller question, no sufficiently large D∆-lattice is isomorphic to the
lattice of overgroups O_G(H) in G=G_2(q) for any prime power q and any H≤G. This has application to the
question of Palfy and Pudlak as to whether each finite lattice is isomorphic to some overgroup lattice inside some
finite group.
Encoding of Low Level Features in the Human Medial Temporal Lobe
Jody Wen
Mentors: Christof Koch and Michael Hill
Within the distal stages of the ventral visual stream lies the medial temporal lobe, a region of the brain commonly
associated with memory functions and object recognition. Research has observed that single neurons in this region
are responsive to selective high level features such as locations or faces. In this study, we now consider if low level
image characteristics, in particular luminance, are also encoded in these higher level areas of the medial temporal
lobe. To do so, we have a massive database containing the activities of monitored neurons when a variety of
images are viewed during recording sessions. The subjects are patients with pharmacologically intractable epilepsy
and therefore implanted with depth electrodes for their pre-surgical evaluation, permitting the detection of single
neuron activity. We first quantify the luminance of each human image that is presented during these recording
sessions, and then conduct a correlation analysis to see if the different luminance values induce positive or
negative neuronal responses. In addition, we also investigate whether the gender or gaze of the presented images
induces activity in certain regions of the medial temporal lobe, particularly the amygdala.
Assessing Stability and the Role of Mo in Ni-Mo Alloy Electrocatalysts
Caroline A. Werlang
Mentors: Harry Gray and James McKone
Ni Mo alloys (Ni-Mo) have been shown as good electrocatalysts for the hydrogen evolution reaction, but the
mechanism for their enhanced activity over Ni or Mo is still unknown. In addition, Ni-Mo is only stable in base, a
medium that limits its performance and applications. Thus we have sought to further understanding of Mo’s role
and utilize that understanding to increase the stability of Ni-Mo in acid. We have synthesized Ni-Mo with varying
compositional percentages of Mo, electrochemically tested them in varying pHs, and analyzed them by SEM, EDS,
and XRD. We have found increased stability in acid with minimal loss of activity by doping with nanofibrous
polyaniline through a new synthetic method. In addition, we have observed that the percentage of Mo affects the
morphology, and thus the behavior, of the alloy particles.
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Optical Characterization of a Superconducting Resonator Bolometer Array
Rebecca A. Wernis
Mentor: Jonas Zmuidzinas
Kinetic Inductance Detectors (KIDs) are a new type of radiation detector being developed at Caltech based on
superconducting resonators. Their simple fabrication process and capacity for high-density frequency multiplexing
should enable drastically larger array sizes than is possible with traditional submillimeter radiation detectors.
Currently, both direct detection and absorption via antennas provide a means for coupling radiation to the array.
We are investigating placement of the resonators on bolometric islands as a new coupling mechanism. This should
enable warmer operating temperatures and an ability to be fabricated with a wider variety of materials, making
them promising candidates for a compact, on-chip spectrometer as well as for satellite-based observations of
Earth.
In order to be established as a viable candidate for such projects, this type of detector must be tested in a lab. An
array was fabricated at the Jet Propulsion Laboratory and brought to Caltech to be tested. The frequency response
for a single pixel as a function of both the device temperature and the temperature of a blackbody illuminating the
device was simulated and measured. In addition the bolometer island time constant was measured as a function of
sample temperature by recording the response from a pulse-modulated terahertz radiation source. These results,
together with noise measurements under optical loading, were used to calculate an optical noise equivalent power,
allowing for performance comparison with other detectors and future application-specific device optimization.
Resonant Ultrasound Spectroscopy for Complex Composite Materials
Theodore Wilkening
Mentor: Dennis Kochmann
Beyond the abundance of materials we find in nature, there are many undiscovered synthetic or engineered
materials out there with unique properties that may be beneficial to different scientific and commercial applications.
Imagine what an extremely light, but strong, material would do for the aviation industry. Once these new materials
are discovered and synthesized, they need to be characterized as to what their elastic properties are, or how they
will react under specified loads and stresses before we can begin to find a use for them. This measurement can be
done using Resonant Ultrasound Spectroscopy (RUS). This project deals with the development of an instrument
used to implement the RUS method, its calibration and the testing of several materials. After researching the
existing ways to implement RUS, we have developed a new RUS system to measure the elastic properties of
materials (in general, the full anisotropic elasticity tensor can be determined). Once it is calibrated, the device will
be used on novel materials developed in the lab, determining their unique elastic properties. The ability to
accurately determine the elastic properties will not only be beneficial to find scientific or commercial applications
for new materials but will also give insight into how to design new materials satisfying specific property
requirements in the future.
4D Visualization of Building Responses to Shaking
Sarah Wittman
Mentor: Monica Kohler
The Community Seismic Network is currently instrumenting a number of buildings in the Los Angeles area with
sensor arrays to collect accelerometer data during earthquakes. The overarching goal of this project is to take data
from these arrays and create intuitive visualizations of the instrumented buildings. Our methods involve creating
simple 3d models of the building structure and illustrating the buildings’ responses from the observed data. We
further predict how a building might respond to a scenario seismic event given some known building properties and
using a shear beam approximation for each building. While we are testing our methods on local buildings in
Pasadena, downtown Los Angeles, Westwood, and Palm Springs, our goal is to generalize the methods so that they
can be applied to any instrumented building.
Algorithm Detecting Radio Transient Events
Chatarin Wong-u-railertkun
Mentors: Gregg Hallinan and Stephen Bourke
The field of radio transients opens up a possibility of discovering a wide range of new astrophysical objects. The
detection of transient radio emission generally indicates dynamic events, for example, high energy particle
populations, gamma-ray bursts, magnetic fields of planets and stars, and, possibly, extraterrestrial transmitters.
Manual searching of data would be extremely time consuming and virtually impossible, given the large volumes of
data, of specific interest for this project, collected by the Very Large Array (VLA), involved. A variability analysis of
each time series that assesses the degree of variability of that time series relative to the mean variability of the
entire sample of time series is used to distinguish variable sources from constant ones. Periodicity of such
astrophysical objects as brown dwarfs is calculated via maximum power of Lomb-Scargle periodogram. As a result,
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images for variability and periodicity with the metric for variability and periodicity for each time-series representing
the pixel value in the corresponding image act as a self-consistent means to assess the significance of any possible
variability or periodicity.
Imaging Plasmas With Coded Aperture Methods Instead of Conventional Optics
Pakorn Wongwaitayakornkul
Mentor: Paul Bellan
The spheromak and astrophysical jet plasma at Caltech emit localized EUV and X-rays associated with magnetic
reconnection. However, conventional optics does not work for EUV or X-rays due to their high energy. Coded
aperture imaging is an alternative method that will work at these energies. The technique has been used in
spacecraft for high-energy radiation and also in nuclear medicine. Coded aperture imaging works by having
patterns of materials opaque to various wavelengths block and unblock radiation in a known pattern. The original
image can be determined from a numerical procedure that inverts information from the coded shadow on the
detector plane. A one-dimensional coded mask has been designed and constructed for visualization of the evolution
of a 1-d cross-section image of the Caltech plasmas. The mask is constructed from Hadamard matrices. Arrays of
photo-detectors will be assembled to obtain an image of the plasmas in visible light range. The experiment will
ultimately be re-configured to image X-ray and EUV radiation.
Scanning Tunneling Spectroscopy of Magnetically Doped Topological Insulator Systems
Nicholas Woodward
Mentor: Nai-Chang Yeh
Kane and Mele predicted 3D topological insulators (TI), characterized by four Z2 topological invariants. Bismuth
alloys were theoretically predicted to be TI, due to their large spin-orbit coupling and inverted band-gap. ARPES
experiments later confirmed the odd Dirac cone band structure characteristic to strong TI in Bi2Se3, Bi2Te3, and
BixSb1-xalloys. Recently the (Bi1-xSbx)2Te3 system was also found to be a TI, with a tunable band. For non-magnetic
impurities, unitary density of states (DOS) resonance peaks around impurities have been observed. It has been
predicted that in the presence of magnetic impurities, the time-reversal symmetry breaking will cause a spin
splitting near the Dirac cone and create dual spin-polarized DOS resonances around the Dirac point, provided that
the impurity interaction is negligible. Additionally, in the limit of high-density magnetic impurities, it has been
theoretically predicted that the gapless Dirac cone associated with the surface states of the three-dimensional TI
will become gapped due to global time-reversal symmetry breaking by the magnetic impurities. We report our
experimental investigation of these theoretical predictions by performing scanning tunneling spectroscopic studies
on pure and Cr-doped (Bi1-xSbx)2Te3 MBE-grown epitaxial films on GaAs substrates.
Experimental Test of Universality Over Boundary Conditions
Matthew Wraith
Mentors: Julia Greer and Robert Maaß
Single crystalline micro-scale pillars deform in discrete bursts in analogy to plate tectonics. A simple mean field
theory (MFT), typically used for earthquakes, is applied to the probability distribution of slip sizes. The probability
distribution follows a power-law with a stress-dependent cutoff. Properties of the system, such as, symmetry,
dimension, and interaction range, dictate the universality class, and thus the statistical properties, of the system.
Here, we investigate whether experimental boundary conditions affect the universality of the probability
distributions. The boundary conditions considered are force-controlled mode and displacement-controlled mode
where the force rate and displacement rate are respectively held constant. Our study of 1, 3, and 5 µm diameter
single-crystalline Au pillars shows that boundary conditions do not affect the distribution of slip sizes via a
predicted scaling collapse. The critical exponents and scaling functions are the same, as predicted by MFT,
regardless of control mode. The answer to this question has implications for other systems, such as, ferromagnets,
earthquakes, the stock market, etc.
Co-Culturing Chondrocytes and Mesenchymal Stem Cells on Electrospun Poly(-caprolactone) Scaffolds
for Cartilage Regeneration Applications
Sarah Wright
Mentors: Antonios Mikos, Kurt Kasper, and John Dabiri
Cartilage defects are common injuries that affect hundreds of thousands of Americans each year and result in
many surgical procedures. A three-dimensional scaffold structure can be created to mimic the extracellular matrix
in these cartilage defect areas. By seeding electrospun poly(-caprolactone) microfiber scaffolds with articular
chondrocytes (ACs) and mesenchymal stem cells (MSCs) and decellularizing the scaffolds after an incubation
period, it is hypothesized that the matrix deposited by the cells mimics the main components of the extracellular
matrix of native cartilage. The efficacy of this approach can be analyzed by quantifying the presence of collagen I
and II, glycosaminoglycans (GAGs), and DNA, as well as performing histology of the 3D scaffolds. Chondrocytes
alone have proven to be good sources of these markers, but they are difficult to harvest and tend to dedifferentiate
when expanded. Because it would not be feasible to harvest enough cells from a patient to adequately seed a
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scaffold with chondrocytes alone, co-cultures of mesenchymal stem cells and chondrocytes are used. Chondrocytes
use trophic factors to drive the mesenchymal stem cells, which are more readily available and expand easily, to
chondrogenically differentiate, producing a construct that is similar in composition and morphology to the cells and
extracellular matrix found in native cartilage.
MicroRNA Regulation of 5-mGFP and 5(D398N)-mGFP Expression in HEK293-T Cells
Adela Wu
Mentors: Henry A. Lester and Crystal N. Dilworth
Smoking is a major public health concern and contributes to many premature deaths. Recent human genomic
studies attempting to classify possible factors for nicotine addiction have identified several single nucleotide
polymorphisms (SNPs) that contribute to smoking-related behaviors. One particular SNP involves an asparagine-toaspartic acid substitution in the nicotinic 5 subunit at amino acid position 398 (rs16969968; 5(D398N)). This
α5(D398N) mutant variant may be associated with an increased risk for greater nicotine use.
Of interest to us is the mechanism by which 5 and 5(D398N) subunits may influence pathological states. In
particular, we look at microRNA regulation of protein expression. miRNAs regulate up to 60% of the human
genome and inhibits translation typically by binding to the 3’ untranslated region of target mRNAs and
incorporating the transcript into an RNA-induced silencing complex (RISC). One microRNA (miR-346) specifically
recognizes and interacts with the 3’ UTR sequences of α5 and α10 subunits. miR-346 itself is apparently
upregulated in mouse cortex with chronic exposure to nicotine, which provides interesting implications for its
involvement in influencing 4β25 nAChRs. With expression of fluorescently-labeled 5 and 5(D398N) subunits
and transfection of miR-346 into HEK 293-T cells and primary mouse cortical neurons, we quantify protein
expression levels using a fluoremeter and use confocal microscopy to determine the actions of miRNA gene
regulation on different variants of the 5 nAChR receptor protein.
Heat Transfer Analysis of the Solar Decathlon House
Xiaotong Wu
Mentor: Melany Hunt
The Solar Decathlon is a biannual competition where universities compete to create innovative, energy selfsufficient homes. Caltech partnered with SCI-Arc to enter the 2011 competition and came in 6th overall. The two
schools have come together once again to enter the 2013 competition. During the early stages of our design
process, a critical component is the heat transfer within the house, including the thermal load and systems for
maintaining the house at the required temperature and humidity.
The thermal load greatly affects energy use. Heat gains from lighting and appliances increase the cooling load while
heat losses to the cold nighttime climate increase the heating load. In order to address these concerns, multiple
mechanical systems for conditioning the house were considered. The abilities of these systems to maintain indoor
air conditions were calculated and a system is recommended based on its efficiency and performance.
Material Optimization of 2D Hexagonal Granular Crystals Using Continuous Gradient-Based Methods
Yue Wu
Mentors: Chiara Daraio and Ivan Szelengowicz
We numerically investigate two-dimensional hexagonally packed, uncompressed granular crystals composed of
spherical particles. We perform continuous gradient-based material optimizations to obtain optimized designs, in
which each particle in the packing is assigned PTFE or steel material properties, in order to optimize the total
energy felt in pre-selected parts of the system (referred to as the target area) after it is impacted from one side by
a striker particle. We investigate three different test cases: energy minimization at the side of the system opposite
to the impact, energy maximization at the side walls, and energy minimization at the center of the system. A new
experimental setup was built to validate the numerical designs. We gauge the efficiency of the optimized designs
by comparing them with numerical results obtained for random and non-optimized configurations. It is observed
that the optimizer takes advantage of stiff/soft interfaces, responsible for reflections inside the packing, to achieve
the goal sought in each case.
EphrinA1 and Collagen IV in Endothelial Cell Migration and Pulmonary Arterial Hypertension
Zhaoying Xian
Mentors: Marlene Rabinovitch, Christopher Rhodes, and Dennis A. Dougherty
An event in the pathology of pulmonary arterial hypertension (PAH) is thought to be dysfunction of pulmonary
artery (PA) endothelial cells (ECs). The Rabinovitch lab has identified loss of ephrinA1 and collagen IV in PAECs
from PAH patients. EphrinA1 regulates EC migration and collagen IV deposition. Collagen IV is a predominant
constituent in the endothelial basement membrane. This project focuses on how loss of these genes affects EC
migration. Migration is assessed by modified Boyden chamber assay in control ECs and ECs transfected with
EphrinA1- or Collagen IV-targeted siRNA, under conditions of 0.2% fetal bovine serum (FBS, negative control), 5%
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FBS (positive control), vascular endothelial growth factor (VEGF, reported EC migratory stimulus), and EphrinA1.
Migration inserts are coated with gelatin (control) or Collagen IV. Efficiency of siRNA transfection is characterized
using quantitative (q) RT-PCR and immunoblotting. ECs with decreased levels of EphrinA1 or Collagen IV show a
decrease in migration. Collagen IV coating appears to enhance migration. Control ECs also migrate in response to a
combination of EphrinA1 and Collagen IV. Decreases in EphrinA1 or Collagen IV may affect collagen deposition in
the endothelial layer, thus inhibiting EC migration and contributing to EC dysfunction in PAH.
MicroRNAs: Small Molecules With Big Impacts in Cancer Development
Catherine Bingchan Xie
Mentors: David Baltimore and Alex So
The mammalian inflammatory response is a complex and rapid physiological reaction to noxius stimuli. MicroRNAs
are emerging as key regulators of the immune system. MicroRNAs are a large class of 21-25 nucleotide small
ribonucleic acids that post-transcriptionally regulate a diverse array of genes. As microRNAs control the regulation
of fundamental processes, their dysregulation has now clearly been linked to cancer and particularly to leukemia.
Our broad objective is to identify and characterize miRNAs that promote leukemic development. We are cloning a
genome wide library of more than 700 miRNAs into the murine stem-cell virus-GFP expression vector. This vector
design allows for the expression of the miRNAs and GFP off the same transcript, allowing the tracking of miRNA
over-expression within cells as a function of GFP positivity. To screen for miRNAs that induce tumorigenesis, we
first use an in vitro system and over-express the miRNAs individuals in primary mouse bone marrow cells. We then
isolate those that accelerate cell proliferation, a hallmark of tumorigenesis for further validation. Our study will
provide an in-depth network of miRNAs that regulate leukemogenesis and have crucial implications in cancer
therapy.
Effects of the Level H-RasG12V Expression on the Tolerance of p53 Expression in Mammalian Cells
Yushu (Joy) J. Xie
Mentors: Cliff Wang, David Tirrell, and Ingrid Lawhorn
Two important genes involved in tumor development are the tumor suppressor gene TP53 and the proto-oncogene
RasG12V. p53 is a transcription factor that is involved in conserving the stability of the genome by regulating the
cell cycle, activating the DNA repair proteins, and initiating apoptosis in cells to prevent mutations in DNA. Ras,
which regulates cell division in response to growth factor stimulation, is also heavily involved in cancers. Generally,
if the cell has wild-type p53 expression, aberrant Ras expression can be kept in check by p53, which can prevent
overactive cell proliferation and unregulated cell survival. However, if the p53 is not expressed or mutated, Ras
expression has the potential to transform the cell into a cancerous one. Recent studies suggest it is possible the
simplest way for a cell to develop constitutive Ras expression is not from a deletion or inactivating mutation in the
p53 gene but rather from decreased expression of p53. In this study, we determine the range of Ras expression
required for PD31 murine and v-Abl and Bcr-Abl transformed pre-B cells to survive and proliferate in the presence
of p53 using an inducible p53 system and a translation-initiation strength library of different Ras inducible
constructs.
Functional Knockdown: Truncation of Novel FT93a Protein
Jing Xu
Mentors: Marianne Bronner and Ankur Saxena
Protein traps resulting from vectors inserted at random into developing zebrafish embryos have been used to
create fluorescently tagged fusion proteins. The previously unknown protein FT93a was discovered this way, and it
is expressed in the developing olfactory system. A potential loss-of-function model was created via a fluorescently
tagged, truncated version of this protein. Here, we performed live confocal imaging of FT93a zebrafish. Results
show that the truncated protein’s localization and expression is disrupted. The protein appears to aggregate in the
nuclei of some cells as the embryo develops and is present beyond its normal expression domain. Preliminary
results suggest that a partially penetrant phenotype of aberrant development may exist in some embryos.
Localizing the Perturbed Fetal Neural Circuitry in the MIA Mouse Model of Autism and Schizophrenia
Zihao Yan
Mentors: Paul Patterson, Wei-Li Wu, and Elaine Hsiao
Maternal infection increases the risk for autism and schizophrenia in the offspring. In the mouse model of this risk
factor, maternal immune activation (MIA) during pregnancy triggers IL-6 surge that ultimately results in offspring
appearing autism- and schizophrenia-like behaviors and neuropathologies. The central role of IL-6 led us to
examine the neural pathway by which this cytokine influences fetal brain development. First, we utilize
immunohistochemistry and qPCR to localize IL-6 receptor (IL-6R) distribution, which demonstrates where IL-6 can
act in the brain. Both approaches indicate that IL-6R is highly expressed in hippocampus and cerebellum, which
are known to exhibit neuropathology of autism/schizophrenia. Next, using immunohistochemistry and laser capture
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microdissection to examine IL-6-stimulated downstream signaling following MIA, we identify regions in the
embryonic brain where IL-6 is likely to be acting. Research on neural circuits involved in the response to MIA will
facilitate our understanding of the pathogenesis of autism and schizophrenia.
Methods for the Observation of Tubule Formation in MDCK and MCF-10A Cells
Jade Yang
Mentors: Chin-Lin Guo and Jiun-Yann Yu
MDCK and MCF-10A cell lines have been previously observed to aggregate and develop into tubules through a
process that involves collagen fibers. While the initial and final stages of tubule formation are known, the specifics
of the intermediary processes and the role of the collagen fibers are still yet to be observed. We have developed a
method for the observation of tubule formation utilizing brightfield and fluorescent timelapse microscopy. Cells are
placed into wells fabricated from a 1% agarose/gelatin mixture. The cells are then immersed in 2% collagen cell
medium and subjected to timelapse microscopy. Thus far, this method has been successfully employed to
demonstrate the tendency of cells to utilize self-constructed collagen fibers to pull together linear aggregates of
cells. Further usage of this method should allow for further investigation and observation of cell self-organized
tubule formation.
Time Sensitive Circuits Used to Characterize FPGA Degradation
Mimi Yang
Mentor: Doug J. Sheldon
The reconfigurability aspect of field-programmable gate arrays (FPGAs) makes them the preferred hardware in
many research and industrial settings. Flash based FPGAs, compared to SRAM based FPGAs, have the advantages
of consuming less power during both static and dynamic operations and requiring less power during
reprogramming. However, the long term reliability of flash FPGAs is untested, so there is a need to model the
degradation of the chip. Environmental and physical factors are two sources of degradation of FPGAs that cause
them to deviate from design parameters. These timing variations can be measured with time sensitive circuits,
such as ring oscillators and windowed shift registers. By analyzing the changes in these propagation delays as a
function of the degradation, one develops a better understanding of the degradation patterns of the FPGAs.
A Germline Gene-Drive System Offers New Possibilities to Control the Spread of Mosquito-Borne
Diseases at Their Source
Ran Yang
Mentors: Bruce Hay and Omar Akbari
Mosquitoes including Anopheles and Aedes aegypti can carry and transmit a range of human diseases, including
malaria and yellow fever respectively. A maternal effect dominant embryonic arrest (medea) construct was created
and tested in Aedes with the purpose of introducing a disease-resistant mosquito population and controlling the
spread of malaria and other mosquito-borne illnesses at their source. The medea element occurs in two main
parts: 1) a maternal promoter driving a miRNA toxin that knocks down genes essential for embryogenesis and 2) a
zygotic promoter driving a recoded version of the miRNA-targeted genes which rescues the individual. This “toxinantidote” system allows the disease-resistant construct to spread when starting from relatively low introduction
frequencies. To create functional toxins, maternal promoters were first identified using the Aedes transcriptome
and their activities at different time points in embryogenesis were assessed. Toxin constructs under candidate
promoters were screened for RNAi-induced female sterility using qPCR on target embryogenesis gene sequences
and comparing their expression levels to those in wildtype individuals. Once germline killing has been established,
the toxin will be joined with an already functional antidote system and these disease-resistant mosquitoes can be
introduced to controlled wildtype populations for further study.
Multi-Resolution Video Streaming in Peer-to-Peer Network Models
Semih Yavuz
Mentor: Tracey Ho
In this paper, we consider multi-resolution video streaming in peer-to-peer networks where source and the peers
can have different upload capacities and there is a link between any two peers. Our purpose is to find the set of all
achievable capacity vectors either using network coding or simply routing in peer-to peer networks. In this regard,
based on some thorough mathematical analysis depending on the properties of given network, we find some
essential restrictions on the set of achievable capacity vectors that have to be satisfied in both network coding and
routing schemes. Moreover, we devise a routing scheme without using any network coding that can achieve any
capacity vector in the essentially restricted region. Therefore, we conclude that there is no coding advantage as
well as finding the set of all achievable capacity vectors in this particular network model.
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Phenotypic Plasticity in Xenopus laevis
Stacy Yeh
Mentor: Lea Goentoro
Phenotypic plasticity is the ability of a single genotype to give rise to alternate forms of morphology due to varying
environmental conditions. Past research has been done on genetic changes in a species, but it is not yet well
understood to what extent physical changes affect a species’ evolution or in exactly what ways the environment
affects a species’ growth. The effects of several environmental factors on the development of Xenopus laevis
embryos were observed in this project with the aid of a high resolution flatbed scanner. These environmental
factors included crowding, water content, terrain, and confinement size and shape. From the scans, a “time lapse”
of embryo development was created, in which the exact point in development that any observable physical
differences arose could be pinpointed. Phenotypic variations observed in this study will lead to further studies
relating to the evolutionary importance of phenotypic plasticity.
Development of a Fluorescent Platinum (IV) Complex to Probe the Reduction of Pt(IV) in a Biological
Environment
Jessica S. Yeung
Mentors: Stephen J. Lippard, Ying Song, and Harry Gray
The coordination compound cis-[PtII(NH3)2Cl2], or cisplatin, is one of the most effective commonly prescribed
anticancer drugs with an impressive efficacy shown by a 90% cure rate for testicular cancer. Nonetheless, toxicity,
adverse side effects, and acquired drug resistance limit the potential of many platinum-based anticancer drugs in
cancer treatments. Pt(IV) compounds have greater stability than Pt(II) complexes such as cisplatin and are inert to
associative ligand substitution owing to greater steric hindrance within the octahedral coordination environment.
Pt(IV) complexes thus may improve upon current platinum-based anticancer drugs and minimize side effects.
Cisplatin can be formed by reductive dissociation of the two axial ligands from Pt(IV). Unshielded, unprotected
Pt(IV) complexes, however, are ineffective as pro-drugs because of fast reduction in blood. A Pt(IV) complex,
cis,cis,trans-[Pt(NH3)2Cl2(OCO(CH2)2NH(FITC))2], was synthesized, characterized, and investigated to probe the
reduction of Pt(IV) in a biological environment. Fluorescence studies in phosphate buffer saline in the presence of
biologically relevant reducing agents, glutathione and ascorbic acid, showed an increase in fluorescence over seven
hours. MTT assays with HeLa and A549 cells showed an increase in IC50 when compared to cisplatin, suggesting
that the Pt(IV) complex is less cytotoxic.
Characterizing Differentiation in Nitrogen Fixation in Azotobacter
Kevin Yin
Mentors: Michael Elowitz and Adam Rosenthal
A fundamental question in biology is the extent to which a single species can generate multiple distinct cell types
that can cooperate with one another. Azotobacter vinelandii is a nitrogen-fixing bacteria species. We hypothesize
that it undergoes division of labor by having only some cells within a population fix nitrogen. To test this
hypothesis, we sought to mark individual nitrogen-fixing cells, either by using fluorescence in-situ hybridization
against nitrogenase mRNA, or by inserting an anaerobic YFP reporter attached to a nitrogenase promoter (nifK).
We observed some preliminary data supporting the possibility of differentiation using fluorescence in-situ
hybridization, but this needs to be verified with appropriate positive and negative control experiments. Future work
on this project would be to characterize differences between the two sub-populations at the genome scale.
Development of a Bio-Image Processing Algorithm to Automate Cell Tagging, Tracking, and Phenotype
Annotation
Patrick Yiu
Mentors: Changhuei Yang, Chao Han, and Sean Pang
Many biological studies make use of high throughput cell imaging technologies that produce data faster than it can
be manually processed. To overcome this limitation, we present an automatic method for the location, trajectory
estimation, and phenotype annotation of cells from both high and low contrast fluorescence microscopy images.
Cell detection is accomplished with a marker-controlled watershed segmentation procedure based on image
intensity normalization, Otsu gray-level thresholding, and distance transformation application. Then an optimal
matching strategy is applied to register multiple cells between images, permitting the robust tracking of cell
movement, merging, and division. Functionality is provided by a simple-to-use graphic user interface. Results from
application of this algorithm are reported and compared with manually-determined analyses alongside existing
tracking methods. The robustness of this algorithm when applied with different parameter values is also analyzed
and discussed.
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Conducting Nano/Micro-Mechanical Back-Action-Evading Feedback Measurements Using a Field
Programmable Gate Array
Joshua Yoon
Mentors: Keith Schwab and Junho Suh
This paper describes the implementation of feedback measurements using a field programmable gate array (FPGA).
We attempt to perform continuous position measurements of a quantum harmonic oscillator by preparing a
squeezed state system, but back action arises for one quadrature of motion. One can avoid this altogether by
performing back-action-evading (BAE) measurements, which allows us to look at one quadrature of motion
exclusively. However, to achieve a squeezed state, we will need to implement a feedback force onto our device
because of its Q reaching on the order of 106, a low spring constant, and susceptibility to outside thermal
fluctuations. This is done by using the Universal Software Radio Peripheral (USRP), which detects signals up to the
radio frequency regime. In addition, by using MATLAB/Simulink, Xilinx® ISE, and GNU Radio, we have the tools
and knowledge to customize filters and other modules which show the versatility of our FPGA. For our controller,
we program a series of second order infinite impulse response (IIR) biquad sections and gain blocks, and
incorporate them within the FPGA framework. By accomplishing this task, we can potentially perform
measurements which are below the standard quantum limit (SQL). Export From the Weddell Sea: Monitoring the Surface Circulation at the Tip of the Antarctic Peninsula
Using Drifters
Madeleine Youngs
Mentor: Andrew Thompson
The complex export pathways between the tip of the Antarctic Peninsula and the greater Southern Ocean are of
importance to both biologists and physical oceanographers for the part they play in shaping ecosystems and global
circulation. In January 2012, 40 drifting bouys, equipped with GPS tracking and temperature sensors, were
released in the northwestern Weddell Sea as part of the Gliders: Excellent New Tools for Observing the Ocean
(GENTOO) project. This project compares this new data to a similar study conducted in 2007 as part of the
Antarctic Drifter Experiment: Links to Isobaths and Ecosystems (ADELIE) project. The satellite-tracked paths from
the GENTOO drifters followed contours of constant depth like the ADELIE drifters but the GENTOO drifters took 5
fewer days to exit the Weddell Sea and took only one of the 3 observed paths in the ADELIE experiment. In 2012
the sea surface temperatures were ~1° C warmer than in 2007. Also, the drifter trajectories were collocated with
maximums in chlorophyll concentration in 2007 but not in 2012. The comparison of these two datasets will provide
insight into temporal variability of the export pathways, as well as the connection between the pathways and
climate and biological productivity.
Gold Litz Wire High-Q Power Coil for Retinal Prostheses
Chia-Chen Yu
Mentors: Yu-Chong Tai and Yu Zhao
Research shows that the retinal prosthesis has great potential for treating blindness diseases due to outer retinal
degeneration and helping patients regain partial vision. Our retinal prostheses system incorporates an extraocular
and an intraocular component that are inductively coupled to transfer data and power efficiently. This work
presents a braided litz design constructed with metal ribbon to serve as the secondary power link to be implanted
intraocularly. Copper foils were used in preliminary rounds to confirm the improvements of quality factor before
proceeding to delicate gold foils. A four-strand braided litz design with foil width 10 mil and thickness 1 mil was
wound into a two-turn coil of 10 mm in diameter. Comparison with copper foil coil with the same amount of metal
shows improvements of quality factor and normalized AC resistance up to 2.6 MHz. Different braiding angles and
increased strands with smaller dimensions are the next steps to further enhance the quality factor of the secondary
coil and extend the applicable frequency range. Ultimately, we wish to build a high-Q power coil that is
biocompatible which can be incorporated into the retinal prostheses system.
Autonomous Information Unit: A Method of Data Protection and User Authentication in a Multi-Domain
Networked Environment
Ben Yuan
Mentor: Simon Woo
The modern technological world consists of a large number of different organizations, all with different
requirements and policies. Occasionally, two different organizations will be required to establish a secure channel
for the purposes of making data available to each other. In the case where a public-key infrastructure cannot be
established, it is difficult to establish both node authentication and forward security. Additionally, organizations
sharing information may require fine-grained control over data access and use policy, including data access
tracking and user authorization. The Autonomous Information Unit (AIU) system is designed to solve these
problems, using password-authenticated key exchange to establish trusted communication and dividing encryption
keys using Shamir’s secret sharing algorithm to protect data at rest. User authentication can be provided using
X.509 or username/password authentication, and authorization can be provided via a defined policy. We have
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refined the method by which trusted communication is established between AIU nodes, as the original scheme
based on reconstruction of a split pre-shared key was found to be vulnerable to a man-in-the-middle attack.
Additionally, we provide APIs for third-party applications to use AIU for their own needs, such as user
authentication and key distribution using AIU as a trusted channel.
Bayesian Rapid Optimal Adaptive Design to Estimate Time Preference Parameters
Jenny Yung
Mentor: Colin Camerer
Intertemporal choice, also known as time preference, refers to how people choose when given a choice between a
small amount of gain immediately and a larger amount in the future. We have several competing models of time’s
effect on utility: exponential, hyperbolic, general hyperbolic, fixed cost, and quasi-hyperbolic. The Bayesian Rapid
Optimal Adaptive Design (BROAD) method will be used to determine which model fits best. The method starts with
a prior belief over likelihood of competing theories and theory-specific parameter values and specifies a space of
possible test questions. To gather data, we create a program and a web interface to generate questions to analyze
the subjects’ responses. With each question, the program gains information to find the most accurate theory, and
chooses the next question with the highest information gain. The program will be used to determine the best model
for intertemporal choice.
Data Acquisition Pipeline Design and Testing for the BetaCage: A Radiocontamination Screening
Detector for Rare Event Searches
Alex Zahn
Mentors: Sunil Golwala and Robert Nelson
Background noise reduction is a critical problem for rare event search experiments. Events of interest are typically
extremely faint and by definition not commonly seen. Even low background levels easily drown out signals and
cause false detections. Indeed background noise is often a primary and fundamentally limiting factor in the
sensitivity of rare event searches. One troubling background source is the presence of trace radioactive
contaminants in the detector hardware itself. The BetaCage is a highly sensitive screening detector capable of
identifying extremely low levels of contamination for the production of unprecedentedly radiopure detector
hardware. We present here the design of the BetaCage data acquisition pipeline and analyze its realtime digital
signal processing performance.
Sparse Time-Frequency Representation in 2 Dimensions
Eric Zhang
Mentors: Thomas Hou and Peyman Tavallali
The analysis of data is essential to advancing science. Every day, new observations and measurements are made
that need careful manipulation to reveal patterns and relationships. Data are also becoming integral to the rest of
society, as technology becomes increasingly involved in the planning, running, and study of business and ordinary
life. Most current data analysis methods make assumptions on the data such as linearity, stationarity, or
periodicity. Real life data often does not satisfy these assumptions. For this reason, more adaptive and robust
methods are needed. Sparse Time-Frequency Representation (STFR) is a method of extracting frequency and trend
information from signal data. It uses the observation that signals are often complicated in time but can be
represented compactly in the frequency domain. Instead of having a set basis, as in Fourier Analysis, SFTR uses a
large and highly redundant dictionary. It then searches for the sparsest representation of the signal in this
dictionary. Currently, the 1 dimensional version of this method has been successfully implemented. Generalizing to
2 dimensions, however, presents some difficulties. Whereas 1D only requires fitting in one direction, 2D must
update in two directions. We are currently exploring methods to overcome this problem.
Visual Search Task: Discriminating Between the Ideal Observer Model and the Max Model
Paul Zhang
Mentors: Pietro Perona and Bo Chen
The ability to locate a target accurately and quickly in a visual search is essential to performing most tasks. Using
few assumptions on the placement of cortical columns, modeled by Poisson distributions, with respect to the
stimulus, two models were derived to predict error rate (ER) and response time (RT) as a function of image
parameters. Furthermore decision thresholds for the Ideal Bayesian observer model were derived independent of
image parameters, signifying that varying the difficulty of the search task will not influence the ER. For the Max
model, however, decision thresholds and ER do depend on the number of stimuli in an image (M) and the
difference in features between target and distractor (TC). This study records 100 trials each for M=[3, 10, 30],
TC=[pi/2, pi/6, pi/18], and target present/absent over 20 subjects. Comparing the RTs, false negative rates (FNR),
and false positive rates (FPR), to those of both models allows us to discriminate between which mechanism is more
likely employed in the human brain.
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Developing a 2D Incompressible Navier-Stokes Solver for a GPU-Based Architecture
Rongxiao Zhang
Mentors: Tim Colonius and Sebastian Liska
Computational fluid dynamics (CFD) is a branch of fluid mechanics that uses numerical methods and algorithms to
solve the Navier-Stokes equations, which are a form of Newton’s second law applied to fluid motion. The solutions
to the Navier-Stokes equations inform a broad range of applications from weather forecasting to the design of airfoils. This SURF project is focused on 2D incompressible flows on an infinite domain. To solve such problems, the
immersed boundary method is used. This method uses the fact that the flow velocity is divergence free and
requires the solution of the Poisson equation. Solving such problems is computationally intensive. Recent progress
in parallel computing using graphic processing units (GPU) can accelerate the Poisson solver. This project is an
attempt to develop a fast Poisson solver using such GPU architectures including both CUDA C programming
language and the MATLAB parallel computing toolbox.
