9:30am – 10:00am
The effect of DNA supercoiling on transcription initiation at the glnAp2 promoter
Abby Knecht (Gelles/Kondev)
Abstract: A quantitative kinetic mechanism for transcription initiation at the bacterial promoter glnAp2 was previously determined using single molecule experiments with relaxed DNA. DNA in E. Coli cells, however, is rarely relaxed but instead is negatively supercoiled. Bulk experiments in the literature report a 10 to 60 times increase in the overall rate of transcription initiation at the glnAp2 promoter with negatively supercoiled DNA compared to relaxed DNA.
To locate where in the mechanism this increase in rate occurs I created circular DNA that contained the glnAp2 promoter, biotin for attachment to a microscope slide, and a dye for visualization. Initiation was then measured using single molecule techniques on both nicked and negatively supercoiled forms of this template. The overall rate of transcription initiation was seven times faster on negatively supercoiled DNA compared to on the nicked DNA. The rate of
RNA polymerase binding, however, was only 1.5 times as fast on the supercoiled DNA, and the rate of open complex decay on the supercoiled and nicked templates was not significantly different. Initial experiments on the RNA polymerase closed complexes suggest that their stability on negatively supercoiled and nicked templates is not very different. Based on those results, I hypothesize that isomerization from closed to open complex is most likely the step in the mechanism that accounts for the difference in overall rate of transcription initiation between relaxed and supercoiled DNA.
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10:00am – 10:30am
Controlling Coupled Chemical Oscillators: Toward Synchronization Engineering and Chemical
Computation
Adam Wang (Fraden/Miller)
Abstract: The collective behaviors of coupled oscillators are ubiquitous in biological systems, with examples including quorum sensing, cardiac muscle contractions, and networks of neurons.
In an effort to better understand the generic properties of such oscillators, we investigated emulsions of diffusively coupled microdroplets containing the oscillatory Belousov-Zhabotinsky
(BZ) reaction with a photo-inhibitive catalyst. We created packed 2D arrays of BZ droplets via microfluidic techniques and studied the behavior of particular geometries with optically-induced boundary conditions. We used optical perturbations to alter periods and phases of oscillation in a controlled fashion, and also to completely suppress oscillations in the BZ droplets. Furthermore, we exploited the observed inhibitory coupling to establish a basis for computation through a chemical substrate by creating a functional NOR gate in a simple 1D arrangement of three BZ droplets.
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10:30am – 11:00am
Inhibitively Coupled Chemical Oscillators as a Substrate for Logic Gates and Larger Circuits
Jacob Gold (Epstein/Pollack)
Abstract: We investigate the Belousov-Zhabotinsky (BZ) reaction in an attempt to establish a basis for computation with inhibitively coupled chemical oscillators. The system consists of BZ droplets suspended in oil. Interdrop coupling is limited to the non-polar inhibitory species Br
2
.
We consider a linear arrangement of droplets to be a NOR gate, where the center droplet is the output and the other two are inputs. Oxidation spikes in the inputs, which we define to be TRUE, cause a delay in the next spike of the output, which we read to be FALSE. Conversely, when the inputs do not spike (FALSE) there is no delay in the output (TRUE). We are able to reliably produce NOR gates with this behavior in microfluidic experiment. We also discuss potential future methods for connecting multiple gates to form larger circuits, and present preliminary simulations to this effect.
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11:00am – 11:30am
Networks of Coupled Chemical Oscillators
Matthew Cambria (Fraden/Epstein/Dogic)
Abstract: The oscillating Belousov-Zhabotinsky reaction (BZ) provides an experimental system with which to study networks of coupled oscillators. By emulsifying BZ in oil with surfactants, stable BZ drops will interact with each other through diffusion. Silicon microfluidics allow these drops to be arranged into custom planar networks with no-flux boundaries. The behavior of BZ drops in weighted star graphs is shown to depend upon two network variables, indicating that control over similar variables could be used to engineer the behavior of other networks of diffusively coupled oscillators.
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11:30am – 12:00pm
Rapid prototyping of microfluidic chips in COC for facilitating protein crystallization and x-ray crystallography.
