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Undergraduate Research Program

2015-16 WRF Fellows

Elliot Abe - Physics

Abe, Elliot 2

Elliott Abe is a senior in the Department of Physics and the Computational Neuroscience
Training Program. His interests involve understanding brain processing through the lens of physics. He began his undergraduate research with Professor Marcel den Nijs working on exploring single neuron action potentials with the Hodgkin-Huxley model. Next, he moved on to working with non-linear dynamics with the FitzHugh Nagumo Model. Professor den Nijs introduced Elliott to Professor Adrienne Fairhall in the Physiology and Biophysics Department and in the Spring of 2015, Elliott began his research with the Fairhall Lab by segmenting and analyzing syllables of zebra finch vocalizations. Currently, his research focuses on analyzing regularities in the silences between syllables to inform the creation of a mathematical model that can describe trial and error learning in brain processing. Elliott is extremely grateful for the support from his mentors Professor den Nijs and Professor Fairhall. In addition, Elliott would like to express his gratitude to the Washington Research Foundation for supporting undergraduate research endeavors. After the completion of his degree in Physics and the Computational Neuroscience Training Program, Elliott intends to pursue a Ph.D. in physics with an emphasis in neuroscience research. His hope is that by integrating his two passions, physics and neuroscience, he can conduct exciting and creative research yielding better understanding of how the brain works.

Mentor: Adrienne Fairhall, Physiology, Biophysics

Project Title: Zebra Finch Song Analysis as a Precursor to Understanding Modulation of Variability in Trial-And-Error Learning

Abstract: Research on the zebra finch song system represents a unique inter-disciplinary collaboration between physics and neurobiology to investigate trial-and-error learning. The objective of this research project, by relying on the recorded vocalizations from four adult male zebra finches, is to analyze repetitive motifs in a song to isolate distinct syllables by developing a reliable approach for identifying the silences occurring. By utilizing sound analysis, the intent is to identify commonly shared underlying structures captured as data in order to represent various relevant dimensionalities such as timing and frequency, with the aim of predicting the neurological activity driving such variation. The outcome sought from this research is to create a modest mathematical model that can serve as an experimental foray for exploring how to combine anatomy with neuro-physiological data and song bird sound recordings to predict the relationship between internal brain activity and the subsequent corresponding behaviors. By investigating such variables as timing and frequency across the songs of zebra finches, the identification of commonly shared dimensionalities can provide a context for considering the manner in which trial-and-error through reinforcement learning occurs. The significance of studying reinforcement learning from the perspective of physics, a physical science, and applying this within the context of neurobiology, a life science, represents the emerging importance for future research to reflect collaborative and cross-disciplinary interdependence in an ever-increasingly complex world.

Gabby Benuska - Bioengineering

Benuska, Gabby

Gabby Bensuka is a sophomore majoring in Bioengineering. She first became interested in tissue engineering when she learned about its potential for addressing the organ failure problem. There is an increasing need for organs, but there is only a limited number of available organs and alternative treatments. This leads to many temporary and short-term solutions and a high death rate—but stem cells and tissue engineering are promising areas of research that could provide more permanent solutions for illness related to organ failure. To become more involved in tissue engineering, Gabby joined the DeForest research group during Winter 2015 as a freshman. She began her research working with graduate student Jared Shadish to create, express, and purify modified protein constructs that were then photopatterned into a hydrogel. Her current research involves using these same photopatterning techniques to control the differentiation of human Mesenchymal Stem Cells (hMSCs) in 4D using BMP-2 (bone morphogenic protein 2) and TGF-β (transforming growth factor beta). This research could greatly impact tissue engineering and provide spatial and temporal control of the growth and differentiation of stem cells outside of the body. Having full control over cell growth in turn will allow us to grow physiological structures identical to those found in the body. Upon graduation, Gabby hopes to continue on to MSTP (Medical Scientist Training Program) to obtain an MD-Ph.D., so she can utilize her research to work directly with patients. She would not have been able to make it this far in her research without her research group. She is especially grateful for all Jared Shadish’s help and for Professor Cole DeForest’s encouraging enthusiasm for science. In addition, She would also like to express her gratitude towards the Washington Research Foundation for their support and generosity as she continues her research.