Psychophysical Rehabilitation and Cross-Modal Plasticity Using Visual Substitution With Audition
Yuqian C. Zheng
Mentors: Shinsuke Shimojo and Noelle R.B. Stiles
The brain is metamodal. While each portion of the brain best analyzes the signals from a particular sense, this does
not preclude its analysis of other senses. We investigated the visual cortex's ability to analyze auditory input by
using two sensory substitution devices (SSDs): the vOICe and the Raindrop. The vOICe turns the visual scene into
a gray-scale image and encodes for brightness and location for each pixel with sound. After training blindfolded
subjects for only ten hours, they easily intuited the coding parameters of vOICe to recognize visual textures by
vOICe only. The blind subjects show ease of use as well. The Raindrop is an SSD in development which is designed
to digitally mimic the sound of rain on a surface to determine location and surface qualities. To determine coding
parameters and to gather baseline psychophysical data, speakers which can mimic the sound of the Raindrop are
being used. Pilot tests on sighted subjects who are blindfolded showcase the practicality of the Raindrop, as the
subjects can navigate a maze or find a seat without any training. Studying cross-modal plasticity advances
understanding of sensory processing, while potentially helping the blind to “see” again.
Algorithmic Self-Assembly With Single Stranded Tiles
Felix Yuran Zhou
Mentors: Erik Winfree, Dave Doty, and Damien Woods
Algorithmic self-assembly is a type of DNA computing which aims to encode and manipulate information using
simple DNA building blocks by exploiting the specificity of Watson Crick base pairings. This idea has been
successful implemented using the DX tile, a rigid 2D DNA structure with 4 exposed single strands which encode
information through appropriate sequence design and act as function inputs and outputs resulting in experimental
demonstrations of Boolean primitives like the XOR function and simple computations like the binary counter.
Recently a simpler building block has been proposed, the Single Stranded Tile (SST); a 42 base long single strand
DNA with 4 concatenated domains which act in the same way as the edges of the DX tile. The simpler structure of
this design admits more flexibility in sequence design and could allow greater scalability in computation. In this
SURF project we investigate the ability to use SSTs for algorithmic self-assembly. Characterisation of the DNA
structures uses a combination of Fluorescence microscopy and Atomic Force Microscopy.
Mathematical Model of Water Flow in the Sacramento-San Joaquin Delta Tunnel Conveyance Facility
Danielle Zhu
Mentor: John F. Hall
One of the goals of preconstruction planning involves programming a model of the motion of water in the
Sacramento-San Joaquin Delta Tunnel Conveyance Facility. The tunnel conveyance facility consists of a surge
tower, weir, pipeline, two shafts, and a 35-mi long tunnel. The program predicts the position of the left and right
ends of the water column using algorithms and the central difference time integration method. The general
behavior of water is to reach a maximum height in the surge tower after the pumps are turned on, reach steady
flow, run out into the tunnel when the pumps are turned off, and oscillate until an equilibrium rest state is reached.
After running multiple cases, analysis shows that the maximum heights and maximum run out positions are
affected by nonlinear flow rates, and the height of the terminating shaft affects the position, period, and magnitude
of the oscillations.
Numerical Simulation of the Electric Field and the Study of Electron Collection Efficiency in a Xe TPC
Julia C. Ziac
Mentors: Elena Aprile, Marcello Messina, and Gil Rafael
The XENON Dark Matter Project uses a two-phase time projection chamber (TPC) with a liquid xenon target to
detect weakly interacting massive particles (WIMPs). WIMP events are categorized by ionization and scintillation
signals. The point of interaction of the WIMP with the xenon nucleus can be reconstructed in three dimensions with
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millimeter precision, when an appropriate fiducial volume cut is made. The electric field inside the TPC must be well
understood in order to reconstruct the interaction vertex with the desired resolution and to select the region where
the electric field is adequately uniform. In preparation for the final phase of the XENON experiments, the electric
field and electron collection efficiency for the Demonstrator TPC and larger TPCs are studied.
Low Temperature Nanoindentation Studies on BCC Single-Crystalline Niobium
Regina Zmuidzinas
Mentors: Julia Greer, Robert Maass, and Seok-Woo Lee
For the last decade, material science research has been focused extensively on studying material properties at
small length scales. As nanotechnology becomes increasingly important in our next steps of scientific discovery and
technological capability, it is necessary to know how materials behave on such a small scale. Understanding
mechanical properties of materials at small length scales and at low temperatures is especially important not only
for acquiring new fundamental knowledge of small-scale plasticity, but also for the design of future mechanical
devices for space exploration. A measure is needed of how different materials perform as a function of size and
temperature. This project focuses on understanding mechanical behavior of body-centered-cubic metals
(specifically niobium) in the range of a few micrometers in length and 130K to 300K in temperature. Using an insitu scanning electron microscope (SEM) with a nanoindentor and cryogenic system, nanoindentation tests were
performed on [001] single-crystalline niobium at 130K, 210K and room temperature (300K). By analyzing data
obtained from these indentation tests, it was discovered that material hardness increases significantly as a function
of decreasing temperature. This finding will be useful for the design criterion of small mechanical devices under
cryogenic environment.
The Effects of IKKβ on Huntington’s Disease
Mario Zubia
Mentors: Paul Patterson and Ali Khoshnan
Huntington’s disease (HD) is a devastating neurodegenerative disorder characterized by cognitive, psychological,
and motor decline. HD is caused by a poly-glutamine expansion in the N-terminus of the huntingtin protein (Htt).
The mechanism by which mutant Htt elicits its disease phenotype is still not fully understood. Interestingly,
inflammation has been detected in HD patients up to 15 years prior to onset of disease. This may indicate that
inflammation plays a crucial role in the disease pathology. IKKβ, an important pro-inflammatory regulator of NFκB—transcription factor—may contribute to HD pathology. To investigate the role of IKKβ in HD pathogenesis, we
have deleted IKKβ from the macrophages/microglia lineage in mice using cre-lox with LysM promoter driving the
expression of cre. Macrophages/microglia cells are the major source of pro-inflammatory cytokines. The IKKβdeleted mice are crossed with HD mice to examine whether deletion of IKKβ in immune cells affect HD pathology.
Characterization of these animals is in progress.
Interactions between Logic and Topological Dynamics
Andrew Zucker
Mentor: Alexander Kechris
We study the universal minimal flows of automorphism groups of Fraisse structures. For G a topological group, we
say that G is amenable if every G-flow admits an invariant Borel probability measure; we say that G is uniquely
ergodic if every minimal G-flow admits a unique such measure. If K is a Fraisse structure and Age(K) admits a
Fraisse expansion class with the Expansion and Ramsey properties, we provide a necessary and sufficient condition
for Aut(K) to be amenable; we use this condition to show that the automorphism groups of the directed graph S(3)
and the random boron tree structure are not amenable. We also answer a question of Angel, Kechris, and Lyons by
exhibiting a uniquely ergodic Polish group with metrizable universal flow with the unique measure not supported on
a comeager orbit.
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MURF
MURF UNDERGRADUATE
RESEARCH FELLOWSHIPS
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Overgroup Lattices in Finite Groups
Levi Biock
Mentor: Michael Aschbacher
To answer the Palfy-Pudlak Question, John Shareshian conjectured that a certain class, DΔ, of lattices are not
overgroup lattices in any finite group. To prove this conjecture one needs the structure of a group G and the
embedding of a subgroup H in G, such that there are only two maximal overgroups of H in G, and H is maximal in
both of these overgroups. In approaching this problem, we look at the minimal normal subgroups of G and we
prove results that describe the structure of G and the embedding of H in G in terms of the minimal normal
subgroups.
Characterizing the Effects of IKK Inhibitors on Cytokine Expression in Immune Cells of Huntington’s
Disease Patients
Kia L. Byrd
Mentors: Paul H. Patterson and Ali Khoshnan
Huntington’s Disease (HD) is a neurodegenerative disorder caused by the expansion of the polyglutamine domain
in exon-1 of the huntingtin protein (Htt). Nuclear factor kappa B (NF-κB) pathway is implicated in the toxicity of
mutant Htt in HD. Mutant Htt fragments activate the IκB kinase complex (IKK), a key regulator of NF-κB. The
IKK/NF-kB pathway regulates the expression of many genes including cytokines, which are responsible for
inflammation. Immune cells from HD patients secrete elevated levels of pro-inflammatory cytokines years before
the onset of motor symptoms. These findings indicate that deregulation of IKK may contribute to HD pathology.
Our study investigates whether IKK inhibition is a viable therapeutic target for HD. Novel IKK inhibitors are
evaluated for their efficacy to block the expression of pro-inflammatory cytokines. Best candidates will be tested for
their safety and therapeutic potentials in an animal model of HD.
Design and Fabrication of a Low Cost Hot-Film Anemometer in Order to Detect Fluctuating Velocities
Adam Chaffee
Mentor: Beverley McKeon
Turbulent flow is the dominant flow regime experienced in everyday life. From the water flowing out of the kitchen
faucet to the air flowing over the wings of an airplane, turbulent flow is all around us. Of specific interest for this
project, is the boundary layer (the region close to the wall where viscosity is important) during the phenomenon of
flow transition from the laminar to turbulent regime. This transition can be caused by, among other things, an
increase in velocity, mechanical perturbation, and an increase in the characteristic length scale. Velocity
fluctuations in the boundary layer signal that the flow has transitioned to the turbulent regime. Hot-films are
currently the tool of choice when studying the features of boundary layers from the wall. Hot-film anemometers are
very expensive and fragile which creates a high risk situation when attempting to place, run, and remove them
during experiments. This project has led to the development of a low cost hot-film anemometer capable of
detecting small changes in velocity. The anemometer consists of low cost electronic components and tungsten wire
which does not present the high risk associated with the commercial anemometers. Subsequent work to be done
consists of further development of the anemometer circuitry, reduction of noise, and refinement of the hot-film
sensor which will be used to determine the frequencies present in the turbulent boundary layer.
End Effector Design and Fabrication for Multi-Surface Adhesion
Phillip H. Daniel
Mentors: Aaron Parness and Matt Frost
There is no reliable way to non-destructively grip the exterior surface of large objects in space, since the earth
orbit environment is unique in composition. Traditional methods which implement suction, magnetism, and wet
adhesion (glue) are ineffective or impractical. Work was done to design an end effector that can adhere to the
unprepared surface of objects with large radii of curvature and varied surface roughnesses. The design constraints
also mandate that the mechanism must function in an environment with 3.2x10-2 Pa of ambient pressure at near
zero gravity and it must have negligible engagement and detachment forces. Such adhesion is achieved through
van der Waals forces, by utilizing a dry and unidirectional synthetic skin that was designed to imitate the climbing
physics of Geckos. When loaded to 12kPa in its preferred shear direction, the current mechanism can adhere to a
geometrically flat plate with a surface roughness of .0015mm, and support 2kPa of normal load. This is
approximately 80% of the ideal adhesion characteristics of the skin alone. Final results will be presented. Future
work will include sensor integration and material selection, for operation at low earth orbit temperatures of 175
degrees Kelvin.
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Selective Labeling of Human Cancer Cells Using a Non-Canonical Amino Acid
Daniela Espinosa
Mentors: David A. Tirrell and Ying (Beverly) Lu
The incorporation of non-canonical amino acids into the proteome introduces chemically unique groups otherwise
unavailable for protein synthesis. This approach allows selective tagging and labeling of proteins with exogenously
delivered probes. Due to the highly analogous translational machinery among different cell types, it is difficult to
restrict non-canonical amino acid labeling to a single cell type without genetic manipulation. Taking advantage of
the intrinsic difference in metabolism between cancer and normal cells, selective labeling of human cancer cells
may be achieved. Glutamine, the most abundant amino acid in plasma, is an important source of cellular energy
and plays a key role in cellular processes such as nitrogen donation during anabolism and ammonium production.
Some cancer cells show lower rates of the glutamine synthetase activity and become avid consumers of
extracellular glutamine. Using cervical cancer HeLa cells, and normal human dermal fibroblasts, we are testing the
incorporation of a glutamine analogue, L-glutamic acid γ-hydrazide (Gah), into cellular proteins. Gah was
introduced to both cultures, followed by reaction with a fluorescent dye through hydrazide-ketone chemistry.
Fluorescence intensity of whole cells was measured and HeLa cells exhibited a 1.6-fold fluorescence enhancement
compared to normal human dermal fibroblasts. Mass spectrometry, western blotting, and fluorescence microscopy
are being used to interrogate selective labeling of HeLa cells using Gah.
A Multivariate Piecewise-Linear Interpolation Approach for Solid Mechanics Simulations
Arturo J. Mateos
Mentors: Michael Ortiz and Malena Español
We present a multivariate piecewise-linear interpolation approach to study the material response of deforming
solids. In particular, we define an approximate variational formulation of nonlinear elasticity by means of a
piecewise-linear interpolation of the potential energy over a simplicial grid. This approach provides a systematic
way to tessellate the domain into simplexes and interpolate the potential energy in one simplex at a time until a
numerical solution is found. Numerical examples demonstrate the performance of this approach in nonlinear solid
mechanics problems.
Investigation of Amide-Amide Intramolecular Hydrogen Bonding in Diamides
Elsy P. Naveo
Mentors: John D. Roberts, Bright Emenike, and William Carroll
The objective of this research is to understand the conformational behavior of N-benzyl-N1-methylsuccinidiamide
(1) in a variety of solvent systems. Diamide 1 can serve as a model for many biologically important molecules
including polypeptides and proteins which contain multiple amide functional groups. The outcome of this research
may aid the proper understanding of the relationship between protein and ligands, which is an important
component of drug design. In line with our interest in the conformations of simple ethane system, 1 adopts both
the gauche and trans forms. Each form is quantifiable using a well-established NMR spectroscopic technique
developed in our lab. In addition to understanding the conditions leading to optimal hydrogen bonding, it is also of
interest to us to elucidate the significance of sp2-hybridized nitrogen atom of the amide in the formation of
intramolecular hydrogen bonds. So far, it has become evident that high fraction gauche is synonymous with
intramolecular hydrogen bonding, and low fraction gauche is indicative of intermolecular hydrogen bonding (mostly
with the solvent molecule). Non-polar aprotic solvents like chloroform and methylene chloride yielded the highest
fraction gauche. Whereas, with polar protic solvents, the fraction of gauche were simply statistical.
Dinitrogen Functionalization Using Metallaboratranes
Sadrach Pierre
Mentors: Jonas Peters and Daniel Suess
The metallaboratrane [(DPB)Fe(Br)] (DPB = bis[2-(dicyclohexylphosphino)-phenyl]borane]) was synthetically
prepared. The synthesis was initiated with the preparation of (2-Bromophenyl)dicyclohexylphosphine which was
prepared in a 67% yield. The DPB ligand was prepared, using the precursor side arm, PhBCl2 and n-BuLi, in a 6%
yield. The DPB ligand was reacted with iron(II) bromide/sodium amalgam to get [(DPB)Fe(Br)] in an 82.5% yield.
The [(DPB)Fe(Br)] was reduced by dinitrogen after adding excess sodium amalgam to get [(DPB)Fe(N2)]Na. A
second reduction of [(DPB)Fe(Br)] was done with excess magnesium to give [(DPB)Fe(N2)]MgBr. [(DPB)Fe(N2)]Na
and [(DPB)Fe(N2)]Mg were further characterized using IR spectroscopy. N2 stretches were observed at 1907 cm-1
for [(DPB)Fe(N2)]Na and 1848 cm-1 for [(DPB)Fe(N2)]MgBr by IR. Yields for the syntheses of [(DPB)Fe(N2)]Na and
[(DPB)Fe(N2)]Mg have not yet been calculated.
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Mechanics of Deformation and Fracture of Soft Fiber Reinforced Composites
Brian Ramirez
Mentors: Guruswami Ravichandran and Michael Rauls
The demand for lightweight materials which can undergo large amounts of deformation and remain in the elastic
region in deployable space structures and tissue engineering, have led to an increase usage of soft fiber reinforced
composites. This provides the motivation for understanding the mechanical behavior of such composites. In the
present work, tensile experiments were conducted on glass fiber/polydimethylsiloxane (GF-PDMS) composites to
study their deformation and fracture response. Digital image correlation (DIC) technique was used to measure the
full field displacements around notches and cracks in the composite. The experiments together with
micromechanical models are used to understand the mechanics of load transfer and failure mechanisms of soft
matrix composites. The mechanics insights gained from this study can be used to design and analyze new
generation of soft fiber reinforced composites for emerging novel applications.
Quick Data Pipeline for Robo-AO
Victoria Ashley Villar
Mentors: Christoph Baranec and Reed Riddle
I have created a fast data analysis and display system for the Robo-AO automated adaptive optics system used at
Palomar Observatory. Because Robo-AO currently corrects for stellar image motion by taking fast frame rate data
and applying post-facto corrections using recentering techniques, it collects a large quantity of raw data. Creating a
quick pipeline that will reduce observational images, calculate basic photometric properties of targets and display
this data is essential in organizing this deluge of information. Beginning with the raw images, the reduction
algorithm can quickly recenter and stack frames to reproduce the expected shape of the target star. Reduced
images are compared to those which have not been corrected by the adaptive optics system in order to give an
estimate of how well the system is working. Information about the target and seeing, as well as a scaled PNG
image of the target, is loaded into an internal website in the form of a table. A version of this program will be
implemented into the automated program and provide realtime updates for Robo-AO users.
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Genotypic and Phenotypic Diversity of Microbial Isolates From the Mars Exploration Rovers
Keith Arora-Williams
Mentor: J. Nick Benardini
Mars-bound rovers such as the Mars Exploration Rover (MER) endure strict planetary protection implementation
campaigns to assess bioburden. The objective of this study is to identify cultivable microorganisms isolated by the
NASA Standard Assay from spacecraft during pre-launch and evaluate their potential to survive conditions on the
Martian surface. Of approximately 350 isolates collected from the MER spacecraft archive, 150 microorganisms
were reconstituted for characterization via 16S rRNA fingerprinting. Assembled sequences show high levels of
sequence similarity to known organisms in the genera Bacillus, Paenibacillus, Brevibacillus, Sporosarcina,
Staphylococcus and others. Samples underwent phenotype characterization employing multiple carbon sources and
ion concentrations in an automated microarray format using the Omnilog system. Working and stock cultures were
prepared to address the immediate needs for day-to-day culture utilization and long-term preservation,
respectively. Results from this study are yielding details about the microbes that contaminate the surfaces of
spacecraft and further characterization will help gauge whether terrestrial organisms can survive interplanetary
transit and/or proliferate on Mars. The overall outcome of this study will benefit emerging cleaning and sterilization
technologies for preventing forward contamination that could negatively impact future life detection or sample
return missions.
Structural Analysis of a Complex of Coat Nucleoporins in Chaetomium thermophilum
Camille Bayas
Mentors: André Hoelz and Tobias Stuwe
The nucleus of a eukaryotic cell is enclosed by a double membrane, which allows for the compartmentalization of
the cell into the nucleus and the cytoplasm, and the separation of transcription and translation. Large protein
assemblies termed nuclear pore complexes (NPCs) along with soluble transport receptors mediate the active
transport of macromolecules into and out of the nucleus. Electron microscopy has provided an architectural
framework of the NPC, but an atomic-resolution structure of the entire assembly has not been obtained primarily
due to its large size and flexible nature. A heptameric Nup84 subcomplex within the yeast NPC forms a continuous
yet porous fence-like coat for the nuclear pore membrane. In the course of this study, the homologous Nup84
complex derived from the thermophilic fungus Chaetomium thermophilum was reconstituted, along with the
proteins Nup37 and Elys, which link the NPC scaffold to cell division. Structural analysis through X-ray
crystallography of this integral part of the NPC coat will be initiated to obtain an atomic model of this complex. The
structure promises to shed light onto the general architecture and ultimately function of one of nature’s most
sophisticated transport channels.
Using Riboswitches to Understand Stem Cell Maintenance
Stephanie Bohaczuk
Mentors: Elliot Meyerowitz and Paul Tarr
Synthetic biology aims to engineer biological systems that elicit preprogrammed outputs. An application is
riboswitches, which are RNA molecules that control translation of an mRNA. A riboswitch consists of a ligand
binding aptamer, which is coupled to a hammerhead ribozyme that mediates mRNA degradation. Binding of the
ligand induces a conformational change in the riboswitch, inactivating the ribozyme and allowing translation. We
use riboswitches to study how dynamic changes in the CLAVATA/WUSCHEL (CLV/WUS) genetic regulatory network
and auxin-signaling pathway regulate stem cell differentiation and specification in the shoot apical meristem (SAM).
We perform a tobacco transient assay to measure the activity of theophylline riboswitches coupled to CLV3 or WUS
mRNA in a plant-based in vivo system. We transformed clv3 mutant Arabidopsis thaliana with theophylline
riboswitches coupled to CLV3 mRNA to look for complementation. The role of auxin in plant organ initiation in the
SAM has been difficult to study due to the lack of a direct reporter. We will implement a riboswitch to act as a
direct reporter of auxin localization by coupling it to a fluorescent protein. The SELEX protocol yielded no aptamers
with sufficient binding affinity for auxin so we consider other options.
Manipulation of the Sex Ratio in an Insect-Parasitic Nematode Using Environmental Factors
April M. Booth
Mentors: Paul W. Sternberg and Hillel Schwartz
The insect-parasitic nematode Heterorhabditis bacteriophora has the potential to serve as a model system for the
molecular and genetic study of parasitism and mutualistic symbiosis. One important obstacle to using this
nematode as an efficient model system in the laboratory is that when grown at low density the animals produce
broods that consist almost entirely of females, with a small proportion of males and a tiny number of self-fertilizing
hermaphrodites. This makes it hard to propagate H. bacteriophora from individuals and at low densities. This
limitation presents particular difficulties for experiments involving genetics and transgenesis. For this reason we are
conducting experimental treatments of the H. bacteriophora hermaphrodites seeking to identify conditions that
induce their progeny to develop as hermaphrodites, as is normally seen for animals that develop at high density or
with little food. We are testing the conditions of temperature, starvation, synthetic ascarosides, and extracts from
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dense populations of stressed H. bacteriophora and some combinations of these conditions. Thus far, starvation,
the combination of starvation and transient heat shock, Caenorhabiditis elegans ascaroside #6.1 and selected
stressed H. bacteriophora extracts may show some ability to induce hermaphroditism.
Self-Assembly of Brush Block Copolymers to Non-Lamellar Nanostructures
Alice Chang
Mentors: Robert Grubbs and Garret Miyake
Brush block copolymers rapidly self-assemble to periodic nanostructures with photonic bandgaps that can be tuned
to span the entire visible spectrum. The peak wavelength of reflectance linearly increases with block copolymer
domain size, allowing the bottom-up fabrication of photonic crystals for specific applications. The goal of this
project is to synthesize brush block copolymers that self-assemble to photonic crystals that reflect infrared
radiation; such polymers could be developed as paints to combat the urban heat island effect, lowering cooling
costs and pollution in cities. Toward this goal, two approaches have been developed: (1) varying the weight ratio of
constituent macromonomers in order to access two- and three-dimensional block copolymer morphologies, and (2)
polymerizing increasingly large macromonomers in order to explore the effect of increasing domain size on selfassembly. Four series of brush block copolymers were synthesized by the grafting-through ring-opening metathesis
polymerization of polystyrene and rigid-chain polyisocyanate macromonomers. Reflection occurred in the visible
spectrum, and novel nonlamellar, unordered morphologies were observed by scanning electron microscopy.
Understanding the Role of miR-146a and Its Targets Traf6, Irak1, and Stat1 in HSC Biology
Prakriti Gaba
Mentors: David Baltimore and Jimmy Zhao
The immune system is an intricate system that aims to destroy any harmful invaders that enter an organism. An
effective immune response typically involves a process called inflammation, which coordinates the recruitment of
the proper immune cell types to eradicate infection. MicroRNAs (miRNAs) are small, non-coding RNAs that have
recently been shown to be important players in the immune system. miRNAs function by targeting mRNAs leading
to repression of their expression. Regulation of miRNA expression and function is controlled by transcription factors
that regulate the production of miRNA containing primary transcripts in specific cell types during development or in
response to various environmental signals. Specifically, we will be studying the transcription of a particular miRNA,
miR-146a, which is present in immune cells and is upregulated further in response to inflammatory stimuli such as
Toll-like receptor ligands or pro-inflammatory cytokines. Hematopoietic stem cells (HSCs) give rise to all blood cell
types, including those found in the immune system. They are located primarily in the bone marrow. In prior
studies, mice that are deficient in ARS2, which contributes to pri-miRNA processing, have bone marrow failure that
is thought to be due to defective HSC function. This experiment suggested that the miRNA pathway is probably
important in HSC function. However, the identity of the responsive miRNAs remains elusive and the mechanistic
basis for miR-146a’s function in HSCs is presently unclear. One aspect of our project is to assess whether overexpression or knockdown of miR-146a leads to changes in proliferation rates of immune cells. Another aspect of
our project is to understand whether specific targets of miR-146a, including IRAK1, TRAF6, and STAT1, contribute
to its biology in HSCs before and after inflammation and whether this occurs in a combinatorial manner. Ultimately,
our aim is to create retroviral vectors that demonstrate over-expression of STAT1 cDNA and other vectors with
siRNAs against one, two, or all three targets of miR-146a to determine which combination can rescue the miR-146a
HSC phenotype.
Comparison of Gaze Patterns on Visual Dynamic Scenes Between Autistic and Neurotypical Individuals
as a Measure of Social Cognition
Neil Gandhi
Mentor: Ralph Adolphs
While specialists can diagnose autism based on behavioral cues, it is difficult to quantify these clinical observations
with experimental, performance-based tasks that recreate complex social interactions. The purpose of this study is
to bridge the gap between clinical observation and experimental tasks by using noninvasive eye-tracking
techniques to map the eye movements of individuals with autism while viewing dynamic social scenes. Gaze data
was collected for 40 control and 15 autistic subjects while watching a full episode of the television sitcom, “The
Office”. The infrared eye-tracking device, Tobii TX300, determined the coordinates of eye-gaze in relation to the
screen. This data was processed and compared using a measure known as the Normalized Scanpath Saliency,
which allows for an across-group comparison of gaze in the spatiotemporal domain. Results are currently being
calculated, and we hypothesize that autistic subjects will demonstrate a different gaze pattern than control
subjects. In addition, we expect to find that the autistic group will direct their visual attention toward areas of high
visual saliency rather than regions containing important social information, such as faces.
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Quantitative Analysis and Depositional Techniques for B. subtilis Endospores
Arin Greenwood
Mentors: Adrian Ponce and Aaron Noell
The Ponce Group at the Jet Propulsion Laboratory has developed an instrument to determine the effectiveness of a
sterilization treatment using resilient bacterial endospores as bio-indicators. In order to improve the methodology
of this process it was necessary to create a reproducible technique for forming a homogenous monolayer of spores
at the highest achievable density, and transfer this monolayer to a variety of useful substrates. Through a series of
filtrations designed to deposit B. subtilis endospores evenly onto a piece of filter paper, and testing multiple
methods of homogenization and transfer, we found that the upper density limit before extensive clumping occurs is
1.4 x 107 spores per square centimeter. At this density, each one-micron long spore is separated by an average
nearest neighbor distance of 1.2 microns. In the filtration process, each increasing concentration and each
homogenization method was imaged in triplicate using an Environmental Scanning Electron Microscope (ESEM). To
test the viability of the B. subtilis spores, their germination process was monitored to determine the number of
recoverable spores. They were then compared quantitatively with data from culturing methods, which are well
established but require much more time to analyze.
Synthesis of Telechelic Elastin-Like Protein-Fluorescent Protein Fusions for Application in Gel Stress
Sensors
Tiffany A. Huang
Mentors: David A. Tirrell and Wen-Bin Zhang
Mechanical stress at a molecular level remains poorly characterized and understood, so mechanical stress sensors
that can detect local force fields exerted on an object and give feedback in a straightforward way (such as a
colorimetric readout) have great potential both as research tools and as biomaterials for applications in fields
where pressure and strain are heavily involved. A gel stress sensor can be created by introducing a mechanoresponsive fluorescent protein into an artificial extracellular matrix. Several different elastin-like protein-fluorescent
protein fusion constructs used for transformation in E. coli were expressed, purified, and lyophilized. These protein
constructs were then cross-linked to form a fluorescent gel using two different chemistries: the thiol-maleimide
chemistry and the strain-promoted azide-alkyne cycloaddition. Rheological and atomic force microscopy tests were
performed on the gels to determine several of their mechanical properties and establish the relationship between
the external force/stress applied and the change in local fluorescence. The study shows promise for the use of
these gels as potential stress sensors.
Fabrication of a Caged Neuron Multi-Electrode Array for Network Recording, Stimulation, and
Connectivity Mapping
Jessleen Kanwal
Mentors: Jerry Pine, Yu-Chong Tai, and Jungwook Park
We have constructed an 8 by 8 array of cages for single neurons to examine the development of
electrophysiological connectivity between identifiable neurons. The device consists of a micro-machined circular
wall (10 um in diameter) around each electrode, dubbed a neurocage, which traps individual neurons in close
proximity to an electrode. Six tunnels (1 um high, 10 um wide) emanate from each neurocage, permitting neurite
outgrowth. Array fabrication employed standard photolithography processes. Photoresist was applied to a thin glass
substrate followed by etching and deposition steps to create a gold, electrode-lead pattern on the glass.
Subsequently, a 1 um film of low-stress silicon-nitride was deposited for electrical insulation. Parylene-C was then
used to form the neurocage structures, as this biocompatible polymer is optically transparent and provides strong
mechanical strength and flexibility. Upon completion, the device will be wire bonded to a printed circuit board and
glued to a Petri dish for culturing neurons and recording their electrical activity. Fabrication of insulated cages at
the cellular scale allows a 1:1 correspondence between neurons and electrodes, and the electrical stimulation and
recording capabilities will further our understanding of how neural networks develop and how they can be modified.
Multiple Ligands and the Tuning and Dynamics of Cell Response
Heidi Klumpe
Mentors: Michael Elowitz and Yaron Antebi
Cell signaling pathways transmit information from the extracellular environment to the cytoplasm. In many cases,
a single signaling pathway, can be activated by multiple ligands that all produce the same downstream response.
For example, BMPs 2, 4, 6, and 7 phosphorylate the same R-SMADs to activate transcription, and the six members
of the interleukin-6 cytokine family activate the Stat3 transcription factor. We propose these multiple ligands are
not fully redundant, but rather, independently and in cooperation, elicit quantitatively and/or dynamically different
responses, in order to provide additional capabilities that would be difficult or impossible to achieve with a single
ligand. This may explain the distinct in vivo functions of highly homologous ligands, such as BMP4’s inability to
rescue BMP2’s role in certain developmental processes, including chondrocyte maturation1 and other processes.2,3
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We employ a systems biology approach to study the relationship between ligands and cell response. To quantify
the magnitude and dynamics of cell response, cell lines were engineered to report on levels of transcription factor
activity with fluorescent proteins. Our results indicate BMP2 and BMP4 differ in the affinity and efficiency of
pathway activation. Further, a systematic scan over a matrix of BMP2 and BMP4 combinations reveals that the
response is non-monotonic; saturating concentrations of both BMP2 and BMP4 decrease overall transcription factor
activity compared with either of the individual ligands on its
own. This is distinct from LIF and CT-1 (IL-6
cytokines which bind the same receptor complex), which have similar efficiencies and produce an increasing
response with increase of either ligand.
1
Shu, et al. “BMP2, but not BMP4, is crucial for chondrocyte proliferation and maturation during endochondral bone
development.” Cell Science 2011, 124: 3428-3440.
2
Lowery and Caestecker. “BMP signaling in vascular development and disease.” Cytokine and Growth Factor
Reviews 2010, 21(4):287-298.
3
Wu, et al. “Multiplicity of BMP signaling in skeletal development.” Skeletal Biology and Medicine, Part A 2007,
1116:29-49.
Structural Analysis of an Essential Interaction in the Nuclear Pore Complex Scaffold
Antoine Koehl
Mentors: André Hoelz and Tobias Stuwe
The evolution of Eukaryotic life to rely on the separation of distinct, membrane bound organelles brought with it
the unique challenge of transport between the nucleus, where genomic information is held, and the cytosol, where
the majority of enzymatic activity takes place. The nuclear pore complex (NPC) is a large multiprotein structure
that fulfills this role, and essentially acts as a gatekeeper between these environments by regulating transport
processes between the two cellular compartments. While the biochemistry of nuclear transport has been well
characterized, structural information of the transport scaffold at the atomic level is so far lacking. In recent years,
the Hoelz lab has pioneered a divide and conquer approach that seeks to unravel the structure of the NPC through
the building up of large subcomplexes that make up the NPC. This study aims to determine the x-ray structure of a
member of the adapter layer of the NPC, Nup192, along with its binding partners Nup53 and Nic 96. As Nup192
shares structural similarity to nuclear transport factors, a high-resolution structure promises to provide insight into
the manner in which it binds these two proteins and how Nup192 organizes the adapter layer.
NF-B Nuclear Oscillation in Varying B Cell Stages and in Different B Cell Signaling Pathways
Philip Kong
Mentors: David Baltimore and Devdoot Majumdar
Nuclear factor kappa-B (NF-B) is an essential transcription factor that orchestrates the activation of several
immune response genes in response to inflammation. It is found in virtually all animal cells and plays a key role in
responding to infection. One hallmark of NF-B is its oscillation from the cytoplasm to the nucleus on a timescale.
The dynamics of this periodic nuclear entry of NF-B and its resulting gene expression pattern have been studied in
populations of cells. While the trajectory pattern of NF-B has been measured in 3T3 fibroblast cell lines, its
oscillation profile has never been fully characterized in B cells due to convoluted signaling pathways of B cells and
the complexity of different B cell maturation stages. By using immunohistochemistry and sodium dodecyl sulfate
polyacrylamide gel electrophoresis (SDS-PAGE), we attempt to answer the existence of NF-B oscillation in B cells
and how they may differ in varying B cell stages and signaling pathways. Our results suggest a possibility of NF-B
oscillation in B cells and also different kinetics of oscillation in certain signaling pathways. We therefore explore the
functional relevance of NF-B’s oscillatory behavior in B cells, which are the very cells NF-B was first discovered
in.
An RNAi Screen for Chromatin Factors Regulating Reproductive Aging in Female Drosophila Germline
Stem Cells (GSCs)
Susan E. Liao
Mentors: Katalin Fejes Toth and Yung-Chia Chen
Germline stem cells (GSCs) give rise to the mature gametes which pass on genomic DNA from one generation to
the next. GSC system aging – termed reproductive aging – is characterized by the progressive diminishment of
gamete production and a significant reduction in the viability of mature gametes. One mechanism which
contributes to GSC maintenance is epigenetic regulation of the GSC chromatin state, but identifying specific
chromatin factors which regulate GSC aging remains an on-going search. To shed light on how specific changes to
the chromatin state affect reproductive aging, we developed a genetic screen to identify candidate chromatin
factors which may regulate reproductive aging in the Drosophila model organism. We targeted these chromatin
factors for knock down using shRNA (small hairpin RNAs) which were expressed exclusively in the germline using
germline-specific drivers and confirmed knock down using RT-qPCR. To quantify the process of reproductive aging,
we measured the number of eggs laid daily in a fecundity assay. By comparing the fecundity of these knock down
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flies with wild type flies, we will be able to identify which knock down flies show a marked decrease in fecundity
later in life and thus identify genes which may regulate reproductive aging. Preliminary results demonstrate shRNA
knockdown efficiency using the nos-GAL4 driver and provisional setup for a fecundity assay.
Progress Towards the Preparation of Acutumine: Accessing the Aza-Propellane Core
Michael Martinez
Mentors: Sarah Reisman and John Butler
Acutumine is an aza-propellane alkaloid derived from the medicinal herb Sinomenium acutum. In addition to being
an intriguing synthetic target, acutumine exhibits selective T-cell toxicity and antiamnesiac activity. Acutumine has
a high level of structural complexity, containing a neopentyl chloride, a spirocyclic cyclopentenone moiety, and two
all-carbon quaternary assembled on the aza-propellane core. Despite its early isolation in 1929, only one total
synthesis of acutumine has been reported to date. This study reports our progress toward the synthesis of
acutumine. The aza-propellane core is constructed by a diastereoselective 1,2 addition to a benzoquinone-derived
sulfinimine, followed by reductive cyclization and [2+2] photocycloaddition. This core can be advanced to the
natural product after a key retro aldol step followed by late stage chlorination and oxidation reactions. The
development of a synthetic strategy to prepare acutumine can allow access to acutumine derivatives and other
aza-propellane akaloids.
Mass-Based Aerosol Separations in Pulsed Electric Fields
Matthew Mayers
Mentor: Thomas F. Miller III
We design and implement a coarse-grained simulation model to study the efficacy of a pulsed applied electric field
in providing mass-based separation of charged micron-sized aerosol particles. The model accounts for the nonNewtonian fluid dynamical effects of the surrounding aerosol suspension on the motion of the charged particles. We
investigate the effects of different pulsing waveforms on the degree of mass separation and predict the plausibility
of feasible experimental applications. The model shows (and we prove mathematically) that mass-based particle
separation cannot be achieved using any periodic pulsing waveform in the absence of non-Newtonian fluid
dynamical effects. We demonstrate that under certain assumptions about the mechanics of the aerosol fluid,
substantial mass-based separation can be achieved using pulsed electric fields. This work provides a theoretical
basis for the application of pulsed electric fields to existing Differential Mobility Analyzers (DMAs) for mass-based
aerosol separations, which are not currently feasible with the DMA's static applied electric field.