Min-Sung (Chris) Hong (Fraden/Dogic)
Abstract: Understanding protein biochemistry and protein structure at the atomic level are key steps for understanding how proteins function, how proteins interact with other proteins and with small molecular weight molecules and how proteins undergo conformational changes. The structural analysis is most commonly done by X-ray diffraction. In addition to acquiring basic knowledge about protein function, structural knowledge can be exploited to create new antibiotics and improve current medications by utilizing structure-guided synthesis. Diffraction requires protein crystals and production of crystals is the major bottleneck in protein structure determination. The conventional protein crystallization methods, such as the hanging drop method, the microbatch method, and microdialysis do not offer sufficient control over the physical-chemical parameters that influence protein crystallization. One possible solution to this problem is using high-throughput microfluidic devices made out of the thermoplastic cyclicolefin copolymer (COC) that can store 1-2
µ m of solution in 380 identical wells that are 400
µ m

wide and 40
µ m deep. The total thickness of this device can be made in the range from 50-80
µ m, which is thin enough to be transparent for X-ray diffraction. This new technique has the promise to revolutionize the way proteins are crystallized for structural analysis by first reducing the amount of reactants needed for protein crystallization and for x-ray diffraction using freeelectron beams and the Synchrotron by increasing the beam efficiency by 100%, and saving the amount of time needed to crystallize proteins significantly. The thermoplastics are inexpensive to manufacture so this method has the potential to be commercialized, which is the only way to make this technology accessible to the broad scientific community. In my thesis I will develop rapid prototyping thermoplastic chips and test them in temperature and pH gradients, which are crucial parameters for controlling the isoelectric point for the proteins. This new technique will have a strong impact on the fields of biomineralization, drug development, structural biology and lab on chip technology.
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1:00pm – 1:30pm
Sclervey: A New Device to Survey the Sclera
Forrest Webler (Wellenstein/Bensinger)
Abstract: The Boston Foundation for Sight (BFS) has successfully restored vision to many patients suffering complex corneal diseases using a prosthesis. PROSE, an acronym for
“prosthetic replacement of the ocular surface” is the treatment process in which BFS designs custom fitted scleral lenses. The prosthesis forms a seal on the sclera holding a saline solution between damaged tissue creating a “new cornea” thus restoring vision. Currently the fitting process is done by trial and error, requiring multiple sessions and trial lenses. Sclervey, our name for our device, surveys the sclera quickly and without contact. Sclervey maps the sclera to tens of micron precision and will provide clinicians with the data necessary to design custom fitted lenses to seal the sclera with high precision.
Sclervey comprises seven cameras mounted inside a plastic spherical shell. Each camera looks at the light spots of LEDs projected onto the eye. Using camera pairs to conduct stereo imaging we reconstruct the 3D position of light spots on the surface of the eye. With our current set-up we have successfully generated surface maps of 12x12mm sections of 1" diameter PVC balls with
σ
= 40µm. Due to the anatomy of the eye, the sclera must be surveyed in sections where the patient is cued to look in six directions first right, up left, down left, then left, up right and down right. At each position a little more than a third of the sclera is exposed to the projected spots and mapped. Each surveyed section overlaps with the adjacent sections. Neighboring sections are stitched together using the photographed unique structure of blood vessels found in overlapping images. The final surface maps are then returned. Sclervey will not only make
PROSE treatment more efficient it will also improve patient experience by reducing the number of fitting sessions.
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1:30pm – 2:00pm
Survey of High-Redshift Quasars using the Jansky VLA
Jose Vargas (Wardle/Roberts)
Abstract: A wealth of information exists for quasi-stellar radio sources (quasars) that lie relatively close to our own galaxy. Sources that are more than 10 billion light years away, however, have not been so intensively studied. A complete sample of 130 quasars with redshift z, a measure of this distance, greater than 2.5, compiled and initially imaged by Teddy Cheung and
Doug Gobeille of Brandeis University, has recently been re-observed using the updated, more powerful Jansky Very Large Array (VLA). With these high-resolution, high-sensitivity data we can, by comparison to quasars closer to us, examine the effects that the environment around galaxies has had on the shape and behavior of quasars and how they have evolved over time.
This examination of quasars in the early universe will be complimented with optical data from the Sloan Digital Sky Survey (SDSS) and x-ray data from the Chandra X-ray Observatory.
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2:00pm – 2:30pm
Implementing Efficient Hybrid Imaging in CASA and An Analysis of Faraday Rotation Measure
Synthesis Techniques in CASA and AIPS
Rachel Harrison (Roberts/Wardle)
Abstracts:
I.