Mentor: Cole DeForest, Chemical Engineering

Project Title: Controlling 4D Stem Cell Differentiation in Hydrogels Using Site-Specifically Modified Growth Factors

Abstract: The ability to recapitulate the dynamic presentation of signals in a stem cell’s microenvironment remains a major hurdle in tissue engineering. Controlling cell growth and differentiation in 4 dimensions (i.e., time and 3D space) would allow for heterogeneous synthetic tissues to be produced that match the complexity of their native counterparts. Combining strategies in both light-programmable hydrogels and recombinant protein engineering, we control the cellular microenvironment using proteins site-specifically modified with a bioorthogonal handle able to covalently bind to a photocaged reactive group in the hydrogel. Previously we’ve demonstrated the ability to photopattern gels with fluorescent proteins that excite at different wavelengths, and have shown that multiple proteins can be patterned independently within the same material with 4D control. These techniques have many potential applications, including improving joint replacement. Current joint replacement therapies often involve use of metals, plastics, and ceramics, and commonly require future revision surgeries. We propose that through our techniques, we can generate a patterned bone/cartilage interface to improve joint replacement, creating a longer-term option for joint replacement. Towards this, we have generated two photopatternable recombinant growth factors, BMP-2 (bone morphogenic protein 2) and TGF-β (transforming growth factor β), known to direct human mesenchymal stem cell (hMSC) osteogenesis and chondrogenesis. I will encapsulate hMSCs in a hydrogel and direct cell differentiation and growth in 4D using a combination of photopatterned BMP-2 and TGF-β proteins. This research will have significant impact in tissue engineering, as it will enable recreation of complex physiological structures, grown outside the body with the patient’s own cells, that can be used for personalized medicine. Our approach is unique in that it allows for unprecedented control over microscale tissue structures, ultimately matching the complexity of native tissue.

Katie Bigham - Oceanography, Earth & Space Sciences: Geology

Bigham, Katie

Katie Bigham is a junior studying Oceanography with a biological focus and Earth and Space Sciences. She is fascinated by the extreme environments found on this planet, and the life that manages to survive there despite the punishing conditions. Her current research project with Dr. Deborah Kelley involves understanding the ecology at one of these extreme locales, a methane hydrate seep off the coast of Oregon. The site, Southern Hydrate Ridge, is a designated 25 year study site as part of the National Science Foundation’s Ocean Observatory Initiative Cabled Array (OOI). Katie’s work to quantify the biology observed before the Cabled Array’s installation and the abiotic factors influencing that life will act as a baseline for the site for years to come. Her undergraduate research has given her the opportunity to participate in two research cruises during the past two summers. The cruises aimed to construct and maintain the OOI Cabled Array. On these cruises a remotely operated vehicle was used to visit Southern Hydrate Ridge and other extreme environments such as hydrothermal vents. These experiences along with her research have bolstered her fascination with these demanding habitats. After completing her undergraduate degrees, she plans to continue her education by pursuing a Ph.D. in oceanographic sciences. She hopes to do further research on the extreme environments of our planet, and someday be the principle investigator of her own lab. She is extraordinarily grateful towards the Washington Research Foundation for their assistance in meeting her academic and professional goals.

Mentor: Deborah Kelley, Oceanography

Project Title: Quantification and Characterization of the Biologic Community at Southern Hydrate Ridge

Abstract: Deposits of methane sequestered along continental margins and their associated seeps are of increasing interest because of their potential as an energy source, their contributions to greenhouse gases, and the unique community of chemosynthetic microorganisms and macrofauna that they host. One of the best-studied methane seep sites is Southern Hydrate Ridge located ~90km west of Newport, Oregon at a water depth of ~800m. Here, methane hydrate is found beneath the seafloor and escapes through the formation of vigorous bubble plumes as a free gas. Despite extensive geophysical and biological research completed here, no studies have quantified the extent of the methane output, or the relationship of seep sites and seafloor geology to the microbial and macrofaunal communities. In 2011, photomosaics of eight individual seeps (comprised of >30,000 high resolution images) were acquired for the first time using the remotely operated vehicle ROPOS. Analyses of the captured images provide the first quantification of the areal extent of venting based on microbial mat distribution, and the relationship of seafloor geology to macrofaunal communities. At the sites each animal has been identified. Results show that both the distribution and abundances of seep organisms are highly variable. Animals avoid the areas of most intense venting at the centers of the seeps, but are seen at highest abundance at the seep margins. This is presumably due to steep methane and hydrogen sulfide gradients. These detailed habitat maps provide baselines to compare changes in the venting locations and animal distributions over time. Preliminary investigations show that the seep sites are highly dynamic with the formation of deep collapse pits, disappearance of some mat sites, and the nascent formation of others.