Mechanistic Studies of Fluorinated Cobaloximes
Rocio Mercado
Mentors: Harry B. Gray and Michael J. Rose
The conversion of solar energy to chemical fuels is an important challenge in the field of energy research. The
combination of light-absorbing materials with catalytic materials or molecules has gained acceptance as a strategy
to generate “Solar Fuels.” Due to its wide availability, the splitting of water into its elemental components is a
particularly attractive approach. One of the missing links in this approach is the identification of molecular catalysts
for hydrogen (H2) generation that are derived from earth abundant metals like iron, nickel or cobalt. In a previous
work, I synthesized a family of cobalt complexes derived from the fluorinated diphenylglyoxime ligand (“dArFgH2”).
These complexes are variations of the extensively studied diglyoxime systems [Co(dRgBF2)2L2] (R = methyl,
phenyl), which have been shown to catalyze hydrogen (H2) evolution at low overpotentials. In electrocatalysis
experiments, [Co(dArFgH-BF2)2(py)2] also minimizes energy losses by generating H2 at negligible thermodynamic
overpotentials (similar to Pt). The similarity in reduction potentials between [Co(dArFgH-BF2)2(py)2] and Co-dpg-BF2
is in stark contrast to the differences in catalytic activities. Such observations prompt the question: Is the proton
bridge an active participant in the catalytic cycle? Cyclic voltammetry, NMR, and a variety of other spectroscopic
techniques have been used to elucidate some of the mechanistic details of the hydrogen evolution pathway in these
perfluorinated cobaloxime systems.
Characterization of nAChR Subunit Stoichiometry in the Medial Perforant and Temporoammonic
Pathways
Mahati Mokkarala
Mentors: Henry Lester and Rachel Penton
Nicotine has been implicated not only in addiction but also in increasing cognitive function, attention and memory.
Increases in cognitive function, attention, and memory could be linked to nicotinic acetylcholine receptor (nAChR)
upregulation in the hippocampal medial perforant pathway (MPP) and temporoammonic pathway (TA). We want to
quantitatively determine  and 2 nAChR subunit upregulation in the MPP and TA pathway after initial exposure to
nicotine using immunohistochemistry and confocal microscopy to detect fluorescently labeled  and 2 nAChR
subunits expressed in recently acquired knock-in -GFP and 2-GFP mice. Exact measurements of 
stoichiometry in the MPP and TA pathway can explain how nicotine and possibly other similar agonists promote
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increased memory and attention. We have currently successfully analyzed some -GFP, GFP and WT
fluorescent images but need more data in order to define the precise nicotine-mediated upregulated 
stoichiometry ratio in the hippocampal MPP and TA pathways.
Elk3 Is Required for Neural Crest Specification
Jacquelyn Phillips
Mentors: Marianne Bronner and Crystal Rogers
Elk3/Net/Sap2 (here referred to as Elk3) is involved in tumor angiogenesis in mice, but is expressed in various
tissues throughout embryonic development. Elk3 expression was characterized using whole mount in situ
hybridization, and we found that Elk3 expression is very dynamic. During development, Elk3 is expressed in the
head folds, the head mesenchyme, the somites, the intersomitic vessels, and in the migratory cranial neural crest.
Because Elk3 is expressed in premigratory and migratory neural crest cells, we believe that it is involved in cranial
crest specification and migration, and it may be required for the formation of many neural crest derivatives. Neural
crest cells migrate throughout embryos and become various types of cells, including neurons, enteric ganglia, and
melanocytes. Based on the Elk3 expression pattern, we performed gain and loss of function experiments to
determine its role in neural crest cell development. Here we show that loss of the Elk3 protein decreased the
number of neural crest cells marked by Sox10 and Foxd3 expression, which supports a role for Elk3 in neural crest
specification.
Mapping the Hypothalamic Anxiety Circuits Modulated by Lateral Septal CRHR2 Neurons
Scott A. Shuster
Mentors: David J. Anderson and Todd D. Anthony
Much work has been devoted to mapping the neural circuits controlling emotional behaviors with the long-term
goal of developing targeted treatments for psychiatric diseases. Recent work has been directed at understanding
the role of a subpopulation of projection neurons in the lateral septum (LS) defined by expression of the
corticotrophin-releasing hormone receptor 2 (CRHR2) and activation in response to stress. Specifically, viral tracing
of these neurons shows that the anterior hypothalamic nucleus, a genetically heterogeneous and underexplored
region, is a major target. Here, we mapped c-fos expression to determine the activation patterns in the medial
hypothalamus following immobilization stress (IMS) and injections of CRHR2 agonist and antagonist into the LS.
While IMS activates many stress pathways, injection of the agonist should activate only the targeted CRHR2
projection neurons, which the antagonist should inhibit. Thus, comparing differences in c-fos-positive cells between
mice subjected to IMS and agonist and antagonist injections will illuminate the specific downstream pathways
modulated by the CRHR2 projection neurons. These results will contribute to a deeper understanding of the
hypothalamic neural circuitry underlying stress-induced anxiety.
Examining a Possible Role of Sensory Stimuli in the Activation of Hypothalamic Neurons Involved in
Aggression: An Extracellular Recording Approach
Clara Starkweather
Mentors: David Anderson and Ryan Remedios
The brain relies on sensory information to instruct behavior. One example of this basic principle is that mice use
pheromones and olfactory cues to direct aggressive and mating behaviors (Corridi et al., 1993; Nowell et al.,
1980). However, the circuit-level details by which the brain harnesses sensory information to promote these innate
behaviors await full elucidation. Recent work utilizing optogenetic and electrophysiological methods facilitated the
identification of cells in the ventral-medial hypothalamus ventrolateral subdivision (VMHv1) that promote
aggressive behavior upon activation (Lin et al., 2011). Specifically, a subset of cells in the mouse ventral-medial
hypothalamus exhibits increased responses as the male mouse is exposed to an intruder animal. These responses
either attenuate or intensify prior to the animal proceeding to mate with/attack the female/male intruder
respectively, raising the possibility that certain VMHv1 neurons may be differentially inhibited and activated by
sensory stimuli specific to the male intruder mouse. For this reason, we are currently asking whether VMHv1
neurons are activated by sensory stimuli, such as male major urinary protein of an intruder animal. We are
addressing this issue by recording multiunit activity in VMHv1 while presenting animals with olfactory stimuli.
Ruthenacycle Mechanism of Z-Selective Ruthenium Olefin Metathesis Catalysts
Alexandra Sullivan
Mentor: Robert H. Grubbs
The synthesis of super-fast initiating catalysts to be observed via VT NMR to confirm Z-selective ruthenium olefin
metathesis catalysts’ structure is ongoing. Additionally, 2nd Generation Piers catalyst was found to be C-H activated
in the presence of sodium pivalate. Such C-H activation of the mesityl group on Piers is a promising step towards
C-H activation on the adamantyl group in future super-fast initiating Z-selective catalysts.
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Directed Evolution of Thermostable Fungal Endoglucanases Using Random Mutagenesis and
Non-Contiguous Recombination
Sabrina I. Sun
Mentors: Frances Arnold and Devin Trudeau
The high cost of enzymatic hydrolysis hinders the feasibility of lignocellulosic biomass as an economically viable
alternative to petroleum-derived materials. A method for reducing this cost is to improve thermostability of
cellulases that break down cellulose chains into component sugars for biofuel production. Here we describe our
initial work towards exploring the evolvability and stability of endoglucanases, a class of cellulases that cleave from
internal points of the polymers, via two protein engineering techniques. Random mutagenesis has been used to
construct a library of Hypocrea jecorina Cel5a endoglucanase variants, and non-contiguous recombination will be
implemented to design a chimeric library assembled from four parent enzymes. Avicel, an industrially relevant
microcrystalline cellulose, has been identified as an effective substrate for screening these libraries for mutants
with improved thermostability. To maintain enzymatic functionality at high temperatures necessary for
lignocellulosic degradation, we aim to create a novel fungal endoglucanase that remains active up to 80C.
Image Processing Techniques for PV-OCT Imaging of Human Eye
Malvika Verma
Mentors: Scott Fraser, Jeff Fingler, and Dae Yu Kim
Phase-variance optical coherence tomography (pv-OCT) visualizes retinal vasculature non-invasively and thus has
potential in the early diagnosis of retinal vascular diseases that include diabetic retinopathy and macular
degeneration. Currently, circulation of the retina in clinical settings makes use of fundus fluorescein angiography
(FA), which involves injection of a fluorescein dye to view the perfusion into the blood stream. The injection makes
this an invasive procedure with complications like nausea and vomiting to anaphylaxis and limited axial resolution
and information regarding structural and functional consequences of vascular disease. These factors necessitate
the development of a non-invasive optical tool for early diagnosis of retinal vascular diseases. The project
concentrates on the clinical development of pv-OCT, which has the advantage of being a non-invasive, threedimensional microvascular imaging method. Developing image processing algorithms for feature extraction and
noise and shadow removal is essential to overcome the restrictions of human motion during imaging and hardware
restriction of the pv-OCT. This project will focus on improving image quality for scientists and ophthalmologists by
removing eye motion effects and artifacts and shadows, producing en face visualizations of the three-dimensional
vascular data with segmented features.
Applying a Novel General Principle for Determining an Enzyme’s Cofactor Dependency to Change the
Preference of a Variety of NADPH-Dependent Enzymes From NADPH to NADH
Ted G. Xiao
Mentors: Frances Arnold and Sabine Brinkmann-Chen
Various biotechnological processes require the usage of cofactor-dependent enzymes, which are either
nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide phosphate (NADPH) dependent. In
general, NADPH is a less favorable cofactor for biotechnological applications since it is less abundant in the cell and
more expensive than NADH. Based on analyses of thousands of protein crystal structures co-crystallized with their
cofactors, we suspected that previously proposed determinants for cofactor preference need revision, suggesting a
novel general principle for cofactor binding. If demonstrated to be applicable for various enzymes, this principle
could be developed into a powerful tool for a great variety of biotechnological processes currently using NADPHdependent enzymes. Putting our hypothesis to test, we here demonstrate how to identify the key cofactorpreference-determining amino acid residues with subsequent mutation to change the cofactor preference of the
enzymes. We thus generated, expressed, and characterized variants of two NADPH-dependent enzymes, alcohol
dehydrogenase 6 of S. cerevisiae and glyoxylate reductase of A. thaliana. We used the ratios of catalytic
efficiencyNADH/catalytic efficiencyNADPH to describe the cofactor preference of our test enzymes.
Multiplexed Detection of Infectious Diseases Using DNA Hybridization in a Microfluidic Chip Setting
Conway Xu
Mentors: Axel Scherer, David Baltimore, George Maltezos, and Devdoot Majumdar
Infectious diseases are prevalent throughout the world and are especially problematic in developing countries.
Specifically, the lack of practical diagnostic tests hinders the treatment of disease in these settings. Without quick
and effective diagnostic tests, healthcare providers in these countries cannot efficiently identify those who are in
need of treatment. While diagnostic machines do currently exist on the market, they are too expensive and slow to
be practical in resource challenged settings. The goal of this project is to optimize the detection of amplicon using
DNA hybridization as a part of the overarching goal of designing a “lab on chip” device which will present a cheaper
and more practical diagnostic tool for resource challenged settings. Microfluidic chips were fabricated because they
offer a protected setting to conduct our hybridization studies in. We then tested several cross linkers to bind
oligonucleotide probes to amino silanized glass. Once the oligonucleotide probes were effectively attached to the
glass surface using the cross linker glutaraldehyde, we proceeded to optimize hybridization between our
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oligonucleotide probes and complementary oligonucleotides with attached fluorophores. After hybridization was
optimized, our microfluidic chip was able to utilize DNA hybridization to specifically detect for double stranded
amplicon sequences.
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LIGO
THE LASER INTERFEROMETER
GRAVITATIONAL-WAVE OBSERVATORY
L
I
G
O
Development of a Cryogenic Silicon Reference Cavity for Laser Frequency Stabilisation
Matthew Arran
Mentors: Rana Adhikari and David Yeaton-Massey
Thermal noise is a major source of frequency variation in lasers stabilised by an external reference cavity. Among
other effects, this is a significant limit on the sensitivity of gravitational wave detectors based on laser
interferometry. Considerable reductions in thermal noise may theoretically be achieved by working at cryogenic
temperatures, due to the reduction of Brownian noise; and near zeros of the coefficient of thermal expansion of the
cavity spacer, due to reduction of thermoelastic noise. Progress was made in developing an optical system with a
laser beam stabilised by a cryogenic fused silica reference cavity, by the attachment of heaters and temperature
sensors, trial cooldowns of the system, and analysis of the thermal system. Transfer functions for the propagation
of temperature perturbations were found analytically and proved, given the appropriate choice of parameters, to
correspond closely to measurements of step responses. Further work will include the design of heater control
systems and analysis of the effect of temperature fluctuations on beam frequency.
Investigating Crackle Noise in Metal Blade Springs
Igal Bucay
Mentors: Rana Adhikari, Jan Harms, and Eric Quintero
Systems crackle when exposed to slowly changing external conditions by responding with impulsive, discrete
events. Crackling (or crackle noise) is the result of crystal domains changing or moving with respect to one
another—the displacement analogy of Barkhausen noise. Some components in the mirror suspension system in
Advanced LIGO (i.e. the cables and metal blade springs) are susceptible to crackle noise, which, in turn, may
interfere with the detection of gravitational waves. In a lab experiment, crackle noise in blade springs will be
quantified using a simple Michelson interferometer where the mirrors at the end of each arm are suspended from a
blade spring. The interferometer sits on top of a seismic isolation stack composed of two steel plates with rubber
legs, all held within a steel chamber which can currently be pumped down to 800 mTorr. When the springs are
driven at a low frequency of 0.1 Hz, any change in the signal will ideally be due to crackle noise. So far, we have
measured the time constants and eigenfrequencies of the two springs, as well as other sources of noise which may
interfere with our measurements, such as seismic noise, laser shot noise, and electrical noise. We are currently in
the process of calculating a noise budget, after which we will collect crackle noise data. At that point, we will
calculate the characteristic coefficients that describe the relationship between the low frequency driving force and
crackle noise, compare it to the current aLIGO noise budget and determine if crackle noise is a significant concern
for the aLIGO detectors.
Visualization of Images Distorted by Black Holes
Darius Bunandar
Mentors: Mark Scheel and Nick Taylor
One of the most promising sources of gravitational waves for potential detection by LIGO is the inspiral and merger
of two black holes. In an effort to aid LIGO data analysis, the Caltech-Cornell SXS collaboration is numerically
solving Einstein's equations for a number of such binary black hole systems with varying mass ratios and spins. In
this project, we investigate a novel way to visualize the structure of such a numerical solution by producing images
of a distorted stellar background in the vicinity of black holes. This involves following the paths of photons through
regions of strong gravitational field—produced by the black holes—from the observer to the light sources at distant
locations in the background. We present some images and movies of the distorted stellar background; among
these are some of the world's first distorted images of merging binary black holes.
The Role of Small Robotic Telescopes in Multimessenger Astronomy With Advanced Gravitational Wave
Detectors
Cutter Coryell
Mentor: Stephen Privitera
Maximizing the scientific returns from observations of compact binary coalescence requires joint observation of
gravitational waves and counterpart electromagnetic radiation. Small, robotic, rapid-response optical telescopes
such as ROTSE III and TAROT were used to follow up gravitational wave candidates in the most recent joint LIGOVirgo science run. We explore the role of such telescopes in following up gravitational wave candidates in the
advanced detector era.
Tools to Analyze LIGO Trend Data
Alexandra Danilet
Mentors: Gregory Mendell and Richard Savage
The initial Laser Interferometer Gravitational Wave Observatory (LIGO) in Hanford, WA produced over 13,000
channels of data, collected at typical rates of 1024 to 16384 sample per second during the last Science Run (S6),
from July 2009 to October 2010. Trends in LIGO data (for example, the mean value of channel computed every
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minute) have been found useful in Photon Calibration studies and Radio Frequency Amplitude Modulation studies,
and can be used to determine correlations between various channels. The motivation of this project is to develop
tools with which data from LIGO can more easily be gathered, formed into new trends, and then analyzed. Code
was written in Matlab, html, php, tcl and condor to create a web user-interface through which researchers may
enter the state vector, channels, duration and functions to be performed on the data to obtain an output file with
the GPS time, the state of the detector and their requested calculations. We also plot the RFAM over S6 for times
when the interferometer was in full science mode and look for trends with the hope of determining whether a
correlation between RFAM and detector sensitivity exists.
Rapid Sky Localization of Binary Inspiral Sources
Ryan Darragh
Mentors: Larry Price, Leo Singer, and Stephen Privitera
Sky localization of gravitational wave sources is done using the time of arrival and signal to noise ratio in each
detector. Taking a Bayesian approach requires creating a likelihood function and choosing priors. Our likelihood
function tells us the probability of our parameters given our signal, and our priors express our beliefs about a given
parameter. We investigate three different distance priors, uniform in volume, uniform in log distance and another
astrophysically motivated prior based on rates of coalescence. We determine how sensitive each prior is to our
parameters and choose the best one to be used in the sky localization procedure.
Detector Characterization Tools for Interferometer Commissioners
Elizabeth Davison
Mentors: Jameson Rollins and Rana Adhikari
The Laser Interferometer Gravitational-Wave Observatory (LIGO) detectors are dual-recycling interferometers with
four kilometer Fabry-Pérot arm cavities. Complex control and data acquisition systems for these instruments are
prototyped at the 40 meter interferometer on the Caltech campus. With the development of increasingly intricate
subsystems, it has become important for the commissioners working at the 40 meter lab to have an accessible,
effective overview of the instrument's behavior. This project required consultation with each scientist and an
overall understanding of the interferometer in order to refine the considerable amount of information from the data
channels into useful plots. Code that had been used for a full-scale interferometer website was modified to suit the
40 meter lab's objectives. The result of this project is a regularly updated website that contains calibrated plots of
relevant channels and images of monitoring screens. It can be further adapted by the scientists at the 40 meter lab
as the need arises and will be a helpful and informative tool.
Directional Gravitational Wave Search
Nick Eminizer
Mentor: Peter Kalmus
Data from two or more gravitational wave detectors contain many coincident glitches: short-duration blips in the
data. We tend to assume these are all from coincident and independent noise events in the individual detectors,
but some of them may actually be gravitational wave signals. Building on past searches, we will develop and refine
a method that associates a sky position with each significant blip, and then we will look for sky directions with a
statistical excess of these blips. The goal is to search the whole sky over long time periods in order to discover
gravitational wave signals from repeating sources. We will characterize the sensitivity of our search via simulated
waveforms that echo plausible astrophysical models and correlate it to simulated point sources and regional
sources, as well as known bright matter.
Simulating the Response of LIGO Data Analysis Pipelines to a Population of Binary Black Hole Mergers
Irina Ene
Mentor: Alan Weinstein
I present an analysis of the response of the LIGO data analysis pipelines to a simulated population of gravitational
wave sources consisting of binary black hole mergers. The analysis determines the detectability of the
astrophysical sources as a function of source parameters (including component masses, sky location, and orbit
orientation) and the detector network. Monte Carlo simulations are used to generate a population of astrophysical
sources that are uniformly distributed across the sky and to map the response of the detectors across this
parameter space. The detectability of each source is computed by determining the maximum distance at which the
source could be located such that both single detector and detector network signal-to-noise ratios (SNR) are above
certain thresholds.
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Low-Noise Seismic Sensing and Actuation
Yaakov Fein
Mentors: Jenne Driggers and Rana Adhikari
Seismic noise is a significant noise source that limits the low frequency range of all terrestrial gravitational wave
detectors. At the 40m Prototype Lab at Caltech, the STACIS 2000 active isolation system was implemented in order
to reduce seismic noise, but proved ineffective at low frequencies. There is a dual motivation for further
investigation of the STACIS: First, implementing active seismic isolation will push down the ever-present seismic
wall and help the interferometer maintain lock. Second, the STACIS can be used as an actuation system to test and
implement adaptive feed forward filtering techniques developed at the 40m Lab.
I have investigated ways to modify the STACIS to provide better isolation at low frequencies. Replacing the
STACIS’ internal sensors with higher quality sensors shows promise, but further work is needed to determine the
extent of the benefit. Other options, such as modifying the STACIS sensors, also require further investigation. To
use the STACIS as actuators, I have investigated two possible input points through which the STACIS can be
actuated with an external signal. These points can be used for external actuation as long as the open loop gain of
the STACIS is known accurately, because that is what determines how an input signal will be converted to motion.
Tools for Collaborative Electromagnetic Follow-Up of Gravitational Wave Candidates
Tobias Fleming
Mentor: Roy Williams
This project aims to provide tools for a collaborative follow-up after the detection of gravitational waves with
electromagnetic telescopes. While the similar project BAYESTAR aims for an optimal follow-up with maximally
coordinated observatories, the object of this approach is to allow observatories to react quickly to LIGO
gravitational wave events on their own terms. The tools provided use generated probability maps or skymaps in
creation of observing plans for available telescopes and known data. This pragmatic and dynamic processing of
available information will enable available observatories and their operators to process detection events
communally, while still allowing a coordinated gathering of valuable scientific data.
Spin Alignment Effects in Black Hole Binaries
Davide Gerosa
Mentors: Yanbei Chen and Emanuele Berti
We use Monte Carlo simulations to investigate the spin alignment of black hole binaries when they enter the
Advanced LIGO detection band. Our simulations start at large separation, where the post-Newtonian (PN)
approximation (a perturbative expansion of the Einstein equations in the ratio v/c, where v is the orbital velocity
and c is the speed of light) is valid. We followed the evolution of a statistical sample of binaries by numerically
evolving the PN equations of motion. We first tested our code by reproducing results in the literature, and then we
add high-order PN corrections recently computed by Marc Favata. Stellar evolution calculations hint that
comparable-mass binaries where both spins have the same misalignment angle with respect to the orbital angular
momentum may be likely, so we focused on these configurations to initialize our Monte Carlo simulations. Our goal
is to understand if the existence of PN resonances, that was originally pointed out by Schnittman, can simplify the
construction of matched-filtering templates in binary black hole data analysis.
Real-Time Calibration of Gravitational-Wave Strain
Eric R. Hendries
Mentors: Jameson Rollins and Rana Adhikari
The Laser Interferometer Gravitational-wave Observatory (LIGO) uses a Fabry-Perot Michelson interferometer to
measure the change in length between two test masses due to an incident gravitational-wave strain. Calibration of
LIGO is necessary for a meaningful physical analysis of strains and their sources. Traditional calibration methods
used multiple measurements of individual transfer functions of elements within the differential arm length control
loop. A real-time calibration system has the advantage of taking the current state of the interferometer’s timevarying components, allowing for a more accurate calibration and smaller errors. Moreover, immediately having
data in calibrated units will allow for quick identification of the type of gravitational-wave event, reconstruction of
the source position, and notification of follow-up telescopes. We begin by simulating the control loop at the LIGO
40 meter prototype. This simulation then guides the real-time model that we implement in the digital control
system to calibrate the interferometer while in operation.
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A Generalized Harmonic Formulation of Modified Gravity With Applications to Black Hole Inspirals
Matthew Heydeman
Mentors: Yanbei Chen and Bela Szilagyi
In this paper, our goal is to extend the Generalized Harmonic form of the Einstein field equations of General
Relativity to a modified system describing effective theories of gravitation such as those arising as classical limits of
string theory and loop quantum gravity. Such classical theories contain a power series of higher order curvature
invariants that deviate from the Hilbert action, and generally the equations of motion of the metric tensor become
fourth or higher order differential equations. These equations have some solutions that are high frequency and
non-causal which makes the system appear ill-posed. Such apparent ill-posedness is a challenge for the
Generalized Harmonic (GH) numerical evolution of black hole inspiral solutions in these modified theories.
However, since these are classical limits of more fundamental quantum theories, these solutions are not expected
to be physical because they involve lengthscales over which the classical theory breaks down. In formulating our
modified Generalized Harmonic system we defined auxiliary fields to reduce the higher order system to a first order
one. The dynamics of the newly introduced fields contain terms which temporally average over the higher
derivative modes so that only the physical long wavelength classical modes appear in the solutions. In certain
cases we have made progress in demonstrating that the system is hyperbolic and extract the characteristic fields
and velocities, but our goal is to generalize our current results to include up to fourth order or higher derivatives of
the metric tensor. In future work we will apply this GH form of the modified theories to black hole inspiral
simulations and observe how the gravitational wave profile is modified by the effective quantum gravity theories.
Distinguishing Gravitational Wave Polarizations in Continuous Waves From Spinning Neutron Stars
Maximiliano Isi
Mentor: Alan Weinstein
According to the theory of General Relativity, gravitational waves (GWs) can present only two polarizations, both of
them transverse to the direction of wave propagation. This is generally taken as an assumption in the models and
templates used in the simulation and searches of gravitational waves. However, Einstein’s theory has never been
tested in the highly dynamical regime of GWs and alternative theories allow for the existence of a maximum of
three extra polarizations. In light of this, we develop methods to identify signals containing all such polarizations in
continuous GWs emitted by spinning neutron stars –the Crab pulsar in particular. We analyze the extent to which
extra polarizations can be detected, making use of simulated signals and preliminary searches in actual LIGO data.
Camera Set-Up for Laser Beam Monitoring
Vidisha Jain
Mentors: Valery Frolov and Rana Adhikari
LIGO (Laser Interferometer Gravitational Wave Observatory) is the research hub aiming at gravitational wave
detection, for which, large Michelson interferometer is used which has laser at its core. The laser beam travel
towards the beam splitter, gets split, approaches the two mirrors placed at perpendicular direction, gets reflected
back and then interfere. Due to the various noises, angular motion is induced in the laser which produces motion in
beam spot. Hence beam spot motion is monitored which can be used to control the angular motion of the arm
cavities and the laser. Camera is set up which takes continuous images of the beam spot. Images are analyzed and
processed to get the beam position. For a continuous set of readings, fluctuations in beam spot are plotted and the
amplitude spectrum obtained which is used to see the various noise levels. To get rid of the maximum noises, Dark
frame is subtracted from all the grabbed images and camera is properly calibrated. Camera characteristics, such
as, linearity and different camera noises are analyzed. This set up can then be used to monitor the angular motion
of laser.
A Model-Independent Test of General Relativity Using Wave Signals of Binary Coalescence
Joon Sik Kim
Mentor: Parameswaran Ajith
Gravitational-wave (GW) observations of coalescing compact binaries (CBCs) are excellent testing grounds of
general relativity (GR). This project aims to develop a model-independent test of GR using such observations.
Since the expected gravitational waveforms from CBCs are well modeled in GR, if we subtract the modeled GW
signal from the data, the residual should be consistent with the detector noise. If the residual is inconsistent with
the detector noise, this would imply that the true theory might be different from GR. The “residual” from multiple
observations can be stacked to enhance the sensitivity of such a test. A chi-square test or Kolmogorov-Smirnov
test may be used to check the consistency between the residual and the detector noise.
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Studying Dynamics of Macroscopic Quantum Entanglement With Future Advanced Gravitational-Wave
Detectors
Oleg Kiriukhin
Mentors: Yanbei Chen and Haixing Miao
Future advanced gravitational-wave detectors will reach such high sensitivity that they possibly allow us to study
quantum behaviors of the macroscopic test masses. One interesting issue, which is also of fundamental
importance, is the observation of the Einstein-Podolsky-Rosen-type of quantum entanglement among macroscopic
objects, for example, the kilogramscale test masses. We explore quantum dynamics of entanglement and study the
possibility of observing it with future advanced gravitational-wave detectors or prototypes. In particular, we
theoretically evaluate the characteristic lifetime of macroscopic entangled states under thermal decoherence in
realistic setups and analyze its dependence on the different parameters of the system.
In this work we consider a system being under the continuous measurements and study the dynamics of quantum
entanglement for the conditional quantum state. In order to obtain the conditional expectations we apply filtering
approach which is a technique of minimization of error dispersion. Filter gives the best possible estimation of the
variable by measurements with incomplete information and noise in the system being under the disturbance of an
uncontrolled stochastic process.
Gravitational Waves From Core-Collapse Supernovae
Hannah E. Klion
Mentors: Christian Ott, Peter Kalmus, and Ernazar Abdikamalov
It was recently discovered that during the iron core collapse of rapidly rotating stars, there are correlated
oscillations at 700-800 Hz in the central density of the star and in the neutrino and gravitational wave signals. It
was hypothesized that these oscillations were due to quadrupolar excitations of the nascent neutron star. We aim
to study this hypothesis by determining the range of initial angular velocities at which these oscillations occur, and
characterizing the oscillations. To do so, we have simulated the iron core collapse of a 12 M⊙ progenitor. To study
rotation effects, we have applied one of ten initial central angular velocities to each model. These angular velocities
ranged from 4.5 to 9.5 rad s-1. We have used a 3-D hydrodynamic code employing octant symmetry. Oscillations
between 700-800 Hz have been found to occur in models with initial angular velocities ranging from 4.5 rad s-1 to
at least 8.5 rad s-1. Models with initial angular velocities greater than 8.5 rad s-1 did not collapse due to centrifugal
support for the infalling matter.
Adaptive Quantum Measurements in Future Gravitational-Wave Detectors
Mikhail Korobko
Mentors: Yanbei Chen and Haixing Miao
Advanced gravitational-wave detectors, such as Advanced LIGO, Advanced VIRGO, LCGT, are expected to be limited
by fundamental quantum noise around the most sensitive frequency band. To further improve the detector
sensitivity, various approaches based upon modifying the input or output optics of the interferometer have been
proposed in the community. They usually require additional low-loss optical cavities to filter the input or the output.
In our work we propose a new alternative type of scheme—adaptive linear measurements—that has not been
explored in the community yet. This approach uses the time-dependent phase of the homodyne detector which
changes depending on the results of the measurement.
Adaptive measurements provide new approach to the measurement of signal with unknown shape and arrival time,
that makes possible detection the gravitational waves from different types of sources without any change in
experimental scheme. In this work we propose the general scheme for such kind of measurements and consider
the special case of detecting the impulse force with unknown amplitude and arrival time.
Modeling the Effect of aLIGO Thermal Compensation on Beam Scatter
Alexander Mauney
Mentors: Aidan Brooks and Rijuparna Chakraborty
A major problem in aLIGO is thermal lensing caused by the absorption of power in the testmass. In order to
compensate for this a thermal compensation system (TCS) is used which uses other heating systems to even out
the overall thermal effects. Understanding how the different distortions used in TCS impact the signal that is
generated further down the beam line is crucial for the alignment of other systems, such as the output mode
cleaner (OMC). In this project we use numerical models to simulate small differences in thermal compensation
between beam lines and the impact they have on the output signal.
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Detection of Short Gamma-Ray Bursts in Coincidence With Gravitational Waves
David Miller
Mentor: Leo Singer
The detection of gravitational waves from compact binary coalescence mergers are likely when the Advanced
LIGO/Virgo detector network goes online as early as 2015. To maximize the science returns, an electromagnetic
counterpart must be detected. I examine the ability of present and future high-energy telescopes to detect short
gamma-ray bursts in coincidence with gravitational wave signals.
Comparing Numerical Relativity and Black Hole Perturbation Waveforms for Intermediate Mass Ratio
Black Hole Binaries
Derek S. Nelson
Mentors: Christian Ott and Christian Reisswig
Advanced gravitational-wave observatories will soon be capable of detecting cosmic phenomena at both lower and
higher frequencies than previous observatory specifications. It is essential to similarly broaden data analysis
strategies and, in particular, improve the bank of template waveforms used to search for compact binary
coalescence at the lower frequency end of the Advanced LIGO sensitivity band. Although post-Newtonian
waveforms are the foundation for current searches at mass ratios near unity, it is unclear whether or not they are
well suited to lower frequency Intermediate Mass Ratio Inspirals (IMRIs). As a possible substitute, the black hole
perturbation waveform generation technique commonly referred to as the Numerical Kludge method is
implemented and compared to waveforms created using full Numerical Relativity. The relative agreements between
the modal decompositions of each waveform are analyzed to determine whether the Numerical Kludge method is a
promising template generation technique for implementation by future Advanced LIGO pipelines.
Exploring the Signal Space of Spinning Compact Binary Coalescence Waveforms
Afina Neunzert
Mentors: Nickolas Fotopoulos and P. Ajith
Gravitational wave signals from the coalescence of compact binary systems (CBCs) are expected to be detectable
by Advanced LIGO. The LIGO CBC search pipeline requires the use of template banks, or families of expected
waveforms, against which to perform matched filter calculations and thereby recover signals. Few previous
template banks have attempted to incorporate spin and precession effects, leading to an overly narrow searchable
parameter space. This project explores and characterizes the signal space of spinning CBCs using a stochastic bank
placement algorithm and several types of waveform approximant, including a reduced-spin and a precessing
model. Preliminary results demonstrate the effectiveness of the reduced-spin template bank in detecting precessing
waveforms, and lend insight into the bank parameter ranges necessary to optimize detection.
Machine Learning Techniques for Seismic Noise Classification and Interferometer Control Systems
Maria Okounkova
Mentors: Denis Martynov, Jenne Driggers, and Rana Adhikari
One of the most significant low-frequency noise sources in the Laser Interferometer Gravitational Wave
Observatory (LIGO) experiment is seismic noise. While 40 Meter Prototype Lab has noise cancellation filters in
place for constant seismic noise, transient seismic disturbances, such as earthquakes, vehicles, and other
unforeseen events, which generate noise in the interferometer signals, require adaptive filtering to be removed.
This project involved gathering training data of seismic disturbances from known sources at the 40 Meter Lab and
applying various machine learning algorithms for online classification, so that a noise source can be identified in
real time, and a specific filter for the noise source may be applied.
Machine learning techniques have other potential applications to the LIGO project as well, including applications to
interferometer control systems. Thus, I experimented with using recurrent neural networks as adaptive control
systems in simulations of noisy dynamic systems in order to assess the feasibility of training a neural network to
internally approximate their dynamics. With rigorous training, such a system could potentially be implemented in
the 40 Meter Lab to control the interferometer test masses.
Investigating Electromagnetic Interference in the Control Electronics of the Advanced LIGO Detectors
Mayowa Omokanwaye
Mentor: Joseph Betzweiser
The aim of this project is to investigate the installed electronics for the LIGO interferometers and examine their
ability to cross talk amongst systems as well as their sensitivity to external electromagnetic fields. In order to
determine if there was any electromagnetic interference in the electronic signals, a magnetometer was placed in
various locations in LIGO’s CDS (Control and Data Systems) Electronics Room. Power spectra for the magnetic field
measured by the magnetometer were then analyzed to determine at which frequencies there were strong peaks in
the magnetic field. These peaks were compared to peaks in the power spectra for various electronic signals. High
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coherence between the magnetic field and the electronic signals suggests that the magnetic field is inducing noise
in the electronics. The strongest measured source of noise is a temporary power supply which will not be a part of
the LIGO’s final setup.
Thermal Noise in Ultra-Stable Fabry-Perot Cavities
Sarah Terry
Mentors: Tara Chalermsongsak and Rana Adhikari
According to calculations, Coating Brownian Noise dooms Advanced LIGO because it limits measurement precision.
The Coating Thermal Noise Measurement experiment aims to measure this noise source at the frequency range of
interest (50Hz - 300Hz). My objective is to further complete, understand the noise budget for the beat
measurement, as well as minimize the technical noise. Further completing the noise budget includes obtaining the
frequency noise due to power fluctuations of the laser (RIN induced noise), as well as finding the frequency noise
due to the effects of acceleration on the cavity. Understanding the results of the noise budget involves identifying
the sources of the different components of noise budget. Minimizing the technical noise consists of designing an
Intensity Stabilization Servo (ISS) to reduce the frequency noise due to power fluctuations, and fixing the cavity
supports to minimize mirror tilt and frequency noise due to acceleration acting on the cavity. The ISS will be
approached by first identifying the RIN induced noise, and then creating a servo with a transfer function
appropriate to suppress the noise to about 10-8 [1/\sqrt{Hz}] at 100Hz. The length noise due to acceleration on
the cavity will be modeled using COMSOL Multiphysics Software. Understanding and optimizing the noise budget
will allow for a more precise measurement on the extent to which Coating Thermal Noise effects the measurements
made by the Advanced LIGO interferometers.
Setting Up the Physical Environment Monitor System for Advanced LIGO
Maggie Tse
Mentors: Robert Schofield and Daniel Sigg
The Laser Interferometer Gravitational-Wave Observatory (LIGO) makes use of an interferometer that is sensitive
to arm-length changes of 10^-18m. Because of this sensitivity, environmental noise sources can make unwanted
contributions to the gravitational-wave channel. Through a network of strategically placed sensors, the Physical
Environment Monitor (PEM) system can be used to identify, characterize, and monitor environmental noise sources
as well as coupling mechanisms and coupling sites through which environmental influences enter the gravitationalwave channel. The upgrade from initial LIGO (iLIGO) to advanced LIGO (aLIGO) will include an upgrade of the PEM
system, as well as the introduction of a new system for locking the interferometer, the Arm Length Stabilization
(ALS) system. We investigated performance issues found in the iLIGO PEM design and propose a new scheme for
mounting accelerometers to optical tables using acrylic cubes and UV-curing epoxy. We are also providing support
for the single-arm test stage of aLIGO commissioning, whose purpose is to investigate the performance of the ALS,
by using PEM sensors to identify noise sources contaminating the signals the recently installed optical levers and
investigate sources of vibration near the reference cavity used to lock the single-arm cavity. We will also measure
environmental coupling to the single-arm test signal, in particular because aLIGO also introduces a new seismic
isolation and suspension system that will be tested for the first time during the single-arm test. In addition, data
from the aLIGO PEM system will be made easily accessible through a web interface we developed that allows users
to search a database of PEM channels and look up calibration factors, sensor locations, and other information.
