REU Projects for Summer 2013
These 38 areas for research projects are proposed for 2013 REU Fellows. Descriptions of these
project areas follow below. The 2013 Application and Project Descriptions are also available by
email from the program director, Martha Absher, at mabsher@duke.edu. Please note that these
descriptions are general and describe the research area which you will learn about and observe as
part of your educational experience here at the Pratt School of Engineering. For some of those
project areas which have been offered previously, brief descriptions of some former Fellows'
projects are presented. The 2013 REU Application and 2013 REU Project Descriptions will be
available online at: http://www.pratt.duke.edu/reu/absher
Project #1: Engineering Gene Expression Systems for Tissue Regeneration
Advisor: Charles Gersbach, Assistant Professor, Biomedical Engineering
The Gersbach laboratory is dedicated to applying molecular engineering to the
development of novel approaches to gene therapy and regenerative medicine. A central focus of
this research involves engineering proteins that coordinate changes in cellular gene expression or
genome sequence. This research involves enhancing the activity of proteins that occur naturally
or engineering entirely artificial proteins to perform these functions. These proteins are then
delivered to cells, either by genetic engineering or other drug delivery vehicles, to coordinate
complex changes that control cell behavior. One example of this research involves using these
proteins to engineer readily available cell types, such as skin cells, to regenerate diseased or
damaged tissues, including bone, muscle, or blood vessels. Another example involves using the
engineered proteins to correct the genetic mutations associated with hereditary diseases, such as
muscular dystrophy and hemophilia.
In this project, the student will be challenged to design these new proteins with
advisement from the advisor and graduate students. The student will then build the DNA
sequences that encode the gene for the protein, including the appropriate gene expression system.
If successful, the student will have the opportunity to test the activity of the engineered protein in
cultured human cells. Through this research, the student will gain expertise in important
laboratory methods, including plasmid DNA propagation and purification, molecular cloning and
DNA recombination techniques, electrophoresis, and potentially mammalian cell culture
including liposomal transfection for genetic engineering. Additionally, they will gain exposure to
the fields of molecular medicine, gene therapy, and regenerative medicine.
Project #2: Advanced Biophotonic Structured Illumination Imaging System Design
Advisor: Joseph Izatt, Professor, Biomedical Engineering
Professor Izatt’s laboratory has REU opportunities in a project sponsored by the National
Science Foundation entitled “Advanced Biophotonic Structured Illumination Imaging System
Design.” The goal of this project is to apply cutting-edge signal and image processing techniques
to improve the resolution of conventional optical imaging devices such as microscopes and
ophthalmoscopes. This will be done by designing novel laser lighting patterns to illuminate cells
and tissues with special patterns of light which are designed to reveal fine structures upon
collection and image processing. This approach will contribute directly to the design of diagnostic
instruments capable of imaging individual photoreceptor cells in the living human retina.
Students involved in this project will gain experience in medical imaging laboratory practice,
optical system design and prototyping, computer interfacing with laboratory instrumentation, and
image processing algorithm design and programming. Students will also interact directly with
physicians on identifying requirements for instrument design and in testing of prototypes.
Theresa Meyer, Sophomore, Computer Science Engineering, Princeton University
Mentors: Dr. Joseph Izatt and Dr. Sina Farsiu, Dept. of Biomedical Engineering at Duke
University
Project Title: Optical Coherence Tomography (OCT) with XFast/YFast Imaging
High resolution volume images of the retina can be taken using a technique called Optical
Coherence Tomography (OCT). Capturing this volume can take four seconds or greater, and in this
amount of time a patient’s eye has the ability to move and cause jumps and distortions in the image,
known as motion artifacts. These motion artifacts make it more difficult for ophthalmology
professionals to diagnose and treat diseases of the retina, such as glaucoma. However, many software
algorithms have been developed to try to fix these motion artifacts after the volume has been captured.
One such software-based program that repairs motion artifacts was developed in the lab of Dr. Fujimoto
of the Massachusetts Institute of Technology, known as XFAST/YFAST. This paper provides an
evaluation of this algorithm. In order to analyze this algorithm, it must be recreated. One hurdle in this
study lies in that the XFAST/YFAST paper was studied to replicate the algorithm, and the exact code
used by Dr. Fujimoto is not available. Therefore, replication of the exact code utilized is lacking and
similarity is only based on results of a completed program. It is known that in XFAST/YFAST, fixing
the motion is done retrospectively by correcting motion on the OCT data sets themselves. Volume scans
with orthogonal fast scan axes are registered and then combined in order to form a final, more accurate
volume with reduced motion artifacts. This goal can be broken into three main steps: preprocessing,
optimizing a cost function, and volume merging. The first of these steps, preprocessing, was
successfully recreated in MATLAB. For the second step, optimizing the cost function, work is currently
being done. Progress is currently being made on creating a program that is able to detect the
displacement of an image when shifted a known number of pixels. Also the multi-resolution
optimization, part of the cost function, used in the XFAST/YFAST algorithm has been duplicated. Due
to time constraints, work on the volume merging step has not begun. If given more time and the
algorithm was successfully recreated, then it would be analyzed for performance and improved upon.
PROJECT #3: Three-dimensional drug distributions in solid tumors
Advisors:
Fan Yuan, Ph.D., Professor, Dept. of Biomedical Engineering
Anticancer drugs will not be able to cure cancer, if they can not reach every tumor cells.
However, it has been shown that drug delivery in solid tumors is non-uniform. The drug
concentration is high in some regions but nearly zero in other regions of tumors. This is one of
the major problems in cancer treatment since local recurrence of tumors can be caused by the
residue tumor cells left from the previous treatment.
The non-uniform drug delivery in solid tumors can be caused by different mechanisms, including
non-uniform blood supply, vascular permeability, and interstitial transport. The goal of our
research is to understand the mechanisms and to improve the delivery of novel therapeutic and
diagnostic agents in solid tumors. Our research is multidisciplinary, which involves quantification
of drug distribution, transport parameters, and vascular morphology in solid tumors. The
approach used in our research involves development of animal and cell culture models,
application of fluorescence microscopy, image and data analysis, and mathematical modeling of
transport processes in solid tumors. The following project will be available for undergraduate
students.
Description: 3D cell culture models will be used to study drug delivery. Students will learn how
to prepare the tumor models and quantify 3D distributions of fluorescent molecules in these
models. The distribution results will be compared with computer simulations, using mathematical
models developed for studying transport of drugs in solid tumors. These mathematical models
will integrate the information of individual experiments, which is crucial for identification of
important factors that hinder drug delivery in solid tumors.
Jazmine Brown, Junior, Biomedical Engineering, North Carolina A & T State University
Mentors: Fan Yuan, Ph.D, Professor and Jianyong Huang, Ph.D, Postdoc Fellow
Project Title: Electrotranfection of DNA into Tumor Cells
Electroporation is a process where rapid pulses of electrical potential are applied to cells
suspsended in medium. This electrical potential causes the cell membrane to break down and
pores to form. These pores allow for the delivery of drugs or genes as well as the delivery of
small molecules such as chemotherapy or the delivery of macromolecules such as DNA. There
are four major components to the elctroporation process: The voltage, the pulse duration, the
number of pulses, and the interval length. The ideal conditions for electroporation process are
short, high frequency pulses or long, low frequency pulses. In order to make the transfection of
DNA more efficient, it was hypothesized that this could be achieved by combining the ideal
conditions as well as increasing the interval length of the pulses. Three different parameters were
used combining a difference in interval length as well as the ideal conditions. A 170 volt pulse
with a pulse duration of 10 milliseconds was used as the base parameter. For the short, high
frequency pulse, 180 volts and a pulse duration of 5 milliseconds was used. For the long, low
frequency pulse, 160 volts, with a pulse duration of 15 milliseconds was used. All three of these
parameters proved that the cells exposed to the pulses with longer interval lengths had a greater
amount of transfected DNA. More research will be done with determine how and why this
phenomenon occurred.
Jason Hallo, Biology Major, Gallaudet University
Chemotaxis Velocity
Mentors: Dr.Fan Yuan, Professor of Biomedical Engineering and Dilip Nagarkar, Pratt Fellow,
Biomedical Engineering
Jason Hallo is a biology major from Gallaudet University. Jason’s project focuses on chemotaxis
velocity of bacteria. Gene therapy might one day cure cancer in our cells. Unfortunately, gene therapy
when placed into a virus is not able to host into a person’s DNA. An alterative method of gene therapy is
to use bacteria instead of viruses. Bacteria can’t get in the host but they are able to give proteins that
hopefully will regulate cancer cells one day in the future. An understanding of bacteria E-coli’s mobility
is required before we can do further experiments on gene therapy. My project aimed to study and
understand the mobility of bacteria E-coli in the presence of four different concentrations of dextrose.
Charts of results are made based on the experimental measurement of the rings of growth of the bacteria
on the petri dishes. Our finding was that bacteria move more when there is a lower concentration of
dextrose present.
These findings will be used in further experiments in the laboratory on the
development of gene therapies using bacteria.
REU Fellow: Kelley Bohm, Bioengineering Major, Pennsylvania State University
Protocol for Microfluidics Tumor Formation
Kelley Bohm is a bioengineering major from Pennsylvania State University. Her project focuses
on Microfluidics, which offers a novel way to observe interactions between therapeutic bacteria and
cancer cells. Culturing the cancerous tumors in microscopic conditions allows for precise manipulation of
the cells and the bacteria that will be introduced. Creating these tumors, before the bacteria are even
introduced, is a complex process that needed to be worked out in order to move on to more complex
topics. Cells need to aggregate effectively within the microfluidic chamber and this involves proper flow
rates, cell concentrations, and possibly a substance to help aggregation. One potential aggregate that was
considered was poly-L-lysine. This was first imaged with cells to choose the concentration that yielded
the desirable amount of aggregation and then the viability of this mixture was tested using trypan blue
stain. The ideal amount – 20% poly-L-lysine – was determined to be too deadly to the cells and will not
be used. Collagen will be considered in the future. Many trials were needed to determine the ideal flow
rates and cell concentrations. The specific numbers are detailed later in this paper. This data was compiled
and a protocol was made for Dr. Yuan’s lab and others to use for microfluidic tumor culturing.
REU Fellow: Danielle F. Garcia, Chemical Engineering, University of New Mexico
Developing a Multicellular Layer Model for Drug Diffusion in Tumors
Danielle is a chemical engineering major from the University of New Mexico. Her project
involved drug diffusion in tumors. An in-vitro model for drug diffusion through solid tumors has been
developed. The development process is comprised of growing a three-dimensional cell culture on a
collagen coated Teflon membrane suspended in stirred media for up to 12 days. HT-29 human colon
carcinoma cells and B-16 murine melanoma cells were used to demonstrate the procedure in developing
these multicellular layers (MCLs). HT-29 cells have been shown to produce an MCL thickness of
160mm after 12 days in suspension. A comprehensive investigation was carried out of variables affecting
growth of B-16 MCLs to achieve maximum reproducibility and comparability to HT-29 MCLs. We aim
to generate a sufficient amount of MCLs, and refine the development process to visualize common
properties of tumors such as necrosis and hypoxia, which affect diffusion properties. These MCLs can
then be used in further studies of drug transport to aid in cancer treatment research.
REU Fellow: Rebekah Lee Smith, Biology Major, Gallaudet University
Project: Quantification of Electrical Impedance of Tumor Tissues
Rebekah's project was in biomedical engineering and its application in cancer research. The goal of her
project was to develop a method to determine changes in the volume fraction of cells in tumor tissues
based on electric impedance measurement. This method can be used directly in the clinic to monitor the
efficacy of any anticancer treatment. In her experiment, different electrodes were used to measure the
impedance as a function of electric field frequency in tumor tissues. The impedence was then converted
to the resistance, capacitance, and inductance of tumor tissues based on the Cole model. The tissue used
in this experiment was a rat tumor, called rat fibrosarcoma. The volume change of tumor cells was
induced by a mannitol solution that would in theory shrink tumor cells due to the osmotic effect. The cell
shrinkage was detected through electric impedance measurement and data analysis based on the Cole
model. After several sets of experiments on fibrosarcoma, Rebekah did find that the mannitol solution
made the cells shrink, and the final impedance graph did fit into the Cole model. Rebekah completed the
formulas for resistance indicating how the tumor reacted and shrank in the mannitol solution. Therefore,
her hypothesis that fibrosarcoma cells would shrink in the mannitol solution was proved true.
REU Fellow: Daniel Lundberg
Project: Viscous Polymer Solutions for Sustained Drug Delivery
Daniel Lundberg is a senior biology major at Gallaudet University. He performed his research
under Dr. Fan Yuan, Assistant Professor, and Yong Wang, graduate student in the Department of
Biomedical Engineering. Daniel’s research focused on a novel method to treat cancers and tumors via
targeted drug delivery systems. As traditional methods and local drug delivery lead to the dissemination
of the drug into the systemic circulation, the side effect impact of a cancer treatment increases.
Temperature-sensitive polymers offer a possible method in containing the drugs within the tumor,
reducing the side effects. In order for a substance to be a successful polymer for this treatment, it has to
have a low viscosity at room temperature yet a high viscosity at body temperature. Polymer solutions,
such as alginate, calcium ion/alginate, Poloxamer, PNIPAAM, and methyl cellulose polymer solutions
were tested as potential agents which can reduce drug clearance into the systemic circulation and improve
drug retention in tumors, reducing the side effect of the anti-tumor drugs. From the data, it was clear that
the alginate and methyl cellulose polymers did not attain the goal, since they were more viscous at room
temperature than body temperature. Certain concentrations of PNIPAAM and Poloxamer polymer
solutions turned out to be promising polymers. Their viscosity had dramatic increases from room
temperature to body temperature, achieving the goal. The ionic environment variable proved to be
effective in increasing a polymer’s viscosity at a certain concentration. The next step of this experiment
would be to focus on the addition of the calcium ions to the successful polymers to observe the results.
Also, the promising polymers need to be tested in mice with the aid of fluorescent drug markers to
observe the progression of the polymer/drug markers. Daniel learned challenging new laboratory
techniques in this project.
