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 RegenerationAdvisor:  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 DesignAdvisor: 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 UniversityMentors: 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 tumorsAdvisors: 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 UniversityProtocol 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 MexicoDeveloping 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 UniversityProject: 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 LundbergProject: 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 EnvironmentsAdvisor: 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 PacificIntegrin 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 GradientsAdvisor: 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 graftsAdvisor: 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 UniversityResponse 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 UniversityProject: Interactions between the Endothelial Cells and the Smooth Muscle Cells in Co-Culture: The Endothelial Cells Confluency in Co-CultureThe overall project in Dr. Truskey’s laboratory, in which Viet worked, aims to construct a tissue-engineered 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 50L 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 UniversityProject 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 non-Matrigel 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 UniversityQuantifying Gap Junctional Coupling between Cardiomyocytes and Other Cell TypesMentors: 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 AustinThe 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 RecorderAdvisor: 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 UniversityMentors: Dr. Patrick Wolf, Associate Professor, Department of Biomedical Engineering and Thomas Jochum, PhD candidate, Department of Biomedical EngineeringProject 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 KansasEncapsulation 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 UniversityBrain-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 UniversitySoftware 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 PXIinterface 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 UniversitySubdermal EEG Recorder for Lifelong MonitoringMentors: 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 UniversityIn 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 UniversityPreliminary Investigation of the Feasibility of a Graphite Radio-frequencyAblation 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 roboticsAdvisor: 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 PlasticityAdvisor: 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 ControlAdvisor: 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 BiophotonicsAdvisor:  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 UniversityLow 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 UniversityEarly 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 UniversityEarly 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 DeploymentAdvisor:  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 ControlAdvisor: 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 CircuitsAdvisor: 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-for-testability (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 BiochipsAdvisor: 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 smallantennas for communication and imaging applications.  The studentwill utlize computer software to design antennas, build antennas inthe laboratory, and perform communication and imaging measurements. Ugonna Ohiri, Computer Engineering Major, University of Maryland- Baltimore CountyUltra Wideband AntennasMentors: 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 CollegeUsing 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 EngineeringProject Title: Recycled Error Bits: Architectural Support for Energy-Efficient and Numerically Accurate Software

In numerical software, double precision is often preferred over single precisionfor concerns relating to the smaller amount of numerical accuracy offered by singleprecision. Rounding error often constrains the accuracy of numerical software due to thefinite 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 moreburdensome to hardware due to the increased transfer of data to and from memory. Thepurpose of this investigation is to facilitate the development of numerical software that isboth accurate and energy efficient. We demonstrate that “recycling” the rounding error ofeach 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 greateraccuracy with comparable performance and energy use or comparable accuracy withgreater 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 multi-layered 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 EnvironmentsAdvisors: 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 NetworksAdvisor: 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 vaccines for anti-tumor immunityAdvisors:  Kam W. Leong, Professor, BME

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 UniversitysiRNA Delivery Into LNCaP Cells Using a Novel, Multivalent NanocomplexMentors: 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 UniversityFabrication of Nanopatterned Surfaces to Study Stem Cell DifferentiationNevija 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 CondensateAdvisor: 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 AdvisorProject 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 GeneratorAdvisor: 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 SurfacesAdvisor:  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 three-dimensional 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 FellowProject 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 KansasMentors: Dr. Pei Zhong, Professor, Duke University and Fang Yuan, PhD Candidate, Duke UniversityProject 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 laser-induced 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 AeroelasticityAdvisor: 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 ClimatesAdvisor: 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 StatesAdvisor:  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.              environmental sensors and sensor networks to monitor, record and analyze environmental quality

2.              cyberinfrastructures (computer networks) to link all CLEANER participants within NC and across the nation

3.              methods to model and remediate environmental pollution on a regional and national scale

4.              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 ConnecticutOptimizing Wireless Sensor Networks in VineyardsMentors: 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 CollegePlanning 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 UniversityFluorescence 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 BrushesAdvisor: 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 MaterialsAdvisor: 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 ChemistryMentors: 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, BiochemistryProject 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 UniversityBrushes 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 UniversityChanging 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 UniversitySingle 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 UniversityThe 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-methylene-acrylamide (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 (F f = 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 cross-link 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 UniversityProject: 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 UniversityAdhesion 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.