Modeling Efficiency of the Global Gravitational Wave Detector Network
Justin Wagner
Mentors: Nickolas Fotopoulos and Alan Jay Weinstein
Assessments of efficiency of the worldwide gravitational wave detector network are needed to draw conclusions
about sensitive distance and the distribution of astrophysical phenomena. Current techniques used to find efficiency
involve simulations of large numbers of sources distributed throughout a volume of space. Due to the high
computational cost of processing these simulations, statistically strong declarations about efficiency consume
computation time that will not be available during online analysis of aLIGO data. A simple model of detectors and
the data analysis pipeline would allow vastly cheaper simulations.
Real-Time Simulation of a Suspended Cavity With the Advanced LIGO Digital Controls System
Alexandra A. Zhdanova
Mentors: Jamie Rollins and Rana Adhikari
An integral part of LIGO’s interferometers are the Fabry-Perot cavities in the arms. Modeling them can show us
how well we understand the noise in addition to serving as a test of the control system used to keep the
interferometer in resonance. While time-domain simulations of the cavity have been done, a real-time simulation
developed with the Real-Time Code Generator would provide a better comparison point for the noise while
accurately modeling the cavity response. This presentation outlines such a real-time simulation, as well as a
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comparison between the results of the “fake” (or simulated) cavity and the “real” cavity. The closer these results
are to each other, the more successful we count our simulation as an accurate representation of the real-life noise
and mechanics in a Fabry-Perot cavity.
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NASA/JPL Programs
PGGURP
Planetary Geology and Geophysics
Undergraduate Research Program
SPACE GRANT
The National Space Grant College
and Fellowship Program
USRP
Undergraduate Student Research Program
JPLSIP
JPL Summer Internship Program
N
A
S
A
Amorphous Metals for Use in Long-Life, Low-Temperature Gearboxes
Laura Andersen
Mentor: Douglas Hofmann
Electromechanical gearboxes used in planetary vehicles and sample-handling systems are required to endure
extreme environments for extended lifetimes. Actuators currently in use require grease lubrication to keep
mechanical wear to an acceptable level when operated below -55 C. Lubrication can only be achieved with external
heating which translates to a heavy drain on the system and greatly affects the overall science return. The
proposed amorphous metal (AM) materials exhibit exceptional wear resistance and good retention of mechanical
properties at low temperatures. Implementing AMs into planetary gearboxes will increase wear resistance and
potentially eliminate the need for wet lubrication and heating. The scope of this preliminary work is to identify the
optimal composition of an AM in order to achieve maximum wear performance. Each candidate composition was
suction cast into a circular plate of a 1 inch diameter and 3 mm thickness. Samples were evaluated using pin-ondisk testing, Vicker’s hardness, profilometry and ultrasonic measurements. Through intensive investigation, the
critical hardness, fracture toughness and shear modulus for minimum wear loss is outlined. From these results,
relations between explicitly measured mechanical properties and the wear resistance for AMs are formulated.
Factors Contributing to Unsuccessful Re-Proposed Missions
Gillian R. Anteau
Mentor: Lynne Cooper
JPL often re-proposes unselected missions following additional technology advancement and/or concept
development, with varying degrees of success. This research provides insight into how changes in the mission
concept over time affect the evaluation of the re-proposed mission. It presents a case study comparing an original
mission to one re-proposed following a multi-year technology development effort. The two mission concepts are
analyzed in eight critical areas (science goals, science objectives, technology maturity, mission design, experiment
design, instrumentation, cost, and mission schedule) and assessed relative to sponsor feedback to gain insight into
the factors that affected perceptions of risk and value.
Development of an iOS Interface for the Mars Science Laboratory Mobility Systems Testbed
Riley A. Avron
Mentors: Jaret B. Matthews, Matthew C. Heverly, and Justin Y. Lin
The Mobility Systems Testbed, known as Scarecrow, is a tool used to characterize the capabilities of the Curiosity
rover over a wide range of terrain types. Since its creation, Scarecrow had implemented a rudimentary
communication protocol through a secure shell, which, while operable, was unwieldy and inefficient. To address this
issue, we aimed to develop an interface for iPhone and iPad devices which would allow the user to interact with the
vehicle more quickly and in a more natural and consistent manner. The result of this endeavor is an application
which includes features such as visual path prediction, realtime vehicle orientation displays and intelligent
command completion. This new interface offers the power of high-level constructs combined with the finesse of
low-level control, packaged for the ubiquitous and convenient iOS operating system. The overwhelmingly positive
response to the application from Scarecrow’s primary users leads us to believe that there is great potential for
mobile platforms to be used as powerful robot interfaces.
Identifying Key Factors Affecting Evaluation of Proposed Spectrometers
Elizabeth E. Baker
Mentor: Lynne Cooper
Over the past ten years, several types of spectrometers have been proposed for NASA missions, e.g. mass, image,
laser, and neutron spectrometers. Each type of spectrometer addresses different proposed science objectives by,
for example, measuring composition of a target body, its atmosphere, or asteroid dust. The central focus of this
work is to identify factors that affect the successful inclusion of spectrometers in advanced mission concepts and
proposals. Using archival data, this research first identifies systemic issues in the use of spectrometers in JPL
mission concepts. Second, it evaluates specific families of spectrometer technology to identify factors influencing
perceptions of risk. Finally, it develops a set of guidelines for the presentation of spectrometer information in
proposals based on type of spectrometer, type of mission, and target body.
A Flexible Quasi-Optical Input System for a Submillimeter Multi-Object Spectrometer
Guadalupe Banales
Mentors: Dave Braun, Michael D. Seiffert, Charlie Fisher, and Joel Kaluzny
Measuring the red shift of galaxies is a valuable technique for studying dark matter and dark energy. However,
dust associated with many galaxies cause half the starlight to be lost when it reaches modern telescopes. Existing
receivers cannot efficiently capture this light nor capture multiple targets due to their sparse distribution in the sky.
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However, these galaxies are observable at submillimeter wavelengths. A proposed solution for performing efficient
redshift surveys of galaxies shrouded in dust is to build an array of multi-object spectrometers (MOS) operating at
submillimeter wavelengths.
Assessing the feasibility of such a system requires a conceptual design and a prototype for the input optical system
for MOS. Efforts this summer were dedicated to developing a design of multiple receiver mechanisms to steer the
light from the array of targets into the array of cryogenically cooled submillimeter spectrometer receivers. To
choose the most cost effective and compact design that met all the requirements, several different approaches
were investigated and 3D CAD models were generated. The success of one of these approaches will allow the
observation of multiple submillimeter galaxies at a one telescope pointing, which would enable scientist to create
surveys, use less telescope time, and further their science.
Incorporating Plant Phenology Dynamics in a Biophysical Canopy Model
Raquel Barata
Mentor: Darren Drewry
The Multi-Layer Canopy Model (MLCan) is a vegetation model created to capture plant responses to environmental
change. The model vertically resolves carbon uptake, water vapor and energy exchange at each canopy level by
coupling photosynthesis, stomatal conductance and leaf energy balance. The model is forced by incoming
shortwave and longwave radiation, as well as near-surface meteorological conditions. The original formulation of
MLCan utilized canopy structural traits derived from observations. This project aims to incorporate a plant
phenology scheme within MLCan allowing these structural traits to vary dynamically. In the plant phenology
scheme implemented here, plant growth is dependent on environmental conditions such as air temperature and soil
moisture. The scheme includes functionality that models plant germination, growth, and senescence. These growth
stages dictate the variation in six different vegetative carbon pools: storage, leaves, stem, course roots, fine roots,
and reproductive. The magnitudes of these carbon pools determine land surface parameters such as leaf area
index, canopy height, rooting depth and root water uptake capacity. Coupling this phenology scheme with MLCan
allows for a more flexible representation of the structure and function of vegetation as it responds to changing
environmental conditions.
ATHLETE: Anchoring Mechanism Modification and Remote Seismic Transducer Development
Joseph R. Bartels
Mentor: Matthew Frost
The All Terrain Hex Limbed Extra Terrestrial Explorer (ATHLETE) is a wheel-on-limb rover developed to support the
exploration of the Moon, Mars, and other near earth objects such as asteroids. To operate in the reduced gravity
environment of an asteroid, ATHLETE must be able to anchor to the ground to keep from drifting off the surface.
An anchoring mechanism has been built to interface with the tool adapter on ATHLETE’s wheels and when powered
is capable of securing the rover to the surface. This mechanism was originally built stronger than required, so finite
element software was used to redesign several components and reduce their weight by over 50%. ATHLETE is also
an excellent platform for scientific studies. One of the project’s long term goals is to demonstrate the capability of
extraterrestrial subterranean mapping and soil composition identification with the ATHLETE rover. To perform this
study, ATHLETE induces a shockwave into the ground and remotely placed sensors measure and record the seismic
activity. By using a geophone and microcontroller equipped with a wireless radio, a remote seismic transducer was
built to collect and wirelessly transmit data to a central database on ATHLETE to be collected for later analysis.
Dust Transport Over Kuwait and the Arabian Peninsula
Carly A. Baumann
Mentors: Olga Kalashnikova and Michael Garay
Satellite images, particularly those showing significant amounts of dust in the atmosphere, are examined to find
the source of dust events, determine meteorological parameters for a severe versus insignificant dust event, and
determine velocity, direction, and height of dust storms to see what other regions are affected.
Linkages between dust plume information at the source and dust properties in downwind transport regions were
evaluated using the MINX software application. Images from the MISR instrument aboard NASA’s Terra satellite
were brought into MINX and height and velocity measurements were obtained. In order to verify the data retrieved
by MINX, other satellites and surface observations were checked for consistency.
Dust events travelling over Kuwait and the Arabian Peninsula have been tracked back to Syria. When winds
become primarily northwesterly and increase to 10 m/s and higher, a severe dust event is likely to occur.
Depending on the season, the height of the dust relates to the depth of the atmospheric boundary layer, which
ranged from 2 km in the spring to 5 km in the summer.
As severity of dust storms may increase in the future, the people of Kuwait will be further affected by health
hazards and low visibility.
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Correlations Between Technical Performance and Cost Growth: A Case Study Using Technical
Complexity
Keith Becker
Mentors: Kevin Rice and Eric Kwan
Flight Projects historically exceed the available budgetary funds allocated by NASA HQ. This group research project
investigates historical data from recent JPL and non-JPL Flight Projects to determine trends and correlations
between technical and programmatic parameters to predict cost growth. Each project is analyzed using 3 data
sets: technical complexity, subcontractor performance and schedule slip. My focus is the technical complexity data
set. Activities in this analysis include: pointing accuracy, instrument count, redundancy level and mission life, along
with 52 additional parameters. Once all technical and cost data is collected a numerical complexity matrix is
created based on technical performance, followed by regression analysis and modeling to establish trends. It is
expected that certain aspects of technical performance parameters will lend themselves to be more accurate
predictors of cost growth than others. As such, a weighting system has been developed with engineering
cooperation and input. Conclusions derived from this research can be utilized to form a historical data base for
future projects and compared against the current in-work flight projects to improve cost growth predictions.
Development and Testing of a New Hinge Technology
Bradley Beler
Mentors: Mark Thomson and Daniel Kahn
The SWOT project plans to put a satellite into orbit that will map the surface elevation of all bodies of water on
Earth within a centimeter of the actual height using a large deployable interferometer antenna. To achieve this, the
boom arms must be incredibly stiff, lightweight, and the hinges must precisely deploy the tip-mounted antenna
multiple times. Current heritage hinge technologies fall short with metallic hinge bodies and motors attached
directly to the hinges that are far too massive for this application. This summer I helped in the design, fabrication,
and testing of a brand new, super lightweight cable driven hinge prototype design which greatly increases the
stiffness and decreases the deployed mass, achieved by positioning the motor remotely on the spacecraft and
hinge mechanism design. The actuation can be repeated a number of times, allowing the antenna booms to be
stowed and deployed when necessary and to enable precise measurement of deployment repeatability and hinge
stiffness. I was in charge of performing hand calculations, ordering standard parts, working with the machine shop,
and assembly of the prototype.
CASSIUS: The Cassini Uplink Scheduler
Earl P. Bellinger
Mentors: Diane Conner and David Mittman
The Cassini Uplink Scheduler (CASSIUS) is cross-platform software used to generate a radiation sequence plan for
message files being sent to the Cassini spacecraft. Because signals must travel through varying amounts of Earth’s
atmosphere, several different modes of constant telemetry rates have been devised. These modes guarantee that
the spacecraft and the Deep Space Network agree with respect to the data transmission rate. However, a message
file will be lost if it is sent across telemetry mode boundaries. Given a list of spacecraft message files as well as the
available telemetry modes, CASSIUS can find an uplink sequence that ensures safe transmission of each file. In
addition, it can predict when the two on-board solid state recorders will swap. CASSIUS prevents the corruption or
loss of transmitted data by making sure that message files are not planned for radiation during telemetry rate
changes or a solid state recorder swap.
Managing the Perception of Advanced Technology Risks in Mission Proposals
Sebastian Bellisario
Mentor: Lynne Cooper
The use of technology in proposals enables new and exciting missions and increases the capabilities of the science
community. The infusion of new technology, however, also increases perceived risk and is a known factor in
missions receiving “high risk” ratings. This research investigates how advanced technology has been incorporated
into proposals and the impact this has had on sponsor perceptions of risk. Using archival data, it evaluates issues
with both the development of the technology and the communication of the technology development efforts in the
proposal, identifying factors that affect success. Finally, this research develops guidelines for how to successfully
present technology development efforts and address concerns related to risk.
Simulating Rope and Parachute Dynamics
Collin J. Bezrouk
Mentors: Benjamin Thoma and John Gallon
The Low Density Supersonic Decelerators (LDSD) program is a technology mission designed to demonstrate two
new Mars Entry, Descent, and Landing (EDL) technologies: inflatable decelerators, and a 33.5 m supersonic ringsail
parachute. One test program leading to the final demonstration test is the Parachute Design Verification (PDV) test,
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which will simulate peak loads on the parachute canopy. This test involves dropping the parachute from a
helicopter, allowing it to inflate, and then towing it with a rope and rocket sled to achieve the 125k lb verification
load on the canopy. In order to predict the response of the parachute and rope to conditions like wind and
helicopter position, a dynamics simulation program was written in MATLAB. This simulation can model the rope as a
variable number of lumped masses separated by a tension-only spring-dashpot to simulate the rope’s stiffness and
damping. The parachute is modeled with a parabolic inflation curve and includes empirical data whenever possible.
Results from several simulations show that the parachute exceeds its verification load several times during the test
and does not exceed its load limit. Additionally, combinations of helicopter positions and wind conditions were
identified that bound the parachute to successfully latch to the rocket sled.
Design of System Engineers Design Analysis Tool Using Maple
Eric F. Bickford
Mentor: Jennifer M. Rocca
The analysis tools used today for performance analysis specific to each spacecraft subsystem are designed by each
individual subsystem engineer. They typically use legacy MS Excel spreadsheets which lack commentary and
expressions for governing equations and when these senior engineers retire, new employees are left with the job to
decode these spreadsheets (or recreate them from scratch). Unlike Excel, the mathematics program Maple does
not have these problems. Equations can be entered symbolically with comments. This allows new users to follow
the tools very easily and understand how the results are produced. Maple also has a feature to link worksheets
together so that various subsystems can be connected together. Then when a design parameter is changed, it will
carry through to all the appropriate subsystems. This makes for a user friendly interface with increased design
productivity. Existing DESDynI (Deformation, Ecosystem, Structure, and Dynamics of Ice) analysis tools will be
converted to Maple and each subsystem will be integrated into a master toolkit, useful for assessing project trade
studies, interpreting science impact due to a given design choice, and analyzing requirement sensitivity to design
changes.
Effects of the Environment and a priori Knowledge on FFT Based Image Correlation for Terrain Relative
Navigation
Pronoy K. Biswas
Mentor: Yang Cheng
In order to autonomously land a spacecraft within a hundred meter target zone on a planetary body, the method
for determining position during Entry, Descent and Landing (EDL) must be well tested. This position can be found
using a Fast Fourier Transform (FFT) based algorithm to locate the image of ground below the spacecraft within an
already known larger reference image. Before using this algorithm, the spacecraft needs to transform the descent
image below to make it look like it was taken from the reference image camera. The goal of this study is to
comprehensively test and characterize the limits of this algorithm by simulating errors in descent image
transformation and interference from various lighting conditions. More specifically, this testing is achieved by first
applying errors on a smaller image to simulate a descent image. Then, the FFT algorithm finds the coordinates of
this image within a reference image for all specified error conditions. Through these trials, the FFT algorithm is
accurate enough for spaceflight if operated within the parameters determined by this study.
Testing the High Resolution Impact Crater Chronology Method for Areally Limited Martian Geologic
Terrains
Nathan J. Boll
Mentors: Matthew P. Golombek and Nicholas H. Warner
Crater-count chronology is the only available means of estimating the relative age of Martian surface features. The
established chronology of major geologic terrains on Mars has been developed by analyzing the number of largediameter (D >1 km) impact craters over vast geographic areas (105 km2). Recently, the availability of imagery
from the High Resolution Imaging Science Experiment (HiRISE) and Context (CTX) cameras of the Mars
Reconnaissance Orbiter (MRO) has allowed for the analysis of much smaller craters (D >200 m) over significantly
smaller areas (102 km2). This project examines the usefulness of such small-scale applications of the crater-count
method for target terrains on Mars. Terrains covering 104 km2 were selected whose approximate ages have been
established by counts of kilometer-size impact craters and for which CTX/HiRISE imagery is available. These
regions were then subdivided into grids of 100 km2 and 1000 km2. The cumulative frequency of craters with D
>200 m was recorded for each grid and individual model ages calculated. Statistical patterns within the data were
used to determine the precision of ages across the entire terrain and the accuracy of these ages relative to
published ages. Our data revealed factors that may limit the usefulness of the technique for 100 km2 surfaces, such
as small sample sizes and resurfacing effects.
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State-Based Behavior Modeling of the Combined SLS-MPCV System
Kevin Bonanne
Mentors: Oleg Sindiy and Otfrid Liepack
In NASA’s effort to foster a human spaceflight capability beyond Earth’s orbit, two systems are being developed,
the Space Launch System (SLS) and the Multi-Purpose Crew Vehicle (MPCV). As of this time, the interactions
between the two systems during launch are not fully detailed. To remedy this situation, a Systems Engineering
approach utilizing models was developed to investigate the behavior of the integrated SLS-MPCV stack during
ascent and abort situations. Specifically, this unique approach combines aspects of Model-Based Systems
Engineering (MBSE) and state analysis to simultaneously model the physical, functional, and behavioral aspects of
systems. This approach focuses solely on the interactions between the systems, leaving much of the internal
workings of either system at a logical level (i.e., black box). By utilizing this newly defined approach, a behavior
model for the integrated SLS-MPCV stack was developed, emphasizing only the subset of interactions between the
systems that impact behavior. Finally, analysis is performed within the model to investigate requirements gaps and
examine the execution times of key behaviors related to various ascent phases and abort scenarios. The work
described in this paper is merely a portion of the outlined effort being undertaken for this project; only a segment
of the SLS-MPCV system behavior will be described.
Trade and Economic Dependency Model for Themis
David Bowerman
Mentors: Leila Meshkat and Ed Upchurch
Themis is a JPL based modeling framework which anticipates possible future states for the world within the next 25
years. The goal of this framework is to determine the likelihood that the US Army will need to intervene in various
countries on behalf of the US strategic interests. Themis will need to know about the relationships and
dependencies between countries. Trade relationships are one key dependency. In order to determine what the
trade relationship between any given pair of countries will look like, it is useful to look at what products each
country imports and exports. A country that imports the same products that another country exports will be more
likely to depend on that country; however, it may not be as dependent on that country if there is a third country
exporting the same product. To determine the future economic relationship between countries, for each of some
given products, the top importing/exporting countries of those products are studied, and a trend line is developed
based on how much of that product that country imported/exported in the past. The trend line is used to project
future expectations of imports/exports by that country, associated with a certain level of confidence, and then the
results are used to determine which countries are most likely to depend on each other.
Correlations Between Technical Performance and Cost Growth: A Case Study Using Subcontractor
Performance
Damien Brinoccoli
Mentors: Kevin Rice and Eric Kwan
Flight Projects historically exceed the available budgetary funds allocated by NASA HQ. Performance data indicated
that JPL flight projects on average overrun their cost targets by 40 to 50%. Unfortunately, the funds to cover these
overruns must come from other projects which often results in those projects slipping or reducing in scope. In
search of a method to predict and reduce future cost overruns on projects, the Program Business Management
Division has appointed a small group of summer interns to conduct extensive studies on cost growth for recent JPL
and non-JPL flight projects. One of the major drivers of such overruns comes from the cost performance of system
contractors. Using their subcontract data to analyze the cost growth between each milestone will provide critical
trends as to the amount of allocated funds being spent on the different milestones of the project lifecycle. These
findings are then broken down to the subsystem level to measure where and how each Subcontractor is spending
the funds. Results from these analyses will provide JPL the cost performance data needed to develop accurate cost
estimations for future flight projects.
Geoid to Topography Ratios and Mantle Plume Implications of Lada Terra Rise on Venus
Noranda Brown
Mentor: Suzanne Smrekar
Understanding the density structure of the Venusian lithosphere may provide great insights into the dynamics of
Earth and Earth-like planets due to its similarity in overall size and density to Earth. While Venus lacks evidence for
active plate tectonics, substantial evidence exists for mantle plume, or ‘hotspot’ activity, analogous to Hawaii on
Earth. To better understand the origin character of these features, geoid to topography ratios (GTRs), derived from
gravity data collected from the Magellan mission to Venus, are estimated for the Lada Terra rise and neighboring
regions located in the southern hemisphere of Venus which allow comparison with terrestrial convection
mechanisms. Local emissivity anomalies which have been associated with mantle plumes on Venus have also been
observed in the Lada Terra region and provide further motivation for this study. An initial estimated GTR of 23 ± 1
m/km is consistent with previous GTR estimates for similar Venusian highland regions which have been interpreted
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to occur over mantle plumes. Subsequent work will further constrain the GTR in this region to increase precision,
helping to interpret key characteristics and relationships within these volcanic features and characterize any
existing mantle plume signature.
Determination of the Shape of Vesta Using Radio Occultation Data From the Dawn Spacecraft
Dustin Buccino and Claudia Pham
Mentor: Sami Asmar
In 2007, NASA launched the Dawn Mission to increase understanding of the geophysical properties of the asteroid
Vesta and the dwarf planet Ceres. Since arrival at Vesta in 2011 before departing for Ceres in 2012, Radio Science
Receivers (RSRs) at NASA’s Deep Space Network (DSN) antennas collected numerous occultation data sets that
occur when the radio signals from Dawn are occulted by Vesta as seen from Earth. By utilizing edge diffraction
theory, the exact time the signal is occulted can be identified. When matched with Dawn’s location in space at the
corresponding occultation time, the radii and chord lengths of Vesta can be determined to good precision,
producing detailed mapping and shape of Vesta, to be later included in the geophysical interpretation when
combined with gravity data. Comparing the radio science occultation solution to already known dimensions and
topography of Vesta, the method can be validated and applied to future missions to determine the size and
topography of other celestial bodies.
Using the IML Ontology to Represent and Reason About Networking Infrastructure
Kalesha S. Bullard
Mentor: Simon Woo
Ontologies provide a shared and common understanding of a domain that can be communicated between people,
and heterogeneous and widely spread application systems. They have been used and developed in Artificial
Intelligence to facilitate knowledge sharing and reuse. This project builds upon a previously-defined ontology,
called Integrated Markup Language (IML). IML is an ontology used to describe computer networking
infrastructures. It describes the relationships and interconnections between all of the different individual
components associated with a potentially complex computer network. After achieving the initial goal of formally
extending the IML syntax, we designed and developed the implementation of the ontology using an objectedoriented structure. Using this implementation, we have applied the IML ontology specification to a specified set of
networking infrastructure data and used IML to represent and characterize relationships present within the given
data set. This representation may now be inputted into a reasoning system to be queried or converted to a
different from of knowledge representation, namely a Resource Description Framework (RDF) document.
Hierarchical State Machine for Automatic Calibration and Control of a Digital Camera System
Kevin Burg
Mentor: Michael McHenry
Digital video cameras can be configured in a wide variety of ways including shutter time, gain, resolution, and
frame rate. More sophisticated cameras offer additional options such as sub-windowing and High Dynamic Range
(HDR) capture. When utilized for teleoperation of a mobile robot there is a need to automatically configure the
camera based on current vehicle velocity and environmental illumination. We provide a solution to this problem
while also demonstrating a way in which programmers without years of flight code experience can write code that
architecturally resembles JPL flight code. This is accomplished by creating components with well-defined looselycoupled interfaces built on a framework of hierarchical state machines (HSM) and message passing based
communication. Our system contains a HSM created using MATLAB’s Stateflow/Simulink toolbox that is later
converted to C code by Simulink coder and interfaced to FireWire video cameras using the libdc1394 API. Control of
the camera system becomes possible through the resulting higher-level software interface that enables automatic
control of camera resolution, frame rate, compression level, and HDR imaging based on vehicle speed,
environmental illumination, and available bandwidth.
Improving the Mars Science Laboratory Payload Code Generation and Testing Process
Brandon Bussjaeger
Mentor: Marcel Schoppers
The Mars Science Laboratory (MSL) contains ten scientific instruments for running experiments on the surface of
Mars. For each of these instruments, the flight software team develops unique code to control the instruments and
handle errors. To both reduce the amount of hand coding necessary for instrument control and testing, a Domain
Specific Language (DSL) was created within an Excel spreadsheet, which is interpreted by a Python script and
translated into C code. However, the generated code had flaws, and required hand editing after generation. By
analyzing the limitations of the spreadsheet and Python script, additional syntax options and formatting were
added to the DSL, closing the gap between generated code and the current hand edited code. This reduced the
amount of C code entered directly into the spreadsheet as well, improving readability and functionality. With these
improvements, the spreadsheet and generator can quickly create a powerful instrument manager strictly for testing
the Instrument Manager Framework that runs underneath each instrument on MSL.
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Space-Based Exoplanet Observation: An Experimental Analysis of the Reflectivity Exhibited by Test
Samples for the Optical Edge of a Starshade Occulter
Robert J. Calderon
Mentors: Doug Lisman and Stefan R. Martin
Direct observation of exoplanets is difficult due to the high contrast between parent stars and their planets; stars of
interest are on the order of 1010 times brighter than earthlike exoplanets. Needed is a way to block the direct light
from the stars so that the nearby planets can be viewed via the light which they reflect from the parent star. One
of the technologies under development by NASA to overcome this challenge is a starshade occulter, operating in
formation with a space telescope. Starshades consist of a central disk with flower shaped petals to create a smooth
apodization function. The amount of sunlight striking petal edges and reflecting forward to the telescope must be
limited. An edge material with reflectivity ≤ 1% and radius of curvature ≤ 50 microns is desired. Theoretical
models show how the reflected light should behave for a range of angles. An experimental setup has been
constructed to mimic the physics of the actual system. The measurements taken over a range of angles and
sample test pieces will be used to validate the models and identify the most suitable optical edge material and
required radius of curvature.
Ulysses Observations of Magnetic Waves Due to Newborn Interstellar Pickup Ions and Why They Are So
Seldom Seen
Bradford E. Cannon
Mentor: Neil Murphy
The sun is a source for a fast moving gas of electrically charged particles called the solar wind. The solar wind and
associated interplanetary magnetic field dominate a region of space which extends past 100 AU from the Sun.
Therefore, it is interesting that neutral atoms, originating in the cold interstellar medium, can penetrate this region
of space relatively freely. The interstellar neutral atoms see no effect from the interplanetary magnetic field until
they experience a rare collision with either a charged particle of the solar wind or photon of solar origin.
At that point of ionization, the previously neutral atom becomes an electrically charged ion which is subject to both
the Lorentz forces of the interstellar magnetic field and the electrically charged particles of the solar wind. The
ionization process creates an energetic component to the interplanetary plasma which, as it scatters, produces
magnetic waves that are observable by Ulysses spacecraft instruments. The purpose of this research is to utilize
the observations made by the Ulysses spacecraft in order to better understand the magnetic wave enhancements
produced by interstellar pickup ions, and why they are so seldom seen.
Analysis of Nearly Simultaneous CloudSat/TRMM Intersect Data
Sam Carp
Mentor: Ziad Haddad
There are currently two radar systems operating in Earth's orbit dedicated to cloud and precipitation
measurements: The Tropical Rainfaill Measuring Mission (TRMM), and the CloudSat radar. These radars have
dissimilar orbital paths, however they do make measurements of the same region within a few minutes of each
other every week or so. Using various statistical and analytic techniques, a pair of algorithms were developed that
transform the data collected by either satellite into data that shows the main features the other would have
measured had it collected data over the region instead. These were then tested against data collected in years that
were not used to develop the algorithms.
Mars Science Laboratory: Qualification Model Dirty Testing (QMDT) Support
Makai A. Cartman
Mentor: Randall Foehner
The Mars Science Laboratory (MSL) rover Curiosity landed on the surface of Mar's on August 5th, 2012. Onboard
the rover is a Sample Acquisition – Sample Processing and Handling (SASPaH) Drill and a Collection and Handling
for In situ Martian Rock Analysis (CHIMRA) system. Both of these components have been and continue to be tested
in Mar's like conditions here on Earth, within the Qualification Model Dirty Testing vacuum chamber. QMDT is a test
program setup to characterize and gain experience with MSL’s SASPAH Drill and CHIMRA and also to
troubleshoot/investigate issues that may arise during Mission operations in a Mars-like environment. The future
success of the MSL mission is directly linked to QMDT's involvement which works to keep things running smoothly
by testing different rock types and various collection methods before performing actual sorties on Mars so that we
know how to proceed with as few complications as possible. My role as a QMDT support intern was to design, test,
and integrate mechanical ground equipment.
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Teleoperation of Robonaut Using Finger Tracking
Rachel G. Champoux
Mentor: Victor Luo
With the advent of new finger tracking systems, the idea of a more expressive and intuitive user interface is being
explored and implemented. One practical application for this new kind of interface is that of teleoperating a robot.
For humanoid robots, a finger tracking interface is required due to the level of complexity in a human-like hand,
where a joystick just isn’t accurate. Moreover, for some tasks, using one’s own hands allows the user to
communicate their intentions more effectively than other input. The purpose of this project was to develop a
natural user interface for anyone to teleoperate a robot that is elsewhere. Specifically, this was designed to control
Robonaut on the international space station to do tasks too dangerous and/or too trivial for human astronauts. This
interface was developed by integrating and modifying 3Gear’s software, which includes a library of gestures and
the ability to track hands. The end result is an interface in which the user can manipulate objects in real time in the
user interface. Then, the information is relayed to a simulator, the stand in for Robonaut, at a slight delay.
Investigation of MER-B’s Microscopic Imager Acquisition Error
Gabriel Charalambides
Mentors: David Mohr and Bill Nelson
This study investigates a recurring acquisition error of MER-B’s Microscopic Imager (MI). The error occurs when the
capture image command is misinterpreted by the MI, and as a result the image is not taken. In this scenario, the
CPU reissues the command. All retry attempts to date have succeeded, however, a recent increase in the
occurrence of these errors indicate that a retry failure may be imminent.
The MI is located at the end of the rover’s arm, whose serial interface is susceptible to connection and impedance
issues. Accordingly, this study’s primary focus was the arm’s various joint angle and temperature values at the
times of the errors. Python scripts were written to mine relevant data gathered over the past eight years in order
to establish whether or not trends existed. Analysis revealed that there is no correlation between particular joint
angle or temperature values and the image acquisition errors. Although the error’s origin remains to be
determined, these results indicate that no adjustments to operations are required. Further investigation may look
more closely at power or voltage levels at the times of the occurrences, or if evidence exists of damage to the MI’s
transmitter and/or receiver.
Cryogenic S Band Test Case
Nathan A. Cheadle
Mentor: Michael Britcliffe
Current methods to test S band low noise amplifiers require large expensive equipment. That is why it was deemed
necessary to develop a small test case that would allow researchers to test S band low noise amplifiers in a lab
setting. The test case that is being developed utilizes a Sunpower Cryotel cryocooler, one of the most efficient
cryocoolers on the market, to cool the low noise amplifiers. By using this cryocooler and mostly off the shelf parts,
this test case will allow researchers to reduce the cost, and allow easy testing of S band low noise amplifiers.
Numerical Simulation of the MSL Dynamic Albedo of Neutrons (DAN) Instrument
Nicholas Cho
Mentor: Insoo Jun
The DAN instrument on the Mars Science Laboratory has been tasked with detecting hydrogen in the Martian
subsurface by measuring neutron thermalization in the Martian Soil. Increased levels of neutron thermalization are
highly indicative of the presence of Hydrogen (and thus Water) in the Soil; however, there are numerous other
factors that influence the process as well. To better understand the significance of these external factors, we used
the Monte Carlo N-Particle Extended (MCNPX) code to study numerous cases simulating conditions on the Martian
surface. The results give us an insight into the varying impacts of factors such as water content, depth, density,
temperature, and composition on the thermalization of neutrons, and ultimately better equip us to interpret real
data from MSL. Going forward, we will use the results of these simulations, and others like it, in attempting to
answer the question of whether water is present on Mars and thus whether Mars was ever capable of sustaining
life.
An Examination of Coarse Sun Sensor Contingencies in Attitude Determination and the Sun Vector
Calculation
Brennan Coffey
Mentors: Ray Welch and Brad Burt
Satellite pointing is vital to the success of a mission. One element of that entails describing the position of the sun
relative to the frame of the satellite. Coarse Sun Sensors (CSS) are typically used to provide the information to
calculate the sun’s position in Safe Modes or contingency operations. In the OCO-2 configuration there are 13 CSS
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total which provide redundant 4  celestial coverage. Failures of the individual CSS elements can introduce holes in
the celestial coverage resulting in potential loss of sun knowledge. These failures must be analyzed to determine if
the contingency plan is sufficient to assure mission success. First the static case was looked at and determined that
at a maximum, 3 CSS failures can be sustained on the bodyand 1 on the array without causing coverage holes.
Also array sensors are more important to mission success. The Sun Vector calculation has been transcribed to
MATLAB code and failure scenarios are being examined to determine the maximum error given a set of failure
scenarios. This activity indicated that if there is a loss of the sun, the sun-searching algorithm could be modified to
use XZ rotation as that is guaranteed to find it whereas the design using the XY rotation misses the sun if it is at
the + or – Y orientation.
ATHLETE Rover: The Design and Build of a Motor Joint Testbed
David R. Connolly
Mentor: Christopher McQuin
Future missions to distant bodies such as the Moon or Mars may require multiple supply landings and a method to
consolidate all of the supplies in a central location. In previous lunar landings it was observed that the landing
process would accelerate lunar regolith to a speed which could effectively sand blast any previously established
equipment. To avoid damaging the first payload of a multi-landing process, future missions would need a
designated landing location with the intent of transporting supplies to a pre-determined site. The All-Terrain HexLimed Extra-Terrestrial Explorer (ATHLETE) is a rover which has the ability to transport bulky cargo across
treacherous terrain without the need of an on-site operator. This paper presents the design and functionality of
ground support equipment used to characterize the performance of various actuators. The resulting motor joint
testbed will provide a method to supply a varying load to robotic joints while allowing for easy access to joint
components. Data obtained from these tests will be valuable in determining the performance and endurance
limitations of robotic arm joints built by the ATHLETE team. This project will also provide the ATHLETE team with
the capability to easily test various robotic joints in the future.
Improving Spacecraft Data Visualization Using Splunk
Matthew Conte
Mentor: Victor Hwang
EPOXI, like all spacecraft missions, receives large volumes of telemetry data from its spacecraft, the Deep Impact
Flyby (DIF) vehicle. It is extremely important for this data to updated quickly and presented in a readable manner
so that the flight team can monitor the status of the spacecraft. Existing tools for monitoring spacecraft telemetry,
while functional, are limited and do not take advantage of modern search technology.
To more easily organize and visualize spacecraft telemetry, the EPOXI team has implemented Splunk, a
commercially-available data mining system. Splunk can take data received from different instruments on board the
spacecraft, often in different formats, and index all the data in a common format. Splunk allows flight team
members to search through the different data formats from a single interface and to filter results by time range
and data field to make finding specific spacecraft events quick and easy. Furthermore, Splunk provides functions to
create custom interfaces which allows team members to visualize the data in charts, tables, or however is most
useful.
Splunk is an excellent solution for the problem of organizing telemetry data. It is far less expensive than
maintaining old ground data systems and is fully customizable, allowing teams to adapt it to their own needs.