Project # 4: Vaccine Engineering Formation of Chemokine Gradients in 3D Environments
Advisor: Dr. William Reichert, Professor, Biomedical Engineering and Varad Vernekar,
Postdoctoral Associate in BME
A key goal of vaccine engineering is to formulate vaccines that generate effective, high-affinity
antibody. The currently available vaccine for anthrax calls for five intramuscular injections over
18 months to establish effective protection. Our motivation is to improve the process of vaccine
development, and in particular, to identify strategies to improve the efficacy of the standard
anthrax vaccine. To achieve our goal, a collaborative team compromising of labs at Duke
University, Yale University, University of Michigan, and North Carolina State University has
been assembled to carry out the many phases of this research effort. The REU Fellow’s
educational experience provide exposure to the exciting area of vaccine engineering in this
laboratory.
The focus of this project is the many cellular interactions that occur in the germinal center.
Germinal centers within lymph nodes and the spleen are the epicenter of the adaptive immune
system. Within the germinal centers, B cells migrate to different areas interacting with T cells
and experience cell proliferation, mutation, and selection. This process can occur many times to
produce a high-affinity antibody to the antigen, such as anthrax. Extracellular gradients of
chemokines serve as the signals that guide cell movement in vivo. However, direct visualization
of chemokine gradients is still in its early stages, largely due to the technical difficulties in
detecting extracellular diffusible molecules.
The purpose of Reichert Lab subproject is to form in vitro models to study the migration of T and
B lymphocytes along well-characterized chemokine gradients within 2 and 3D environments. The
goal of the REU fellow will be to help optimize and characterize chemokine gradients in a 3D
environment.
Sharis Steib, Senior, Biological Engineering, Louisiana State University
Mentors: Charles S. Wallace, PhD, Assistant Research Professor and William M. Reichert, PhD,
Professor of Biomedical Engineering and Chemistry, Associate Dean for Diversity and PhD
Education, Director of the Center for Biomolecular and Tissue Engineering
Project Title: Characterization and Comparison of SDF–1 Mediated Cell Migration Across
Various Cell Lines
Cell adhesion and migration are essential processes in many body functions. Cells secrete
special proteins called chemokines. These proteins have the ability to produce a migration
response by surrounding cells. Stromal cell-derived factor–1 (SDF–1/CXCL12) is the chemokine
being studied in these experiments. Two- dimensional (2D) haptotactic migration – the
directional motility of cells up a gradient – must to be explored and understood in order to
discover better solutions to enhance the former of processes listed above and tackle the latter.
Current literature on cell migration describes multiple methods to assess three-dimensional (3D)
chemotactic migration – when cells direct their movement according to certain chemicals and
stimuli in the surrounding environment. None of these have been successful at creating the
chemistry necessary to form a SDF–1 gradient and using endothelial progenitor cells (EPC) and
human umbilical vein endothelial cells (HUVEC) for migration. In this study, I introduce a way
to capture overnight haptotaxis studies using the aforementioned cell lines, propose methods that
can be used to quantify this data, and conduct both 2D and 3D migration studies. I also describe a
series of Boyden chamber transwell assay experiments involving EPCs, B cells, and Jurkat cells
(immortalized T cells). I also show that haptotatic migration studies can be conducted overnight
using EPC and HUVEC cells on a SDF–1 gradient to track cell migration. By creating this
controlled in vitro environment to study cell locomotion, we expect this new approach to
dramatically change cell migration studies and potentially discover the exact effects of various
chemokine gradients.
REU Fellow: Sean McNary, Bioengineering, University of the Pacific
Integrin Density in Adherent Fibroblast Cells
Sean McNary is a bioengineering major from the University of the Pacific. The location and
distribution of RGD-recognition integrins in confluent fibroblasts is important for developing cell
layering studies and other investigations involving RGD-recognition integrins. To this end, fibroblasts
were incubated with RGD-Streptavidin (SA), with the RGD site being recognized by the cell?s ?v?3 and
?5?1 integrins. Through a high affinity ligand-receptor bond, SA was labeled with biotinylated Alexa
Fluor 488 dye or biotinylated FluoSphere microspheres. Cells and the fluorescent markers were imaged
through confocal microscopy. Control experiments verified that both biotinylated fluorescent markers
labeled only RGD-SA treated cells. Imaging revealed biotinylated Alexa Fluor 488 penetrated the cell
membrane and remained in the cytosol, preventing analysis of RGD-recognition integrins. Limited
experimental evidence suggests biotinylated FluoSphere microspheres bind to selected fibroblasts. More
research is required to fully assess the viability of labeling RGD-recognition integrins with FluoSphere
microspheres.
Project # 5: Vaccine Engineering: Lymphocyte Migration on Chemokine Gradients
Advisor: Dr. William Reichert, Professor, Biomedical Engineering and Varad Vernekar,
Postdoctoral Associate in BME
A key goal of vaccine engineering is to formulate vaccines that generate effective, high-affinity
antibody. The currently available vaccine for anthrax calls for five intramuscular injections over
18 months to establish effective protection. Our motivation is to improve the process of vaccine
development, and in particular, to identify strategies to improve the efficacy of the standard
anthrax vaccine. To achieve our goal, a collaborative team compromising of labs at Duke
University, Yale University, University of Michigan, and North Carolina State University has
been assembled to carry out the many phases of this research effort. The REU Fellow’s
educational experience provide exposure to the exciting area of vaccine engineering in this
laboratory.
The focus of this project is the many cellular interactions that occur in the germinal center.
Germinal centers within lymph nodes and the spleen are the epicenter of the adaptive immune
system. Within the germinal centers, B cells migrate to different areas interacting with T cells
and experience cell proliferation, mutation, and selection. This process can occur many times to
produce a high-affinity antibody to the antigen, such as anthrax. Extracellular gradients of
chemokines serve as the signals that guide cell movement in vivo. However, direct visualization
of chemokine gradients is still in its early stages, largely due to the technical difficulties in
detecting extracellular diffusible molecules.
The purpose of Reichert Lab subproject is to form in vitro models to study the migration of T and
B lymphocytes along well-characterized chemokine gradients within 2 and 3D environments. The
goal of the REU fellow will be to characterize the migration properties of T and B cells when
exposed to various chemokine gradients. At the end of the fellowship, the REU fellow will have
gained experience in many areas, such as surface chemistry, cell culture, and mathematical
modeling.
Project #6: Characterization of peripheral blood endothelial progenitor cells for use in prosthetic
vascular grafts
Advisor: Dr. William Reichert, Professor, Biomedical Engineering and John Stroncek, and Michael
Nichols, Biomedical Engineering Graduate Students
Cardiovascular disease is the leading cause of death in the US. Blockage of the coronary arteries is the
most deadly form of cardiovascular disease and is one of the main causes of sudden cardiac arrest. One
surgical solution for blocked coronary arteries is coronary artery bypass surgery. These bypass grafts are
isolated from a patient's mammary artery or saphenous vein. However, this surgery can only be
performed if autologous vessels are healthy. Not all coronary bypass surgery candidates have healthy
vessels available, and thus there is scarcity of suitable small diameter vessels for patients.
Synthetic grafts made out of ePTFE or Dacron have been looked to for a possible replacement of
autologous vessels. However, currently synthetic grafts are limited to vessels with an internal diameter
larger than 6 mm due to the thrombogenicity of the material. Investigators have attempted to improve the
performance of these materials by coating the lumen with endothelial cells, and successful seeding of
endothelial cells has been shown to improve the long-term patency of these grafts. Still, major technical
hurtles include finding a relevant autologous cell sources and improving the attachment of endothelial
cells to prosthetic grafts.
This research focuses on isolating a type of high proliferation potential endothelial cells that are found in
an individual's circulating blood, called endothelial progenitor cells (EPCs). We are currently attempting
to determine whether EPCs represent a viable and easily isolated autologous cell source for the seeding
onto synthetic vascular grants. The strength of adhesion and the antithrombotic properties of the EPCs on
synthetic graft materials will be determined through in vitro assays. Gene therapy will be used to regulate
the expression of antithrombotic molecules. Seeded grafts will eventually be tested in animal models.
This project involves cell culture, gene expression analysis, and phase/fluorescent microscopy.
Project #7: Engineering Bacteria for Medical Applications
Advisor: Lingchong You, Assistant Professor of Biomedical Engineering
We are engineering bacteria for medical applications by constructing synthetic gene circuits.
These projects involve development of genetic sensors that can detect changes in the
environment, and containment modules that limit un-intended bacterial proliferation. These
projects will expose students to both mathematical modeling and experimentation. The summer
student will primarily participate in design, construction, or characterization of synthetic gene
circuits. Prior experience in mathematical modeling, cloning, or bacterial growth experiments is
preferred.
Project #21: Energy Conservation through Unobtrusive Activity Detection Advisor: Matt
Reynolds, Assistant Professor, Electrical and Computer Engineering The two largest
contributors to domestic energy consumption are heating, ventilation, and air conditioning
(HVAC) and lighting. We propose to reduce domestic energy consumption by allowing an
automated system to detect when no-one is home, and to automatically turn off unnecessary
lighting or HVAC loads. The solution we will explore is based on sensing activity in the home
from a single point, using sensors such as air pressure or vibration in the structure of the home.
We will build on prior research that has demonstrated that these signals can provide an
unobtrusive, anonymous source of information about the occupancy of a building. We will focus
on developing new algorithms for processing these signals and extracting a binary result: Is a
person home, or not? If nobody's home, we will consider various strategies for minimizing
HVAC and lighting power consumption. This research will be conducted in a unique facility on
the Duke campus. The Home Depot Smart Home is a unique residential laboratory housing 10
undergraduate students who share an interest in "smarter living" from many perspectives. The
project will involve deploying simple sensors in the Smart Home and capturing sensor data
during times when the Smart Home is occupied and un-occupied. We will analyze this data both
in post-processing and real time to develop and improve algorithms for occupancy detection,
providing feedback to the home's residents, and potentially controlling the HVAC or lighting
systems. Experience Needed: Prior experience with MATLAB and one course in signals and
systems.
PROJECT #8; Application of Endothelial Progenitor Cells for Vascular Repair
Advisor: Dr. George Truskey, Professor and Chair, Biomedical Engineering
Endothelial progenitor cells derived from adult and umbilical cord blood represent a
promising source of cells for applications in tissue engineering, repair of blood vessels and
seeding of vascular grafts, stents and ventricular assist devices. Work in our lab is focused upon
determining the properties of these cells when cultured with smooth muscle cells under flow
conditions, understanding ways to optimize the dynamic adhesion of the cells and furthering the
development
of
tissue
engineering
applications.
REU FELLOW: Kristen Hambridge, Biomedical Engineering Major, North Carolina State University
Response of Human Umbilical Vein Endothelial Cells in Co-culture With Aortic Smooth Muscle Cells
In vitro cell culture systems are important for modeling diseases such as Atherosclerosis.
Atherosclerosis is a disease of the intima, resulting in plaque formation on the inner lining of the
artery walls. Low Density Lipoprotein (LDL) accumulation within the vessel wall leads to an
immunological response with inflammatory attributes. The increased permeability of the
endothelial layer to LDLs has played a major role in Atherosclerosis. The study aims to research the
role of human umbilical vein endothelial cells (HUVECs) in co-culture with aortic smooth muscle
cells (AoSMCs). Specifically, it aims to discover whether the inclusion of smooth muscle cells will
improve the physiological nature of endothelial cells. This was tested by performing albumin
permeability tests on a HUVEC monolayer, AoSMC monolayer, co-culture, and the membrane
containing no cells. Cells were grown in media containing 3.3% and 10% Human Serum (HS).
Permeability was tested on days 2,3, 5, and 7 post seeding. Days 5 and 7 were found to be optimal
days. Average albumin permeability for HUVECs was 1.35 +/- 0.47 for 10% HS at Day 5, 0.75 +/.04 for 3.3% HS at Day 5, 1.95 +/- 0 for 10% HS at Day 7, and 1.34 +/- 0 for 3.3% HS at Day 7.
Average albumin permeabilities for AoSMCs at Day 5 were 4.05 +/- 0.69 and 1.72 +/-0.62 for 10%
and 3.3% HS respectively while Day 7 were 4.95 +/- 1.33 and 5.2 +/- 0.93 for 10% and 3.3% HS
respectively. Lastly, the co-culture average albumin permeabilities were found to be 1.97 +/- 0.35
and 0.83 +/- 0.4 at Day 5 for 10% and 3.3% HS respectively while values for Day 7 were .089 +/0.34 and 1.77 +/- 0.66 for 10% and 3.3 % HS respectively. Overall, most permeability values at
3.3% HS were lower than at 10% HS. At day 7, the permeability of the co-culture was lower than
the ECs at 10% but not for 3.3% HS. It can be concluded that with time, the ECs respond better in
co-culture than alone when in 10% HS.
REU Fellow: Viet Le, Chemistry Major, Gallaudet University
Project: Interactions between the Endothelial Cells and the Smooth Muscle Cells in Co-Culture: The
Endothelial Cells Confluency in Co-Culture
The overall project in Dr. Truskey’s laboratory, in which Viet worked, aims to construct a tissueengineered blood vessel and a synthetic (polymer) vessel, so it can be put into a human body that has a
clotted vessel. The tissue-engineered blood vessels are made from cells that grow into tissue on a
degrading scaffold. Current tissue-engineered blood vessel form clots over relatively short periods of time
because the endothelial cells tend to rip off synthetic vessel that clots easier. The endothelial cells need to
adhere and function properly in the tissue-engineered blood vessel to prevent clotting. After the smooth
muscle cells have grown to a confluent layer on the slideflask, the endothelial cells were seeded and
cultured for several day for growth. Antibody Labeling was used to specifically stain cell junction
proteins so that the visible cell junction protein appear under the fluorescent microscope. In Viet’s
research, attempts were made to stain three type of cell junction proteins: VE-Cadherin, -catenin, and
PECAM. VE-Cadherin and -catenin were specifically localized to the inter-endothelial cell junction and
PECAM was specifically localized to the outer-endothelial cell junction. Two variables for staining the
cell junction proteins which must be considered are (1) the concentration of antibody labeling solution to
specifically stain for cell protein and (2) the incubation time. The VE-Cadherin and -catenin antibody
did not stain the cell effectively in the endothelial cells monolayer, under all the varying concentrations
and incubation times. VE-cadherin and -catenin antibody did not show its visible borders where two
cells had merged together under the fluorescent microscope. PECAM was considered as the next cell
junction protein and the results show that PECAM successfully stained the cell borders alone with
concentration of 20 L to 50L PECAM antibody solution in the endothelial cells monolayer. Dapi was
added to the PECAM protocol that stains cell nuclei to indicate the visible stained nuclei within each
visible PECAM border under the fluorescent microscope. The isotype was used as a control group that
should not show any visible cell junctions protein with the same PECAM protocol. Viet hypothesized that
the PECAM antibody will stain the endothelial cell borders on the smooth muscle cell. His results showed
the PECAM protein did not stain effectively the endothelial cells monolayer at low concentration. For
staining the PECAM protein in future investigation, Viet concluded that an increasing concentration of
PECAM antibody solution should stain the entire cells in co-culture, and the incubation time must vary
with the antibody concentration.