Implementing Efficient Hybrid Imaging in CASA
The Common Astronomy Software Applications package (CASA) is a set of software applications being developed by NRAO for reducing and processing data from radio telescope arrays such as the ALMA and the VLA. We present a Python wrapper for
CASA that automates the software’s self-calibration process. The workflow of this script is meant to parallel that of Caltech’s program Difmap. We also present the results of using this script to create total intensity and polarization images of the microquasar SS 433.
II.
An Analysis of Faraday Rotation Measure Synthesis Techniques in CASA and AIPS
We present a comparison of the results of Faraday rotation measure synthesis algorithms in CASA and AIPS (the Astronomical Image Processing Software). The original goal of this project was to use the output of the AIPS task FARS to run spectral cube analysis of the polarization of SS 433’s jets. We also aimed to build simple analytic/numeric models of the polarization of the jets. This proved more difficult than expected, and we were unable to build models of SS 433’s jets.
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2:30pm – 3:00pm
X-Shaped Radio Galaxies Polarimetry
Jake Cohen (Roberts/Wardle)
Abstract: The purpose of this experiment was to collect polarization information on a collection of X-Shaped Radio Galaxy candidates. A relative intensity, a polarization, and a fractional polarization map were produced for each of 47 X-Shaped Radio Galaxy candidates using the
Astronomical Image Processing System and were collected in this paper for the purpose of further analysis. Some complications in the polarization calibration process were encountered but a solution was successfully developed and implemented and is also explained in this paper.
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3:00pm – 3:30pm
Simulation of Alignment Error and Distortion of Chambers in the New Small
Wheel in ATLAS, CERN
Michael Frederikse (Blocker/Bensinger)
Abstract: The Large Hadron Collider (LHC) in Geneva, Switzerland, has recently been restarted after a two-year hiatus for repairs and upgrades. The LHC now runs at a higher operational energy of 13TeV. To compensate for the higher beam energies, many components of the ATLAS detector needed to be improved or replaced. The Brandeis High-Energy Group in particular is responsible for upgrading the alignment system of the New Small Wheel (NSW)[1]. The small wheel is a key component of the muon detection system; the alignment of which needs to be very accurate in order to adequately describe collisions. This study simulates these upgrades to the
NSW in order to determine the effectiveness and potential problems with the NSW alignment system. Simulations focus on the exclusion of alignment components to see how the alignment system can cope with possible engineering issues such as line of sight violations in optical sensors, the geometry of the NSW, as well as long-term deterioration and its potential effects.
These simulations allow the Brandeis group to address potential future issues with the NSW, accurately compensate for the warping of NSW detection chambers, and provide insight for future upgrade solutions.
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3:30 – 4:00pm
The large-N O(N) model on hyperbolic space
Stefan Stanojevic (Lawrence/Headrick)
Abstract: We studied the thermodynamics of the critical interacting O(N) model in three spacetime dimensions, in the large-N limit, when the spatial dimensions are two-dimensional hyperbolic space. The question of ordering in the theory at low temperature is considered.
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4:30pm or 5:00pm
Detector region- and momentum-specific event selection to improve the transverse momentum resolution of high-energy muons of the ATLAS Detector
Wei Zhong Goh (Sciolla/Blocker)
Abstract: The Large Hadron Collider (LHC) collides protons and produces new particles, such as the Higgs boson, that rapidly decay into other particles (decay products) that we are able to reconstruct in our detectors. For instance, one key decay product in the study of the Higgs boson is the muon, a heavier cousin of the electron. The better we measure the momentum of the decay products, the better we can infer the properties of the exotic particles, such as their energy, quantum properties and interactions with other particles. We may estimate how well we measure the momentum of a stable particle, such as the muon, using the “resolution”. The resolution is the width of the distribution of the difference between the particle’s generated and reconstructed momenta in Monte Carlo simulations. In the ATLAS Detector, the tracks of muons are traced as they hit Monitored Drift Tubes (MDT) and other components of the Muon Spectrometer, which allow their momenta to be deduced. To improve the resolution, requirements are made on the number of MDT hits. These requirements are uniform for all detector regions and momenta. This study explores the possibility of tuning the three- and two-station requirements based on the effects on efficiency and resolution, in specific regions of the detector and momenta ranges, in order to achieve a better momentum resolution. It was found that the existing requirements cannot be made more stringent, as the improvement in resolution is overshadowed by a rapid decrease in efficiency, in all cases examined. To achieve better resolution, event selection criteria based on other variables would have to be optimised instead.
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