Designing a Graphical User Interface for Display of Multicore Processors Operation
Eric Corbett
Mentors: John Lai, Kim Gostelow, and Leonard Reder
This paper describes the development of an interactive user interface (UI) to display the operation of the Tilera
TILE64 processor. The Tile64 is a multicore processor system with an array of 64 individual cores or processing
elements on a chip containing an array of processing elements and a network with a switch engine at each core for
data routings. The purpose of the UI is to demonstrate the design and operation of fault tolerant software deployed
in test and showcase the TILE64 processor for use in future space missions. The UI will indicate the current
execution state of each core and the applications/processes being ran using a simple color scheme displayed in real
time based on information retrieved from the Tilera processor. Specific commands can also be sent to Tilera via the
UI for invoking the execution of software functions.
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Low-Latitude Ethane Rain on Titan
Paul A. Dalba
Mentor: Bonnie J. Buratti
Cassini ISS observed multiple widespread changes in surface brightness in Titan's equatorial regions over the past
three years. These brightness variations are attributed to rainfall from cloud systems that appear to form
seasonally. Determining the composition of this rainfall is an important step in understanding the “methanological”
cycle on Titan. I use data from Cassini VIMS to complete a spectroscopic investigation of multiple rain-wetted
areas. I compute “before-and-after” spectral ratios of any areas that show either deposition or evaporation of rain.
By comparing these spectral ratios to a model of liquid ethane, I find that the rain is most likely composed of liquid
ethane. The spectrum of liquid ethane contains multiple absorption features that fall within the 2-micron and
5-micron spectral windows in Titan's atmosphere. I show that these features are visible in the spectra taken of
Titan's surface and that they are characteristically different than those in the spectrum of liquid methane.
Furthermore, just as ISS saw the surface brightness reverting to its original state after a period of time, I show
that VIMS observations of later flybys show the surface composition in different stages of returning to its initial
form.
Testing and Characterization of an IR CBIRD FPA
Tanya Das
Mentor: Sir (Don) Rafol
High performance IR cameras are in great demand for a variety of applications, including defense (e.g. night vision,
missile detection) and space (e.g. imaging at IR wavelengths). IR focal plane arrays (FPAs) are an essential
component of IR cameras. An FPA is a collection of detectors at the focal plane of an imaging device, where each
detector can be thought of a pixel in the image it is detecting. The FPA in this study is composed of Complementary
Barrier InfraRed Detectors (CBIRDs). The CBIRD FPA was tested by imaging black body targets at three different
temperatures, 20ºC, 25ºC, and 30ºC, with images captured using SEIR/WinIR software. The important figures of
merit for an IR FPA, NEDT (noise equivalent differential temperature), NEI (noise equivalent irradiance), detectivity,
responsivity, and QE, were extracted from the image data for each individual detector using a MATLAB program, as
was the array MTF. The test results show a mean NEDT of 16.98mK and an MTF of about 0.34 at the Nyquist
frequency. Overall, the array performs well in the MWIR range and takes quality IR images.
Finite Element Model Report for SMAP
Willem A. DeBirk
Mentors: Darlene Lee and Michael Long
This presentation summarizes the FEM Report for the SMAP Satellite. The SMAP Satellite will provide information
about ground water content and distribution that will be used to predict water availability in the future. The mission
depends upon a sound structural system that will protect and support the instrument during launch and throughout
its operation. To analyze and ensure an adequate structural system, a finite element model (FEM) is created and
analyzed. A FEM is a discretized set of small elements arranged to resemble the actual item. Each element is small
enough to be analyzed using conventional engineering practices, but the discretized nature of the model implies a
certain level of idealization and approximation. To ensure that there aren’t any serious errors inherent in these
idealizations and approximations, a model report is created. The model report explains the configuration of the FEM
and explains the idealizations and approximations. It then contains reports from a series of checks performed with
Nastran that ensure that the model behaves properly and can be used as a valid representation of the real system.
Finally, the report contains the model’s complete data deck so that the FEM can be recreated and the results
corroborated.
Software Analysis of New Space Gravity Data for Geophysics and Climate Research
Rupert H. Deese
Mentor: Erik R. Ivins
Both the Gravity Recovery and Climate Experiment (GRACE) and Gravity field and steady-state Ocean Circulation
Explorer (GOCE) satellites are returning rich data for the study of the solid earth, the oceans, and the climate. Lack
of software capability prevents researchers from realizing the full potential of this data. Methods of data
computation, analysis and visualization are explored to improve current capabilities. These include the ICGEM’s
(International Center for Global Earth Models) web server interface, the GOCE User Toolbox, Wolfram Mathematica,
the Generic Mapping Tools, and Tesseroids. Particularly, the efficiency of the ICGEM web server and Mathematica
are compared to better-established methods of computation with spherical harmonics. For producing Bouguer
corrections of the gravity tensor, the gravity field modeling software Tesseroids is tested for the first time. These
methods streamline the analysis of deep crustal structure using space gravity data. Such analysis is further
enhanced where the incorporation of terrestrial data is possible, as in Earth Gravity Model 2008. The Gulf of
Mexico, Antarctica, and the region of the 2010 Maule earthquake are focuses of this analysis. Research into
calculating the gravity tensor using a combination of Mathematica, Python, and Tesseroids suggests promising
results.
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GRIFEX Mechanical Design
Jeffrey DeLucca
Mentor: Paula Pingree
CubeSats provide a low cost option for flight testing and establishing heritage for next generation hardware. GEOCAPE Readout Integrated Circuit In-Flight Performance Experiment (GRIFEX) will provide on-orbit verification of a
high performance focal plane array (FPA) consisting of an innovative in-pixel analog-to-digital converter (ADC)
readout integrated circuit (ROIC) hybridized with a silicon detector array. In order to ensure the payload survives
integration, testing, launch, and orbit, finite element analysis (FEA) must be done with consideration towards both
mechanical and thermal stresses. After completing a redesign of preliminary sketches in SolidWorks, ANSYS was
used to analyze stress due to 200 G acceleration in each direction, and thermal stress resulting from an 87 K
difference from room temperature (22 degrees C). All parts were within the margin of safety at these loads. Modal
analysis indicated the resonant frequency of the weakest part was 226.27 Hz, and the first resonant frequency of
the entire structure was 978.89 Hz.
Applying Modeling Tools to Ground System Procedures
Peter J. Di Pasquale
Mentors: Oleg Sindiy, Kathleen Crean, and Patricia Lock
In the Ground Systems (GS) engineering domain, Mission Operation System Engineers (MOSEs) and Ground Data
System Engineers (GDSEs) perform systems engineering functions that are typically learned from years of on-thejob experience. These activities have traditionally been captured in a way that makes it difficult for newer
engineers to learn the desired GS engineering procedures. While GS procedures exist, the current set lacks a
desired level of granularity, traceability, clarity, and consistency. Furthermore, GS processes and products do not
consistently utilize a standard taxonomy. To provide GS engineers with a more descriptive guiding set of
procedures that define the roles and responsibilities of MOSEs and GDSEs throughout a given project Life Cycle,
the processes and products of the MOS and GDS domains have been updated and modeled using the MagicDraw
Software Tool via Business Process Model and Notation (BPMN) and Systems Modeling Language (SysML).
Currently, the resulting preliminary model describes the tasks completed by the MOSE and GDSE throughout the
Life Cycle phases of a project, and the products that are produced during those phases. After the model is refined
and expanded, it will become a reference that GS engineers can use to efficiently and consistently identify and
execute their responsibilities.
Optimization of KINETICS Chemistry Calculation FORTRAN Code
Cristina A. Donastorg
Mentors: Karen Willacy and Mark Allen
NASA JPL has been creating a code in FORTRAN called KINETICS to model the chemistry of planetary atmospheres.
Recently there has been an effort to introduce Message Passing Interface (MPI) into the code so as to cut down the
run time of the program. There has been some implementation of MPI into KINETICS; however, the code could still
be more efficient than it currently is. One way to increase efficiency is to send only certain variables to all the
processes when an MPI subroutine is called and to gather only certain variables when the subroutine is finished.
Therefore, all the variables that are used in three of the main subroutines needed to be investigated. Because of
the sheer amount of code that there is to comb through this task was given as a ten-week project. I have been
able to create flowcharts outlining the subroutines, common blocks, and functions used within the three main
subroutines. From these flowcharts I created tables outlining the variables used in each block and important
information about each. All this information will be used to determine how to run MPI in KINETICS in the most
efficient way possible.
JPL Cyber Defense Research Laboratory
Christopher Dorros
Mentors: Bryan Johnson and DJ Byrne
JPL and NASA are increasingly becoming the target of advanced cyber attacks, many of which can occur completely
unnoticed. The initial design phase was completed for a Cyber Defense Research Laboratory (CDRL). Once
deployed, the lab will allow for the development of new mitigation techniques for cyber attacks and allow for
verification of such techniques via realistic test bed exercises. The CDRL will serve an immediate need for research,
test, and validation for JPL’s work with the Los Angeles Department of Water and Power relating to Smart Grid
security. The architecture allows for interfacing with disparate physical equipment, a feature critical to control
systems security and absent in most cyber security test environments built on emulation. Additionally, the CDRL
will support rapid creation of accurately represented systems and test bed sanitization following an experiment.
Initial components of the lab were used to conduct several unique investigations of existing JPL systems, including
an assessment of the JPL wireless network and a forensics evaluation sparked by anomalous network behavior on
an employee’s workstation.
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Simulating an HMMWV in an Urban Terrain and Updating the DARTS Lab Software to Work With an
Upgraded Physics Engine
Matthew C. Dughi
Mentors: Abhinandan Jain, Jonathan Cameron, and Calvin Kuo
The Dynamics and Real Time Simulation (DARTS) Laboratory creates high fidelity simulations of vehicles on land
and in space. It develops software designed to perform highly accurate and computationally efficient dynamic
simulations. The DARTS lab has been sponsored by the Tank Automotive Research, Development, and Engineering
Center (TARDEC) to create a simulation of a High Mobility Multipurpose Wheeled Vehicle (HMMWV). This involves
simulating the HMMWV in an urban environment, in multiple scenarios. These include, but are not limited to,
accelerating the HMMWV to a high speed and performing a change of lane procedure, and driving the vehicle
around in a suburban environment and normal to high speeds. Another part of the task is assisting in the shift from
the old physics engine that the DARTS lab wrote and used to their newer version, which supports closed chain
dynamics and contact dynamics.
Measurement and Modeling of Clathrate Hydrate Thermodynamic Stability in the Presence of Ammonia
Marc T. Dunham
Mentors: Mathieu Choukroun and William Smythe
Clathrate hydrates are structures formed under high pressure and/or low temperature in which gas molecules are
trapped individually in ice-skeleton cages. As the temperature increases or pressure decreases, the cage structure
may become unstable and dissociate, freeing the trapped gas molecule. It is known that the presence of ammonia
decreases the melting temperature of ice. Experiments have been conducted using a high-pressure cryogenic
calorimeter to examine the effects of ammonia-water solutions with different concentration (0-30 wt%) on the
stability of methane clathrate hydrates at pressures below 10 MPa and temperatures of 123-293 K. Previous works
have assumed a comparable effect on the stability of clathrates to the stability of ice in the presence of ammonia.
Preliminary results suggest that ammonia does reduce the dissociation temperature, but potentially only by half the
temperature reduction observed for the melting point of ice. The experimental results obtained from the
calorimeter system will be used to construct a thermodynamic model for methane clathrate hydrates in the
presence of ammonia. As these conditions and compounds are believed to exist on icy satellites such as Titan, such
a model may help to explain the sustainability of methane in Titan’s atmosphere.
Retrieval, Analysis, and Quality Control of MINX Derived MISR Stereo Heights
Benjamin Dunst
Mentor: Veljko Jovanovic
The MISR instrument aboard the Terra satellite collects data in four spectral bands from multiple viewing
directions. Using an in-house, interactive program called MINX to retrieve the stereo heights and winds from the
MISR data, we collected climatological datasets on wildfires in areas such as the whole of North America in 2000.
The pattern-matching algorithm in the MINX program has several distinct options for retrieving this data; of
particular interest is the option for switching the band used for finding stereo matches. Two bands were used for
retrieving heights and winds, a high-resolution red band, and a low-resolution blue band. These two bands give
noticeably different results over a variety of terrains and aerosol densities. The goal of this project was to
determine the significance of multi-band retrievals and if there is information in the differences. A secondary goal
was to determine if there is a significant difference in data collected between different MINX users. The source of
this question is that over several years of the MISR plume height project there are large differences in the users'
criterion for digitized plumes. We examined whether or not it is scientifically appropriate to make comparisons
between years of data generated by different MINX users.
Technology Development for Exoplanet Missions
David Dyrda
Mentor: David Webb
An external occulter is a flight instrument that is used in tandem with a space telescope whose purpose is to view
exosolar planets. The occulter—or starshade—is designed to block light coming from the host star in such a manner
as to allow direct observation of the desired exoplanet. The structure of a starshade can be likened to a flower,
with a circular truss supporting as many as thirty petals which can fold around the central truss and then unfurl.
Past investigations into starshade technology have focused on the development of these petals in order to first
demonstrate their feasibility and to then demonstrate the levels of accuracy and precision necessary for their
functionality.
This summer four petals were constructed for the ultimate goal of demonstrating deployability. The idea is to
demonstrate that the petals can be folded around a central truss and then unfurled back to their original position
within a small degree of error. The petals were successfully assembled to a relatively high degree of precision with
the aid of both physical and optical measuring devices. Soon these petals will undergo testing in order to determine
their ability to accurately deploy.
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Synthesis and Thermoelectric Properties of Filled p-Type Skutterudites
John Elliott
Mentors: Danny King, Sabah Bux, Jean-Pierre Fleurial, and Thierry Caillat
Thermoelectric generators are a key technology for powering space missions. They take advantage of the
thermoelectric effect, which is the conversion of a temperature difference to electric voltage. Current state of the
art thermoelectric materials are very inefficient and must be improved. For a material to be viable it must possess
a combination of properties: low metal-like resistivity, a high Seebeck coefficient, and low thermal conductivity.
Skutterudites based on the formula FexCo4-xSb12 have the most favorable p-type electric properties observed so far.
However, thermal conductivity in these compounds is too high to result in high ZT values. One way to reduce
thermal conductivity is to prepare filled skutterudites in which the empty octants in the unit cell are filled with large
rare or alkaline earth elements. This reduces the thermal conductivity through phonon scattering by the filling
atoms. Different metals will scatter phonons of different frequencies, making some more effective than others.
Currently, filling the skutterudite structure with cerium in the fraction Ce0.9Fe3.5Co0.5Sb12 is the state of the art
p-type material with a peak ZT around 1 at 600 °C. This project seeks to create a p-type thermoelectric material
with a higher ZT using different filler atoms to reduce the thermal conductivity and different ratios of iron to cobalt
to further improve the electrical properties.
Carbon Dioxide and Aerosol Data Validation for the Orbiting Carbon Observatory-2
Dillon E. Elsbury
Mentor: Gregory Osterman
The objective of the project has been to compare data sets of carbon dioxide and aerosol measurements to ensure
the validity of the Atmospheric CO2 Observations from Space (ACOS) data. Validation indicates what magnitude of
carbon dioxide and aerosol measurements can be expected from OCO-2 and sheds light on how to analyze these
results. For this project, carbon dioxide and aerosol measurements are plotted against time and other criteria using
the programming language Python. These plots are created using measurements from multiple data sets and then
are compared to each other and the ACOS data set in particular, because it is the set being validated.
Among the carbon dioxide vs. time plots, there are great correlations, which suggest that the methodology and
criteria chosen for recording carbon dioxide measurements is correct. However, among the aerosol vs. time plots,
correlations are not as strong, which suggest that there are inaccuracies in the retrieval algorithms used to create
the data sets. Another aerosol data set has been compiled and its measurements will be used to make more plots
for comparison to the ACOS data set.
FT-IR Analysis of Bacillus subtilis Spores Under Vacuum Ultraviolet Irradiation Buried Beneath
Water Ice
Tucker Ely
Mentors: Paul V. Johnson and Robert Hodyss
Resistance to extreme environmental constraints has made bacterial spores the focus of astrobiological models
depicting extremophile life within Europa’s subsurface ocean. Should detectable deposits find their way to the
surface via geologic processes, they may display unique spectroscopic signatures as a combined result of the
intense solar UV radiation incident on Europa’s surface, high energy bombardment from plasma trapped in Jupiter’s
sizable magnetic field, and ice-photoproduct interaction. In an effort to mimic the temperature, UV flux, and waterice interaction aspects of the Europan surface, Fourier transform infrared (FT-IR) spectroscopic analysis of a
monolayer of Bacillus subtilis spores was carried out at 100K and ~10-9torr, and evaluated for alterations
generated by exposure to sun-like ultraviolet radiation (130-335nm). Tests were carried out with both bare spores
and spores buried beneath water-ice, and deposited on silicon-oxide coated aluminum mirrors. The uncovered
spores irradiated with photon fluxes of ~2 x 1014 s-1 cm-2 for 16 hours displayed unique absorptions bands at 2169
and 2249 cm-1, in the general region of nitrile containing functional groups. Disappearance of the bands with a
return room temperature while still under vacuum suggests against pyrimidine dimer formation, and for
photoproducts with a relatively small size. Ice coverage of 0.25-0.5μm appeared to have no effect on the
absorptive characteristics of the spores themselves, aside from the addition of the expected water-ice spectra, and
a general diminishing of the spore spectra signal.
Analysis of the Relationship Between Project Cost and Schedule
Kevin P. Ferris
Mentors: Kevin Rice and Eric Kwan
Historically, flight projects exceed their allocated budgetary funds. As a result, the Program Business Management
Division has become interested in finding additional early warning cost analysis tools to address this issue. Over the
past few years, JPL has begun to assemble a comprehensive historical cost analysis database relative to a standard
Work Breakdown Structure which provides a more thorough breakdown of project costs in a consistent manner.
The database contains project cost totals by year for Level 1 and 2 of the Work Breakdown Structure. Using these
data, a model was fit which can be used to reasonably estimate the true mean cost of historical projects at given
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times in the project’s schedule. For example, the model will estimate the true average amount spent by previous
projects when those projects are 30% complete. JPL will then be able to tell how future projects are performing
when they are 30% complete relative to historical projects. A time series analysis of selected parameters and
characteristics from historical projects was used to build this model. This provides a mathematical relationship
between a project’s schedule and cost at specific times during construction of the project.
Systems Engineering: Integration, Testing, Verification, and Validation for a Small Flight Project at JPL
Logan Finch
Mentors: Parker Fagrelius, Marcus Wilkerson, and Robert Witoff
Flight projects form the heart of NASA’s Jet Propulsion Laboratory (JPL). However, not all flight projects at JPL have
large budgets like the Mars Science Laboratory program. There are flight projects that operate on a smaller scale
and budget, like the Optical PAyload for Lasercomm Science (OPALS), which is a small optical communications
technology demonstration payload that will fly on the International Space Station (ISS) in 2013. The OPALS project
is currently in the integration and test (I&T) phase of development which includes activities like the calibration of
the two-axis gimbal, testing the flight laser that will downlink video, and final integration of structural components.
This internship has been focused on supporting I&T for the OPALS project. For example, a problem with a solidstate relay circuit on the laser power circuit was found during the testing of the power board, which routes power
to the payload. A solution was found through troubleshooting on a representative board and then solved with a
small circuit design change. In parallel to I&T, documentation has to be created to demonstrate compliance with all
JPL and ISS requirements. When I&T and all verification activities are complete, the OPALS payload will be ready to
deliver.
Particle Tracking and Quantification
Veronica Flesch
Mentors: Ying Lin and Moogega Cooper
SAC (sample acquisition and caching) systems for MSR missions are required to meet strict planetary protection
and contamination control requirements, but no proper protocol currently exists to track microbial contamination.
The objective of this project is to develop a methodology for quantifying and tracking biological contaminants,
experimentally represented by fluorescent particles. A method of depositing an even monolayer of FluoSpheres
ranging in size from 0.2 microns to 4 microns onto titanium coupons was established. It was found that the
number of FluoSpheres on any particular area of a coupon could be determined with only 3% error by
photographing the area with an AxioPlan 2 imaging microscope and analyzing the picture with ImageJ software.
The effects of basalt, MMS dust, and sand on the images of fluorescent particles were studied. Much work was done
to set up a microscope, stage, and camera system that is compatible with new software, AxioVision 4.8.
AxioVision’s MosaiX program will make it possible to scan an entire coupon and automatically stitch together
individual images to produce a complete picture. This feature will be utilized during wind and drilling particle
transfer experiments, since particle movement can be studied by quantifying the number of particles that have
flown onto different coupons.
Flight System Power Modeling for Mission Scenarios
Timothy W. Fong
Mentors: Raymond V. Welch and John B. Burt
The Orbiting Carbon Observatory (OCO-2) mission will be launching an Earth-orbiting satellite that will record high
resolution measurements of carbon dioxide in the atmosphere. During its two-year mission, the OCO-2 will be
powered by four solar array panels and a rechargeable Nickel-Hydrogen battery. They will be powering the
components and the instrument operating on the spacecraft. For this project, the Multi-Mission Power Analysis Tool
(MMPAT) was used to predict the overall power budget of the OCO-2 spacecraft for various simulated mission
scenarios and off-nominal scenarios. The MMPAT was adapted for the OCO-2 power subsystem design and orbital
parameters and provides graphical data of battery state of charge, bus voltage, and load power of the spacecraft
for various mission scenarios. Several mission scenarios are assessed using the MMPAT including launch,
separation and deploy, and driving science scenarios: nadir, target, and glint modes. By determining the power
budget of OCO-2, the spacecraft power margin can be found to determine if it is compliant with JPL design
standards.
Planetary Ices Spectroscopy
Jeffrey T. Foster
Mentors: Robert Carlson and Kevin Hand
The goal of this research project is to develop a robust and highly sensitive spectrometer that can be used to scan
water ice and liquid samples on Europa for organic compounds. The aim is to find signs of life on the ice covered
moon orbiting Jupiter because it has been shown to have liquid water underneath its icy crust. To work towards
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this goal I am helping set up and perform spectral analyses on several different sample types relevant to Europa.
The tasks I perform are varied but the focus is infrared spectroscopy of ice grains containing organic molecules.
Progress is being made on obtaining spectra similar to those that would be obtained from Europa.
Comparing Solar Wind Prediction Models at 5.2 AU
Alexander J. Freed
Mentors: Henry B. Garrett and Michael Kokorowski
The solar wind is the main driver of Earth’s magnetosphere, but at the gas giant Jupiter, where the rotation period
is only ~10 hours and the solar wind is much less dense, its role is unclear. Previous studies investigating the role
of the solar wind on Jupiter’s have been limited to the time and place spacecraft were able to take measurements.
This study, in contrast, has created a continuous database of solar wind conditions near Jupiter. Such a database
was constructed from the solar wind propagation model ENLIL and the Wang-Sheeley-Arge (WSA) solar corona
model by averaging the model output into 10-minute bins to match the Galileo database. An analysis of the
database will be used to resolve a discrepancy between two former studies of the database. In the future, the
accuracy of the predicted solar wind parameters will be verified with the Galileo data taken outside Jupiter’s bow
shock. Also, an investigation of models such as the Michigan Solar Wind Model (MSWiM) or the Hakamada-AkasofuFry version 2 (HAFv.2) model may provide more accurate results at 5.2 AU. Predictions from these models,
however, were not available during this study.
Characterizing Crosstalk in a Single Camera Stereoscopic System
Eric Fritz
Mentor: Youngsam Bae
Traditional stereoscopic vision (3D) is achieved through use of two cameras arranged to emulate human eyes.
While this method works on large scale projects, it becomes impractical to use on small scale designs, such as
surgical endoscopes, where the working area doesn’t allow the bulk of dual camera systems. This project is focused
on developing a stereoscopic endoscope using a single camera and Conjugated Multiple-Bandpass Filters (CMBF) to
create the 3D images. Each filter is designed to allow only a distinct spectrum through. A stereoscopic image can
be obtained by using filters that are complementary to one another.
A major concern in all stereovision is crosstalk, which is defined as the light from one eye image that leaks into the
other eye image. This incomplete isolation causes deterioration of the 3D image. In our system, the crosstalk
comes from imperfect filters. The filter spectrums overlap at certain wavelengths. This allows a dim outline of the
right eye image to leak into the left eye image and vice versa, in phenomena known as ghosting. Knowing the
extent of this is critical to creating sustainable stereovision.
Effects of Oxidation on Clay Mineral Precipitation: Implications for Mars
Seth R. Gainey
Mentor: Joel A. Hurowitz
Spectral observations from orbiter space craft have detected clay minerals in ancient rock deposits exposed at the
Martian surface, formed from the hydrolysis of silicate minerals, indicating the past presence of liquid water. The
Mawrth Vallis region contains large deposits of phyllosilicate-rich rock, and is stratigraphically characterized by a
Fe- and Mg-rich nontronite overlain by an Al-rich montmorillonite. The stratigraphy and chemical transition of the
Mawrth Vallis region could be explained through a sedimentary origin, later modified by a paleo-oxidation front.
Under this hypothesis, the alteration of the sedimentary material would occur under anoxic conditions deep within
the profile, the increased solubility of iron in its ferrous form may have allowed for the formation of the gibbsite
structure leading to the precipitation of nontronite. Whereas the insoluble ferric iron would not be incorporated into
any clay like structure, leading to the precipitation of Al-Mg rich clay minerals. To test hypothesis we conducted a
series of batch experiments aimed at replicating the results of Harder (1972; 1976; 1978) in order to determine
whether oxidation state is the critical parameter determining whether nontronite versus montmorillonite form from
similar starting chemistry. Experiments, contained similar starting material as those of Harder (1972; 1976; 1978)
and were allowed to age for one month, oxic experiments were exposed to atmospheric O2 concentrations, while
anoxic experiments were run in a glove box with an O2 concentration less than 2 ppm. Samples were pulled each
week to determine the aging effects on clay mineral formation. Mineralology was determined thorugh X-Ray
diffraction, solution chemistry was analyzed through ICP-OES. The results of this study may be useful in
determining the paleo-enviroments of Mars, and give insight where life had the highest potential to develop.
Development of a Martian Atmospheric Sample Collection Canister
Charles E. Galey
Mentors: Eric Kulczycki and Ryan Van Shilfgaarde
Retrieval of the Atmospheric sample is a vital but often overlooked element of the Mars Sample Return mission.
Engineers at NASA’s Jet Propulsion Laboratory have worked to correct that oversight using advanced equipment
and simulation tools. To demonstrate sample collection and integrity researchers simulated a sample return
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mission on a compressed timeline. This was accomplished by varying the pressure in a vacuum chamber and
actuating a valve at key mission steps. A medical grade commercial off-the-shelf micro valve was selected to
enable fast prototyping and testing of the system. This valve was mated with a first-generation sample canister
incorporating a pressure transducer. Results will quantify mass, power and sensing requirements for a sample
return mission. Discussion will also cover science requirements and a storyboard for sample collection to loading in
the orbiting sample capsule. A path to flight will be indicated including discussion of the valve used and steps
needed to bring the sample canister to a flight ready state.
Development of a Purely Mechanical System for Obtaining Cometary Soil Samples
William J. Gallagher
Mentor: Paul Backes
Comets are composed of material from the early formation of the Solar System, and are therefore of interest for
scientific study into its origins. This is best accomplished by designing a mission to visit and sample the surface of a
comet. However, several challenges arise in obtaining the soil sample. The region very near the surface of a comet
has a high level of dust due to material being ejected from the comet, preventing a spacecraft from approaching
too closely. Therefore, a sampler mechanism should be deployed from the spacecraft to the comet's surface. This
sampler mechanism should be simple and reliable, with an ideal system being purely mechanical and eliminating
the possible failures associated with electronics and control software. It must also be capable of obtaining a sample
from a wide range of possible soil densities and hardnesses, since the exact nature of cometary surfaces is still
uncertain. The design requirements of such a system are discussed, and a trade space of possible sampler
elements is developed. After evaluating several likely concepts chosen from this trade space, a final system is
proposed. This system relies solely on mechanical action and motion rather than robotic actuation to penetrate the
surface, obtain a sample, and eject the sample back to the parent spacecraft. A prototype of the proposed system
is fabricated and tested to evaluate its viability.
Addition of an Automated Cometary Activity Detection Algorithm to the WISE Moving Object Processing
System, an Enhancement to the Rareness of Active Main Belt Objects (RAMBO) Survey
Thomas N. Gautier IV
Mentors: Amy Mainzer, James Bauer, and Rachel Stevenson
The Wide-Field Infrared Survey Explorer mission is a 4-band all-sky infrared survey that operated between January
and December 2010. The WISE Moving Objects Processing System (WMOPS), an addition to the WISE mission, is a
processing pipeline that looks for moving objects in the WISE dataset. Prior to this project, WMOPS had no
provision for detecting cometary activity. The purpose of this addition to WMOPS is to detect cometary activity
among asteroids observed by WISE. Specifically the system is looking for Active Main Belt Objects (AMBOs), a
newly discovered and unusual phenomenon. The system is divided into tail detection and coma detection
algorithms, which will analyze each of the expected 158,000 potential moving objects detected by WMOPS in the
next iteration of the pipeline, which will launch in December 2012. The system was tested on over 100 coadded
WISE detections of active comets and about 100 coadded WISE detections of known inactive solar system objects
in order to determine effectiveness of the system and optimum criteria to minimize false positive detections while
maintaining a near-zero false negative rate.
Distributed Motor Control Life Testing in Extreme Temperatures
Reza Gheissari
Mentors: Mohammad Mojarradi, Colin McKinney, Zack Pannell, and Jeremy Yager
Current NASA spacecraft utilize a central motor control mechanism that while straightforward to implement,
requires significant wire mass and must be placed in a warm box to keep it within operating temperature range. A
distributed motor control (DMC) architecture uses up to an order of magnitude less wiring and does not use a warm
box. As a result, however, it will be exposed to extreme temperatures ranging from -180⁰C to +125⁰C. We seek to
ensure DMC performance in temperatures of up to -150⁰C for an extended period of time. Four integrated circuits
from DMC must be tested at these temperatures; they will be subjected to them through life testing in a
cryochamber cooled by liquid nitrogen. The four ICs will each have a dedicated testing board with five setups for
characterizing various parameters. Over the past month test procedures have been intricately detailed and the ICs
have been made test-ready. Requisite DMC documentation has been prepared at the module level and testing
results have been tabulated to aid testing. For six weeks after testing commencement, measurements will be taken
at increasing intervals to validate component performance and to move forward with eventual DMC
implementation.
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Model-Based Engineering of SMAP System Structure and Behavior
Corrina L. Gibson
Mentor: Shaun Standley
Using the Model Based Systems Engineering (MBSE) and Model Based Verification and Validation (MBV&V)
approach, complex system structure is architected to promote consistency, reusability, and systems engineering
robustness. After system structure is statically modeled, a simulation of system behavior is natively generated in
MBSE System Modeling Language (SysML) tools. The ability to generate a simulation directly from a static model
separates SysML tools from former systems engineering methods where behavior engineering is difficult to
express. The execution of these models provides insight to the reaction of the system given various inputs. Thus,
SysML can be used to perform design validation and verification throughout project life cycle phases far earlier than
more traditional highly capable simulations would be available. MBSE and MBV&V techniques have been used in the
development of the Soil Moisture Active Passive (SMAP) flight project to demonstrate Model-Based Engineering’s
effectiveness in complex space systems. Three such models that have been developed are the SMAP Thermal
Control System, SMAP Mission Scenario Tests, and SMAP Operational Readiness Tests.
Effect of High-G Impact on Rock Core Integrity
James Gilbert
Mentor: Charles Budney and Lori Shiraishi
The goal of the proposed Mars Sample Return mission is to collect rock samples from the Martian surface and
return them safely to Earth where in-depth scientific analysis can be performed. However the impact of the sample
carrying vessel as it undergoes a hard landing would create a mechanical shock that could potentially cause the
samples to be fractured and degrade their scientific value. This research is particularly interested in determining
the limits of mechanical shock which Martian-like rock cores can endure without fracturing. To quantify these limits,
a drop test apparatus which produces and measures acceleration as a function of time was developed to simulate
the shock that could be felt by the samples during return landing. Terrestrial rock samples from various locations
were selected as Martian rock simulants based on planetary scientists’ expectations of what will be found on Mars.
As the research continues, these rocks will be subjected to a spectrum of shock loads using the experimental setup
to identify a limit for the survivable shock load. The results of this research should be valuable for ascertaining the
feasibility of the proposed Mars Sample Return landing.
Robot Teleoperation and Perception Assistance With a Virtual Holographic Display
Charles O. Goddard
Mentor: Victor X. Luo
Teleoperation of robots in space from Earth has historically been difficult. Speed of light delays make direct
joystick-type control infeasible, so it is desirable to command a robot in a very high-level fashion. However, in
order to provide such an interface, knowledge of what objects are in the robot’s environment and how they can be
interacted with is required. In addition, many tasks that would be desirable to perform are highly spatial, requiring
some form of six degree of freedom input. These two issues can be combined, allowing the user to assist the
robot’s perception by identifying the locations of objects in the scene. The zSpace system, a virtual holographic
environment, provides a virtual 3D space superimposed over real space and a stylus tracking position and rotation
inside of it. Using this system, a possible interface for this sort of robot control is proposed.
The Creation of an Aerosol Retrieval Algorithm for the Airborne Multiangle SpectroPolarimetric Imager
Michael Goetz
Mentors: Olga Kalashnikova and Michael Garay
The composition, size, and reflecting properties of aerosol particles determine the overall magnitude of solar
radiation reflected back into space or absorbed. JPL’s Airborne Multiangle SpectroPolarimetric Imager (AirMSPI)—a
multi-directional, multi-wavelength, high-accuracy polarization imager—is one of many instruments designed to
measure the characteristics of aerosols within our atmosphere. Both polarization and intensity information are
obtained in the blue, red, and near-infrared spectral bands. However, a retrieval algorithm does not currently exist
that takes AirMSPI’s observations and links them to specific aerosol properties. Analysis was performed using Mie
Theory, a Dynamic Light Scattering code, and a Successive Orders of Scattering code to understand the effects of
an aerosol’s microphysical properties on simulated AirMSPI observations. By varying the reflecting properties, size,
composition, or a combination of the three, it was noticed that the single scattering albedo decreases while the
percentage of light being polarized increases with increasing reflecting properties for fine mode particles.
Understanding trends such as these will help in creating a future retrieval algorithm for AirMSPI.
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Correlations Between Technical Performance and Cost Growth: A Case Study Using Schedule Slips
Austin Gomez
Mentors: Kevin Rice, Kevin Endo, Eric Kwan, and John Jack
As a group project, this AO investigates the possibilities of linking the performance assessment data of the most
recent JPL missions with the associated cost and schedule delays. Specifically, the schedule slip data collected in
the previous year were enhanced and analyzed at a lower level in terms of Integration and testing, spacecraft, and
payload. These three subsystems contribute bulk of the schedule uncertainty within the Phase B-D portion of the
JPL mission life cycle. In order to increase the data sample size, this investigation also includes the recent missions
from various other NASA centers. This is considered the most crucial period for both schedule and cost growth.
Although interpretation of the schedule data within the Project Status Report proved to be difficult, incorporation of
the statistical program “R” has resulted in appealing graphical representations of the data.
Analysis and Feasibility Study of Radio Science CubeSat Missions
Carlos E. Gonzalez
Mentors: Sami Asmar and Kamal Oudrhiri
NASA JPL’s Radio Science Systems Group specializes in using the communication link between a Spacecraft and
Earth’s Deep Space Network to perform valuable radio science experiments and studies. The group studies the
effects on the radio signal as it travels through different materials such as the atmosphere of a planet or through
the rings of Saturn. By evaluating the signal, the group can determine information about the planet that many
sensor systems may not be able to or require a dedicated instrument on the spacecraft. All of this evaluation is
done using instruments that are not specific to the radio science group. The use of compact satellite systems
continues to grow in the Aerospace industry due to their compact package, low weight, and relatively low flight
cost. The radio science group is looking into the feasibility of using CubeSat systems as a means to performing
radio science experiments at a low cost. This could open the door and provide more opportunities and chances to
perform radio science experiments on a wider range of targets.
On-Chip Sample Preconcentration of Thiols for Sensitive in situ Extraterrestrial Analysis
Matthew Gordon
Mentors: Peter Willis and Maria F. Mora
The search for signs of life on extraterrestrial planetary bodies is among NASA’s top priorities in Solar System
exploration. Because all life on Earth is based on common biochemical roots and genetic history, one essential
astrobiological question is whether there is life elsewhere in the universe, and if so whether it has a similar
biochemical nature to us or not. Due to the anticipated complexity of extraterrestrial samples, identification and
quantification of individual species is extremely challenging or impossible without a method to separate them prior
to detection. Microchip capillary electrophoresis (μCE) is a powerful separation technique that has progressed
greatly in the last two decades and offers short analysis times, small sample and solvent consumption, and low
waste generation. Furthermore, μCE meets the size, weight, and power consumption requirements of a flight
mission. This technique has been successfully employed for analyses of a wide range of compounds in relatively
simple samples (e.g. water) to highly complex ones (biological fluids), demonstrating its powerful analytical
capabilities. We have designed a new microfluidic architecture that incorporates a preconcentration chamber into
existing automated microfluidic technology. This preconcentration chamber encapsulates milligrams of
functionalized silica beads (40µm) for the trapping of target molecules (thiols), which ultimately allows for ultralow
levels of detection. While preconcentration methods have been demonstrated for a range of molecules, they have
never been integrated into fully automated μCE devices. We have created a microfluidic device capable of
completely automated end-to-end analysis of thiols following an initial preconcentration step; this device would
allow detection of traces of sulfur-containing molecules in an automated, miniaturized fashion, which is crucial for
planetary studies.