Project #9: Cell and tissue engineering therapies for heart disease
Advisors: Nenad Bursac, Associate Professor, Biomedical Engineering and Mark Juhas,
Biomedical Engineering Graduate Student
This project involves understanding how changes in the geometry and environmental cues alter
the functional properties and fate of stem cell derived and primary cardiomyocytes. Cell
microfabrication techniques will be employed to alter the shape of cardiomyocytes while
maintaining their connectivity. Relationships between stem cells and cardiomyocytes will be
examined in these cell cultures. Electrical stimulation may be employed to understand its role in
maturation of cells. Modulatory roles of cardiac non-myocytes such as cardiac fibroblasts on the
function the cardiomyocytes will be examined. Educational exposure to variety of
immunostaining, gene and protein expression, and functional studies in cells and engineered
tissues will be given to the REU student and these areas will be utilized to accomplish the goals
of this project.
Leigh Atchison, Senior, Biomedical Engineering, North Carolina State University
Mentors: Dr. Nenad Bursac, Principle Investigator and Dr. George Engelmayr, Research
Scientist, Department of Biomedical Engineering at Duke University
Project Title: Optimizing a Cell Culture Medium for the Expansion of Skeletal Muscle-derived
Satellite Cells and Myoblasts In Vitro
Skeletal muscle tissue engineering is an exciting field of research that has the potential to
solve many medical conditions or injuries resulting in large volumetric muscle loss as in battle
wounds or muscle degradation as in muscular dystrophy. The ability to create this muscle in
large, cost effective quantities is currently limited. The two critical issues with skeletal muscle
engineering are 1) the small number of skeletal muscle derived myoblasts and satellite cells that
can be isolated as well as 2) the purity of these cells for skeletal muscle reconstruction. In order
to overcome these limitations, we tested different growth environments in order to determine the
optimal conditions for maintaining large number of phenotypically pure cell populations.
Neonatal rat skeletal muscle cells were enzymatically isolated and seeded on Matrigel and nonMatrigel coated tissue culture flasks in growth medium containing 0 ng/mL, 2.5 ng/mL, 5 ng/mL
or 10 ng/mL basic fibroblast growth factor (bFGF). After passaging the cells four times cell
counts were taken and the cells were grown in differentiation medium in PDMS molds to create
muscle bundles. Cell counts showed that the greatest number of cells occurred in the population
grown on Matrigel in a growth medium containing 5 ng/mL. After two weeks the muscle bundle
functionality was tested by their force output. The population grown in 10 ng/mL of bFGF
produced the greatest force even with low cell counts. The bundles were then stained in order to
characterize the cell types present in each of the populations. The population grown in 2.5 ng/mL
bFGF showed the greatest number of cells, but the population grown in 10 ng/mL bFGF showed
a purer population with a larger ratio of myoblasts to fibroblasts. In summary, this study shows
that bFGF and Matrigel are necessary for creating an optimal growth environment to grow
skeletal muscle derived cells. Also, increasing the concentration of bFGF creates a purer
population of cells by limiting the growth of fibroblasts in culture.
REU Fellow: Alice Welsh, Biomedical Engineering Major, Senior, North Carolina State University
Quantifying Gap Junctional Coupling between Cardiomyocytes and Other Cell Types
Mentors: Dr. Nenad Bursac, Assistant Professor, and Luke McSpadden, Graduate Student, Biomedical
Engineering
Alice Welsh is a senior biomedical engineering major at North Carolina State University. The
purpose of her project was to determine gap junctional coupling between cardiomyocytes and other cells
types. Cardiac cells are connected to each other by channels called gap junctions; these channels allow
ions and small molecules to pass between adjacent cells. The presence of these junctions allows for
electrical signals within the heart to propagate from cell to cell, causing the contraction of the heart which
pumps blood throughout the body. The formation of gap junctions between other cell types and
cardiomyocytes results in slowed conduction of the action potentials of the heart, leading to unpredictable
signal propagation. It was hypothesized that gap junctions would only form between cardiomyocytes and
other cells that contain connexins, which are important gap junctional proteins. In order to quantify the
gap junctional coupling between cardiomyocytes and other loading cells, a technique involving dye
transfer followed by fluorescent-activated cell sorting (FACS) analysis was implemented. Donor cells
were stained with two dyes: one small enough to move through gap junctions, calcein AM, and one that
was too large, DiI. The percentage of cells which uptake the calcein but not DiI can be used as a measure
of gap junctional coupling between the cell types. The appropriate dye concentration and absorption
times were determined, as was the most effective staining procedure and donor to recipient ratio. The
initial results were good but the theory that yielded promising results with human embryonic kidney
(HEK) cells did not hold up for cardiomyocyte donor cells. This study helped clarify what process would
not work for cardiomyocytes, and gives some direction for procedures and approaches in future studies.
procedures. This project let Alice know for sure that she wishes to continue research in biomedical
engineering and she is currently applying to graduate programs, including Duke.
REU Fellow: Kassandra Thomson, Biomedical Engineering, University of Texas at Austin
The Visualization and Quantification of Collagen
Deposition by Cardiac Cell Cultures
Kassandra Thomson is a biomedical engineering major from the University of Texas at Austen.
Cardiac fibrosis is a major component of heart disease, and can lead to heart failure as the cardiac muscle
stiffens. It is important to build models of diseased heart tissue in order to study the effects of fibrosis on
the electrical properties of cardiac cells. The aim of this study was to develop a method to visualize and
quantify collagen deposition by 2D cardiac cell cultures in vitro to determine if collagen was being
deposited between cardiomyocytes, thus interrupting electrical propagation. Collagen deposition was also
compared between samples of different age, with different concentrations of ascorbic acid, and isotropic
versus anisotropic. Immunostaining was the primary method of visualization used. A new method was
developed to stain extracellular collagen separately from intracellular collagen. A hydroxyproline assay
was tried in order to quantify the amount of collagen present in cell cultures. Extracellular collagen
staining was achieved in cardiac fibroblast cultures, but not with cardiomyocytes. For fibroblasts, there is
a visible increase in the amount of collagen deposition with cultures of increasing age and with increasing
amounts of ascorbic acid. Changes in collagen deposition with cellular patterning have not yet been
determined. The hydroxyproline assay is currently being formatted to our cell cultures, and has not yet
worked successfully.
Project #10: Implanted Biopotential Recorder
Advisor: Patrick Wolf, Ph.D., Associate Professor, Department of Biomedical Engineering and
Thomas Jochum, Biomedical Engineering Graduate Student
A student involved in the Implanted Biopotential Recorder project will partake in the
development of an implanted medical device to measure, store, and telemeter biopotentials such
as electroencephalograms. The long range goal of the research is a novel medical system
comprised of a miniature electronic device implanted beneath the skin that measures and stores
biopotentials and a desktop device that extracts the data stored in the implanted device. An
important piece of this project is discovering how the devices electrically and thermally interact
with the body. The student will design, construct, and apply measurement systems that quantify
the electrical or thermal performance of prototypes or emulations of the Implanted Biopotential
Recorder. The ideal student should have an interest in electronics and computer-controlled
measurement systems. Experience with or prior course work in these areas is a real plus.
Susannah Engdahl, Senior, Physics, Wittenberg University
Mentors: Dr. Patrick Wolf, Associate Professor, Department of Biomedical Engineering and
Thomas Jochum, PhD candidate, Department of Biomedical Engineering
Project Title: Subcutaneous Electroencephalography Electrodes
Although electroencephalography (EEG) is frequently used in the diagnosis of
neurological disorders, it remains inadequate in situations where long-term data collection is
required. It is possible for patients to wear ambulatory EEG systems for up to months at a time,
but this can cause both physical and social discomfort. This problem may be circumvented with
the use of subcutaneous electrodes which interfere less drastically with patients’ lives. These
recently developed electrodes need to be tested against the conventional external electrodes to
ensure they perform equivalently. Testing will be performed by comparing the power of the
signals detected by the two electrode types in the traditional EEG frequency bands. Consequently,
a system has been developed which is capable of acquiring EEG signals, and then calculating and
displaying signal power across the frequency bands. It relies upon LabChart software to perform
calculations and Microsoft Excel to display the results in a color-coded format that represents the
relative power of the EEG signal in each frequency band. This system has been verified to
correctly detect changes in alpha band power resulting from a patient opening and closing his
eyes. Further testing must be done to ensure that it performs in a manner comparable to that of a
clinical EEG system.
Clarissa Shephard is a biomedical engineering major from North Carolina State University. Her
research focused on the Subdermal EEG Recorder for Lifelong Monitoring, which will provide a low cost
alternative to currently available EEG monitoring devices. The Recorder will be a thin cylindrical device
implanted along the top of the skull, below the scalp. Because the device is fully implanted, charging of
the device and data transmission will occur transcutaneously. To test the transcutaneous capabilities of the
device, a saline phantom model of the human head was created using acrylic, saline, and copper wires to
mimic the electrical properties of the human head. This model was built using the HEALPix (Hierarchical
Equal Area isoLatitude Pixelation) model as a conformal mapping model for the scalp and skull. The
scalp and brain were represented by saline layers and the skull was represented by a perforated acrylic
sheet. These materials gave the desired electrical properties and resistivity ratios. The copper wires were
used to electrically connect the physical discontinuities present in the HEALPix model. The completed
model was tested and the results were compared to a computer simulation to determine the relative error.
Initial findings show that the model has limited error when compared to the computer simulation, but
future research must be done to determine if this is an accurate representation of an anatomical human
head.
Erin Lewis, Mechanical Engineering Major, Junior, University of Kansas
Encapsulation Methods for a Neural Data Acquisition System
Erin Lewis is a junior mechanical engineering major at the University of Kansas. Her project
focused around neural data acquisition, which translates neural signals into digital signals that can be
interpreted by a computer to perform specific motions such as moving a prosthetic arm. Current
technology is progressing toward a three-component system that can be considered for complete
implantation. However, the system must be encapsulated in appropriate materials that will protect the
human body and the electronic components, as well as meet the government’s standards and Erin’s
project was to research and begin testing on this encapsulation methodology. She created a handbook
outlining each detail of the encapsulation procedure and outlining the methods and materials of two
components of the system: the Transcutaneous Energy Transmission System (TETS) coil and the Internal
Central Communications Module (ICCM). In the process learned about properties of several materials:
compatibility, durability, flexibility, and water-vapor permeability, as well as FDA approval. She
performed many compatibility tests, learning which materials worked well together. Through her
research and lab testing, encapsulation methods and materials for two of the components have been
documented. The Transcutaneous Energy Transmission System (TETS) coil is encapsulated in Silicone
Adhesive and Silicone Dispersion to create a flexible, durable, and water-vapor preventative coating. The
Internal Central Communications Module (ICCM) is coated first with Parylene-C, a pin-hole free
covering, and then by a mold of Hysol Medical Grade Epoxy; the combination provides durability and
water vapor permeation protection. The procedure for the encapsulation of each component will help the
neural data acquisition system be one step closer to the market.
Patrick Conway, Computer Science Major, Gallaudet University
Brain-Machine Interface
Patrick Conway is a computer science major from Gallaudet University. His project involved a
portable neural interface developed by Dr. Iyad Obeid for his Ph.D. under the supervision of Dr. Patrick
Wolf, which has been undergoing some revisions and needed a new software program to run it.
Specifically, there are two data processing boards operating in tandem rather than a single one and the
6533 Digital I/O data acquisition card from National Instruments is being used for the first time to collect
the data from the data processing boards. At this point, the program is also being transferred from a
command line interface to a graphical user interface. The software is capable of acquiring data from the
FIFOs of the brain-machine interface, converting the data from the packed 8 bit word formats to the
unpacked 16 bit word format, saving the data to a selected file, and graphing all channels simultaneously.
The software uses parallel processing to improve speed and dynamic queues to allow the threads to
proceed at their own pace. There are a few software and hardware bugs to work out yet, but nearly
everything is fully functional at the time of this writing.
Eric Turevon, Biology and Computer Science Major, Gallaudet University
Software for a Brain Machine Interface
Eric Turevon is a biology and computer science major from Gallaudet University. His project
focuses on the Brain Machine Interface, and his research was performed in collaboration with Patrick
Conway, also an REU Fellow, with Dr. Patrick Wolf, Associate Professor of Biomedical Engineering, as
their mentor. Eric’s task was to learn to program software to accompany the Brain Machine Interface.
The three components of a brain machine interface are: a 16 channel headstage module, an analog front
end and mezzanine,a personal computer with a National Instruments NI-DAQ PXI-6533 PXI
interface onboard. The software programmed to interact with these components was written in a
LabWindows/CVI environment. Eventually, the purpose of this brain machine interface will be to assist
severely disabled people to lead a more productive, independent life.
Clarissa Shephard, Biomedical Engineering Major, North Carolina State University
Subdermal EEG Recorder for Lifelong Monitoring
Mentors: Dr. Patrick Wolf, Associate Professor, Department of Biomedical Engineering and Thomas
Jochum, Biomedical Engineering Graduate Student and Zachary Abzug, Pratt Fellow in Biomedical
Engineering
Renee Miller, Biomedical Engineering Major, Marquette University
In Vitro Differentiation Between Multiple Cardiac Ablation Lesions using Acoustic Radiation Force
Impulse (ARFI) Imaging
Renee Miller is a biomedical engineering major from Marquette University. Her project focused
on acoustic radiation force impulse (ARFI) imaging, which may be an effective method of imaging
cardiac ablation therapy in real-time. Many cardiac ablation treatments, used to treat arrhythmias, require
doctors to make multiple lesions in a line or ring. Consequently, ARFI imaging must enable doctors to
distinguish between separate lesions and show gaps between them. In this study, a V shaped lesion was
made in porcine and ovine myocardial tissue samples and imaged using ARFI imaging. A digital picture
of the image was also taken. The images were aligned using needles which were visible in the digital and
bmode images. Then, a thresholding algorithm was used to determine lesion from non-lesion in the ARFI
image. And finally, at the point of separation, the distance between the actual lesions was calculated in
order to determine the relative resolution between lesions using ARFI imaging. The average distance
between distinguishable lesions was 0.22 cm. With this information, doctors can potentially perform
cardiac ablations with greater accuracy. In addition, a standardized method for creating the V shaped
lesions was determined. Ablating endocardial tissue at 30 W for 60 sec proved to be most effective in
creating a defined V shaped lesion visible on both the surface and ARFI images.
Emily Dingmore, Biomedical Engineering Major, North Carolina State University
Preliminary Investigation of the Feasibility of a Graphite Radio-frequency
Ablation Catheter
Emily Dingmore is a senior biomedical engineering major from North Carolina State University.
Developments in Acoustic Radiation Force Impulse (ARFI) imaging have provided useful imaging of
lesions during cardiac Radio-frequency ablation procedures. By measuring stiffness in soft tissue, ARFI
imaging can determine the effectiveness of procedures to treat cardiac arrhythmias. This imaging
technique, however, cannot take place while a metal catheter is in the imaging window due to noise
created on the ARFI image. Alternate catheters were tested by placing various carbon materials on
porcine heart tissue and producing ARFI images at incremental distances. It was predicted that by using a
graphite coated radio-frequency ablation catheter instead of a metal tip catheter there would be a
reduction of noise present in the Acoustic Radiation Force Impulse image. This reduction of noise would
allow for improved imaging of lesions created during clinical cardiac ablation procedures. By using
MATLAB computer code to analyze the average amount of noise produced by each material it was
determined that the graphite samples produced less noise on the ARFI image than that produced by the
metal catheter. The region of tissue affected is also smaller for the graphite materials. It is also possible
that the transducer used for capturing the ARFI images can be closer to the catheter placement site for the
graphite materials than it can be while imaging the metal catheter. Further testing may provide more
insight into the benefits of using various materials for the ablation catheter.
Project #11: Tissue-engineered model of muscle disease
Advisors: Nenad Bursac, Associate Professor, Biomedical Engineering and Mark Juhas,
Biomedical Engineering Graduate Student
Duchenne Muscular Dystrophy (DMD) is a debilitating disease that occurs due to lack of the
protein dystrophin. The disease effects 1 in every 3500 males and in most cases results in patients
being wheelchair-bound by age 12 and dying before age 30 due to respiratory or heart failure. In
this project we will apply genetic and tissue engineering methodologies to generate novel tissue
model of DMD muscle and by altering expression of membrane-matrix binding proteins
(integrins) attempt to decrease cell death, improve force generation capacity, and restore normal
myofiber architecture of the DMD muscle. A variety of tissue engineering techniques, gene and
protein expression analyses, and physiological tests will be utilized to accomplish goals of this
project.
Project # 12: Neuronal circuits in the primate brain and their implications for robotics
Advisor: Marc A. Sommer, Dept. of Biomedical Engineering and the Center for Cognitive
Neuroscience
The primate brain is a network of highly interconnected areas. Most of the areas have
been studied at this point, and we know much about them. Little is known, however, about how
the areas talk to each other. Somehow their connections form highly synchronized, widespread
circuits that mediate our perception, cognition, and movements. The overall goal of my
laboratory is to study the interaction of brain areas at the circuit level. Our primary method is to
record from single neurons in behaving rhesus monkeys. The animals perform tasks similar to
video games that involve visual stimulation, decision-making, and eye movement responses. We
study the signals carried by neurons between brain areas while the animals perform the tasks,
analyze what the signals represent, and design computer models that help us to interpret our
findings and apply them to technology. We are currently designing a model of the visual system
that rotates a video camera in a way that approximates real eye movements. Input from the
camera guides a robotic arm, and the bioengineering challenge is to design the system so that the
arm makes accurate visually-guided manipulations even as the video camera moves around -- just
like we are able to inspect and manipulate tools even as we move our eyes around. A good
undergraduate candidate for a position in our laboratory would have studied biology (including a
basic understanding of neurons), would be comfortable with animal research, and should have
familiarity with computer programming (e.g. Matlab or C), engineering, or both.
Project#13 (WISeNet): Robotic Saccadic Adaptation and Visually-guided Auditory
Plasticity
Advisor: Dr. Marc Sommer, Associate Professor, Biomedical Engineering and Dr. Jennifer
Groh, Professor, Psychology & Neuroscience (WISeNet)
Many items in the world make sounds, so to understand the world coherently biological brains
must colocalize visual and auditory inputs. This is important not only for perception, but also
for action. If you suddenly hear something next to you, looking at it quickly and accurately
could save your life. Sensor fusion and learning based on heterogeneous sensor data, and
subject to changing environmental conditions, are very challenging problems that are yet to be
overcome in artificial sensor systems. Currently, robotic sensors deployed to perform both
sensing and motor or navigation tasks, such as mapping an environment and manipulate
objects while avoiding collisions, must first stop and process the sensor data, and then execute
the motion. Their ability to process data, and coordinate across different sensor modalities is
far removed from that observed in biological systems.
The focus of this project is to transfer findings of on-going research on biological sensory
systems to the design of artificial robotic sensors. This research will aim at reproducing some
of the capabilities of biological sensors, such as, coordinating sensor movements and fusing
heterogeneous sensor data, while performing motor tasks, such as, manipulating an object, or
moving across an obstacle-populated room. A servo-mounted camera will be used to send the
visual input to the robot’s computer (e.g. coffee mug), and the computer must rotate the
camera at saccadic velocities. The sensorimotor system will be simulated using a neuronal
sheet structure designed with the program Topographica, and the experiment is set up to
examine presaccadic remapping, and mediation of our sense of visual continuity while we
move our eyes.
Research in the Sommer Laboratory involves recording from single neurons and studying the
effects of inactivating or stimulating well-defined brain areas. Our goals are to understand how
individual areas process signals and how multiple areas interact to cause cognition and
behavior. Results from the work are guiding the design of vision-based models and robots.
The goal of the REU fellow will be to help test a computational sensorimotor system on a
robot comprised of a servo-mounted video camera, microphone, and sound card, soon-to-be
equipped with a robotic arm.
Project # 14 (WISeNet): Sensorimotor Modeling and Control
Advisor: Dr. Marc Sommer, Associate Professor, Biomedical Engineering Dr. Craig
Henriquez, Professor and Chair, Biomedical Engineering, and Dr. Silvia Ferrari, Associate
Professor, Mechanical Engineering and Materials Science (WISeNet)
Recent results in the neuroscience literature indicate that the sensorimotor system functions as
a feedback controller that optimizes neuronal representation of behavioral goals, such as,
regulatory and exploratory behavior. Several experiments have also shown that exploratory
actions, such as, whiskers deflections in rat’s tactile exploration, are optimized for sensory
input, and that the adult primary somatosensory (SI) cortex compares the meaning encoded in
new sensory inputs with internal representations, or models, of the sensory experience
accumulated during a lifetime. For example, an internal dynamic may be used by the brain to
represent the behavior of the external environment, as in the case of saccadic adaptation where
the frontal eye field may use an internal model of the motor-to-sensory transformation, in
combination with the current state of the motor system to predict the sensory input. This
prediction may be compared to the actual, reafferent sensory input to inform the brain of
sensory discrepancies evoked by environmental changes, and generate shifting receptive fields.
Drs. Sommer, Henriquez, and Ferrari are currently collaborating to develop a computational
sensorimotor systems comprised of a network of neural networks each representing an internal
model and controller, and inspired by their biological counterpart. Their laboratories are
investigating the use of biologically-plausible paradigms, such as spiking neural networks and
synaptic time-dependent plasticity, to simulate and adapt both the internal models and
feedback controllers in the sensorimotor system subject to changing environments and external
stimuli. The REU fellow will test intelligent control designs, such as, model-reference
adaptive control, temporal difference, and adaptive critics through robotic and computer games
conducted in the Ferrari Laboratory, as well as through real-worlds experiments on saccadic
adaptation and visually-guided auditory plasticity conducted in the Sommer Laboratory.
Project #15: Early Cancer Detection with Biophotonics
Advisor: Adam Wax, Associate Professor, Biomedical Engineering
My research is based on using non-invasive optical techniques to measure the features of
biological cells in a way that is not possible with traditional methods. We have developed a new
technique capable of diagnosing cancer at the cellular level based on using scattered light and
interferometry. Currently, we are developing these techniques for application to detecting cancer
in vivo. Research in my lab involves designing and implementing electronic and optical systems,
programming in Labview for instrument control, as well as computer modeling of light scattering
using C++ and Fortran. This project can include hardware (optical and electrical systems) and/or
software (Labview and/or C++) components
Jenna Woodburn, Chemistry Major, Gallaudet University
Polarization effects on plasmonic coupling of gold nanosphere pairs
Jenna Woodburn is a chemistry major from Gallaudet University. Her project hypothesis was
“will parallel polarization direction show a strong redshift of the surface Plasmon peak?” or “will
orthogonal polarization show a strong redshift of the surface Plasmon peak?” She studied and worked
with gold nanoparticles by taking many images of gold nanoparticles in order to find and measure
interparticle distance. She learned to use a Scanning Electron Microscipe (SEM) as part of her training,
and also learned many laboratory techniques which were new to her. While using the SEM (Scanning
Electrons Microscope) for her project, she realized that she still could not find the measure of the
interparticle distance. She found that the difficulty was due to the very hard problem of keeping the gold
coating on the slides. Instead of the gold coating, she then used Indium tin oxide coating, which worked
well. The laboratory is still working on this project and this work will continue. Her mentor and other
workers in biomedical engineering will continue to work towards results for this research.
Matthew Meleski, Chemistry Major with Minors in Biology and History, Gallaudet University
Low Coherence Interferometry (LCI) for Microbicide Gel Measurements: Optical Signal to Noise Ratio
(OSNR) and Resolution
Matthew Meleski is a senior chemistry major and biology and history minor at Gallaudet
University. Everyday, the cases of HIV and AIDS are rapidly increasing due to unprotected sexual
activities, especially in third world countries in Africa. In order to prevent the rising cases of HIV and
AIDS, scientists around the world are developing many different preventative methods against HIV and
AIDS. One method being developed to prevent the spreading of HIV/AIDDS is by using microbicide
gels. These gels are topical products that act as a physical barrier and as a carrier of an active drug. Based
on the Michelson Interferometer geometry, the 6-channel low coherence interferometry (LCI) will be
used, and the optical signal-to-noise ratio (OSNR) and axial resolution of each channel will be
determined. LCI uses broadband light to perform depth ranging measurements of layers in a sample. If
improvements are made to the LCI device, particularly in optical signal-to-noise ratio (OSNR) and axial
resolution, then there will be increased accuracy of measurements using the device. In order to obtain the
OSNR data of each channel, a Matlab routine program was developed to calculate the OSNR for an input
signal. Also, a Matlab routine was made that plots the data as an a-scan graph and calculates the
resolution of each channel. The resultant resolution values were then compared to the predicted
resolution of 6.2 micronmeters. All of the actual resolutions are higher than the theoretical resolution
(6.2), which means that all these channels are not optimized due to possible contamination (dirt and dust),
or the channels are not aligned well. It is therefore concluded that more work and adjustments need to be
done on the 6-channel LCI device in order to reduce the actual resolution as close as possible to 6.2
microns.
Ryan Kobylarz, Chemistry Major, Junior, Gallaudet University
Early Detection of Cancer with Biophotonics
Ryan Kobylarz is a junior chemistry major from Gallaudet University. The objective of Dr.
Wax’s research project was to develop a biomedical tissue imaging technique. In this research Ryan
learned about how optics can affect the properties of light and how interferometry is based on the physical
principle of light waves; two light waves in phase amplify while those in opposite phases cancel out.
Ryan and the research team developed a non-invasive optical technique, Digital Hologram Microscopy,
which utilizes both interferometry and microscopy. They used a modified Mach-Zehnder interferometer
type, adding acoustic-optical modulators to create a frequency offset. The frequency offset then caused a
phase shift and allowed insight on the sample analyzed through the microscope. The resulting images
provided a three-dimension informative view of the sample. Images from stationary objects were obtained
and analyzed, and the next step will be to complete the dynamic cell imaging technique.
Michele Patterson, Biosystems Engineering Major, Clemson University
Early Cancer Detection with Biophotonics
Michele Patterson is a Biosystems Engineering Major from Clemson University. Her project
focused on low coherence interferometry, which allows information to be gathered concerning nuclear size
and depth resolution. When light is directed at a spherical particle it will demonstrate characteristic
reflection patterns. A new system named Fourier-domain Low Coherence Interferometry (fLCI) is
introduced to detect the size and location of cell nuclei. It is hypothesized this information can potentially
offer a noninvasive cancer diagnostic system since it has been determined that malignant cells display an
abnormally large nucleus compared to benign cells.
Upon reaching a spherical particle, such as a cell nucleus, light waves will both reflect off and
travel through the particle. Of the light that passes through the lower boundary of the particle, again some
will reflect off the upper layer of the particle and some will pass through. The reflected rays will meet and
display a distinctive interference pattern. This scattered spectrum is then Fourier transformed to determine
particle size and also depth resolution. The fLCI system provides a non-invasive, cost effective technique
for noticing nuclear irregularities at various depths within tissues.
Particles of different sizes were measured to optimize the data collection technique. First uniform
microspheres were used to mimic nuclear size. The 1.0 micron beads produced credible results with the
fLCI system yielding an average size of 1.099 microns. Second, E. coli cells were measured. Although
these cells are much smaller than human cells, they display the natural variations in size unlike the uniform
microspheres. Several different samples were tested; the average sizes, in microns, were 0.398, 0.423,
0.819, 0.828, 0.753, and 0.429. E.coli cells are known to range in size from around 0.5 microns to 1.0
microns, so these results were very accurate. Finally, yeast cells were measured since these display
roughly the same shape as cell nuclei.