Aerodynamic Performance of the Orion Drogue Parachutes and Designing Small Satellites for Europa
Brooke Goree
Mentor: Anita Sengupta
Primary Task: The Orion Multi-Purpose Crew Vehicle drogue parachutes are currently being analyzed for their
performance in the wake of the Orion Capsule. Data from 10% scale wind tunnel tests provided key insight
regarding the dynamic properties of the drogues, including drag, dominant frequency, and shape variation with
Reynolds’s number, capsule angle of attack, and trailing distance. In addition, the aerodynamic performance of
drogue clusters and reefed parachutes was obtained. This analysis provides the first quantitative insight into the
fluid structure interaction of the parachute and the Orion Capsule. A survey of pressure measurement technologies
was also completed to assist in future wind tunnel test planning efforts.
Secondary Task: The ice moon Europa is of great interest to scientists and NASA engineers studying solar system
habitability. A study is being conducted to determine the feasibility of adding a multiple nanosatellite augmentation
to a Europa orbiter mission as a low-cost means of obtaining geophysical, organic, and particle radiation not
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currently included in the orbiter’s payload. The nanosatellite study is currently seeking to define the radiation
environment, determine new radiation shielding options, select nanosat-scale instruments to accomplish the
science objectives, and provide a conceptual design for the nanosat that includes mass, power, and subsystem
definition.
Understanding and Predicting Landing Site Hazards on Mars
Jeffrey Green
Mentors: Matthew Golombek and Nicholas Warner
When sending missions to Mars, the safety of the spacecraft is paramount. In order to ensure the safe landing of
the vehicle, a thorough study of the landing site must be made. An important consideration when choosing a
landing site is the quantity of rocks on the surface. The abundance of harmful boulders can be measured and
compared in order to best choose a landing site using high resolution images of the surface from HiRISE, and
thermal data from IRTM and TES. HiRISE images are georeferenced to a global map of Mars and the thermal data
is overlain so that the image matches corresponding data. The images, which have a resolution of about
0.25m/pixel, can resolve boulders one meter in diameter or larger, allowing them to be observed and quantified.
Understanding the distribution of boulders gives insight into the safety of areas not covered by HiRISE, the
reliability of the thermal data, as well as the geology of the area. In the northern plains, boulders tend to be
distributed mostly around fresh impact craters.
Methods and Analysis in Electronic Packaging Engineering
Jacob G. Greenburg
Mentors: Charles J Kaczinski, David C Barr, and Mau-Huu Tran
Electronic packaging provides a fundamental role in any space exploration project that needs circuitry to operate.
The main aspects of the field include; system design and drawing generation, manufacturing, computer simulation,
final testing, and quality assurance. The primary topics for this summer’s research involve mostly system design
and drawings and computer simulation (i.e. finite element methods, FEM). In playing a supporting role in design
and drawings this research looks to optimize the efficiency of the design process by the creation of tool and method
standardization based on requirements for manufacturing. Furthermore, FEM plays a role in verifying the reliability
of a design before actual testing is conducted to check the final product. Both aspects of this summer’s research
piece together a critical aspect of the larger picture of a mission’s success.
Lander Vision System Estimator and Simulator Performance
Spenser C. Guerin
Mentors: Andrew E. Johnson, Nikolas Trawny, and Milan Mandic
The Lander Vision System (LVS) is an autonomous navigation system providing accurate state information of a
spacecraft for precision landing on a cosmic body. The estimator computes the optimum position, velocity, and
orientation by processing measurements from an inertial measurement unit (IMU), a light detection and ranging
(LIDAR) unit, and a camera. Descent images are processed to extract two measurements: feature matching
between the image and a ground map, and displacement measurements between consecutive images. A MATLAB
implementation of the estimator reads in the different measurements and produces quantitative results. Simulator
code was improved to simulate both image measurement types with the ability to adjust noise parameters.
Validation of the simulator ensured more realistic noise characteristics and exposed bugs on the image processing
side before integrating into the MATLAB environment. Future work includes modeling noise of a real IMU, so a more
accurate representation of IMU measurements can be incorporated into the estimator. Sensitivity studies for
different trajectories, IMUs, sensor noise parameters, and other factors will follow to evaluate estimator
performance in a more realistic, noisy simulation.
Telemetry Decomposition Analyzer
Matthew B. Gumport
Mentors: Lermont Khachikyan and Bonnie Theberge
The main goal was to be able to quickly transform Dawn's telemetry into a human readable format while identifying
gaps and potential errors in the data. There are two data structures that were subjects of the tool: frames and
packets. Packets sit within frames, but do not start in one fixed place and can also span multiple frames. The flight
software team would gets reports of missing data from science teams with no easy way of determining whether the
flight software, the instruments, or the network was responsible for the missing data. The result of the project was
a tool that expedited the investigation. The tool also finds and reports on flight software packet filtering
discrepancies. Frame and packet gaps were determined by taking the first difference between a given type of
frame or packet as the correct difference and reporting any deviations from that standard. The new difference
would be set to be the standard, since the change would probably be the result of a change in mode onboard the
spacecraft.
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Extreme Environment Electronics Design
Richard K. Harris
Mentors: Mohammad Mojarradi, Colin McKinney, Zack Pannell, and Jeremy Yager
The main objective of my projects this summer has been to develop electronics capable of operating in extreme
environments. For the Next-generation Integrated Camera project, I am assisting in the design and layout of the
application specific integrated circuit (ASIC) that will be used in a test imager. This imager will need to be able to
operate over a wide range of temperatures in order to be used in space-based applications. For the Distributed
Motor Controller project, I will be life-testing off-the-shelf electronic components to determine whether or not they
are operational after long exposure to very cold temperatures. This testing will help determine whether or not they
are capable of being used in space.
Actuation Using Piezoelectric Materials: Application in Augmenters, Energy Harvesters, and PiezoMotors
Jennifer Hasenoehrl
Mentors: Yoseph Bar-Cohen, Mircea Badescu, and Stewart Sherrit
Piezoelectric actuators are used in many manipulation, movement, and mobility applications as well as transducers
and sensors. When used at the resonance frequency of a piezoelectric stack, the actuator performs at its maximum
actuation capability. In this Space Grant internship, three applications of piezoelectric actuators were investigated
including hammering augmenters of rotary drills, energy harvesters, and piezo-motors. The augmenter shows
improved drilling performance over rotation only. The energy harvesters rely on moving fluid to convert mechanical
energy into electrical power. Specific designs allow the harvesters more freedom to move and thus generate more
power. The piezo-motors that were studied are based on the use of a ratcheting mechanism to convert vibration to
rotation. Friction inhibits this motion and is to be minimized for best performance. Tests and measurements were
made during this internship to determine the requirements for optimal performance of the studied mechanisms and
devices.
Thermal Interface Materials in Electronics Packaging Applications
Kevin Hischier
Mentors: Don Schatzel and Don Hunter
Thermal management in electronics packaging is one of the major drivers behind the design of the packaging
system. This analysis is specifically interested in the heat transfer between the individual printed circuit board
chassis and the adapter plate that connects to the radiator. The space between these is filled by a thermal interface
material to form a solid conductive path between the board and the radiator. This analysis compared high polish
gold finish to three thermal interface materials: eGRAF HITHERM, Chomerics Therm-a-gap 575NS and Chomerics
Therma-a-gap 579. These materials were evaluated in the following categories: thermal conductivity, removability,
contamination, and compressibility. Based on these criteria, the Chomerics Therm-a-gap 575NS has been chosen
as the baseline for the interface material, pending flight qualification.
The Development of a Sub-Kelvin Grating Spectrometer Test Bed
Jeremy Hodis
Mentor: Charles M. Bradford
There are many benefits to using a parallel plate waveguide grating spectrometer, the most important of which is
its small size for a given resolving power (R=lambda / delta lambda). When fabricated out of silicon its size
decreases by a factor equivalent to the index of refraction of silicon (3.4). We are working to prototype must be
made to demonstrate the benefits of using such a spectrometer. In making the prototype we must couple as much
light as possible into the spectrometer. A silicon lens was chosen to couple the light into the spectrometer. To we
must make measurements of the spectrometer. The simplest and fastest way to demonstrate the spectrometer is
to couple a high-power source into the input and scan the output with a warm detector.
The actual detectors which will be used on the spectrometer are still being developed. These detectors are
numerous, extremely sensitive, and work at very low temperatures (.050 Kelvin). A new testbed must be made to
efficiently test so many of these sensitive detectors. A modular design was chosen for more efficient use of space
and to reduce possible errors in testing.
LTP Performance Analysis Over Variable Arrangement
Andrew Hogue
Mentor: Amalaye Oyake
As Delay/Disruption Tolerant Networking emerges as the prevalent means of communication between deep space
entities, the realization is that DTN and its related protocols begin to exchange efficiency and prompt delivery of
information in exchange for the security and integrity of the data. The following report investigates the optimization
of the use Licklider Transmission Protocol, within a Deep Space Network; specifically designed for ensured delivery
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of high priority data, LTP ensures a relatively secure method of communication under harsh conditions where
standard UDP or TCP would fail. The question that arises concerns the point where LTP becomes a necessary
precaution in a Deep Space Network, and this report should make significant strides towards pinpointing that
threshold.
After creating a thorough and comprehensive simulation/testing suite, which interfaced with ION software to
simulate a DSN and its conditions, and writing a capture suite to capture, plot, and analyze the data output by the
software, I iterated through several permutations of tests, varying the light delay time between nodes, the error
rate or level of disruption within the network, and the arrangements of the LTP transmission loop to find the
optimal setup. The data and analysis collected provide insight into the practicality and efficiency of each
arrangement of the LTP loop within a simulated Deep Space Network.
Prime Focus Spectrometer (PFS) Fiber Positioner Testbed Development
Andrew C. Houck
Mentors: David Braun, Charlie Fisher, and Joel Kaluzny
Spectroscopic observation of cosmologic targets allows galactic archaeology studies and dark energy surveys,
which help us understand large-scale structures in the universe. An instrument capable of conducting wide surveys
is required, as previous technologies have had limited capability in the number of observable targets and amount
of data collected. The Prime Focus Spectrometer (PFS) is being developed for this purpose, and will be mounted on
the Subaru Telescope on Mauna Kea, Hawaii. This instrument includes an array of 2400 optical fibers, arranged in a
close-packed hex layout and positioned by Cobra rotary mechanisms. Each fiber can observe a distinct light source,
allowing simultaneous analysis of many targets. An improved Cobra positioner was developed this summer, and
the Cobra testbed is being upgraded to enable multi-positioner testing. This will allow implementation of collisionavoidance algorithms, as well as positioner characterization and improvement studies. NX was used for mechanical
design of testbed components, and MATLAB was used to develop the motor control and collision-avoidance
algorithms. Tests performed with the new setup will assess positioner performance, help finalize positioner design,
improve projections for full-scale target reconfiguration times, and be used to develop software and discover issues
for final instrument design.
Study of Discrete Element Modeling for Robotic Manipulation and Mobility
Ryan Houlihan
Mentor: Rudranarayan Mukherjee
Properties of granular media and the interaction of granules with robotic systems are important in the design and
optimization of the robotic systems. Through massively parallel granular media simulations based on Discrete
Element Method (DEM) much of the difficulty in quantitatively analyzing the interactions of robotic systems with
granular mediums can be alleviated. In our research we develop new methodologies for simulating such
interactions using DEM on regions composed of aspherical granules as well as grass. We run our models on the
parallel computing resources available at JPL. We modeled drilling on terrestrial and extra-terrestrial granular
surfaces. The results from our DEM based simulations were validated against experimental data developed at JPL.
We also perform a parametric study of wheeled mobility on granular media by analyzing the effects of parameters
such as bulk density, static friction, and rolling friction. The results of these mobility simulations are also validated
against experimental data on single wheel tests.
Development of Anion Exchange Membranes (AEMs) for Fuel Cells and Electrolyzers
Gevorg Hovakimyan
Mentor: Thomas I. Valdez
Anion exchange membranes (AEMs) are being developed for use in the next generation of polymer-based fuel cells
and electrolyzers. The benefits of AEMs for fuel cells and electrolyzers include increased efficiency, system
simplicity, and low cost. Understanding polymer properties such as anion exchange capacity and conductivity is a
requirement for this materials development. Traditional ion exchange capacity and conductivity testing was
conducted on anion exchange membranes. The ion exchange capacity was measured by immersing the polymer in
hydrochloric acid, exchanging the hydroxide ions in the polymer with chloride ions, and back-titrating to a
phenolphthalein endpoint to measure the number of hydroxide ions that came out of the membrane. Conductivity
testing was conducted with a four point probe, which feeds a constant current through the sample. Voltage is
measured at two known points on the sample, thereby allowing the resistance and conductivity of the sample to be
determined. The results of these tests as well as the performance of AEMs operating in fuel cells will be presented.
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Research on Highly Accurate Time Synchronization Over Wide Area Networks Using Precision Time
Protocol
Edward W. Huang
Mentor: Simon S. Woo
Precision time protocol is a method of synchronizing the internal clocks of independent computers to account for a
phenomenon called clock offset, the accumulated time difference between clocks. Current methods of time
synchronization include Network Time Protocol, which is accurate to milliseconds, and Global Positioning Systems,
which is expensive to maintain. Precision Time Protocol has been shown to be both accurate to microseconds and
inexpensive, offering a compromise between GPS and NTP. Since PTP has only been shown to function effectively
over Local Area Networks, discovering a configuration of PTP for Wide Area Networks will help increase the
precision and accuracy of time synchronization for increasingly large networks. Therefore, this work’s focus is to
explore the use of PTP in WANs, characterize the clock synchronization performance, and determine the
effectiveness of PTP by comparing the results of different configurations. The test results showed that peer-to-peer
mode, utilizing the peer-delay mechanism, yields the most accurate synchronization. Thus, we can conclude that
using the peer-delay algorithm would also be the most efficient PTP configuration for Wide Area Networks. Accurate
offset computed with PTP will be used to conduct more complex distributed network simulations, improve policybased network management, and develop predictive smart dead-reckoning.
Improving Resolution of Canopy Height Estimation Using Random Forests
Sebastian Imlay
Mentor: Marc Simard
Wall to wall canopy height maps of the globe have been created [Marc Simard and Baccini, 2011] with spatial
resolution of 1 km. This summer has been dedicated to increasing the spatial resolution and accuracy of these
models. We present a method for estimating canopy heights bundled with validation for said results. These
methods and tools are used to improve canopy height maps of Canada, the United States, and Mangrove forests in
Latin America.
Automating Performance Measurements of NASA Modems
David Isenberg
Mentor: Mike Cheng
NASA is in the process of replacing legacy modems that support the Space Network. The new modems are being
characterized under various service modes. The current method of testing involves many hours in the lab with the
modems, with little to no automation of the test process. This project aimed to streamline the process of testing so
that the instruments can be reconfigured for use with less human oversight. There are three main pieces of
equipment in use: the modem itself, a Bit Error Rate Tester (BERT), and a white noise generator. Each has a
unique method of remote control. Using the remote control specifications for each of the machines, a script was
created that features easy to understand, extensible methods of quickly generating test scripts that communicates
with all three machines in tandem to create the desired experiments. This script greatly reduces both human
oversight and work time in optimizing the modems.
Thermal Conductivity and Young’s Modulus Measurements on Icy Compositions
Aurya Javeed
Mentors: Martin Barmatz, Fang Zhong, and Mathieu Choukroun
Evolutionary models of icy satellites—e.g. Enceladus, Europa, and Titan—are predicated by an understanding of the
satellites’ constituent materials. Therefore, to further constrain these models, an apparatus is being developed to
simultaneously measure the thermal conductivity and Young’s modulus of icy satellite analogs as functions of
composition and temperature. My summer task is to calibrate this apparatus.
Methodologically speaking, two cylindrical, copper platens sandwich a sample. Because of the simultaneity of
measurements, the presence of a load coaxial with the platens necessitates support and inhibits a standard, axialflow measurement of thermal conductivity; thus uniaxial heat flow constitutes merely a zeroth-order
approximation.
After improving upon this zeroth-order approximation, fused quartz’s1 measured thermal conductivity between 190
and 300 kelvin falls within 2 percent of the NBS standard. Unfortunately, preliminary measurements of the
apparatus’s response to applied loads suggest a more complex mechanical characterization.
We intend for the apparatus to be fully calibrated at the time of presentation. Presently, we are going beyond
zeroth-order to develop first-order corrections to the apparatus’s thermal conductivity measurements. Also, we are
working to characterize the apparatus’s response to applied loads.
1
Fused quartz was chosen as its thermal conductivity is on the order of ice’s.
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Quantum Gravity Gradiometer
Justin Jeet
Mentor: Nan Yu
Gravitational field mapping is important to characterize planets. It can help map earth, ice, and oceans; and even
allow better understanding of dynamic processes within. The atomic gravity gradiometer utilizes matter-wave
interferometry based on stimulated Raman transitions using neutral atoms. This technique was first demonstrated
in 1991, and many atom interferometer-based sensors have been demonstrated since then. The quantum gravity
gradiometer in the laboratory utilizes two cold atom interferometers. Each interferometer can measure
gravitational acceleration directly, but this would require an inertial frame of reference, which is difficult to
accomplish even in a laboratory setting. Instead, the two interferometers measure the differences in gravitational
fields in between two locations. The use of a common reference frame allows non-inertial accelerations to be
cancelled out as common noise. The sensitivity of the gravity gradiometer increases with the square of
interrogation time, making it better suited for applications in space. To realize such a gradiometer on a satellite
platform, a more efficient and robust setup will be necessary. While work has been ongoing to achieve these goals,
optimization of the system is crucial. So far, we have increased atom signal significantly by simply adjusting the
Raman beam alignment and polarization. As part of this effort, I have developed a data analysis program which is
used to characterize the Rabi oscillations in the Raman transitions. Among other parameters, this program is able
to determine the Pi pulse length for the Raman transitions employed in the atom interferometers. A very
interesting discovery that resulted from analyzing previous data was an exponential decay term in addition to the
typical linear term which describes the decoherence of the Rabi oscillations. We also discovered that the oscillation
period and the required Pi pulse length seem to increase as the cloud of atoms is allowed to expand. We continue
to analyze data and to develop physical explanations for the phenomenon we are observing, all the while making
improvements to achieve the ultimate goal in realizing a satellite-based quantum gravity gradiometer for global
gravity field mapping.
Computing Surface Coverage From Optical Images
Breanna Johnson
Mentor: Ryan Park
In satellite operations, it is often crucial to determine how much of the area has been surveyed using optical
cameras. The purpose of this study is to develop a robust algorithm to efficiently compute this surveyed area.
Research in this area will serve as the groundwork for a future program that will combine this algorithm with an
image database to determine how much of the total area has been covered and where the gaps in coverage are
located. The simplest algorithm features a spherical finite element model, which is then tailored to an elliptical
model, and finally modified to some arbitrary shaped model. This final algorithm will better calculate the surface
area of the complex geometrical bodies often found in space.
Methods for Improving Long-Range Wireless Communication Between Extreme Terrain Vehicles
Paul Johnson
Mentor: Dimitri Zarzhitsky
JPL is developing an Extreme Terrain Mobility platform using of a combination of multiple, two-wheeled Axel
vehicles connected via a passively actuated central module. Reliable wireless communication between system
components is required to coordinate driving, docking, and science activities over large distances. Extensive use is
made of commercial, off-the-shelf technology, including the IEEE 802.11 “WiFi” communication protocol, receivers,
and access points. This research aims to develop methods and software tools for finding the optimal configuration
of the Linux operating system kernel modules, wireless router firmware, and antenna placement to overcome radio
frequency transmission challenges posed by the cylindrical, metal alloy body of the Axel rover. Early experiments
revealed detrimental effects of multiple active emission sources in the unregulated 2.4 GHz frequency spectrum,
resulting in inconsistent, intermittent, and unpredictable quality of service. In the follow-on study, new scripting
tools and system monitoring utilities are employed to assist with data collection and analysis, resulting in a
parametric characterization of the rover communication bandwidth and range in terms of protocol settings, network
congestion, and materials used to protect the vehicle.
Performance of Model-Based Aerial Reconstruction From Vision
Brandon M. Jones
Mentor: Curtis Padgett
Algorithms for the accurate and efficient estimation of a 3D scene and an airborne trajectory from a sequence of
2D imagery are critical to the success of real-time aerial navigation systems. Sensor measurements from onboard
instrumentation such as inertial measurement units (IMUs) and GPS aid in the estimation of the aerial trajectory,
but are known to suffer from the ill-effects of biases and measurement noise and provide no information relating to
the observed scene (which motivates the use of camera imagery). In this work, we evaluate the performance of
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the current techniques for jointly estimating both a vehicle trajectory and landmark states on a large scale and
discuss the applications of these techniques to unmanned aerial vehicles. Simulation and experimental results are
provided comparing the performance of the various methods.
Robotic Control and Perception Assistance Using Six Degrees of Freedom Input and 3D Display
Mark Jouppi
Mentors: Victor Luo and Heather Justice
Controlling complex robots with many degrees of freedom (DoF) such as the All-Terrain Hex-Limbed ExtraTerrestrial Explorer (ATHLETE) can be difficult and unintuitive for operators using conventional input modalities. An
application was built to allow operators to control the position and orientation of a simulated ATHLETE’s end
effector using zSpace, a system incorporating a virtual-holographic 3D display and a tracked stylus providing 6 DoF
input. Operators can command ATHLETE’s end effector to match the position and orientation of the stylus in a
natural manner. This application could be used by operators to plan, simulate, and control ATHLETE movements as
it drills into the surface of an asteroid in future missions.
A second project using zSpace was undertaken to allow operators to provide perception assistance and control for
dexterous, humanoid robots doing manipulation tasks with significant time delay. Perception is extremely
important for these tasks. However, current robots have limited autonomous perception and cannot always reliably
select and use tools in a cluttered, complex environment. zSpace is used to display a virtual-holographic 3D scene
showing simulated point cloud data from Robonaut 2 (R2). Using the stylus, the operator drags wireframes of
objects over the corresponding point cloud data in the scene representing that object, which gives the robot
segmentation information and allows the robot to use a priori knowledge about the object such as how to grasp it
and what actions can be performed on it. Operators can then compose command sequences and simulate how R2
would execute them.
Analysis of ISS Attitude Profiles via Analysis of Payload Data
Benjamin Katz
Mentor: Armin Ellis
One of NASA’s major thrusts for current and future planned earth-observing payloads is adopting the International
Space Station as a platform. Many of the desired missions require an ability to direct the payload’s observation to
specific locations on earth; doing so requires foreknowledge of the payload’s attitude, which in turn requires that
the attitude be predictable. Sets of attitude data for both the ISS ‘core’ (consisting of both internal slew rate
measurement gyros and micro-acceleration sensors) and for a specific payload on the station (the HREP payload,
located on JEM-EF) were considered for regularity, predictability, and correlation. This examination provides both
further clarification as to the ISS environment for payloads in terms of both suitability and concerns; in addition it
establishes a much better bound on predictive ISS attitude than that provided by ISS construction specifications,
which give an accuracy of +/- five degrees per axis.
Improved Maneuver Reconstructions for the GRAIL Orbiters
Mason L. Keck
Mentors: Tung-Han You and Peter Antreasian
Maneuver reconstructions for the Gravity Recovery and Interior Laboratory (GRAIL) A and B lunar orbiters were
improved through updates to the orbit determination filter and dynamic models. Consistent reconstructions of the
28 GRAIL A and B maneuvers from the Trans-Lunar Cruise phase in the fall of 2011 through the Transition to
Science Formation phase in February 2012 were performed. Standard methods of orbit determination were applied
incorporating the latest dynamic models and filter strategies developed by the GRAIL Navigation and Science
Teams, including a high resolution, 420x420 degree and order Lunar spherical harmonic gravity field model.
Maneuver execution model values were largely found to agree with the nominal designed values within one
standard deviation. These maneuver reconstructions will enable the GRAIL Navigation Team to better characterize
each spacecraft’s main engine performance. This will help the Navigation Team to navigate low (>10 km) altitude
orbits during the extended-mission phase in the fall of 2012.
Passive CubeSat Tracking: A Distributed Radiometric Approach to Tracking Near-Earth Small Satellites
Benjamin Kempke
Mentors: Eric Gustafson and Andy Klesh
Current passive tracking methods for small satellites are limited in their accuracy and are anonymous in their
identification. These techniques require early-on input from satellite operators in order to heuristically distinguish
between multiple satellites commonly grouped together after launch vehicle separation. While some missions may
make use of GPS- or transponder-based tracking, these technologies are usually prohibitively costly in terms of
space, power, or mission cost. By tracking the difference-based measures of Doppler and time-of-arrival of satellite
transmissions received at multiple synchronized ground stations, characteristics of the satellite's orbit can be
carefully refined without requiring any modification of the underlying satellite radio architecture. A system has been
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developed which gathers, processes, and filters one-way difference-based Doppler and time-of-arrival
measurements to help with early-mission satellite identification and supplement other (potentially unavailable)
tracking services. The system has shown superior performance when evaluated using current on-orbit satellites and
has also helped to identify the radio technologies and packet contents which are best suited for obtaining high
fidelity measurements.
Analysis of Cleaning Methods for Enhanced CO2 Composite Spray Cleaning Technology
Amanda L. Kessel
Mentors: Fei Chen, Ying Lin, and Moogega Cooper
Mars missions with a sample acquisition and handling system require strict contamination controls for Mars
samples, and for the release of Mars particulates into Earth’s atmosphere. Current cleaning technologies do not
address sub-micron particulate contamination issues. As a result, CO2 composite spray cleaning technology is being
developed as a precision cleaning tool for surfaces with complex geometries and fragile mechanical features. In
particular, Nitinol plugs are proposed to hermetically seal sample tubes containing core samples on future Mars
missions. Nitinol is sensitive to high temperatures, and exposure to dry heat microbial reduction temperatures may
put its material properties at risk. Initial evaluation of the CO2 composite spray technology’s ability to remove
particles from Nitinol surfaces is being conducted, and a validation method is being developed to analyze the
material surface and quantify particle removal efficiencies. This method is being upgraded for use with a Zeiss
microscope and software system which includes a motorized stage and MosaiX and ImageJ software. Nitinol
coupons are used as target surfaces and fluorescent spheres are used to represent particulate contaminants on 2D
coupon surfaces. Five different CO2 device cleaning parameters: temperature, pressure, distance, angle, and
crystal size are varied and analyzed for cleaning effectiveness.
Multibody Simulation Software and Modeling
Isaac S. Kim
Mentor: Rudranarayan Mukherjee
The goal of this project is to model and better understand vehicle terrain interactions through the simulation of
multibody systems. Both numerical accuracy as well as visualization of the system are required of the simulation.
One simulation method of granular media systems provided understanding between granular terrain such as sand
and single rigid bodies. Our main simulation software implements multibody constraints, allowing for more
macroscopic interaction. To further model interaction between bodies and terrain, we implemented multiple contact
force models as well as sliding friction models within the simulations. These models, along with the multibody
constraints allow us to construct systems in which a vehicle and basic sloped terrain interact. In addition,
documentation and code cleanup have furthered the software development. Thus, we have established the
fundamentals needed for simulation and can begin modeling and understanding more complex systems.
Feasibility Study of Nanosatellites as Radio Science Instruments
Jonathan Klein
Mentor: Kamal Oudrhiri
Radio Science studies the propagation of electromagnetic waves as they pass through fields and particles in space.
These measurements require extremely stable signals and high signal to noise ratios. They are typically done by
transmitting from a spacecraft, either with a frequency referenced to an ultra stable oscillator (USO) or using an
on-board transponder to relay signals from the Deep Space Network on Earth.
The feasibility of transmitting from a satellite to earth is limited on nanosatellites due to constrained mass, surface
area, and power. An alternative is to transmit from Earth and receive with a radio science receiver on-board the
spacecraft. This permits several orders of magnitude higher transmit power.
Another alternative to direct to earth communication is to use a constellation of two or more satellites flying in
formation. This reduces the path loss of the radio link and permits faster coverage of the target. This type of
mission may be suitable for nanosatellites. Nanosatellites deployed from a larger spacecraft could enable faster
coverage of targets and more efficient use of the Deep Space Network.
My presentation will review the feasibility of nanosatellites as interplanetary radio science instruments and describe
possible radio science missions.
Energetic Oxygen Ions Near Europa
Nicholas R. Knezek
Mentors: Michael Kokorowski and Henry B. Garrett
A study of energetic oxygen ions near Europa is conducted using data from the Galileo orbiter Heavy Ion Counter
(HIC) instrument. Ions with energies from 5 to 50 MeV/nucleon are examined to determine phase space densities,
radial diffusion rates, and losses near Europa’s orbit. Large-scale inward diffusion is found to occur for oxygen ions
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in this energy range, reproducing results derived from Voyager data by Gehrels et al. (1983). Depletions in the
phase space density are found for all energies near Europa’s orbit, even when excluding data taken within 1 RJ of
Europa, indicating strong losses outside of Europa’s direct wake. Radial diffusion coefficients are derived assuming
lossless diffusion and found to be similar to past results by Cohen et al. (2001) and Gehrels et al. (1983). Europa
as a sweeping mechanism is then examined as a possible explanation of the near-Europa depletion in phase space
density by considering ion drift velocities, radial diffusion rates, and possible ion loss mechanisms.
Soil Moisture Active Passive (SMAP) Thruster Testing: Flow Meter Calibration With LabVIEW
Hannah Kolus
Mentor: David Vaughan
SMAP requires ACS thruster performance that exceeds the thruster qualification. It is necessary to certify the
thrusters for the mission requirements. This thruster testing is scheduled to begin at the end of August. One source
of data recorded during testing is the propellant flow rate. This is measured by a flow meter which digitally outputs
the total mass throughput to the LabVIEW program during each test run. The flow meter must be calibrated
correctly with the LabVIEW program that controls the test and records test data to ensure that the data from both
sources correlate. For this calibration, Group 353A is conducting flow meter testing using a simple system set-up.
The propellant is water, in place of hydrazine, due to comparable densities, and a solenoid valve emulates a
thruster. Through this testing, we will determine how to analyze the flow meter’s data output to calculate the total
throughput.
Statistical Characterization of Solar X-ray Flux and Solar Energetic Particle Events for Use in Launch
Commit Criteria
Katelyn M. Kufahl
Mentor: J. Martin Ratliff
The protons in solar energetic particle (SEP) events can cause spacecraft anomalies that result in data loss and
service outages. Immediately following launch, spacecraft cannot afford to have certain vital operations disrupted
or delayed by severe conditions. As a result, it is undesirable to launch spacecraft during SEP events. Space
weather theory is not mature enough to predict such events, thus an empirical probabilistic approach to space
weather modeling is necessary. If a statistical relationship can be established between solar X-ray flux and the
proton flux measured by the GOES satellites, it can be used to predict imminent SEP events at launch time. The
X-ray data is useful because solar flares often occur in conjunction with SEP events, which can arrive at Earth
within a few hours. The Space Weather Analysis for Launch Criteria Tool provides the framework for such analysis,
producing estimates for the probability of an SEP event following an X-ray event. The functionality of the tool has
been expanded to account for noise in the data and to characterize the time delay between events, which yields
more comprehensive and accurate results.
Integration of Two Divide and Conquer Based Algorithms for Closed Loop Flexible Multibody Systems
Jeremy Laflin
Mentor: Rudranarayan Mukherjee
Modeling and simulation of robotic systems using physics based methods is an important tool to that enables
scientists and engineers to better predict the behavior of such systems. Modeling these multibody systems with the
Divide and Conquer Algorithm (DCA) [1] has been shown to be a highly efficient method of solving large system
dynamics. Two variations of this algorithm have been developed, the Orthogonal Complement based Divide and
Conquer Algorithm (ODCA) [3] for closed loop systems, and the Flexible body Divide and Conquer Algorithm
(FDCA) [2] for multibody systems which contain flexible bodies. The goal of this work is to demonstrate that these
two algorithms can be combined to efficiently model closed loop systems that contain flexible bodies.
References
[1] Featherstone, R.: Robot Dynamics Algorithms. Kluwer Academic Publishing, 1987.
[2] Mukherjee, R.; Anderson, K.S.: A Logarithmic Complexity Divide-and-Conquer Algorithm for Multi-Flexible
Articulated Body Systems. Computational and Nonlinear Dynamics, Vol. 2, No. 1, pp. 10–21, 2007.
[3] Mukherjee, R.; Anderson, K.S.: An Orthogonal Complement Based Divide-and-Conquer Algorithm
for Constrained Multibody Systems. Nonlinear Dynamics, Vol. 48, No. 1-2, pp. 199–215, 2007.
Pleiades and OCO-2: Using Supercomputing Resources to Process OCO-2 Science Data
Nick LaHaye
Mentors: Charlie Avis and Paul Springer
The OCO-2 satellite will be taking measurements and recording data regarding CO2 sources and sinks in the
Earth’s atmosphere. This data will then get downlinked and sent to JPL for processing. About 6% of the data will be
processed into deliverable science data locally and close to real-time. At the end of the mission, the data will need
to be reprocessed with the new calibration data and algorithms refined throughout the project. In order to meet
project requirements either an increase in size of the local cluster, or the use of an outside supercomputing source,
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in this case Ames Research Center’s Pleiades, is necessary. Summer efforts have been to create an end-to-end
prototype of an interface between the project’s local cluster and Pleiades in order to see if this is a feasible
solution. This prototype will do preprocessing at JPL, upload the data to Pleiades, process the data, and then
download the processed data from Pleiades. It also will have the capability of monitoring jobs being run on
Pleiades. There is a possibility that instead of having 6% of the data reprocessed locally in 6 months, that 30% of
the data can be processed by Pleiades in 2 months.
Cal9000: A Next Generation Earth Science Instrument Calibration and Validation Software Package
Alexander M. Lalejini
Mentor: William Johnson
Continuous monitoring stations in Lake Tahoe and Salton Sea are maintained by the Jet Propulsion Laboratory and
are instrumental in gathering relevant data on water surface and bulk temperature as well as various
meteorological measurements. National Institute of Standards and Technology (NIST) certified radiometers are
used to measure the surface temperature of the water; in order to maintain certification, the field radiometers are
calibrated in a controlled laboratory environment. A water bath, environmental chamber, and thermometer are
used to simulate a variety of conditions allowing for an accurate and reliable calibration process, and in order for
this process to work efficiently, a software package is required to manage the radiometer and laboratory
equipment. I have created a software package, developed using the Enthought Python distribution, to replace the
outdated software previously used to manager the radiometer calibration process. The new calibration application
has a user friendly interface and is able to provide real time plots of data collected during the calibration; the
software is now multithreaded allowing efficient management of serial requests sent to the instruments and the
subsequent responses, and a new output format has been designed to allow for easier data interpretation upon the
completion of an experiment.
Soil Moisture, Active and Passive (SMAP) Flight Software (FSW): Increasing Testing Autonomy and
Accelerating Module Validation
Richard Connor Lange
Mentors: Tom Fouser and Cindy Oda
Ever since Explorer-1, the United States’ first Earth satellite, was developed and launched in 1958, JPL has
developed many more spacecraft, including landers and orbiters. While these spacecraft vary greatly in their
missions, capabilities, and destination, they all have something in common. All of the components of these
spacecraft had to be comprehensively tested. While thorough testing is important to mitigate risk, it is also a very
expensive and time consuming process. Thankfully, since virtually all of the software testing procedures for SMAP
are computer controlled, these procedures can be automated. Most people testing SMAP FSW would only need to
write tests that exercise specific requirements and then check the filtered results to verify everything occurred as
planned. This gives developers the ability to automatically launch tests on the test bed, distill the resulting logs into
only the important information, generate validation documentation, and then deliver the documentation to
management. With many of the steps in FSW testing automated, developers can use their limited time more
effectively and can validate SMAP FSW modules quicker and test them more rigorously. As a result of the various
benefits of automating much of the testing process, management is considering this automated tool’s use in future
FSW validation efforts.
The Design of Extreme Environment Electronics for Space Based Applications
Matthew I. Laurence
Mentors: Mohammad Mojarradi, Colin McKinney, and Zack Pannell
Electronics intended for spaced based applications are fundamentally different from those we use on a day to day
basis. The extraterrestrial environment is harsh and unforgiving, yet the electronics deemed for space exploration
must be able to handle the wide temperature swings, high energy particles, and ionizing radiation that Earth’s
atmosphere typically shields us from. This extreme environment requires the electronics be designed with the
hazards in mind since repairing and replacing a module is improbable and in some cases, such as a rover on Mars,
impossible. The Application Specific Integrated Circuit (ASIC) referred to as NIC, or the Next Generation Integrated
Camera, is planned to be a small robust ASIC capable of operating on the Martian surface. NIC is to be a
replacement for any future missions that require a low-power engineering imager capable of detecting the visible
light spectrum. The design is currently in progress, which requires many computer simulations to verify our
designs. A test chip, that will validate our initial design, will be submitted for fabrication on August 20.