Since the readings from the fLCI system consistently provided convincing results, hopefully this
device can be used in a clinical setting to identify cell dysplasia.
Project #16: Heterogeneous Datacenter Design and Deployment
Advisor: Benjamin Lee, Assistant Professor, Electrical and Computer Engineering
Demand for computing capacity is driven by the data deluge. Over the past 45 years, computer
engine,ers have transformed exponentially increasing transistor density into exponentially
increasing capacity. At present, energy costs jeopardize further scaling. The US Environmental
Protection Agency estimates datacenters already consume 1.5% of total nationwide electricity,
which is comparable to the consumption of 5.8M US households. No combination of existing
datacenter architectures can improve computing capacity by the desired three orders of magnitude
within datacenter power budgets, which are already at megawatt scales. This project examines
the design and deployment of heterogeneous datacenter architectures that improve efficiency by
10x. Heterogeneity deploys a mix of specialized hardware for a mix of software needs,
improving efficiency as unnecessary hardware resources are eliminated. To build heterogeneous
datacenters, we explore design spaces for processors, memory, network, and storage using
techniques in statistical inference and machine learning. To deploy heterogeneous datacenters,
we use multi-agent markets in which applications bid for heterogeneous architectures,
maximizing utility. REU students participating in this project may participate in data collection
and analysis. Responsibilities may include (1) analyzing performance and power for a variety of
processor and memory designs, (2) simulating future processor and memory designs, (3)
performing data analysis and design optimization. While not required, some knowledge in
computer architecture and a major programming language (e.g., C, C++, Java) is helpful.
Project # 17 (WISeNet): Dynamic Optimization of Enterprise Systems Using Real-Time
Sensor Measurements and Adaptive Feedback Control
Advisor: Dr. Krishnendu Chakrabarty, Professor, Electrical and Computer Engineering and Dr.
Silvia Ferrari, Associate Professor, Mechanical Engineering and Materials Science (WISeNet)
The goal of adaptive feedback control for enterprise systems (ES) is to develop data-centric
techniques for designing an adaptive ES to enable the highest level of agility, performance, and
efficiency. Adaptive model reference and reinforcement learning techniques will provide the
foundation for a smart software mediation layer that enables the ES to be self-learning,
adaptive to dynamic/diverse service requests and resource availability, based on real-time
sensor measurements from ES nodes, as well as support a network of service providers and
users within a complex information ecosystem.
The focus of this project is integrate, for the first time, policy management and production
planning with data-driven adaptive control to realize a dynamic information ecosystem. Our
vision is a smart enterprise-wide system that automatically adapts to emerging system
behaviors by dynamically evolving optimization strategies in real-time and without disruption.
This level of adaptation, seamless efficiency, uninterrupted service from the perspectives of
users and providers, is a significant step forward towards smart enterprise systems. To date,
most adaptive control methods, including MRAC, are applicable to linear or, in some cases,
nonlinear dynamical systems that can be modeled by an ordinary differential equation or
transfer function derived from first principles. This research will develop an adaptive control
method for influence diagram (ID) models of enterprise systems that can be learned from data,
and that can take into account uncertainties and errors inherent to all ES and their users.
Professor Chakrabarty’s research is focused on testing and design-for-testability of integrated
circuits; digital microfluidics, biochips, and cyberphysical systems; optimization of digital
print and production system infrastructure. His research projects in the recent past have also
included chip cooling using digital microfluidics, wireless sensor networks, and real-time
embedded systems. The goal of the REU fellow will be to develop and influence diagram
model of an enterprise systems using learning algorithms and simulation data from an existing
virtual printing factory.
Project #18: Design-for-Testability Methods for Multicore Integrated Circuits
Advisor: Krishnendu Chakrabarty, Professor Electrical and Computer Engineering
Multicore integrated circuits (or “muticore chips”) are being used today in microprocessors to
achieve high performance under power constraints. Processor chips with four cores from
companies such as Intel and AMD are now common, and up to 16 cores are going to become
mainstream quite soon. These multicore chips are giving us unprecedented computing power for
scientific applications, gaming and entertainment, control systems, and business software. For
graphics applications and graphics processors (GPUs) from companies such as Nvidia, many
more cores are integrated in a single chip. This project is focused on cutting-edge design-fortestability (DFT) techniques for multicore chips. We are developing DFT solutions that can
reduce manufacturing cost and make these chips more dependable for user applications. Our
research involves collaboration with Intel and AMD.
Desired skillset: A first course in logic design and computer hardware, basic knowledge of
electronic circuits, some understanding of computer architecture/organization, programming in
C/C++.
Project #19: Optimization Methods, Chip Design, and Software Development for Digital
Microfluidic Biochips
Advisor: Krishnendu Chakrabarty, Professor Electrical and Computer Engineering
Advances in digital microfluidics have led to the promise of biochips for applications
such as point-of-care medical diagnostics. These devices enable the precise control of nanoliter
droplets of biochemical samples and reagents. Therefore, integrated circuit (IC) technology can
be used to transport and process “biochemical payload” in the form of nanoliter/picoliter droplets.
As a result, non-traditional biomedical applications and markets are opening up fundamentally
new uses for ICs. In this interdisciplinary research project, we are studying ways to design
biochips that can produce accurate results for clinical diagnostics in the shortest possible time and
with minimum chip area. We are collaborating with other faculty and a start-up company in
Research Triangle Park.
Desired skillset: A first course in logic design and computer hardware, high-school or freshmen
Chemistry lab work, programming in C/C++, basic knowledge of optimization and computer
algorithms.
Project #20: RF and Antenna Design for Communication and Imaging
Advisor: Qing H. Liu, Professor of Electrical & Computer Engineering
The objective of this project is to design and fabricate small
antennas for communication and imaging applications. The student
will utlize computer software to design antennas, build antennas in
the laboratory, and perform communication and imaging measurements.
Ugonna Ohiri, Computer Engineering Major, University of Maryland- Baltimore County
Ultra Wideband Antennas
Mentors: Dr. Qing Liu, Professor, Department of Electrical and Computer Engineering and Luis Tobon
Llano, Graduate Student, Department of Electrical and Computer Engineering
Ugonna Ohiri is a computer engineering major from the University of Maryland-Baltimore
County.
His research focused on antennas with both multiple frequencies of resonance and
widebroadband performance which have played a major role in the functionalities of wireless
communication systems. In his project, he used the Sierpinski Carpet Mod-P fractal antenna based on
fractal geometry. In our experiment, we constructed three iterations using both software simulations and
experimental validation as measurements to test various parameters. The effect of further fractal iterations
on the overall efficiency of the antenna is studied. Both the simulations and experiments show consistent
results when weighed against each other. Overall, the results show the third iteration as being the most
efficient iteration, when compared to the preceding three.
Wesley D. Sims, Physics Major, Morehouse College
Using Microwave Imaging for Breast Cancer Detection
Wesley Sims is a senior physics major from Morehouse College. Microwave imaging for breast
cancer detection is based on the contrast in electrical properties of healthy breast tissues and malignant
tumors. My project contributed to the research of breast cancer detection using microwave imaging as an
REU Fellow at the Pratt School of Engineering at Duke University. The purpose of this project is to assist
in the ability to detect breast cancer by using microwave imaging. Microwave imaging is a much healthier
methods for breast cancer detection than current methods in use. I assisted in the proposed design of a
clinical system to be used at Duke University to do testing through multiple clinical trials. I helped to
design the bed-like structure with an integrated chamber that will collect images of a patients’ breast
tissue. In addition, I helped to design and simulate major components of the proposed switching system.
Part of my research involved making schematic drawings of a proposed clinical system and a single pad
of a circuit board layout. I also performed tests and obtained results from simulations done in Agilent
Automated Design System to be used in refining the system for future use.
Jack Skinner is an electrical engineering major from Ohio Northern University. Microwave
Imaging (MWI) is an emerging technique for the detection of breast cancer and other biomedical
anomalies. The success of microwave imaging is due to the distinct differences in electrical properties
between malignant tumors and healthy mammary tissue. This new imaging technique uses non-ionizing
radiation to produce a full 3-D image of the anomaly based on scattered microwave energy. This paper
focuses on the research and construction of an experimental 3-D MWI system, as well as some of the
theory behind microwave imaging. The MWI system will use a 3-D array of folded patch antennas to
send and receive an RF signal. The transmitted signal will be scattered by an object (tumor) and then
recorded by various antenna combinations. These measurements, known as S21 parameters, will be used
in an inversion algorithm to reconstruct the inverted dielectric constant and conductivity of the medium
and the target itself. This research discusses the major components of the MWI system: the antenna array,
imaging chamber, switching system, network analyzer, and PC used to run LabVIEW software and record
the data. The conclusion of Jack’s research has resulted in a functional 3-D MWI system, with only issues
of the switching system and matching fluid to be resolved before a series of tests will be run to
reconstruct sample images.
In addition, another new imaging technique, microwave-induced
thermoacoustic imaging (MITI), was discussed and reviewed. This imaging technique will use short
pulsed, high power microwave energy to irradiate the mammary tissue and possible tumors. The tissue
and tumor will then heat up and expand, causing a variation in fluid pressure. The difference in pressure
will induce an acoustic signal that will be recorded by an ultrasonic transducer and amplified. The
amplified signal will be converted to a digital signal to be used in image reconstruction.
Project #21: Programming A New Type of Multicore Processor
Advisor:Dan Sorin, Electrical and Computer Engineering
Prof. Sorin's research group has developed a new type of multicore
processor that includes general purpose cores (CPUs) and graphics
processing units (GPUs). The novelty of the new system is in how the
CPUs and GPUs communicate with each other, and this new communication
is vastly more efficient than previous schemes. To take advantage of
this faster communication, we need to re-write programs that were
written in CUDA or OpenCL. The potential for performance improvement
is very large (10-100x speedups), and we seek students who can learn
new programming skills and incorporate knowledge of the hardware to
write better software.
Bryan Anthonio, Sophomore, Engineering Physics, Cornell University
Mentor: Dr. Dan Sorin, Associate Professor, Department of Electrical and Computer Engineering
and Ralph Nathan, PhD Candidate, Department of Electrical and Computer Engineering
Project Title: Recycled Error Bits: Architectural Support for Energy-Efficient and Numerically
Accurate Software
In numerical software, double precision is often preferred over single precision
for concerns relating to the smaller amount of numerical accuracy offered by single
precision. Rounding error often constrains the accuracy of numerical software due to the
finite precision of FPUs, making the use of double precision more prominent. However,
the use of double precision often leads to significant energy costs, as it can be more
burdensome to hardware due to the increased transfer of data to and from memory. The
purpose of this investigation is to facilitate the development of numerical software that is
both accurate and energy efficient. We demonstrate that “recycling” the rounding error of
each floating-point operation and allowing it to be utilized, if desired, can achieve this.
Our experiments show that by doing this, numerical software can either achieve greater
accuracy with comparable performance and energy use or comparable accuracy with
greater performance and less energy use.
Project #22: Design and Evaluation of a Computer Processor that Tolerates Faults
Advisor:Dan Sorin, Electrical and Computer Engineering
Prof. Sorin's research group is developing the first low-cost
multicore processor that can tolerate faults as it runs, without the
user ever knowing that any problems had occurred. There are many
challenges to be solved, including how to detect when certain errors
occur and how to demonstrate that the chip design actually achieves
its goals at reasonable power and chip area costs. We seek students
who want to "get their hands dirty" in hardware design and
experimentation
Project #23: Thickness Variation in Polymer Thin Films Deposited by Resonant Infrared
Matrix-Assisted Pulsed Laser Evaporation
Advisor: Adrienne Stiff-Roberts, Associate Professor, Electrical and Computer Engineering
Resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) is a promising
deposition technology for the fabrication of conjugated polymer-based optoelectronic devices for
two primary reasons: i) the ability to control film morphology, and ii) the ability to deposit multilayered heterostructures. The Stiff-Roberts group has developed a variation of RIR-MAPLE that
uses emulsified targets of organic solvents and water such that the incident laser wavelength
(Er:YAG at 2.9 µm) is resonant with hydroxyl (O-H) bonds in the host matrix, which are absent
from the guest material. The novelty of the approach lies in the fact that while most polymers of
interest and many compatible solvents do not resonantly absorb the laser energy at 2.9 μm, the
emulsion with water enables high-quality, thin-film deposition with minimal photochemical and
structural degradation for almost any polymer of interest. In order to fabricate polymer-based
optoelectronic device heterostructures, careful control over film thickness across a substrate is
required. In this project, atomic force microscopy (AFM) will be used to characterize film
thickness of polymer thin films across an entire substrate as a function of RIR-MAPLE growth
parameters. The goals is to determine the thickness uniformity of the thin films for application to
optoelectronic devices.
Project #24 (WISeNet): Decentralized Sensor Guidance and Control in Complex
Obstacle-Populated Environments
Advisors: Dr. Michael Zavlanos, Assistant Professor, , Mechanical Engineering and Materials
Science, and Dr. Silvia Ferrari, Associate Professor, Mechanical Engineering and Materials
Science (WISeNet)
Methods for vehicle guidance (or motion planning) and control typically are designed to
compute a vehicle’s trajectory between two or more waypoints subject to navigation
objectives, such as collision avoidance and minimum-fuel consumption. Mobile sensors
consist of sensor-equipped vehicles that are deployed primarily to perform target detection,
classification, surveillance, and/or tracking. Thus, they require the sensor’s field-of-view
(FOV), or visibility region, to intersect the target geometry in order to obtain measurements
from the target. Since the FOV typically is bounded, the sensor’s position and orientation
determine what targets can be measured at any given time. Thus, the vehicle’s trajectory must
be planned in concert with the sensor’s measurement sequence. Finding optimal vehicle
trajectories is intractable even under simple constraints. This problem is aggravated by the fact
that many modern sensors are deployed as a part of a network that is possibly heterogeneous,
and must account for communication constraints, to allow sensors to communicate with each
other and/or a base (central) station.
The Zavlanos Laboratory specializes in the area of networked dynamical systems and
distributed control, with applications to robotic, sensor, biomolecular, and social networks. The
goal of the REU fellow will develop new guidance methods for mobile sensor networks by
investigating how approaches such as optimal control, potential field, and probabilistic
roadmap methods can be modified to account for the expected information value of the targets,
based on the local environmental conditions.
Project # 25 (WISeNet): Biologically-inspired Intelligent Sensor Networks
Advisor: Dr. Silvia Ferrari, Associate Professor, Mechanical Engineering and Materials
Science and Dr. John Alberston, Professor, Civil and Environmental Engineering (WISeNet)
Intelligent sensor networks consist of multiple heterogeneous vehicles, such as ground, air, and
underwater robots, each equipped with heterogeneous sensing and wireless communication
devices that work together toward a common objective. By cooperating and exploiting their
complementarities, these networks can exhibit enhanced sensing performance and navigation
in complex environments through the use of sensor fusion and data-sharing algorithms. As a
result, heterogeneous sensor networks are now being increasingly utilized to remove humans
from monitoring and surveillance tasks that are hazardous, tedious, or must last over long
periods of time.
Some of the applications we will consider in this project include alpine search-and-rescue;
robotic serpentine monitoring to detect leaks of greenhouse emissions from covered landfills or
from CO2 sequestration fields; environmental monitoring of air quality near major highways;
monitoring of physical variables in agricultural and greenhouse environments; and monitoring
of oil leaks in refineries for Leak Detection and Repair (LDAR). In all of these applications,
the robotic sensors must carry out multiple complex tasks, such as, cover a region of interest,
detect, track, classify, and possibly pursue multiple targets, while simultaneously avoiding
obstacles and maintaining connectivity with a base station.
Dr. Ferrari’s Laboratory for Intelligent Systems and Control (LISC), develops guidance and
control methods for mobile sensor networks, using interdisciplinary methods inspired by
biological systems, statistics, and computer science. As part of this project, the REU fellow
will help develop and test a hierarchical command and control software architecture for the
coordination and control of sensor networks, which will be comprised of three modular
components for mission planning, trajectory planning, and vehicle control.
Project #26:
Development of mRNA
Advisors: Kam W. Leong, Professor, BME
vaccines
for
anti-tumor
immunity
Nanoparticle-mediated delivery of mRNA vaccines warrants attention because of its potential for
direct in vivo administration of mRNA vaccines without ex vivo manipulation of dendritic cells.
We have previously shown that primary dendritic cells can be efficiently transfected by mRNA
encapsulated in nanoparticles. We have also identified intranasal and intravenous routes as
optimal vaccination sites, and further characterized associated transfection efficiencies and
transgene expression kinetics. In this project, we will investigate the efficacy of intranasal
vaccination of mRNA encoding antigen protein for inducing anti-tumor immunity in both
prophylactic and therapeutic settings. We envision that the student will assist in the following
aspects of the project:
1) Optimize the formulation of mRNA nanocomplexes for transfection
2) Assist in conducting animal experiments;
3) Characterize the immunological response of mRNA tumor vaccination.
Krystian Kozek, Materials Science and Engineering Major, North Carolina State University
siRNA Delivery Into LNCaP Cells Using a Novel, Multivalent Nanocomplex
Mentors: Dr. Kam Leong, James B. Duke Professor, Department of Biomedical Engineering and Dr.
Hanying Li, Postdoctoral Associate, Department of Biomedical Engineering
Krystian Kozek is a materials science and engineering major from North Carolina State
University. His research focues on short interfering ribonucleic acid (siRNA) delivery into prostate
cancer (LNCaP) cells, which was attempted using a novel and multivalent nanocomplex. The complex
was a three-armed deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) hybrid structure, where the
arms were connected through dithio-bismaleimidoethane (DTME) by disulfide bonding. The disulfide
bonding of the arms was not as efficient as desired; however, conjugation was successful, although with a
low yield. A three-armed and fully formed complex has not yet been completely successful proven;
however, preliminary data points towards assembly of the full nanocomplex. Application of this
nanocomplex for the receptor-mediated endocytosis into the LNCaP cells has been preliminarily
successful, with the aptamer guiding uptake and the siRNA knocking down chosen genes; future research
will aim to prove the efficiency and study the application in cancer research.
Nevija Watson, Chemical Engineering Major, North Carolina A&T State University
Fabrication of Nanopatterned Surfaces to Study Stem Cell Differentiation
Nevija Watson is a junior chemical engineering major from North Carolina A & T State University. The
hypothesis of her research project over the summer was that cells react to nanotopographic cues under
static conditions and flow alters the cells behavior. We wanted to engineer a synthetic surface with
topographic cues in the nanoscale to mimic a stem cell niche. We want to use this synthetic niche to
expand and differentiate human mesanchymal stem cells for cellular therapies. In my time here over the
summer, we found that the topographic cues on the synthetic patterned surface we created do affect the
cells. Cells seeded on the patterned surfaces grew and moved along the ridges of the pattern compared to
cells seeded on a flat surface which spread out along the surface in a normal fashion. We have found that
flow increases the elongation of the cells on the patterned surface and the cells become oriented in the
flow direction on the flat surface. Our findings from the duration of my project are still preliminary; there
is still extensive research to be done on the reaction of the cells to flow and the nanotopographic cues
Project #27: Hotspot Cooling by Jumping Condensate
Advisor: Chuan-Hua Chen, Assistant Professor, Department of Mechanical Engineering and
Materials Science chuanhua.chen@duke.edu 919-660-5343
The objective of this project is to develop a novel phase-change cooling technique for
hotspot thermal management of microprocessors and power electronics. The hotspot cooling is
enabled by the self-propelled jumping condensate on water-repellant superhydrophobic surfaces,
on which condensate droplets spontaneously jump by themselves. (The detailed process can be
watched on the Discovery Channel: http://watch.ctv.ca/clip231340).
This project is primarily experimental but will also involve the development of scaling
laws. The student will have the opportunity to fabricate the nano-structured superhydrophobic
surface and integrate it into a phase-change cooling system for hotspot mitigation.
More information about the Microscale Physicochemical Hydrodynamics Laboratory
(µPHYL) can be found online at http://www.duke.edu/web/uphyl/. Interested students are
encouraged to visit our lab at 181 & 183 Hudson Hall.
Chance Bozeman, Junior, Mechanical Engineering, University of Virginia
Mentors: Dr. Chuan-Hua Chen, Assistant Professor and Dr. Xiaopeng Qu, Post-Doc Research
Advisor
Project Title: Kelvin Water Dropper
The Kelvin Water Dropper is a high voltage gravity driven generater that has failed to be
implimented due to its sensitive and otherwise impractical set up. Developments into the field of
hydrophobicity has uncovered alterative mechanisms that may drive the Kelvin Water Dropper.
In the onset of such technology, our project aided to create a functioning and testable Kelvin
Water Dropper to first determine the most important parameters in assembly. A series of Kelvin
Water Droppers were made with each interation improving upon the previous. The most
important building factors was minimization of leakage, consistant flow rate at the nozzles, hoop
stability and a fixed distance between the nozzle and hoop assembly. The results of the calibration
test proved that the performance of the generator is indeed influenced by its enivornment. Further
testing with liquid conductivity implied that higher conductivity liquids would generate more
voltage. The current system will allow us to proceed with a control experiment to determine the
limitation of our unique generator. The results of this experiment will aid in the development of a
hydrophobic driven Kelvin Water Dropper.
Project #28: Thermohydroelectric Generator
Advisor: Chuan-Hua Chen, Assistant Professor, Department of Mechanical Engineering and
Materials Science chuanhua.chen@duke.edu 919-660-5343
The objective of this project is to develop a new technique to generate electricity by
harvesting waste heat. In a closed-loop phase change system, condensate drops can self-propel
themselves upon coalescence on a superhydrophobic condenser. (The detailed process can be
watched on the Discovery Channel: http://watch.ctv.ca/clip231340). Electricity can then be
generated from the jumping drops via electrostatic induction.
This project is primarily experimental but will also involve the development of scaling
laws. The student will have the opportunity to develop a thermohydroelectric generator from
scratch. High-speed photography will be used to study the energy conversion processes.
More information about the Microscale Physicochemical Hydrodynamics Laboratory
(µPHYL) can be found online at http://www.duke.edu/web/uphyl/. Interested students are
encouraged to visit our lab at 181 & 183 Hudson Hall.
Project #29: Transformative Skin: Controlled Electromechanical Instability on Polymer
Surfaces
Advisor: Xuanhe Zhao, Assistant Professor, Mechanical Engineering and Materials Science
An integrated theoretical, experimental, and computational effort is proposed to
systematically investigate novel polymer systems capable of transforming their surface patterns
and roughness under applied voltages. These transformative skins have a broad range of
important applications including on-demand superhydrophobicity, adaptive optics, controlled
adhesion, anti-biofouling and transfer printing. The technology is based on a surface
electromechanical instability, which frequently triggers electrical breakdowns and failures of
various polymers in energy applications including insulating cables, organic capacitors, polymer
actuators and generators. The opposite roles of the same instability require precise controls of the
instability in various applications, based on a fundamental understanding of its mechanism.
However, such an understanding is still missing in the basic knowledge of surface and materials
engineering, since previous studies are focused on air-polymer systems.
Recently, the PIs at Duke University have invented a new system (i.e. the transformative
skin) for studying the surface electromechanical instability. The new system represents a dramatic
departure from the conventional understanding in the field, which relies on the permeability
difference between air and polymer as the driving force for the instability. Although this driving
force does not exist in the new system, the transformative skin nonetheless yields a rich variety of
instability patterns strikingly different from conventional ones. The proposed project will
integrate a suite of experimental, theoretical, and computational tools to systematically
understand the surface electromechanical instability. Specific tasks include: 1) to develop an
experimental system to simultaneously generate instability patterns and characterize their threedimensional topography; 2) to develop a non-linear field theory to analyze the formation of the
instability patterns; and 3) to develop coupled-field models and numerical methodologies to
simulate the formation and evolution of instability patterns. The proposed research will constitute
the first systematic understanding of the surface electromechanical instability, with the potential
to significantly expand the use of functional surfaces and electrical polymers in energy
technologies.
Nia Christian, Sophomore, Carnegie Mellon University,
Mentors: Dr. Xuanhe Zhao, Assistant Professor and Jianfeng Zang, Postdoctoral Fellow
Project Title: Superhydrophobicity of Graphene on a Flexible Surface
Since 2010, when researchers studying it won the Nobel Prize in physics, graphene has
generated a significant amount of interest in the scientific community. With an incredible strength
and an ability to conduct heat and electricity extremely well, the potential applications for
graphene are extensive. Our research aims to unlock even more potential applications for
graphene by making it superhydrophobic. We increased the hydrophobicity of graphene samples
using a dual focused approach, which concentrated on altering the material’s micro and nano
scale structure along with its chemical structure. This process involved stretching and relaxing the
graphene samples and subjecting them to oxygen plasma treatment to increase their surface
roughness, and then treating the graphene samples with fluorosilane solution to alter their
chemical structures. Our experimental results demonstrate that, using this approach, graphene is
able to achieve a superhydrophobic state, which we defined as having a water contact angle
greater than 150 degrees. We also used these experiments to discover the optimal treatment
conditions needed in order to maximize graphene contact angle. Additionally, the results of our
experiments also give us insight into the structural properties of crumpled graphene and the
potential for further improvement in this area.
Project #30: Targeted drug delivery to single cells by cavitation bubbles
Advisor:Pei Zhong, Professor, Mechanical Engineering and Materials Science
We have developed a unique microfluidics-based system for investigating cavitation bubble(s)cell interaction with potential applications in targeted drug delivery and mechanical stimulation of
individual cells. The REU Fellow will have the opportunity to participate in this exciting new
project, specifically in conducting high-speed imaging experiments to correlate bubble and
associated fluid dynamics with resultant membrane permeabilization and macromolecular uptake
in the target cells assessed by optical and fluorescent microscopy.The REU Fellow may also be
involved in additional work in microfluidic device design, fabrication and integration with an
ultrasound applicator. A solid engineering background in MEMS and BME, and strong
motivation and dedication for scientific research are required.Appropriate technical training will
be provided to the student at the beginning of the project.
Emily Schapker, Senior, Mechanical Engineering, University of Kansas
Mentors: Dr. Pei Zhong, Professor, Duke University and Fang Yuan, PhD Candidate, Duke
University
Project Title: Tandem Microbubbles for Single Cell Manipulation
Microbubble collapse and the resulting jets have been used in a variety of biological
applications, such as shockwave lithotripsy. The use of bubble jets for cellular manipulation
offers great promise for drug delivery and cell differentiation. Recent studies in tandem bubble
dynamics have shown that laser-induced cavitations can produce jets of controlled speed in a
microfluidic chip for cell deformation and poration. In order to ensure that pores can be formed
without resulting in cell death, it is necessary to determine the maximum strain that a cells can
withstand during jet interaction. It is also necessary to understand the parameters that may affect
cell strain, such as media viscosity and the shape of the adhesion pattern between the cell and the
substrate. To investigate this, cells were seated in a microfluidic chip and 3μm polystyrene beads
were attached to the cell surface. The chip was fabricated to include two gold dots for laserinduced bubble generation, along with a substrate pattern in “H” and “I” shapes. Experiments
were conducted in a control solution of culture media as well as a Ficoll solutions was prepared to
increase the media viscosity to approximately that of blood. Jets with speeds of approximately 50
m/s were generated in the chip 20 μm away from the cell. Deformation was recorded using a
high-speed camera and displacement of the markers was tracked using Matlab code. These
discrete points were then used to calculate the maximum strain and shear stress on the cell.
Analysis of the markers showed that maximum displacement was 2.4 times greater for “I”
adhesion patterns. It was also observed that average maximum shear stress on the cell was 3.7
times higher for the 0% Ficoll solution over the 8% Ficoll solution. While these results provide
valuable information for understanding the parameters that impact cell poration, the study only
allowed for a limited collection of data points. In order to increase the statistical significance of
the findings, it is recommended that more data points be collected, in addition to revising the
algorithm of the code to improve accuracy. It is also suggested that data be collected for cell
viability following poration, to compare the maximum principal strains with the occurance of cell
death.