Assessing Ground Support Equipment for the Hyperspectral Thermal Emission Spectrometer
Gloria T. Lee
Mentor: William R. Johnson
The Hyperspectral thermal emission spectrometer (HyTES) is an airborne imaging spectrometer system for the long
wave infrared range that is being developed at JPL. Data from the HyTES will be used for several applications such
as high-resolution surface temperature and emissivity measurements as well as allow insight into examining the
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behavior of volcanoes and their effect on atmosphere and climate, wildfires, urbanization, water use and
availability, and land surface composition and change. The HyTES is a pushbroom imaging system which has a
downward facing camera. Some ground support equipment is necessary in order to test and calibrate the
instrument. Infrared light from a blackbody source passes through a monochromator in order to achieve a narrow
wavelength bandpass. The signal from the monochromator can then act analogously to a delta function and be
used to test individual pixels of the HyTES instrument for responses to specific wavelengths. Since the HyTES
instrument and the monochromator are large and mostly immobile, an adjustable system of mirrors directs and
focuses the signal between pieces of equipment. The system including the monochromator and blackbody has been
used with different mid and long wave infrared cameras in order to determine if the system will produce a strong
enough signal for calibration and testing with the HyTES.
Plot-Oh-Matic: Graphical User Interface for Plotting MSL Telemetry Data
Kaiying Liao
Mentors: David Y. Oh and Erisa K. Hines
The Mars Science Laboratory (MSL) is the Jet Propulsion Lab’s most recently launched Mars rover, designed for the
purpose of exploring and studying Mars’ climate and geology while searching for evidence of life on Mars.
Throughout the mission, scientists and engineers keep track of the state of the rover through information gathered
via Engineering Health and Accountability (EHA) channels, event records (EVRs), and data products. All of this data
is compiled in databases and thoroughly organized; however, the data may be difficult to understand when queried
for directly. One way to view and analyze data quickly and easily is through a display tool created by David Oh and
Daniel Alkalai called Plot-Oh-Matic. Plot-Oh-Matic is an intuitive graphical user interface that uses Multi-Mission
Data Processing and Control System (MPCS) tools to query telemetry data from the MSL databases and present the
information in interactive charts. This presentation will discuss its new features, which aim to process queried data
more quickly and conveniently as well as provide more flexibility to its users for data analysis.
Building a Massive Volcano Archive and the Development of a Tool for the Science Community
Justin Linick
Mentor: Dave Pieri
The Jet Propulsion Laboratory has traditionally housed one of the world’s largest databases of volcanic satellite
imagery, the ASTER Volcano Archive (~10Tb), making these data accessible online for public and scientific use.
However, a series of changes in how satellite imagery is housed by the EOS Data Information System has meant
that JPL has been unable to systematically maintain its database for the last several years. We have provided a
fast, transparent, machine-to-machine client that has successfully updated JPL’s database and will keep it current
in near real-time. We have also provided a publicly available tool that interfaces with NASA’s Earth Observing
System Clearinghouse (ECHO) that can provide functionality not available in any of ECHO’s Earth science discovery
tools.
HierarchThis: An Interactive Interface for Identifying Mission-Relevant Components of the Advanced
Multi-Mission Operations System
Krystof Litomisky
Mentor: Eleanor Basilio
The Advanced Multi-Mission Operations System (AMMOS) is NASA’s collection of tools and services that are
reusable across different NASA missions, supporting tasks such as Planning and Sequencing, Communications,
Navigation, or Ground Data System Integration. The Jet Propulsion Laboratory is currently creating a unified
database of all the tools and services in AMMOS. This database is in the Systems Modeling Language (SysML), and
is maintained through the MagicDraw modeling program. I created HierarchThis, a MagicDraw plugin that
automatically generates hierarchical, interactive diagrams of the tools in AMMOS. The plugin allows customers to
see the tools available in all function groups as well as the functional requirements that those tools satisfy. This
allows the customer to identify and interactively select only those tools that are relevant to the customer’s mission.
HierarchThis then connects to existing software to automatically generate a Service Level Agreement tailored to the
specific mission.
Capture and Documentation of Standard Ground System Solutions for Earth-Based Missions Using
Model Based Systems Engineering
Benjamin Liu
Mentors: Eleanor Basilio and Gregory A. Welz
The purpose of this research is to capture and document standard ground system designs contained in a Earthbased missions using systems modeling. The task included determination of fundamental subsystems and analysis
of its characteristics/features such as functionality and interconnectivity. Analysis of potential alternative solutions
was also performed and documented through model based engineering methods.
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Through exploring the ground systems structure of two major Earth missions, the Wide-field Infrared Survey
Explorer (WISE) and Soil Moisture Active Passive (SMAP) spacecraft, multiple models were created describing the
variety of aspects inherent in a ground system. Additional modeling was done evaluating the data and process
flows, providing a better understanding of the operations of the ground system as a whole. This research will aid in
the proposal and selection for ground system solutions of future missions through concise exposure of different
system elements as well as introduce potential opportunity to improve ground system design.
Transcendent Political Systems and the Gravity Model
Connor A. Lock
Mentors: Ed Upchurch and Leila Meshkat
Themis is a JPL based modeling framework that anticipates possible future states for the world within the next 25
years. The goal of this framework is to determine the likelihood that the US Army will need to intervene on behalf
of the US strategic interests. Key elements that are modeled within this tool include the world structure and major
decisions that are made by key actors. Each actor makes decisions based on their goals and within the constraints
of the structure of the system in which they are located. The goal of this research effort is to explain the function
and interaction of specific actors within varied political systems. In order to do so, a specific case study is
considered. This case study is the United States. This research elaborates on the government structure of the US
and the different influences involved in key decisions made by the government. The application of a Gravity Model
for the purpose of determining the actor interactions is explored. This analysis has proceeded in a top-down
fashion, analyzing key actors and organizations first, then distinguishing differences across various systems. The
framework in which the actors make decisions is the structure of the political system in which they are located.
Furthermore, the structure of the system is somewhat static and therefore easier to abstract into a useful model.
The way in which actors interact is of critical importance to the modeling of any political process, and an adapted
Gravity Model of Trade is explored to advance this modeling.
MMRTG Renderings and General 3D and Design Support
Alexander Y. Lu
Mentors: Victor X. Luo and Matthew Clausen
The purpose of my internship at JPL was to primarily assist the Conductor team in any 3d or 2d related work. The
majority of my time went to working on the renderings of the Multi-Mission Radioisotope Thermoelectric Generator
(MMRTG) and the General Purpose Heat Source (GPHS) for use by NASA and the DOE. I would first organize the 3d
model in Autodesk Maya (in the case of the GPHS, I also created some extra geometry). I then brought the model
into Luxion Keyshot for rendering. This project is almost complete.
Another project I worked on is a 3d data visualization written in Processing (which has the same syntax as Java).
Using a Microsoft Kinect and SimpleOpenNI, I tracked two separate hands to navigate the scene. I also had the
program store the initial depth of the hands upon recognition, allowing the user to simulate a mouse click simply
by moving their hand forward as opposed to the usual hovering over desired menu items in typical Kinect
interfaces. I am currently in the process of getting the visualization running in WebGL.
Designing, Building, and Testing the Planetary In-Situ Capillary Electrophoresis System (PISCES)
Eugene Lynch
Mentors: Peter Willis and Amanda Stockton
The PISCES instrument is a portable, miniature, modular instrument designed to analyze organic molecular
signatures of life. PISCES uses microcapillary electrophoresis (µCE) with laser-induced fluorescence detection
(LIFD) to analyze fluorescently labeled analytes pneumatically prepared and transported on a multi-layer
microfluidic chip. As a modular instrument composed of five independently functioning units, each module can be
easily detached from the system and used for subsystem testing in different environments, e.g. low temperature.
The pneumatic module contains circuitry and solenoid valves required to control pneumatic, on-chip sample
processing and transport. A prototype LabVIEW program and two printed circuit boards (PCBs) have been designed
to operate the pneumatics using an Arduino microprocessor, and a tentative design for the module’s housing has
been developed. The high-voltage module contains the circuitry required to apply varying electrical potentials to
the electrophoretic channel of the microdevice. Work is currently being done with Advanced Designs, Incorporated
to design the circuitry and a PCB for this module from a schematic developed for a similar instrument in
collaboration with our SBIR partners at Los Gatos Research. The optical electronics module contains the
spectrometer, laser, and circuitry required to power the laser. The mounting components for the electronics and
housing for the module have been designed, assembled, and tested. The optical module contains an optical
pathway through which light travels from the laser to the electrophoretic channel to the spectrometer. The housing
for this module has been designed and assembled with the aligned optical components inside.
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A Service Portal for the Integrated SCaN Network
Sarah R. Marx
Mentors: Oleg Sindiy, Mike Levesque, Peter Shames, Shan Malhotra, and Paul Wolgast
The Space Communication and Navigation (SCaN) program office owns the assets and services provided by the
Deep Space Network (DSN), Near Earth Network (NEN), and Space Network (SN). At present, these individual
networks are operated by different NASA centers—JPL for DSN—and Goddard Space Flight Center (GSFC) for NEN
and SN—with separate commitments offices for each center. In the future, SCaN’s program office would like a
deployment of an integrated service portal which would merge the two commitments offices with the goal of easing
the task of user planning for missions requiring services of two or more of these networks. Proceeding interviews
with subject matter experts in this field, use cases were created to include the services mission users would like to
see in this new portal. These use cases act as a guideline as the mock-up for the design of the user interface for
the portal. The benefit of this work is that the new portal will join the two commitments offices, as well as include
the feedback from the subject matter experts, in order to ease the time required and streamline/standardize the
process for planning and scheduling SCAN’s services for future space missions.
A Measurement System for Magnetic Characterization
Timothy R. Mastny
Mentors: Pablo Narvaez and Richard Kuberry
DC Magnetic characterization of the SAFT Battery Subsystem for the Geostationary Operational Environmental
Satellite-R (GOES-R) begins in November 2012 at JPL, building 150. The GOES-R magnetic requirements have
imposed strict magnetic cleanliness specifications on the battery due to the inclusion of a sensitive magnetometer
experiment. Prior to the battery magnetic tests, a Helmholtz coil and magnetics testing apparatus and procedures
are required to be verified, tested, and codified. As part of this preparation, the previous older version of the
magnetic measurement system was organized, prepared, and debugged to ensure future testing would have a
backup in case of unforeseen circumstances with the updated magnetics measurement system. The current
procedure was debugged on new and updated test hardware. We confirmed complete system functionality by
determining the magnetic moment of a known quantity of magnetic material and comparing against expected
theoretical magnetic moment results. The Helmholtz coil system was successful in nulling Earth’s magnetic field,
critical for the most accurate measurements of flight hardware. The SAFT Battery Test Procedure was developed
and updated to accommodate the actual GOES-R magnetic requirements and to encompass new procedures and
processes for future JPL projects requiring magnetic cleanliness requirements.
Rover Resizing Project
Christopher Matthes
Mentor: Kobie Boykins
The six-wheeled rocker-bogie suspension system used in all four planetary rovers built by JPL and sent to the
surface of Mars provides exceptional climbing ability; however, increasing the number of wheels will better
distribute ground pressure and in turn provide better traction for improved performance in soft sand. A prototype
was designed in NX Unigraphics to physically model the rover mobility with a completely new geometry of pivoted
links. A primary need to initiate prototype creation was the design and fabrication of adapter housings,
manufactured using stereolithography, for a set of existing surplus motors and harmonic drives. Linkage and wheel
design was focused on proper interface with these housings.
The obstacle-climbing performance of the rover is dependent on several factors, including location of the obstacle
relative to the wheels, the direction of travel, and the coefficients of friction between the terrain and obstacle.
Therefore, it was necessary to consider trade-offs between various suspension dimensions to optimize the
geometry. A four-wheeled rover was considered for software development, and a set of static equilibrium equations
was created for each obstacle position. This allowed for comprehensive optimization in sizing the rover’s wheel
base and wheel radius.
Statistical Evaluation of Climate Model Simulations Using CloudSat Observations
Kelsey McCullough
Mentor: Amy Braverman
Clouds exert enormous influence over the Earth’s hydrological cycle as well as over the exchange of energy in the
atmosphere. Any slight change in cloud abundance or distribution could cause drastic changes in Earth’s climate.
Therefore, developing accurate models of clouds is key to better understanding of the climate system. The goal of
this project is to quantitatively evaluate climate model simulations of cloud water content as a function of sea
surface temperature and altitude by comparing them to remote sensing observations from JPL’s CloudSat
instrument. We evaluated two models used in the Intergovernmental Panel on Climate Change’s Coupled Model
Intercomparison Project: one from the Bjerknes Centre for Climate Research and one from NOAA’s Geophysical
Fluid Dynamics Laboratory. CloudSat observations and both models covered the period between 2006 and 2010.
These data sets were individually stratified into cells of a matrix defined by ranges of values for altitude and sea170
surface temperatures. Using non-parametric statistical methods, we tested the hypothesis that the models’ and
CloudSat matrices came from the same underlying population. We were unable to reject this null hypothesis, and
thus conclude that the model simulated relationship between sea surface temperature, altitude, and cloud water
content are not significantly different from that of CloudSat for the time period tested.
Integration of Innovative Sensor Payload for Flight Test and Associated Ground Station Design
Casey Meehan
Mentor: Paula Pingree
The GEO-CAPE ROIC In-Flight Performance Experiment will attempt to provide on-orbit verification of a Focal Plane
Array (FPA) with an in-pixel analog-to-digital Read Out Integrated Circuit (ROIC) mated with a silicon detector
array. The ROIC/detector atmospheric imaging technology will be tested on a 3U CubeSat developed by the
University of Michigan. To ensure proper mechanical integration and cable routing of the payload, 3D printed
prototypes of its components and of Michigan’s chassis must be developed. CAD models of each part are generated
and evaluated for prototype integration. Parts are printed such that the prototype offers a useful evaluation of the
CubeSat’s structure, including but not limited to board spacing, fit check, hardware check, and cable routing.
Necessary edits are then added to create drawings for fabrication. To validate the technology on orbit, data will be
received and commands uplinked to and from the CubeSat’s telemetry system. An amateur band Yagi antenna
ground station is being constructed at JPL for communication with GRIFEX and future CubeSats. Ground station
hardware is selected and circuitry designed/programmed to allow rooftop integration of the antenna. Prototype
development and ground station construction are still in progress. Results and conclusions will be drawn after
further development.
Development of Advanced UV/Visible Detector Characterization With Avenues for Future Collaboration
Alex Miller
Mentors: Shouleh Nikzad and Timothy Goodsall
Recently, space-based telescopes such as GALEX and Hubble have utilized UV light detectors with great success.
However, new experimental devices are being developed that will revolutionize the field. New understanding of
physical and chemical interactions on quantum scales enables precise manipulation of atomic structure. This has
lead to the creation of some of the most advanced UV detectors to date. Moreover, experimentally designed
photodetectors must undergo in-depth testing to establish their characteristics. By mounting a photodetector in a
vacuum dewar and manipulating light sources with a monochromator, characterization can be conducted over
specific ranges of the spectrum. Providing a vacuum environment along with cryogenic cooling ensures that the
experimental device will receive the wavelengths of light with minimal atmospheric or quantum interference. When
we have conducted sufficient testing, the experimental detectors will be tested in collaboration with ASU. The
detectors will first be tested in ground-based telescope with implications for space-based deployment.
Verification and Validation: A Discussion of Its Process and Applications on SMAP
Michael Murry
Mentors: Carolina Barltrop and Shaun Standley
Verification and Validation (V&V) is widely recognized as a critical component in system engineering and is vital to
the success of any space mission. V&V is an independent process that is used to check that a system meets its
design requirements and specifications in order to fulfill its intended purpose. Verification often refers to the
question “Have we built the system right?” whereas Validation asks “Have we built the right system?” In this
presentation, a brief overview of the process will be discussed while focusing on the examples of its application on
a spacecraft project called Soil Moisture Active Passive (SMAP). These examples include verification reports, test
plans, anomaly investigations, and V&V tools.
Curiosity Rover: Surface Operations, System Verification, and Validation
Teresa Nguyen
Mentor: Tracy Van Houten
The Curiosity Rover, otherwise known as the Mars Science Laboratory (MSL), is scheduled to land in the late
evening of August 5, 2012. Before surface operations on Mars can begin, operational readiness tests (ORTs) and
thread tests (mini-ORTs) must be conducted to ensure that MSL’s operational system is working properly. In
preparation for the last remaining test, ORT-14, a surface operations notebook was created in order to provide the
Engineering Operations team a hard-copy reference of all relevant data produced by the team. MSL system
engineers have also been working on verifying and validating the completion of mission system requirements. The
top-level requirements are broad and considered to be level 1 (L1). Further specification of these requirements
branch down from L1 to L2 and continue down the ladder. The mission system requirements live at L3 and have
been supplemented by hundreds of verification items (VIs) to be tested at the system level. All the requirements
are housed in an electronic database called DOORS. From the ORT test results, many VIs and L4s (team-level
requirements) were passed and subsequently implemented the pass and sign off process for L3s and required
thorough updating within the DOORs database.
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Accuracy of the Ideal Point Heat Source Approximation in the Dual Probe Heat Pulse Method Using
Water
Christine Odabashian
Mentor: Fang Zhong
The objective of this experiment is to step toward a deeper understanding of the three-dimensional crystallization
network in cryogenic slurries. This crystallization in cryovolcanic lava flow is hypothesized to play an important role
in land formation on icy bodies such as Titan. Because crystallization follows the cold temperature gradient, the
slurries’ thermal properties are required for rheological modeling. Here the dual probe method is adapted to
measure the thermal conductivity and thermal diffusivity in icy slurries. The dual probe setup first must be
calibrated with pure water, whose thermal conductivity and thermal diffusivity are well known, in order to evaluate
any necessary corrections to the mathematical approximation of an ideal point heat source and sensor.
Experimental parameters such as the heat pulse amplitude and duration, AC exciting frequency and amplitude, and
lock-in low-pass time constant are determined for a desired 10% systematic uncertainty in measured properties.
Once the experimental set-up is finalized, experimental calculations of water’s thermal diffusivity and conductivity
can be compared with the widely-accepted values in order to determine the nature of any correction factors
necessitated by the ideal point heat source approximation in the dual probe heat pulse method.
Testing Saliency Parameters for Automatic Target Recognition
Sagar G. Pandya
Mentor: Thomas Lu
A bottom-up visual attention model (the Saliency model) is tested to enhance the performance of Automated
Target Recognition (ATR). JPL has developed an ATR system that identifies regions of interest (ROI) using a trained
OT-MACH filter, and then classifies potential targets as true- or false-positives using machine-learning techniques.
In this project, Saliency is used as a pre-processing step to reduce the space for performing OT-MACH filtering.
Saliency parameters, such as output level and orientation weight, are tuned to detect known target features.
Preliminary results are promising and future work entails a rigorous and parameter-based search to gain maximum
insight about this method.
Instrument Payload Proposal for the JUpiter Icy Moons Explorer (JUICE) Mission Announcement of
Opportunity
Andrew Park, Jr.
Mentor: Kevin Hand
The JUpiter Icy moons Explorer (JUICE) spacecraft constitutes the European element of the Europa Jupiter System
Mission (EJSM), a joint NASA-ESA flagship mission originally proposed to characterize Europa’s ocean and ice shell
by investigating the complex chemistry and geological features present on Jupiter’s icy moons. The recently
released Announcement of Opportunity, which recognizes NASA as a minor instrument payload contributor for
JUICE, will be used to select science instruments that can guarantee the greatest “science per dollar” benefit for
the mission. As part of an ongoing effort to better understand icy moons such as Europa, which many scientists
and astrobiologists believe to be habitable for extraterrestrial life, the heritage aspects of the proposed Fourier
transform infrared spectrometer (FTIR) will be carefully evaluated. Once the advantages of the FTIR are identified
based on the mission’s science objectives listed in the JUICE Science Traceability Matrix, a comprehensive proposal
detailing the applicable features of the FTIR will be submitted to the Science Programme Committee of the
European Space Agency for approval.
Fabrication and Design Testing of a Deployable Starshade Prototype
Laurel Paxton
Mentor: David Webb
One of the next steps in the exoplanet search is the development of occulter technology. Starlight supression for a
telescope would provide the ability to more accurately find and characterize potential true-Earth analogs.
Coronographs have been the subject of much research in recent years but have yet to prove themselves a feasible
approach. Attention has now turned to external occulters or starshades. A large occulting mask in front of a
telescope should provide a comparable optical resolution to a coronograph Under a TDEM grant, a proposed
starshade design was demonstrated to exceed coronograph resolution by at least an order of magnitude. The
current project is to demonstrate that the current design can be manufactured and then properly deployed. Four
sample starshade petals were constructed, ready to be attached to a pre-existing deployment truss. Time was
spent detailing and modifying the petal construction process, so that future petals could be constructed at a more
accurate and faster pace.
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Determination of the Shape of Vesta Using Radio Occultation Data From the Dawn Spacecraft
Claudia Pham and Dustin Buccino
Mentor: Sami Asmar
In 2007, NASA launched the Dawn Mission to increase understanding of the geophysical properties of the asteroid
Vesta and the dwarf planet Ceres. Since arrival at Vesta in 2011 before departing for Ceres in 2012, Radio Science
Receivers (RSRs) at NASA’s Deep Space Network (DSN) antennas collected numerous occultation data sets that
occur when the radio signals from Dawn are occulted by Vesta as seen from Earth. By utilizing edge diffraction
theory, the exact time the signal is occulted can be identified. When matched with Dawn’s location in space at the
corresponding occultation time, the radii and chord lengths of Vesta can be determined to good precision,
producing detailed mapping and shape of Vesta, to be later included in the geophysical interpretation when
combined with gravity data. Comparing the radio science occultation solution to already known dimensions and
topography of Vesta, the method can be validated and applied to future missions to determine the size and
topography of other celestial bodies.
Graphic Design in Human Interfaces
Christopher Joseph Phillips
Mentors: Victor X. Luo, Matt Clausen, Scott Davidoff, and Jeff Norris
The way humans interact with computers is a constantly evolving process. Graphic Design serves as an aid to how
a user navigates an interface.
The overall objective was outreach focused to inform the general public on the MSL landing. My methodology is to
assist programmers by generating the necessary assets via Photoshop, Illustrator, Processing and Maya.
The results have been various graphics created for the Conductor team such as 3d models, A user interface
mockup for a game, MSL Video, ZSpace Demo Video, research new logo, and designed asteroid game concept with
Charlie Goddard and Mosaic Poster of Curiosity.
In Conclusion, I have found the JPL working environment allows for me to foster my skill set within a high speed
work environment which gears me for a job after school.
Benchmarking for High-Performance Computing of NASA Flight Missions
Jennifer Piccione
Mentors: William Whitaker and Yutao He
Benchmarking is the process of running a computer program to assess the performance of the computer’s
architecture. Many benchmark suites exist for ground computer systems, such as LINPACK for supercomputers and
EEMBC for embedded systems. My objective is to gain a better understanding of how benchmarking can be
modified to target space flight computer systems as opposed to ground systems. I first studied benchmark
applications, such as Dhrystone and LINPACK, to become familiar with the process. Then I chose to analyze a
specific space navigation application, Terrain Relative Navigation (TRN). More specifically, I looked at the Fast
Fourier Transform (FFT) part of the navigation source code and modified it to access a different number of
processors on the Tilera TILE64 multicore processor. After running the program with different numbers of cores I
noticed that the higher the number of cores gets, the less it affects the runtime of the FFT portion of the TRN code.
The next step is to analyze the floating point operations per second to see how the number of cores might affect
that aspect of the application. Finally, I will analyze the application with respect to spatial and temporal locality to
explain how it accesses memory.
Adapting an FFT-Based Image Matching Algorithm for Air-MSPI
Bryan A. Plummer
Mentor: Veljko Jovanovic
The Multiangle SpectroPolarimetic Imager (MSPI) is a candidate for a science instrument to fly aboard the AerosolCloud-Ecosystem mission. Air-MSPI is part of the second phase of a three-stage development plan in which the
instrument is tested aboard aircraft. This software development project adapts a proven phase correlation based
image alignment method to be used in cloudy Air-MSPI images. At first, a particular image-matching algorithm is
extracted from a much larger but well-tested library. The code was then refactored and its interface altered to fit
the design of the GeoCal library underlying existing MSPI data production software. Also, support to HDF-EOS5
image file formats was added so that dependencies on specialized image formats and interfaces of the legacy code
have been removed. The converted algorithm is then tested on using known solutions given by the original method
and then on raw image data collected from Air-MSPI. As the final procedure in the test cycle, a transformgenerating image warping to match two images is used to map one image onto the other. The FFT-based approach
used in this algorithm has seen promising results in previous applications.
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DKF Syntax/Logic Checker
David Powell
Mentors: Joseph Hunt, Luis Morales, and Ricardo Torres
A DSN Keyword File (DKF) is created by a spacecraft project to give the DSN stations instructions on how to
interact with the spacecraft. These files often are created with errors which, up to this point, mostly needed to be
manually located by JPL personnel. There are two general categories of errors that are found in the DKF: syntax
errors and logic errors. Syntax errors occur when either the DKF is badly formatted or when the variables given to
the keywords do not follow the requirements of the keywords. Logic errors occur when the sequence of keywords
does not give reasonable instructions in a given scenario. Because of the length and intricacy of the DKF, it can be
difficult and time-consuming for one person to proofread a DKF. The task was to create a tool to automate the
process of checking syntax and logic in a DKF.
The tool was designed to be run from a command prompt. The name of the DKF is given as an argument, as well
as flags to indicate which of the tests are to be run. The tool creates a “.basic” and/or a “.logic” file which contains
a log of all the detected errors. Because the logic rules for the DKF are filled with exceptions and quirky behavior,
some warnings also may be included in the “.logic” file to signal strange behavior that is not necessarily incorrect.
A breakdown of the tasks is as follows:
1.
2.
3.
4.
Create a program that can perform tests on a DKF and export the results to an error file
Write comprehensive checks to detect any syntax errors
Write some basic logic checks with the capacity for expansion
Test the program using existing DKFs and specific test cases
After running hundreds of DKFs through the syntax checker, as well as running hundreds of test cases for specific
scenarios, the behavior appears to be as desired. Errors in format and keyword construction are identified and
logged as expected.
The logic check was also run with the same DKFs, and the error files appear fine. Because of the intricacy of the
logic, this tool was designed with the intent of signaling the Sequence Engineer to issues that may have been
overlooked. For this reason, files that are logically correct may still have lines flagged in the error file because of
the possibility that something was missed by accident. This is in contrast to the syntax checker, which flags only
(and all) instances that the DKF does not comply with the DSN documentation.
The logic check has been designed in such a way that a software engineer should be able to add scenarios to the
check when desired.
Mars Science Laboratory Mobility Visualization
Ben Province
Mentor: Justin Lin
Reliable navigation of an extraterrestrial rover is imperative. Wheel slip and uneven terrain affect both the total
distance that a rover travels during a commanded movement and its change in orientation. The Mars Science
Laboratory (MSL) relies on gyroscopes, accelerometers, and visual odometry to determine the rover’s change in
position and orientation for each step of commanded movement. Given the differences between Mars and Earth
gravity, the drive characteristic testing is performed with Scarecrow, the Mars-weight MSL mobility testbed. The
telemetry data from Scarecrow is combined with the position and rotation data from a Vicon motion tracking
system used to animate a virtual model of the rover, which drives over a surface constructed from laser scans of
the test terrain. In this manner, MSL mobility performance can be easily evaluated and documented. This test data
can be useful when determining best driving practices on various terrains on Mars.
Automatic Retrieval and Filtering of DSN Monitor Data for RFI Analysis
Charity Quijano
Mentor: Selahattin Kayalar
The Deep Space Network (DSN) is susceptible to radio frequency interference (RFI), which may seriously affect the
telemetry reception. The DSN is susceptible to interference from the high-power transmissions of near-Earth
satellites and terrestrial transmitters operating in or near the DSN frequencies. In addition, there has been on rare
occasion mutual interference between DSN missions. With the growing number of ground-based and airborne
transmitters, the likelihood of having an interference is higher. Once an RFI event is observed, it is important to
quickly identify the source of and subsequently mitigate the interference. This project is to develop a tool to
achieve this goal. This tool automatically scans, retrieves, filters, and archives DSN monitor data based on
frequency separation and spatial separation between two spacecraft or satellites. It will reduce the engineering
time needed to conduct RFI investigations.
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Balloon Fitting Drop Test
Jennifer N. Quintana
Mentors: K. Charles Wang and Andrew Kennett
The Balloon Fitting Drop Test is a functional verification and validation ground test of vehicle equipment associated
with the Low-Density Supersonic Decelerator (LDSD) project. The objective of the LDSD project is to raise the
Technology Readiness Level (TRL) of three new Entry, Descent, and Landing (EDL) technologies – a 6-meter
attached torus Supersonic Inflatable Aerodynamic Decelerator (SIAD), an 8-meter attached isotensoid SIAD, and a
30-meter Supersonic Ringsail (SSRS) Parachute. The Drop Test encompasses test equipment design, test
requirements generation, data acquisition, deviations of the test equipment and assumptions, testing methods,
safety considerations, and testing facilities. In the present test, the Balloon Fitting is proof-tested to loads up to
20,000 pounds at elevation hang angles between 15º and 30º. Additional permutations include lateral hang angles
of +/- 30º. Special test fixtures are designed to interface with the Balloon Fitting, including the Balloon Fitting
Platform. Structural analysis is performed to ensure adequate margins of safety on the fixtures, initially with
closed-form equations followed by detailed finite-element analysis. The test will be conducted in September 2012
as one of the tests in preparation for the Supersonic Flight Dynamics Test (SFDT)—the integrated test of the new
LDSD technology, planned for June 2014.
State Machine for the DESDYnI CTT Subsystem
Eashwar Rangarajan
Mentor: Robert Smythe
This project will create a prototype State machine and communication interface for the Control, Timing, and
Telemetry (CTT) Board on the DESDynI (Deformation, Ecosystem Structure, and Dynamics of Ice) Radar
Instrument. The radar techniques utilized by DESDynI require proper flow of information and timing signals,
necessitating an onboard dedicated management system. The CTT State machine residing in this board will allow it
to precisely control the data collection process. Development of the State Machine will be done through a Xilinx
ISE-based tool Chain and on a JPL-designed custom Xilinx Virtex 5 board. In addition to creating the state
machine, this project will implement a serial interface between the CTT board and the rest of the radar
instrumentation. This interface will allow the instrument operator to control radar instrumentation data and timing
as well as interact with other software modules in the radar instrumentation. Though DESDyI is still in prototype
phase, the project aims to establish a working base for future project development.
Stereo Photogrammetry of Volcanic Domes and Flows on Venus
Jonathan Reeves
Mentor: Karl Mitchell
During the Magellan Mission of 1990-1992, nearly 20% of Venus’s surface was imaged in same-side radar stereo
imaging. Due to technical issues and computing power, many of the pairs of images necessary for stereo imagery
were never matched. A stereo processing chain is currently being developed in order to automatically match the
stereo images and create the first high-resolution stereo model of Venus. I am testing the automated stereo
matcher and adjusting the match parameters in order to produce disparity maps over volcanic terrain. These
disparity maps will be processed to produce elevation data at the highest resolution to date, allowing the first
systematic study of the morphometry of lava flows and domes. In order to quickly examine the volcanic surficial
morphology once the stereo processing chain is functioning, I am compiling a catalogue of volcanic domes and
flows within the stereo coverage. With accurate elevation data from the stereo processing chain, we will be able to
more carefully analyze these geologic features, and gather a better understanding of the lava rheology and
emplacement dynamics of Venus.
Ultrasonic Spray Deposition of Platinum Black on Polymer Membranes for Fuel Cell Electrodes
William A. Rigdon
Mentor: Thomas I. Valdez
Proton exchange membrane (PEM) fuel cell systems are being developed to enable future NASA space missions.
The power producing element of a fuel cell system is the membrane electrode assembly (MEA). A process was
developed to prepare MEAs for polymer electrolyte fuel cells using a direct ultrasonic spray deposition of platinum
black catalyst suspensions. The ultrasonic spray head with frequency of 60 kHz is utilized for coating a thin and
uniform electrode layer on the substrate. These electrodes are designed to run at high efficiency conditions, low
current (200 mA/cm2) and high potential (> 900 mV) when operated under H2 and O2 in pressurized systems to
meet the NASA fuel cell voltage efficiency goal (> 72%). For the spray deposition, catalysts were suspended in a
mixture of water and isopropanol solvents and an ink formulation was optimized. The addition of hydrophobic
additives to enhance water transport in the cathode was also analyzed. An improvement in the conductivity
between the ion pathways can be realized by this direct deposition method on to the polymer. As a result, this
electrode preparation process leads to a benefit in cell performance over conventional methods.
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Carbon Isotope Chemistry in Molecular Clouds
Amy Nicole Robertson
Mentor: Karen Willacy
Few details of carbon isotope chemistry are known, especially the chemical processes that occur in astronomical
environments like molecular clouds. Observational evidence shows that the 12C/13C abundance ratios vary due to
the location of the 13C atom within the molecular structure. The different abundances are a result of the diverse
formation pathways that can occur. Modeling can be used to explore the production pathways of carbon molecules
in an effort to understand and explain the chemical evolution of molecular clouds.
GRAIL Ultra-Stable Oscillator Characterization
Nicholas G. Rodriguez
Mentor: Kamal Oudrhiri
An ultra stable oscillator (USO) is a clock used for communication by spacecraft when transmitting a very precise
signal. This is important, particularly to radio science, because a lot of information can be derived from changes in
a radio signal as it travels through space. In the GRAIL mission, Ultra Stable Oscillators generate a very precise
timing, allowing the DSN to use Doppler measurements to detect very precise changes in each spacecraft’s
velocity. This information is then used to generate a lunar gravity field map. Knowing the gravity field map of the
Moon helps to increase our understanding of the Moon’s interior and its thermal history. In my characterization of
GRAIL’s USOs, flight data is used to compute the Allan deviation and USO frequency for each Orbiter in order to
measure the stability of the USOs in space.
Correlations Between Technical Performance and Cost Growth: A Case Study Using Historical Cost Data
Dean Rowley
Mentors: Kevin Rice and Eric Kwan
As Flight Projects historically exceed the available budgetary funds allocated by NASA HQ, this AO investigated the
possibilities of linking the performance assessment data of the most recent JPL missions with the associated cost
and schedule delays. Project lessons-learned indicated that there are common reasons for cost growth where
strong correlations existed between technical performance and cost/schedule performance. This group research
project investigates historical data from the 13 most recent JPL flight projects to determine trends and correlations
between technical and programmatic parameters to predict cost growth. Each of the 13 projects is analyzed using
3 major data sets: technical complexity, subcontractor performance, and schedule. Each data set is analyzed to
determine which correlations exist. Last summer, research was done to explore correlation between projects of
cost growth per month. In order to continue research performed last summer, my area of focus was to establish
the cost per month and per milestone for each project, and to set a baseline for the 3 data sets that acts as a
common comparison between the analyses and to perform regression analysis and modeling to establish
relationships among the projects. Conclusions derived from this group research can be utilized to form a historical
data base for future projects and compared against the current in-work flight projects to predict cost growth by
milestone and percentage complete.
DARPA F6 Trade Studies and Data Analysis
Tyler J. Ryan
Mentor: Steven L. Cornford
I have now experienced the complete lifecycle of programming. Last summer, I built foundational discrete event
simulation models in Arena that have since evolved into automatically generated modules written in Python. The
first few weeks of my time here were spent familiarizing myself with the new models, and the tool of which they
are just a single part. Since then, I have been analyzing, debugging, and adding functionality to the models in an
attempt to generate usable, verifiable data. As this DARPA F6 project nears the end of Option Period 1, we need to
generate a fully functional tool that produces outputs consistent with the inputs provided. To this end, I have
performed hundreds of test runs, locating interesting regions and edge cases, and set up large scale Designs of
Experiments in these regions. This allows for the examination of the effects of input parameters such as data rate
and battery capacity on important outputs such as data downlinked and Present Strategic Value, a real options
cost-benefit analysis. I will present the findings of these studies in my final report.
Sequence Revitalization: Timeline Management Service
Justin Saletta
Mentor: Paul Wolgast
It takes a significant amount of planning to operate spacecraft, especially at such great distances. Every aspect
must be carefully planned out and modeled ahead of time to ensure the greatest probability of mission success. For
some missions, it is necessary to plan out every activity weeks or even months ahead of time. The purpose of this
project is to develop new sequencing software to better model these spacecraft operations. This software includes
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database development, REST interfaces, and visualization capabilities. Especially pertinent to what I am doing is
the visualization, in which it is necessary to determine and implement the best way to represent and display
namespace and timeline data.