Project: #31: Construction of an atomic force microscope for combined mechanical and
optical measurements
Advisor: Piotr Marszalek, Professor, Mechanical Engineering and Materials Science
The objective of this project is to provide hands-on experience to undergraduate students
in the design and construction of a robust high-precision and research-grade atomic force
microscope that can be operated on top of an inverted optical microscope for combined force and
fluorescence measurements. We note that a complete home-made AFM instrument was already
designed, constructed and successfully used in the Marszalek laboratory by several
undergraduates and its design was published by Rabbi and Marszalek (Mr. Rabbi was a Duke ME
undergraduate student). This AFM instrument will require a complete design overhaul to be able
to work on top of an inverted microscope. (Some details of this overhall follow, and below that in
italics, is the impact and value of this project): To capture fluorescence from the molecule being
stretched by the AFM, the microscope objective needs to be inserted into the AFM head and
positioned right below the sample. It will occupy the space that in a traditional AFM is taken by
a high precision piezoelectric stage that translated the sample in the z direction for the mechanical
stretching of molecules. Therefore, in the new AFM, the Z-stage that moves the sample will need
to be located outside of the AFM head. One of the main difficulties for the new AFM to operate
successfully will be to keep the molecule stretched within the focal depth of the microscope
objective. To achieve this goal, the whole AFM head will need to be also translated in the Z
direction, relative to the sample. This can be achieved by attaching another high precision
piezoelectric Z stage directly to the top of the AFM head and mounting it on the body of the
optical microscope. This modification will force the relocation of the laser from the top of the
head to a horizontal location inside the head. )
This project will involve undergraduate students who will work over the summer in Dr.
Marszalek’s laboratory to design and construct such an instrument. This project will provide an
extremely fulfilling experience for these undergraduate students in the planning and execution of
their real-world engineering activities whose final product will be a sophisticated research-grade
instrument. The students will directly get experience in designing and constructing an instrument
which is composed of very precise mechanical, electrical, electronic, and opto-elecronic
components, which need to be perfectly aligned and actuated/probed by digital to analog
interfaces controlled by a computer. Thus, their practical experience will integrate many areas
of engineering. Importantly their product will be later used for real research activities done by
their undergraduate peers. These activities will focus on simultaneous measurements of the
elastic and optical properties of single molecules such as DNA and various proteins (force
spectroscopy) that will be labeled with fluorescent probes.
Project: #32: Mechanical Folding of Individual Polypeptide Chains by AFM
Advisor: Piotr Marszalek, Professor, Mechanical Engineering and Materials Science
The folding of proteins is one of the most important yet not completely understood topics
in biology. The question “Can we predict how proteins will fold?” was listed in 2005 as one of
the 125 most important unsolved problems in science by the Science magazine. Significant
progress has been made toward understanding the protein folding through in vitro experiments
and computer simulations, but much less is known about folding in vivo. During co-translational
folding, the nascent polypeptide chain (NPC) is extruded sequentially in a vectorial manner from
the ribosome exit tunnel and starts folding under severe conformational constraints. It is presently
unknown how such 1D constraints affect the folding pathway.
The long-term objective of this proposal is to advance understanding of protein folding
by:
a) studying the vectorial folding of single proteins under 1D constraints by Atomic Force
Microscopy(AFM)-based single-molecule force spectroscopy (AFM-SMFS) and computer
simulations using steered molecular dynamics (SMD) calculations.
b) directly examining the folding behavior of the nascent polypeptide chain emerging from the
ribosome using AFM imaging and mechanical manipulations (Fig. 1).
Atomic force microscopy is a novel form of (non-optical) microscopy that can be mastered easily
by undergraduate students. Although some knowledge of biology as it relates to proteins and their
“folding” problem would be desirable it is not a pre-requisite for participation
Project: #33: Nonlinear Aeroelasticity
Advisor: Earl Dowell, Professor & Dean Emeritus, Mechanical Engin.& Materials Science
Our research is concerned with the dynamic interaction of a fluid and an elastic structure, a field
termed aeroelasticity, i.e., aerodynamics plus elasticity. Recent research has emphasized
nonlinear aspects of the phenomena. Research has often been motivated by aerospace
applications such as the oscillations of aircraft wings, turbine blades in jet engines, hypersonic
inflatable aerodynamic decelerators (HIAD) and solar sails. However, we also study applications
to biomedical engineering, e.g., blood flow through arteries or airflow through the mouth; civil
engineering, e.g., wind loads on bridges and buildings; electrical engineering, e.g., wind induced
oscillations of power lines; and to many other aspects of engineering. Current projects involve
either theoretical or experimental research. These include the following: (1) dynamic response of
airfoils and wings due to self-excitation and external forces; (2) high performance airfoils; (3)
wing planforms that deform as plates; (4) long span, highly flexible wings typical of uninhabited
air vehicles; (5) novel geometries that lead to enhanced aeroelastic performance including oblique
wings and folding wings; (6) control of and energy harvesting from such systems; (7) HIAD and
(8) solar sails.
Project #34 (WISeNet): Drought Monitoring and Prediction in Semiarid Climates
Advisor: Dr. John Albertson, Professor, Civil and Environmental Engineering (WISeNet)
A secure supply of drinking water is a fundamental human need that goes unmet for much of
the world’s population. Although water quality can be ensured through engineered treatment
and delivery facilities, the quantity of future water availability remains surrounded by
significant scientific uncertainty. This project will utilize data and simulations developed
using a long-standing NSF-funded broad network of soil moisture sensors and lower
atmosphere sensors on the island of Sardinia that are designed to address an important
knowledge gap, i.e., how changes in the seasonality of precipitation in semi-arid regions
interact with vegetation dynamics to affect available surface-water resources.
Developing mathematical models that capture not only the dynamics of the environmental and
ecological system, but also its interactions with the wireless sensors, is critical both to sensor
management and data processing algorithms. A fundamental challenge in environmental
sensing and prediction is accounting for the coupling between the sensor performance and the
local environment, which greatly influences the sensor’s visibility region and communication
signal.
This research project aims to develop interdisciplinary models of global environmental
dynamics coupled with spatiotemporal models of sensor measurements for the environmental
process of their choice. The goal of the REU fellow will be to develop probabilistic sensor
models that capture the most significant relationships between local environmental conditions
and the sensor’s measurements, mode, and communication signal. Using available
optimization algorithms, the fellow will then use the sensor models to obtain optimal sensor
deployments for the design of the field site, and repopulation by means of new and possibly
mobile sensors.
Project #35 (WISeNet): Aforestation, Climate Change Mitigation and Prediction
Advisors: Dr. John Albertson and Gabriel Katul, Professors, Civil and Environmental
Engineering / Nicholas School of the Environment (WISeNet)
Distributed sensing is crucial to understanding environmental change, and to protecting the
health of humans. Federal agencies are already in a planning phase for their integration with
national research platforms such as NEON and CLEANER. Dr. Albertson’s and Dr. Katul’s
research addresses a primary question in climate change pertaining to the mediating role of the
biosphere on elevated atmospheric CO2 concentration, and their influence on rainfall and mean
air temperature. The ability of terrestrial ecosystems to absorb CO2 is sensitive to atmospheric
conditions, and is characterized by feedback loops that, if characterized by intensive sensor
data, can lead to far more accurate predictions.
This research project gives students the unique opportunity to employ a wide array of wireless
sensors, e.g. gas analyzers, anemometers, and sap flux sensors, presently deployed in the Duke
Forest, to collect measurements of precipitation, soil moisture, vapor pressure deficit,
temperature, and, more importantly, photosynthetically active radiation. The REU fellow will
use simulation and data processing algorithms to develop improved models that capture the
rich spatial variability in ecosystem carbon dynamics, and natural feedback loops from the
environmental controls to surface radiative, physiological, and aerodynamic process, to predict
their effects on warming potential.
Project #36: Planning for CLEANER (Collaborative Large-scale Engineering Analysis
Network for Environmental Engineering) River Basins Across the United States
Advisor: J. Jeffrey Peirce, Associate Professor, Department of Civil and Environmental
Engineering
The National Science Foundation is planning and preparing for a nationwide system of
environmental quality sensors and information to be networked among university researchers,
public health officials, industry representatives, public interest groups, environmental policy
experts and K-12 educators. Under the direction of Professor Peirce Duke University is in the
process of planning and preparing for one of the eight river basin components, the Neuse River in
Eastern North Carolina, in this nationwide network. Pratt Fellows will collaborate on all aspects
of this research project including the study of:
1.
2.
3.
4.
environmental sensors and sensor networks to monitor, record and analyze
environmental quality
cyberinfrastructures (computer networks) to link all CLEANER participants within
NC and across the nation
methods to model and remediate environmental pollution on a regional and
national scale
business management plans to enhance the operation of Duke’s CLEANER facility
Undergraduate students with interests and training in engineering, science, business management,
public policy, and public health are encouraged to consider joining this research program.
Catie Bishop, Civil Engineering Major, University of Connecticut
Optimizing Wireless Sensor Networks in Vineyards
Mentors: Dr. Jeff Peirce, Associate Professor of Civil Engineering, and Adam Price-Pollak, Pratt
Research Fellow in Civil Engineering
Catie Bishop is a civil engineering major from the University of Connecticut. Her project focuses
on the fact that The optimal location of a few wireless environmental sensors can help viticulturists
monitor water and air in the vineyard and promote grape growth. The cost of the system can be offset by
reduced expenses and increased production. Vineyards are especially suitable for the use of an
environmental sensor network due to grape sensitivity to microclimates within the vineyard. The methods
presented in this paper for identifying the optimal sensor locations are general enough to be applied to
many different sized vineyards. In addition to maximizing healthy grape production, smart viticulture can
be used for other objectives, such as reducing water consumption and intervention to prevent frost
damage
Lizz Michael, Chemistry Major, Grove City College
Planning for CLEANER River Basins across the United States
Elizabeth Michael is a chemistry major from Grove City College. Her project was on “Planning
for CLEANER River Basins across the United States,” which is a means to ensure the success of a
Collaborative Large-Scale Engineering Analysis Network for Environmental Research (CLEANER)
facility to monitor water quality, pollution problems, and other environmental issues in the Neuse River
Basin through careful and systematic planning. In conjunction with Associate Professor Dr. Jeff Peirce,
two journal articles were written: “Innovative Approaches for Managing Public-Private Academic
Partnerships in Big Science and Engineering” for publication in Public Organizational Review and
“Progression of the Size, Management, and Motivation of Big Science and Engineering Projects” for
publication in History of Science. “Innovative Approaches for Managing Public-Private Academic
Partnerships in Big Science and Engineering” analyzes public-private academic partnerships (PPAPs) in
terms of management, organization, funding, and partner relationships; three case studies are presented,
selected to display a range of partnership models. The increasing challenges of Big Science seem to
demand the merging of the public, private, and academic sectors into a single collaboration. Three
conclusions are drawn: (1) complex PPAPs can be successful if partner’s roles are clearly defined; (2) Big
Science needs PPAPs to achieve results; and (3) the management style for CLEANER should make use of
a hierarchical PPAP organizational style. “Progression of the Size, Management, and Motivation for Big
Science and Engineering Projects” tracks the evolution of Big Science and Engineering to allow recent
and ongoing Big Science to be viewed as the product of a gradual shift in human motivations, capacity to
explore and experiment, and competition between nations. The dissemination of Big Science and
Engineering from culture to culture is examined; findings indicate that Big Science could continue to
spread and that more Big Science and Engineering projects may arise in the next several decades as
scientific research continues to evolve. The new applications and complexities presented by Big Science
and Engineering are analyzed to determine the future of Big Science and the most efficient approach to its
management and finance. This analysis of the evolution of Big Science and Engineering concludes that
the scope of Big Science and Engineering may continue to grow, along with the number of possible
management approaches for it, and that the motivating forces driving Big Science have changed through
the ages.
Lauren Raup Civil and Environmental Engineering Major, Geosciences Minor, Virginia Polytechnic
Institute and State University
Fluorescence in-situ Hybridization (FISH)Applications in Complex Soil Systems: Emerging Counting
and Analysis Techniques
Lauren Raup is a civil and environmental engineering major and a geosciences minor from
Virginia Polytechnic Institute and State University. The purpose of her research was to facilitate the
development of counting and analysis techniques for results given by Fluorescence in-situ Hybridization
(FISH) applications in complexly engineered soil systems. The FISH method and a Chemiluminescence
NOx analyzer are used in laboratory experiments to study soil microbial populations and the NO
emissions levels from the amended soil samples. NO emissions are examined for two other reasons: first,
NO plays a significant role in lower-tropospheric Ozone (O3) production, and secondly, NO is a common
byproduct of agricultural soil enhancements. In order to supervise the amount of NO emissions from soil,
bioremediation monitoring techniques are employed. The examination of microbial-NO relationships is
needed to develop better approaches to bioremediation. In order to insure the relevance and contiguity of
the data in question, the soil samples are checked for integrity and consistency using NO emissions data
taken from the NO analyzer and results from previous research. This same previous research shows that
FISH is much more efficient than other methods in so far as it is used to monitor the effectiveness of
bioremediation; however, it is also evident that FISH does not have an expedient, existing method for
counting and analysis. This research specifically focuses on the construction of a counting and analysis
technique, with the eventual aim being the creation of a more efficient experimental procedure that would
effectively utilize; FISH. The development of a precise counting and analysis method for Fluorescence in
situ Hybridization in soil compounds can firmly establish the full capacity of FISH for future usage in
bioremediation processes. The experimental design calls for 3 Mineral Fertilize (MF) amendments
(.0004, .0008, and .0016 g/g soil) with 3 different glucose amendment levels for each MF amount (0, 3, 6
mg/g soil); all samples are given a 1 day incubation period. Three replicates of each treatment
combination are used, thus creating a total of 27 individual experiments. The consequent data from the
NO emissions tests shows that the soil properties are acceptable. Two accurate, simple counting methods
thus result from these experiments. The first is designed to count microbes in a slide well being viewed
through a microscope; the method created cuts the counting time in half. A second method was
developed for counting microbial colonies that have been photographed using a digital camera. These
images are often cluttered by the presence of other microbial species or are unclear due to the
fluorescence of the samples. By using a combination of IrfanView and Microsoft Paint software the
colonies become more accurately mapped. These new methods increase the experimental utility of FISH
with respect to bioremediation, environmental, and agricultural research sciences.
Janelle Heslop, Environmental and Chemical Engineering, Columbia University
Environmental Science and Engineering for CLEANER WATERS in the Neuse River Basin: Designing
Laboratory Procedures for Sensing Water Quality
Janelle Heslop is a junior environmental and chemical engineering major at Columbia University.
In a response to the need for environmental science and engineering outreach programs in early
education, activities for water quality sensing protocols were created as a part of the CLEANER
WATERS network. For the program to be successful, it was determined that it must integrate the
laboratory research of scientist and engineers with academic merit. In order to select water quality sensing
procedures that would be successful in these two areas two set of criteria, one for research and the other
for education, were developed. Using the two established criteria, from a wide gamut of water quality
tests, five procedures were selected to be developed for middle school students. After their development,
the criteria for both success in research and education, were used to evaluate each protocol in order to
determine if expectations were met. From the assessment, it was determined that the protocols do
successfully integrate research and education. Furthermore the two sets of criteria are sufficient in
determining the success of any educational scientific activity.
Projects #37 and #38: Laboratory of Dr. Stefan Zauscher (see below Project #38 for
many project descriptions of students in Dr. Zauscher’s laboratory).
Project #37: Biomacromolecular Block-Copolymers and Brushes
Advisor: Stefan Zauscher, Sternberg Family Professor of Mechanical Engineering and
Materials Science, Professor of Biomedical Engineering and of Chemistry
Practical design of biologically inspired materials has large potential for positively impacting
society's well-being, as biomolecular materials can deliver medical therapeutics, are employed in
sensors to detect biological and chemical threats, and biomolecular nanostructures are used as
scaffolds and templates to imbue novel function for inorganic materials. While most man-made
polymeric materials serve structural purposes, they do lack precise sequence specificity and do
not approach the functional sophistication of biomolecular materials. Biomolecules, however,
provide structural and informational properties, whose functions are encoded within distinct
sequences of diverse monomer sets. At present, however, there still is a lack of fundamental
understanding to control or influence the hierarchical self assembly of biomolecular building
blocks, although this step is critically necessary to unlock the potential of biomolecular materials.
We have shown that the template-independent polymerase, terminal deoxynucleotidyl transferase
(TdT) can catalyze the growth of ssDNA from a short oligonucleotide initiator attached to a
surface or create high molecular weight (up to 8 kb) homopolymer and copolymer DNA in
solution with exquisite control of chain lengths. Furthermore, we have shown that a broad range
of unnatural nucleotides with unique chemical functionalities (biotin, amine, and aldehyde
groups) can be directly incorporated into the ssDNA by TdT catalyzed synthesis. The use of TdT
to create complex DNA based hybrid materials in situ from a range of substrates and from
genetically engineered polypeptides, is a rich and untapped area of soft matter research that we
will exploit in the framework of the newly established NSF Materials Research Science and
Engineering Center (MRSEC) in Softmatter at Duke. For example, temperature-triggered
microphase separation of diblock DNA-polypeptide copolymers could lead to micelles that
consist of a hydrophobic core (polypeptide) and a hydrophilic shell (polynucleotide), and will
depend on the relative size of the blocks and their relative difference in solvation properties.
The REU student will engage with graduate students in the characterization of these
biomacromolecular materials, including transmission electron microscopy, AFM, and Small
Angle X-Ray Scattering.
Project #38: Harnessing Bacteria for the Fabrication of Inorganic Materials
Advisor: Stefan Zauscher, Sternberg Family Professor of Mechanical Engineering and
Materials Science, Professor of Biomedical Engineering and of Chemistry
In this project we seek to demonstrate that bacteria can be harnessed for the biosynthesis and
deposition of semiconducting nanoparticles and thin films that have useful technological
properties in areas as diverse as energy generation, microelectronics and biosensing. Specifically,
we use engineered bacteria (You laboratory) to generate well controlled cadmium sulfide (CdS)
particles and thin films. CdS thin films play an important role in photovoltaic technology and for
optoelectronic devices. The currently used chemical bath deposition for the synthesis of CdS thin
films remains, however, a continuing challenge. Here, biology may offer complementary, and
possibly vastly better, options. The bacterial biosynthesis and precipitation of CdS nanocrystals
intracellularly and extracellularly has been prototypically shown, and useful biochemical
reduction pathways have been engineered. Here we harness engineered bacterial expression
systems for the deposition of nanocrystalline CdS thin films and particles with core-shell
morphology. The REU student will work with a graduate student on nanoparticle synthesis and
characterization using advanced surface analytical tools, such as AFM, XPS, SEM.
REU Students in Dr. Zauscher’s laboratory:
Chelsie Stallings, Senior, Chemistry, Gallaudet University, Department of Chemistry
Mentors: Stefan Zauscher, Professor of Mechanical Engineering and Materials Science, Professor
of Biomedical Engineering and of Chemistry, and Zehra Parlak, Post-doctoral Fellow,
Mechanical Engineering and Materials Science, Biochemistry
Project Title: Investigation of Protein-A by QCM
In this research, we describe a method to observe unfolding kinetics of surface proteins
by quartz crystal microbalance (QCM) when they are tethered to a surface. Kinetic studies on the
unfolding of surface proteins, such as Staphylococci aureus bacteria’s surface protein, protein-A,
have been conducted in solutions so far, but these proteins are attached to surfaces in their natural
state. In our method, we first use a protein solution to create a monolayer of protein on the gold
electrode of QCM. Then, we induce unfolding of the protein by injecting guanidine chloride
(GCl) solutions of varying concentrations. Since GCl solutions have high density and viscosity,
traditional QCM systems cannot decouple unfolding of the proteins from the effects of the
solutions. However, the recently introduced fluid density and viscosity compensated QCM
method of Zauscher lab can decouple these two parameters and observe protein unfolding. In this
study, we verified the fluid density and viscosity compensated QCM method by using glycerol
solutions of different concentrations, which solely changes the fluid properties. We measured
protein-A adsorption kinetics on the gold surface of QCM and we compensated fluid properties
during the introduction of GCl. We were able to observe conformational changes of the protein-A
on the surface by using this compensation method.
Jesse Fuller, Chemistry Major, Gallaudet University
Brushes on a Lead Zirconium Titanate (PZT)
Jesse Fuller is a chemistry major from Gallaudet University. His project objective was to create
end-tethered polymer brushes grafted from lead zirconium titanate [Pb (Zr0.48Ti0.52)O3] surfaces. By first
forming monolayers on PZT, followed by surface initiated polymerization, our findings present the results
of the polymer brush properties on PZT using Atomic Force Microscopy (AFM) in a contact mode. This
research outlines, for the first time, how using traditional grafted from polymerization conditions is able
to grow N-isopropylacrylamide polymer brushes on PZT Stimulus response characterization was
performed in a variety of environments including, 100% deionized water and 50% deionized water/50%
methanol. The polymer brushes in 100% deionized water responded with the highest length in brush
height.
Joshua Doudt, Chemistry, Gallaudet University
Changing the Crystal Structure of PZT Thin Films with Self-Assembled Monolayers
Joshua Doudt is a senior chemistry major at Gallaudet University. In 1983, Nuzzo and Allara
used alkanethiol molecules to form Self-Assembled Monolayers (SAMs) on a gold substrate. Ever since
this discovery, many different researchers have used monolayers for a wide variety of applications. The
goal of this project is to recognize the effect of SAM to change the surface properties of Pt to influence
Lead Zironcate Titanate (PZT) crystal structure. SAMs is single layer of organic molecules. It will form
spontaneously through adsorb on any types of the substrate such as metals, semiconductors, or insulators.
For this project we will use platinum coated silicon wafer as our substrate. The SAMs will be using in this
project to aiding the development of PZT crystal structure through heating process. The procedure of
developing sol gel PZT will be making through spinning coat process. The result of PZT crystalline will
be developed when it is heated up to specific temperature for thirty minutes. The X-Ray Diffraction
measured the PZT crystalline peak in the order to recognize the PZT crystal structure. The results showed
that SAMs changed the surface properties of Pt to influenced the PZT crystal structure yet, the SAMs
didn’t give us great PZT (100), (110), and (111) crystal structure.
Alexander Matsche, Chemistry Major, Senior, Gallaudet University
Single Molecule Force Spectroscopy of Lubricin
Alexander Matsche is a chemistry major and senior from Gallaudet University. The objective of
his research was to collect evidence in support of the hypothesis that reduced lubricin shows different
mechanical behavior due to pH induced alterations in its conformational state. The nanomechanical
properties were measured by single molecular force spectroscopy with an Atomic Force Microscope. The
results of studies of a single molecule of reduced lubricin prove that a molecule with a pH 4.1 has less
force and distance than one with a pH 7.4. Also, the molecule with pH 4.1 is more flexible with regard to
persistence distance than is the molecule with pH 7.4. These results show that various pH’s do affect the
lubricin’s behavior with regard to force, pull off distance, contour length, and persistence length, and are
significant with regard to research into joint problems in the future. During his research, Alex learned
many new procedures in Single Molecule Force Spectroscopy.
REU Fellow: Alexander Matsche, Chemistry, Gallaudet University
The Influence of Relative Humidity on Particulate Interactions in Carrier-Based Dry Powder Inhaler
Formulations
Alex Matsche is a chemistry major from Gallaudet University. The goal of his project was to
study the adhesion between the carrier and the active ingredients for an asthma drug called AdvairTM, a
dry-powder inhaler containing Fluticasone Propionate, Salmeterol Xinofoate, and Lactose . Alex’s
hypothesis was that dry air had a more positive effect on the adhesion force between the drugs and
the carrier, and that the amount of humidity can make a big difference in the adhesion force
between the active ingredients and carrier. If a certain level of humidity does indeed make a big
positive difference, then this result can help improve the drug’s manufacture and use as an asthma
medicine. The Atomic Force Microscope can read and measure the topography and adhesion force
from smooth surfaces with a cantilever probe technique. An Atomic Force Microscope with a
humidity control chamber is used to investigate the effect of relative humidity from 5% to 90% to
measure the adhesion force of the recrystallized drugs. The difference in humidity between dry
and humid air can make a big difference in the adhesion force of the active ingredients and carrier.
An X-Ray Photoelectron Spectrometer is used to study and compare the chemical structure of the
original powder drugs and the recrystallized drugs before we test them in the Atomic Force
Microscope. The adhesion force will be measured on the recrystallized drugs’ surfaces by placing a
lactose coated, tiny crystal of the recrystallized drugs on the cantilever’s tip. The Scanning Electron
Microscope is used to measure the tiny crystal on cantilever’s tip. The results showed that the
humidity of the air does affect adhesion force of each drug. These results can lead to improvements
for asthma medicine users and for the manufacture of drugs by pharmacology companies using the
correct humidity control in the factory.
John Thuahnai, Biology Major, Gallaudet University
Project: Friction Behavior of Stimulus-Responsive Hydrogels
The purpose of this research project is to study the friction behavior of stimulus-responsive
hydrogels at three different levels of cross-link density (high, medium, and low). This project also
explores the gel preparations with different cross-link density by adding N’N-methyleneacrylamide (MBAAm). The hypothesis was “high” cross-link density gel would handle shear strain
rate more than “low” cross-link density gel. The friction measurements were obtained with
controlled strain rheometer. To report the coefficient of friction, we need a measure of normal
force, which requires normal load cell to be installed in the rheometer. However, load cell was not
available so we could only report the friction force (Ff = t * r^2/2). Measurements were performed
with shear rates with gel sliding against the metal surface of the measurement geometry. “High”
and “medium” cross-link density gels proved to be only feasibility for this experiment. Low crosslink density gels were unstable in this experiment. Despite failure of low cross-link density gel, the
result proved the hypothesis to be acceptable.
REU Fellow: Lucas Barrett, Mathematics Major, Gallaudet University
Project: PNIPAAM Contact Angles as a Function of Temperature
In his project, Lucas hypothesized that contact angles will change as a result in temperatures, with some
being hydrophobic and others being hydrophilic. The goniometer experiments were to determine
temperature to contact angle graph for the prepared samples. The experiments were unable to determine a
graph that validates the current pNIPAAM LCST graph. The primary reason was that there is little
material published regarding pNIPAAM and its effect on contact angles. PNIPAAM is widely used
because of its ease of use. S. Balamurugan, et al, gives the theoretical LCST graph of pNIPAAM in a
published paper but the paper does not give much detail into their methods as to how they developed their
data. In addition, Lucas suffered numerous equipment failures ranging from power and temperature loss
to problematic wiring. Lucas was forced to develop many different possible strategies of angle
measurement. For example, he attempted to saturate the ambient atmosphere around the samples in
regards to humidity; he left the samples to stabilize at a set temperature on the stage for a period of 20
minutes for each temperature. Lucas placed the stage at an angle to force the sessile drops to move
minutely to determine advancing and receding angles. He heated the water from which he made his
sessile drops. He soaked the samples overnight to re-hydrate the polymer brush, in case it collapsed. The
second possibility could be that Lucas’s samples were not adequately clean. It could be that
contamination of the sample neutralized the pNIPAAM. Despite all these different attempts, he found no
significant difference in angles as the temperature moves across the LCST region
Pia Marie Paulone, Biology Major, Gallaudet University
Adhesion between Carrier and Active Ingredients in Dry-Powder Inhaler Formulations
Measured by Single Molecule Force Spectroscopy
Pia Marie Paulone is a biology major from Gallaudet University whose project involved the
adhesion between carrier and active ingredients in inhaler formulations. The formulation of
Advair™ includes two drugs, Fluticasone Propionate (FP) and Salmeterol Xinofoate (XP), and an
inactive lactose carrier. Production of Advair™ includes an extremely short initial mixing time, but
requires a longer amount of time to ensure that drug particles are sufficiently bound to the carrier
particles. Understanding and quantifying adhesion forces between the drug and lactose using single
molecule force spectroscopy (SMFM) will lead to improved efficiency in production lines. Model
surfaces composed of dissolved drug and dissolved lactose are created and coated on two surfaces:
a cleaned glass slide and a 10 micron borosilicate glass bead mounted on the tip of an Atomic Force
Microscope (AFM) cantilever with the ultimate goal of accurately mimicking adhesion behavior
between the two substances. Based on data acquired from both AFM and Scanning Electron
Microscope (SEM), it is known that lactose and FP interaction is of far greater magnitude than
either glass on glass interaction or lactose on glass interaction. This presents a definite
confirmation of the feasibility of the preliminary material system.