Survival of B. horneckiae Spores Under Ground-Simulated Space Conditions
Bradley R. Schanche
Mentor: Parag Vaishampayan
To prevent forward contamination and maintain the scientific integrity of future life detection missions, it is
important to characterize and attempt to eliminate terrestrial microorganisms associated with exploratory
spacecraft and landing vehicles. Among the organisms isolated from spacecraft-associated habitats, spore-forming
microbes are highly resistant to various physical and chemical conditions, which include ionizing and UV radiation,
desiccation and oxidative stress, and the harsh environment of outer space or planetary surfaces. Recently a
radiation resistant, spore forming bacterial isolate, Bacillus horneckiae, was isolated from a clean room of the
Kennedy Space Center where the Phoenix spacecraft was assembled. The exceptionally high tolerance of extreme
conditions demonstrated by spore-forming bacteria highlighted the need to assess the viability of these microbes in
situ (in real) space. The proposed BOSS (Biofilm Organisms Surfing Space) project aims to understand the
mechanisms by which biofilm forming organisms, such as B. horneckiae, will potentially be able to withstand harsh
space conditions.
The objective of this study was to establish reference data on the survivability rates of B. horneckiae spores after
exposure to ground-simulated space and Martian conditions. B. horneckiae spores were recovered from metal
coupons after exposure to experimental conditions, using polyvinyl alcohol, after which serial dilutions were
performed to determine the total number of viable spores in each coupon. The results showed that simulated UVspace exposed spores had a lower survivability rate than simulated space conditions without UV exposer. Similarly,
simulated Martian UV had a greater reduction in spore survivability than simulated Martian conditions without UV
exposure. The data generated is important to assess the probability and mechanisms of microbial survival,
microbial contaminants of risk for forward contamination, in situ life detection, and to safeguard the integrity of
sample return missions.
Future Prototype Assessment for Cockpit 2.0 (FPAC)
Michael P. Scherer
Mentors: Scott Davidoff, Heather Justice, and Victor Luo
There is a steep learning curve for sequencers and mission planners to create mission plans for landing and driving
robotic vehicles on current text-driven interfaces. Touch screen interfaces are quickly growing in popularity as a
means to effectively and intuitively interact with computers and robotic systems. Future Prototype Assessment for
Cockpit 2.0 (FPAC) is designed as a system for assessing the effectiveness of various touch-based paradigms for
mission planning and sequence development. Operations for approach, landing and investigation of near-earth
objects (NEO’s) with the ATHLETE platform are chosen as the use case for this system. Scientists, engineers, and
other mission-planning roles are the primary audience for FPAC. Usability and training minimalization are the
primary metrics for this system, in order to optimize the workflow of sequencers and mission planners. Flexible
touch-based camera controls, interactive timeline, sequence comparison options, and 3DConnexion SpaceBall
integration are all included features in the assessment package.
Model-Based Systems Engineering: Creation and Implementation of Model Validation Rules for MOS 2.0
Conrad K. Schmidt
Mentors: Christopher Delp, Louise Anderson, and Elyse Fosse
Model-based Systems Engineering (MBSE) is an emerging modeling application that is used to enhance the system
development process. MBSE allows for the centralization of project and system information that would otherwise be
stored in extraneous locations, yielding better communication, expedited document generation and increased
knowledge capture. Based on MBSE concepts and the employment of the Systems Modeling Language (SysML),
extremely large and complex systems can be modeled from conceptual design through all system lifecycles. The
Operations Revitalization Initiative (OpsRev) seeks to leverage MBSE to modernize the aging Advanced MultiMission Operations Systems (AMMOS) into the Mission Operations System 2.0 (MOS 2.0). The MOS 2.0 will be
delivered in a series of conceptual and design models and documents built using the modeling tool MagicDraw. To
ensure model completeness and cohesiveness, it is imperative that the MOS 2.0 models adhere to the
specifications, patterns and profiles of the Mission Service Architecture Framework, thus leading to the use of
validation rules. This paper outlines the process by which validation rules are identified, designed, implemented
and tested. Ultimately, these rules provide the ability to maintain model correctness and synchronization in a
simple, quick and effective manner, thus allowing the continuation of project and system progress.
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Improving Mission Sequencing Using Cloud Resources
Benjamin A. Schwartz
Mentors: Paul A. Wolgast and Khawaja S. Shams
Mission critical spacecraft sequencing requires a highly performant, reliable, secure, and durable solution. To
support the nature of spacecraft communication, the software must support horizontal scaling to support users in
bursts. The Sequence Revitalization (SEQR) project at NASA JPL is chartered with delivering the next generation of
sequencing software adhering to these requirements.
Currently, this support is provided through a restful application server backed by a database server. This project
explores novel use of cloud computing to enhance the elasticity, performance, cost, security, and flexibility for
SEQR through a principled, quantifiable approach. In this project, we will benchmark network, file, and database IO
for the SEQR deployment, identify bottlenecks, and leverage the latest cloud offerings to optimize our deployment.
We contribute deployment automation and optimize existing architecture in the cloud. Simulated client loads are
used to test data throughput, latency, and consistency to evaluate if the software meets its use case requirements.
Results show that cloud computing provides unprecedented scalability and performance, while delivering ultimate
flexibility through an elastic deployment model. Deployment is automated to make it fast and easy to maintain for
multiple missions, cost is a fraction of using local resources, and data replication and security is robust.
People and Vehicle Tracking: Developing Ground Truth
Sean Sharma
Mentor: Curtis Padgett
Designing a robust algorithm in order to track people and vehicles requires a great deal of knowledge about their
movement behavior beforehand. To acquire this understanding, surveillance imagery must be looked at and
evaluated in order to develop models that can be applied by the tracking algorithms. A person must identify where
the people or vehicles are in various frames before developing these models; this is called Ground Truthing. The
Ground Truth is used to derive the models and as a baseline for evaluating how the algorithm performs.
Research and Development of a New Prototype Comet Sampler
Rory (Jesse) Shevin
Mentor: Paul Backes
Comets are relics of the creation of the solar system, and sampling comets will allow us to have a better view of
the formation of sun and everything orbiting it. Obtaining a sample of the comet can be very difficult though,
because there may be debris in the vicinity of a comet which can interfere with system function. Additionally, there
are a wide range of possible surface properties that are expected, so any sampler must be robust enough to handle
a wide range of possibilities. The objective of this project is to design, build, and test a device which can sample a
comet without using any actuation. The lack of actuation makes the task harder to accomplish, but also it simplifies
the overall concept and increases the reliability and feasibility of the device. The goal of the mission is to fire a dart
type sampler at a comet from a distance and have it collect the material, close sample container, and then eject off
of the comet surface to be collected by the spacecraft. We explored many different concepts, but ended up settling
on a hemispherical, spring loaded sampling design that uses a free mass system to trigger the events in sequence.
We built and tested the sampling device to prove that the concept is valid.
Juno Earth Flyby Public Outreach Project
Bora Shin
Mentor: Dan Goods
The Juno Earth Flyby Project is a series of experiential events that are designed for middle school students
nationwide to collaboratively learn about NASA’s Juno Mission. These experiences allow the students to celebrate
the moment that Juno passes by the Earth on its way to Jupiter, and build excitement around the possible
discoveries Juno will make when it arrives on the distant planet. This educational project creates outreach using
interdisciplinary art, science, and technology that can help students imagine Jupiter’s scale, atmosphere, aurora,
and gravity field. The students will partake in this unique experience by encountering a series of creative tools and
methods that include: an art installation that uses satellite photography to illustrate Jupiter’s scale and appearance,
a light painting activity with accompanying audio narrative to imagine Jupiter’s aurora, and a time-capsule building
exercise that uses a data-cataloguing web-interface to allow students to understand the role of Jupiter’s gravity
field within our solar system. Each project will kick off when Juno performs the Earth flyby on October, 2013.
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Revisions to Photochemical Data for Use in Atmospheric Modeling
Joshua D. Shutter
Mentors: Karen Willacy and Mark Allen
Stellar flux incident on an atmosphere can cause molecules to dissociate into highly reactive species and allows for
photochemical processes to play a fundamental role in atmospheric chemistry. While models have tried to simulate
such processes, they are extremely sensitive to photoabsorption cross-sections and quantum yields: two
parameters that are important in determining the photodissociation rate, and hence the lifetime, of atmospheric
compounds. Obtaining high-resolution and current data for these parameters is therefore highly desirable. Due to
this, database and literature searches for high-quality cross-sections and quantum yields were performed and
compiled for KINETICS, a chemical/transport model that can be used in modeling planetary atmospheres, such as
those of Titan or Mars. Furthermore, terrestrial atmospheric models are presented to verify the completeness of
these latest revisions.
Variable Coding and Modulation Software Simulation
Thomas A. Sielicki
Mentor: Jon Hamkins
Currently most NASA missions use fixed codes, modulations, and symbol rates for space communications. The
objective is to vary the use of codes, modulations, and symbol rates to deliver the optimal data throughput on links
that have dynamic conditions due to changing geometry, weather, interference, launch plumes, etc. The proposed
variable coding and modulation system consists of low density parity check codes and turbo codes from the CCSDS
standards; using modulations of BPSK, QPSK, 8PSK, 16APSK, and 32APSK. The end-to-end simulation consists of a
random data stream that is encoded, modulated, channel simulated by Gaussian noise, demodulated, decoded, and
finally compared to the original data input for errors. To ensure proper performance of the system, bit-error-rates
for various signal-to-noise ratios are checked with theoretical values for all combinations of codes and modulations.
Data throughputs are observed on the new communication system from running a simulation of a known link
budget, for example an overhead passing satellite with varying signal levels due to geometry. Comparing the best
fixed transmission scheme to the software simulation’s variable transmission scheme shows the degree of data
throughput improvement for any particular telecommunication application with a dynamic link.
Investigating the Properties of RF-Driven CO2 Plasma for Mars Instrument Applications
Vritika Singh
Mentor: James Polk
Although past missions have observed and sampled Mars, Mars continues to be a focus of space exploration. The
Mars Exploration Program Analysis Group established four goals for Mars exploration: determining if life ever arose,
understanding the processes and history of the climate, determining evolution of the planet’s surface and interior,
and preparing for human exploration. To work towards these goals, an instrument, the Plasma and Laser Ablation
System for Multi-element Analysis (PLASMA), was proposed by the Jet Propulsion Lab that will use a laser and
plasma to ablate a sample and transport it to a mass spectrometer. PLASMA will allow highly sensitive, multielement, geochemical analysis and radiogenic dating on Mars. Over the summer, the properties and behavior of a
CO2 plasma generated using radio frequency (RF) power were studied. After the experimental setup, diagnostic
probes, and data collection system were operational, plasma potential, plasma density, electron temperature, and
ion saturation current were measured over a range of RF power levels, discharge chamber pressures, and
discharge chamber dimensions. The data were analyzed to resolve trends over the varying parameters, and
information gathered from this project will feed into the next stage of development for PLASMA.
Technical Facilities Management, Loan Pool, and Calibration
Jacob W. Smith
Mentors: Ibrahim Khayat, Alejandra Gomez, and Lois Lewis
Two important facilities offered at JPL are cleanroom maintenance and equipment maintenance. The maintenance
of cleanrooms involves certifications, cleaning, and servicing. Cleanrooms must be certified when working with
mission critical or flight hardware and this falls under the Technical Facilities Management (TFM) group. There are a
multitude of items and rooms to be certified through TFM such as cleanrooms, airlocks, HEPA vacuums, clean
benches, and marking the occasional non-certified room. All of the certifications consist of measuring particle
counts; as well as air velocity and differential pressure in the cleanrooms. From this data, certification reports are
developed and sent to the cleanroom manager. In addition to the certifications the TFM group also evaluates and
replaces HEPA filtration systems located in the various cleanrooms around the lab. The airflow of the HEPA filter
and the differential pressure are measured to determine whether it needs to be serviced or replaced. Along with
the TFM group, is the Metrology and Instrumentation Services group which is responsible for the repair and
calibration of loan pool owned equipment on lab. The calibrations range from electrical equipment to mechanical
equipment and items that used around the lab. Along with calibration and repairs, the Instrument services group is
responsible for shipping out broken items to be fixed by the manufacturer.
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Bringing Mathematical Capabilities to SysML Within MagicDraw
Akshaya Srivastava
Mentor: Frank Dekens
SysML is a visual language used for concept visualization and systems engineering. JPL has chosen MagicDraw as
their current tool to support this visual language. A current limit of the tools is that it requires the use of plugins
and other disparate math tools, such as Mathematica and Matlab, to do simple first order calculations within the
mode. Integration between such math tools and MagicDraw/SysML has yet to be standardized, as currently,
different tools are being used for different tasks. With the immediate task of cost roll-ups, a trade study was
performed to find the best tools to attempt to integrate a math tool into the SysML/Magicdraw infrastructure.
Current, we are evaluating both Python scripts within MagicDraw, and using a third party plugin, which provides an
interface to MATLAB for performing mathematical functions. The latter uses the Cameo Simulation Toolkit plugin.
On-Board Calibration Device for In-Flight Data Collection of Imaging Spectroscopy Instruments
Michael Stange
Mentor: James Coles
The on-board calibrator (OBC) in the AVIRISng imaging spectrometer allows for the recording of reliable data.
Inaccuracies in the spectral signature of light entering the instrument can be removed by cross-referencing the
known spectra of the calibration device. Data sets decrease in dependability when the instrument is not calibrated.
To produce optimal accuracy, in-flight calibration is conducted after each data collection, providing for the most
applicable adjustments to the raw spectral signatures previously recorded. Through temperature and voltage
stabilization, a halogen bulb shines with a constant spectral signature within the OBC. The OBC is connected to the
instrument by fiber-optic cables, which carry the bulb’s light into the imaging spectrometer, recording the
quantitative data from the halogen light source. The spectral signature of the bulb varies by less than 1%,
providing a reliable calibration source for imaging spectroscopy instruments. Previous versions of the OBC did not
facilitate easy assembly of the device, so simple modifications have been made for swift construction of the OBC.
Design and Fabrication of a Stereoscopic Multi-Angle Rear-Viewing Endoscopic TooL (MARVEL)
Andrew D. Strongrich
Mentors: Sam Bae and Ron Korniski
The use of minimally invasive neurosurgical techniques has experienced a growing interest among patients and
surgeons alike due their the numerous advantages over more traditional operations. Current methods employ the
use either rigid or articulating endoscopes, both of which are inserted through a small diameter opening in the skull
near the intended surgical region. Although these devices aid the surgeon in viewing the operating site, they are
severely limited by their inability to provide dimensional awareness to the user. The Multi-Angle Rear-Viewing
Endoscopic TooL (MARVEL) has been designed such that the compact form of existing endoscopes is been
maintained while also providing the user with an enhanced 3-dimensional stereo view.
The design of the alpha prototype for MARVEL was completed over the course of three months. In parallel with
development, the device’s optics were characterized and several software programs were generated. Once
assembled, MARVEL will hold many advantages over existing endoscopic tools. It is expected that the device will
greatly outperform its traditional counterparts by both increasing safety and decreasing the duration of surgical
procedures. After completion, the device will be demonstrated to the project sponsors at the Skull Base Institute
where it will undergo full evaluation and a feasibility analysis.
Mars Science Laboratory: Surface Parameter Audit, 16 Hour Tactical Timeline Model
Matthew T. Stumbo
Mentor: Tracy Van Houten
The Mars Science Laboratory (MSL), also known as Curiosity, is landing on Mars on August 5th. There is still much
work that needs to be done to prepare for surface operations. In the first several sols of surface operations the
flight software will be updated many times. During this time the state of the rover, a series of approximately
40,000 parameter values, will need to be verified against documented truth. This ensures the updates will make
the correct changes to the flight software. The MSL operations team members attend a series of meetings that are
a part of the 16 hour tactical timeline. The teams review the data from the previous sol and plan ahead for the
next. Operational Interface Agreements (OIAs) establish which teams are responsible for producing certain items
and the teams to which those items are delivered. A Unified Modeling Language (UML) model was created to
document the OIAs and other aspects of the tactical timeline. This model is outdated. Many of changes to the OIAs
in the past year are not reflected in the model. These changes needed to be made to the model to make it a useful
tool.
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A Study on the Perceived Development Risk of Surface Sample Collection Systems in Proposal
Formulation
Cecily M. Sunday
Mentor: Lynne Cooper
Both the 2003 and 2013 Decadal Surveys challenge scientists to investigate the processes that “mark the initial
stages of planet and satellite formation.” This question offers continued interest in missions that prioritize sample
collection and return from comets, Mars and the Lunar South Pole Aitken Basin. The purpose of this work is to
understand the design and development of previously proposed sample acquisition instruments in order to assist
future mission formulation. Twelve sample collection missions proposed from 2002-2010 are studied first to map
system commonalities and second to identify potential gaps in communication that arise during the proposal
process, particularly in relation to NASA’s three identified challenges of sample handling, system mass, and mission
design. This information is used to understand the perceived risk associated with acquisition systems so that
instrument descriptions can be clarified and strengthened in future proposals.
Using Maple as a Systems Engineering Design Analysis Tool
Andrew S. Tang
Mentor: Jennifer M. Rocca
The current use of legacy Excel spreadsheets for subsystem analyses varies from engineer to engineer without
explanatory commentary of important parameters and assumptions. Unlike Excel, Maple is a useful tool that can
express the underlying math that is not explicitly defined by the Excel tools as symbolic math and line-by-line
execution. This allows new users to familiarize with how the tool works and to visually understand the generic
equations used to calculate parameters. Maple also allows us to cross-link worksheets for common input
parameters. We make various subsystem tools available by analyzing existing tools for DESDynI (Deformation,
Ecosystem Structure, and Dynamics of Ice) and converting them to Maple such that the tool keeps the original
functionality and adds more functionality for new and unfamiliar users. Using Maple also allows a Systems
Engineers to access a “Master Tool” to link the tools and output useful datasets of the entire system. The
overarching goal is to combine multiple subsystem analyses into a linked toolset, capable of assisting in projectlevel trade studies, science value function generation, and requirement sensitivity analyses.
Integration of Force Sensing Into Robotic Microspine Gripper
Nitish Thatte
Mentors: Aaron Parness and Matthew Frost
Future robotic missions to near-Earth asteroids require a method of anchoring to surfaces without aid from gravity.
Microspine grippers that can grasp rocky surfaces are a potential solution to this problem. In order to enable
robotic control of microspine grippers, the grippers must include force sensors that allow the robot to discern when
grip has been established and how load is distributed within a gripper. In this paper, the design of a hand-actuated
test microspine gripper that integrates several methods of sensing is outlined. Load readings obtained by
measuring force directly via load cells and indirectly by measuring the extension of springs using an array of Hall
effect displacement sensors are compared. Additionally, obtaining force data at the microspine toe level is also
explored through the development of urethane flexures that feature measureable resistivity that is highly sensitive
to strain.
Guidance Studies for a Lunar Descent Vehicle
Grace V. Tilton
Mentors: Abhinandan Jain and J. Bob Balaram
The JPL DARTS (Dynamics and Real Time Simulation) Lab develops simulations for design and testing of spacecraft
systems. This 10-week internship in the DARTS lab focused on two major tasks involving the development of
guidance algorithms and software for integrated mission simulation.
The first task was to assist in the development of test cases to display different capabilities of the DARTS tool.
Starting with a base case of a simple cannonball on a trajectory around Earth, each test case added a different set
of useful additions to the code such as aerodynamics, spacecraft geometry, topography and maneuvering. These
test cases will be used to teach others what the DARTS tool offers and how to implement different situations.
The second task was to extend an existing lunar simulation of gravity turn and landing to ascend to orbit, travel in
the orbit, deorbit, perform a gravity turn and land on the lunar surface. These tasks have some overlap in the
sense that some of the cannonball examples mimic simplified stages of the lunar simulation and some stages or
capabilities are easier to implement first on a cannonball script than to work into the complexities of the Lunar
rover simulation.
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Using the DARTS capability, a study was performed on the effects on trajectory and landing position due to use of
guidance and control schemes at two different fidelity levels: using an inertial anti-velocity set thrust, or the use of
a kinematic slew command to control thrust direction. A parametric study was also performed to observe the
sensitivity of descent, and landing to thruster dispersions in rocket specific impulse and maximum thrust. Data
generation consists of plotted trajectories, landing positions and errors, as well as a movie to demonstrate the
flight and landing simulations.
RAPID and HTML5’s Potential
David Torosyan and Manuk Hovanesian
Mentors: Jay Torres and Lucy Abramyan
Communicating with robots is inherently difficult. Specialized hardware and software are often required to perform
simple tasks. If a system was developed such that any communication interface, be it smartphone, tablet, or
computer, with access to a browser was able to render the information required by the operator, the process would
be simplified. The communication protocol used as a standard for the Human Exploration Technology (HET) Project
is the Robot Application Programmer Interface Delegate (RAPID). It requires specialized software and hardware for
its pipeline. A mobile-compatible website, on the other hand, can enhance the accessibility of RAPID. By delegating
the work to an Amazon Cloud server, anyone with Internet access can receive relevant data presented with HTML 5
features and interactive 3D graphics. The server gathers telemetry from ATHELTE, a lunar/asteroid rover currently
in development, providing a use-case of RAPID while exploring the capabilities of HTML 5.
Tools to Be Used by Mission Controllers for the Juno and Spitzer Missions
Daniel Vélez
Mentor: Luis C. Morales
Throughout the years of operating spacecraft missions, JPL has been using the Deep Space Station Complexes
located in Madrid (Spain), Canberra (Australia), and Goldstone (United States). In order to properly operate each
of the Deep Space Network (DSN) antennas that form part of each of complex, and successfully command the
spacecraft and receive telemetry data, each antenna needs to be properly configured in coordination with the
configuration of the spacecraft. The configuration for each DSN antenna is documented and coordinated using the
DSN Keywords File (DKF). Up to this point, the DKF has been reviewed and checked for possible errors in a manual
manner. This manual review is of course prone to missing errors that might have the potential to delay
commanding of the spacecraft, or loosing data transmitted by the spacecraft. Errors present in the DKF can be
detected in a fast manner and without being susceptible to human error by the use of automated software tools.
We have design and developed two tools for Juno and Spitzer that serve this purpose: 1) the Mission Controller
DSN Keywords File Checker, and 2) the Mission Tracking Support and Display Web Page.
BioSleeve: A Wearable Hand-Gesture Sensor for Human-Robot Interaction
Matthew T. Vernacchia
Mentors: Michael Wolf and Christopher Assad
This project describes Biosleeve, a wearable hand-gesture sensor for controlling robots and actuated prostheses.
Hand-gesture based control of robotics systems helps facilitate faster and more natural human-robot interaction.
While cameras are commonly used to determine hand state, hand state can also be discerned by measuring muscle
action via surface electromyography (EMG). EMG offers improved portability, force estimation, and the ability to
collect data from residual muscle in amputees, which camera systems cannot match. Biosleeve is an arm garment
for interpreting hand motions via EMG, and arm orientation via inertial sensors. This project focuses on improving
many features of Biosleeve, including: choice of gestures, physical placement of electrodes, hardware packaging,
classification features, classification algorithm optimization, robot control software, and reliability. Additionally, this
project adds a new point-to-goal functionality, in which the user can point to a location to order a robot to travel to
that spot. In this operation, arm orientation data from Biosleeve’s inertial sensors is used to determine a ‘pointing
ray’, which is intersected with a terrain map gathered from the robot’s sensors to locate where user is pointing.
Seasonal Variations of Jupiter’s Atmosphere From Observations of Mid-Infrared Thermal Emissions
Laura Wakefield
Mentor: Glenn Orton
Over the last few years, some major visual changes have been appearing at multiple depths in Jupiter’s alternating
axisymmetric banded atmosphere, such as the disappearance of 5-micron hot spots and the fade and revival of the
SEB. In order to understand what is happening in the complex interplay of chemistry and dynamics, we must
analyze changes over a long time frame. To do this, mid-infrared images of Jupiter’s thermal emission, spanning
~1.5 Jovian years, and taken at wavelengths from 7.8 to 24.5 m that are sensitive to temperatures, clouds and
the abundance of minor constituent gases are used. Imaging reduction processes are then completed and the data
are sent through the NEMESIS algorithm [1] to retrieve continuous profiles of gas abundance, temperatures, and
aerosols. These retrievals are then adapted into IDL plots and compared to similar plots generated from absolute
flux calibrated data. Further analysis is needed to ensure the accuracy of the calibrated data before they are
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compared to visual images, but we found that the variability over time is consistent in both data sets, with a slight
difference in absolute radiance. These results directly show seasonal variation in the upper-troposphere despite
Jupiter’s small axil tilt.
[1] Irwin et al. 2008. The NEMESIS planetary atmosphere radiative transfer and retrieval tool. J. Quant. Spectr.
Radiative Transf. 109, 1136.
Mars Sample Return Core Sample Shock Testing
Kelly Wang
Mentor: K. Charles Wang
What lies in the future of NASA’s Mars Exploration Program? Recently, there has been interest in bringing rock core
samples back to Earth for further study. With this proposal, the samples may have to survive the impact of an
Earth landing, which may be accomplished within a ballistic capsule in order to keep the landing system as simple
as possible. A test using the 30-foot drop tower facility at JPL was designed to examine the durability of such cores
by simulating the impact of an entry vehicle. In order to accurately reflect the impact, the samples need to be
exposed to acceleration loads of at least 1500 g. The results of this shock test may prove crucial to assessing the
feasibility of a hard landing that could result from bringing Martian rocks back to Earth’s surface.
High Power Transmit/Receive Module Development for Spaceborne Radar
Jean Weatherwax
Mentors: James Hoffman and Stephen Horst
The proposed DESDynI (Deformation, Ecosystem Structure and Dynamics of Ice) radar instrument plans to
measure changes in the Earth’s surface deformation to monitor and help predict natural disasters as well as track
the changes in ice sheets. In order for the radar instrument to operate as accurately as needed, the
transmit/receive (TR) module must be thermally stable and reliable, and be able to handle a high power output.
Accurate modeling and testing of the TR module’s components are therefore critical for estimating performance..
This project includes the testing and modeling of individual components of the TR system including filters and
couplers, as well as simulation and modeling of the full TR module system, so that it could be compared to the
ideal and actual performance. Statistical analyses of key parameters in the TR module circuit (including in-band
insertion loss, rejection at band edge frequencies, deviation from linear phase, group delay, and ripple) are
important to quantifying the stability and repeatability of the circuit in action. These tests are critical to determining
the absolute accuracy and unit-to-unit consistency of the DESDynI TR module, as it impacts the entire instrument’s
performance. The results will be used to guide the next revisions of the TR module.
Rock Sample Destruction Limits for the Mars Sample Return Mission
David Kutai Weiss
Mentor: Charles Budney
Sample return missions, including the proposed Mars Sample Return (MSR) mission, propose to collect core
samples from scientifically valuable sites on Mars. These core samples will undergo extreme forces during the
drilling process, and during the reentry process when the EEV (Earth Entry Vehicle) performs a hard landing on
Earth. Because of the foreseen damage to the cores, it is important to evaluate each core for rock quality.
However, because no planetary core sample return mission has yet been conducted, it remains unclear as to how
to assess the cores for rock quality. In this report, we describe the development of a metric designed to
quantitatively assess the quality of the rock cores returned from MSR. We report on the process by which we tested
the metric on core samples of Mars analogue materials, and the effectiveness of the core assessment metric (CAM)
in assessing rock core quality before and after the cores were subjected to shocking (g forces representative of an
EEV landing).
Experimental Methods to Evaluate Science Utility Relative to the Decadal Survey
Cynthia Widergren
Mentor: Lynne Cooper
The 2013 Decadal Survey prioritizes specific questions and topics for NASA to address in future missions and it
includes a section on specific goals for the inner planets. The purpose of this work is to assess the extent to which
prior mission concepts address the objectives presented in this most recent Decadal Survey. This work will test
approaches for measuring the degree to which science goals meet goals established in the 2013 Decadal survey. It
will also test algorithms to calculate scientific utility for different mission concepts and science goal combinations.
The results of this research will be used to assess the potential impact of the 2013 Decadal Survey in formulating
future missions.
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Material Testing for Robotic Omnidirectional Anchor
Kevin S. Witkoe
Mentors: Aaron Parness and Matthew Frost
To successfully explore near-Earth Asteroids the question of mobility emerges as the key issue for any robotic
mission. When small bodies have extremely low escape velocities, traditional methods, such as wheels, would only
send the robot spiraling off of the asteroid’s surface. To solve this problem JPL has begun researching the
applications of microspine technology. Through this research, an omni-directional anchoring mechanism was
developed that is ideal for robotic exploration. These microspines are placed in circular arrays with 16 independent
carriages biasing the surface of the rock. The asperities in the surface allow the gripper to hold nearly 150N in all
directions. While the gripper has been proven successful on consolidated rock, it had yet to be tested on a variety
of other surfaces that are expected to separate the large boulders on an asteroid. Since asteroid surfaces vary
widely, from friable rocks to loose ponds of regolith, the gripper will be tested in a variety of materials such as,
bonded pumice, sand, gravel, ice, and loose rocks. In the experiment the gripper is anchored to the test material.
A steel cable attaches to the gripper to a winch, as the winch is wound the tension in the cable is slowly increase.
The forces from the cable that act on the gripper are applied tangent to, at 45 degrees to, and normal to the
surface of the material. The immediate results from this experiment will give insight into the gripper’s effectiveness
across the wide spectrum of materials found on asteroids.
Frontend Graphical User Interface Creation for an Automatic Testing System
Kyle Wolma and Brandon Benjamin
Mentor: Barbara Streiffert
The Mission Planning and Sequencing element at Jet Propulsion Laboratory provides space missions with multipurpose software. This software is crucial to operations teams to be able to send commands to spacecraft that
have been verified not to harm it. In order to ensure that the multi-mission software operates properly, extensive
testing is performed prior to delivery to the operations teams. Automatic testing scripts have been created to
mirror operations’ use of the multi-mission software. The scripts are run and then comparison of the outputs to a
baseline is performed. Part of the testing software is a graphical user interface that helps operators work more
efficiently. Currently, the graphical user interface for the testing system is out of date and does not work well
across operating systems, resulting in lost time and efficiency. This task is creating a new graphical user interface
with improved performance and added features to expedite the testing process.
Programming Calibration Data Utilities Using Agilent Visual Engineering Environment (VEE)
Alexander Wolpe
Mentors: Lois Lewis and James R. Lewis
Metrology Services provides calibration and repair on a wide range of Instrument Measuring and Test Equipment
(IMET) where Metrologists and technicians are constantly analyzing data from various measurement disciplines
(physical, dimensional, optical, etc.) using a variety of analysis methodologies. Using Agilent VEE (Visual
Engineering Environment), and under the supervision of my mentors, I have developed the Calibration Data
Utilities (CDU) program that will become the baseline analysis tool for all measurement disciplines in the metrology
laboratory. This tool represents a significant increase in efficiency and overall process quality. The CDU performs a
variety of regression calculations, error analysis, and will provide users with detailed and customized tables and
graphs. The CDU will be used to generate calibration datasheets for all instrumentation calibrated at JPL. In
addition, the CDU interfaces with the existing offsite INFOR database for instrument specific data based on the item
identification number, thus eliminating the need for a user to manually login and copy information. CDU is
complete, and is currently being tested.
The Design of an Extreme Environment Capable Microprocessor
Austin Womac
Mentors: Mohammad Mojarradi and Zack Pannell
High performance microprocessors are desired to operate in extreme environments such as space or deep
oil-drilling operations. In the past, bulky, hermetic enclosures have been used to protect the sensitive electronics.
Pre-designed high-temperature, radiation-hardened microprocessors also exist. Both these solutions add cost to a
project, either in the form of additional mass in a design or expensive IP. A less expensive solution is to make use
of an available high resolution CMOS silicon-on-insulator (SOI) integrated circuit (IC) fabrication process that is
inherently immune to latchup, resistant to total ionizing dose (TID) radiation and capable of operating over a wide
temperature range. ARM provides soft processor IP that can be synthesized on this fabrication process. A digital
standard cell library is created that provides the building blocks for the ARM Cortex M0 processor to be
synthesized. Analog feedback control circuitry is designed to monitor the threshold voltage of the transistors in
these cells and control it over temperature variations. Two CPUs are synthesized and run in lockstep; any single
event upsets (SEU) are detected as mismatches in the CPUs’ states and the CPUs are reset. Overall, this solution
provides an economical microprocessor capable of operating in extreme environments seen by NASA and other
commercial industries.
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Improving Polarimetric Processing in the InSAR Scientific Computing Environment
William W. Woods
Mentor: Marco Lavalle
This internship focuses upon the InSAR Scientific Computing Environment (ISCE), under development within the
Radar Science and Engineering group, Section 334 at NASA JPL. ISCE is a fully modular and open source
computing environment which aims to provide the scientific community with the tools necessary to perform radar
interferometric, polarimetric and polarimetric-interferometric processing. ISCE currently implements interferometric
and polarimetric processing separately. The polarimetric module, however, is dysfunctional for certain input data
formats, does not perform geocoding, and lacks any sort of comprehensive documentation. We first troubleshoot
the polarimetry application using ALOS-PALSAR data and find that incorrect calculation of the peg point causes it to
fail for level 1.0 input data. We then develop a complete workflow for the polarimetry application and add it to the
growing ISCE documentation. Finally, we begin to incorporate geocoding, mapping the processed data to its actual
earth-bound coordinates, into the application before the duration of the internship expires.
Deployable Starshade for Exoplanet Imaging
Rick M. Zang
Mentor: David Webb
Exoplanet research and observations are greatly hindered by the light from nearby stars. External occulting
provides a solution to this problem and will allow the imaging of many planets that were previously only viewable
through indirect detection. External occulting involves masking the parent starlight with a deployable structure
called a Starshade that roughly resembles the shape of a flower, which is composed of 24-30 petals precisely
shaped and positioned around the circumference of a large opaque disc. Four petals will be built for attachment to
a truss for deployment tests. Future steps should include testing of petal functionality (stiffening rib deployment
and stowing around hub) and analysis of mechanical hardware/mechanism for the full size Starshade.
Fuel Cell Simulations of Hadean Hydrothermal Chemical Energetics in the Establishment of a Primitive
Metabolic Pathway
John L. Zeytounian
Mentors: Laura M. Barge and Michael J. Russell
It is theorized that life emerged at off-axis hydrothermal springs on the sea floor. The porous inorganic mounds
precipitated at these submarine springs were partly composed of iron sulfides in diverse ratios. With other
minerals, they constituted the well-ordered precipitate membranes enclosing the pore spaces. These mediated
interactions of a CO2-rich, cool, mildly acidic ocean with an H2 and CH4-rich, alkaline, warm submarine seepage,
driven by the steep proton, redox, and thermal gradients imposed across them. These semipermeable membranes
also contained trace amounts of molybdenum and nickel, with the potential to catalyze hydrogenation of oceanic
CO2 to CO, as well as the oxidation of hydrothermal methane. The electrochemical propensities of artificiallyprecipitated FexSy membranes were assayed for their potential to catalyze these redox reactions under varied
conditions of reactant concentrations and cell temperatures. Varying initial experimental conditions induced
variations of membrane structure and catalytic potential as revealed by voltage/pH measurements, ESEM, and
EDX. In addition, cyclic voltammetry was utilized to study membrane surfaces as catalytic electrodes that may
drive redox reactions over a range of applied electrical potentials. Future work will encompass the synthesis of
hypothesized simple organic molecules such methane thiol, acetate, and achiral peptides as well as energy-rich
pyrophosphates.
NASA Instrument Cost Model (NICM) Version VI
Zipeng (Hunter) Zhao
Mentor: Hamid Habib-Agahi
The NICM is an essential parametric cost estimation tool. NICM Version VI is in the early stages of instrument
development. Previous versions of the tool have sequentially improved the functionality and robustness to the
Microsoft Excel and Visual Basic for Applications (VBA) engine. The latest version, NICM VI, is currently under
development and contains major changes to its operating platform. The newest version will shift the Excel based
engine to a web-based platform. Major advantages of the change include but are not limited to: synchronized and
universal version management, elimination of risks associated with non-authorized redistribution, cleaner and more
intuitive user-interface, and possible data mining to pinpoint and therefore optimize the most popular aspects of
the tool. NICM VI implements Drupal content management system, and the new web-based user interface contains
a network of extensive Asynchronous Javascript and XML (AJAX) components. During the preliminary stages of
software development, the web-based front-end will communicate with the Excel engine through specially
formatted text files.
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Compliant Space Mechanisms
Shannon A. Zirbel
Mentors: Brian Trease and Greg Agnes
Compliant Mechanisms (CM) perform their function through the elastic deflection of their members. The
advantages of compliant mechanisms include increased performance, reduced or eliminated assembly, no friction
or wear, fewer parts, lower cost, and lower weight. These advantages make compliant mechanisms ideally suited
for space or aerospace applications, where low weight and no lubrication are essential. Space applications are a
large, mostly untapped field that will benefit from compliant mechanism technology. This project will contribute
largely to the knowledgebase on compliant space mechanisms, particularly through the development of design
models and “building block” mechanisms.
Under the guidance of Brian Trease, I have created bistable mechanism designs in titanium and amorphous metal,
two materials that are ideal for compliant space mechanisms. Further work in applying compliant mechanism
theory to create compliant-space-mechanism designs will enable the primary benefit of significant performance
gains in critical applications. The resulting shift in mechanism design will increase robustness and simplify
manufacturing, leading to reduced risk and cost in space mission planning. Coupling compliant mechanism
technology with adaptive structures technology will integrate these functions in fewer components, reducing mass
and cost while increasing reliability.
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Abstracts
Student–Faculty Programs
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