Ian Christen- Mathematics, Physics

Christen, Ian 2

Ian Christen is a junior at the University of Washington majoring in Physics and Mathematics. He works in Kai-Mei Fu’s Optical Spintronics and Sensing Lab as part of her Quantum Information Processing (QIP) Project. The aim of this project is to develop an integrated platform for scalable quantum computation using nitrogen-vacancy (NV) centers in diamond as quantum bits, with the end-vision of having networks of NV centers connected by gallium phosphide waveguides, all on a tiny chip. So far, Ian’s research has involved the parameterization of NV centers and the testing of QIP devices. Specific projects include the construction of a tunable-frequency laser to examine NV optical transitions and the development of an automated testing setup that can test thousands of QIP devices overnight. He is extremely grateful for the opportunity that the WRF poses, as it has the potential to allow him to move from the testing side of his research to the fabrication side. Support from the WRF will be used to fund his use of the Washington Nanofabrication Facility (WNF) where he will use state-of-the-art techniques to build nanoscale gold electrodes around NV centers for the application of electric fields. These electric fields will correct inherent error in NV center optical transitions and allow quantum entanglement between NV centers. After graduation, he plans to pursue a Ph.D. program in Physics. Outside of school, Ian enjoys running, swimming, and competing in triathlons.

Mentor: Kai-Mei Fu, Physics, Electrical Engineering

Project Title: Dynamic Tuning of Nitrogen-Vacancy Center Optical Transitions to Integrated Optical Cavities

Abstract: The nitrogen-vacancy (NV) center is a defect in diamond that has promising applications in quantum information processing. Such applications require the spin states of multiple NV centers to be entangled. This can be achieved by interfering single zero-phonon line (ZPL) photons from different NV centers. Moreover, for entanglement to occur, the frequencies of the ZPL photons must be indistinguishable between NV centers. We can fabricate integrated optical cavities, in the form of disk resonators, to enhance the collection of ZPL photons. However, inherent manufacturing error in the cavities causes incorrect resonance with the ZPL frequencies. Furthermore, local electromagnetic fluctuations within the diamond crystal can cause the ZPL frequencies of NV centers to vary over time and between separate centers. Here we present a solution to these issues in order to further our lab’s goal of demonstrating integrated NV-based entanglement generation. First, the application of electric fields to NV centers can individually tune the ZPL frequencies. Second, photoluminescence excitation (PLE) spectroscopy can quickly and accurately determine the frequency of individual NV centers. We propose to individually tune the ZPL frequencies of NVs to resonance with our integrated cavities, using PLE as feedback for dynamic stabilization and equilibration.

Gina Hansen - Bioengineering

Hansen, Gina

Gina Hansen’s research involvement began in high school, when she studied crayfish sensory perception at the University of Maryland and at her high school in Virginia. From this project, she realized a desire to perform research with more depth and impact on human health, which led her across the country to study bioengineering in Seattle. As a freshman at the UW, she joined the lab of Dr. Daniel Ratner in the Department of Bioengineering, where they develop phenotyping applications for real-time, label-free silicon photonic biosensors. Working in the Ratner Lab over the last three years has helped Gina cultivate an interest in translational research—the application of knowledge gained from basic research to benefit our medical abilities as a society. Ultimately in her professional career, Gina wishes to research and develop diagnostic methods that better healthcare for both doctors and patients. After graduating in Spring 2016 with a B.S. in Bioengineering, she plans to work in biotechnology industry before pursuing graduate research. Gina is a peer tutor at the Odegaard Writing and Research Center, a volunteer with the non-profit organization Casa Latina, and an active scone/muffin enthusiast. She also advocates for engineering students in administrative initiatives and decisions through the College of Engineering Student Advisory Council. Gina is indebted to her mentors Dr. Daniel Ratner, Dr. James Kirk, and Pakapreud Khumwan for their continued guidance and encouragement. She would like to sincerely thank the Washington Research Foundation for its support in her research and professional development.

Mentor: Daniel Ratner, Bioengineering

Project Title: Cellular Phenotyping of Processed Cells and Tissues by Silicon Photonic Biosensors

Abstract: Proteins presented on cell surfaces are clinically useful as diagnostic markers and therapeutic targets. While certain surface antigens may be detected after chemical or mechanical breakdown of the cell membrane, such sample processing may compromise the conformation of proteins with multiple transmembrane domains or that are sensitive to membrane integrity. It would be advantageous in simplifying workflow in sample preparation to perform phenotyping with minimal disruption of the cell membrane. A method for simple, specific, and direct cell characterization in a point-of-care or lab-on-a-chip design is desirable for clinical or laboratory settings without access to or need for a complete flow cytometry unit. In this project, we seek to develop a rapid, simplified method of cellular phenotyping in an immortalized cell line as a proof-of-concept for diagnostics utilizing cell surface molecular markers. A silicon photonic biosensing surface will be functionalized for specific capture of HeLa cell-derived microparticles by binding of the CAIX surface antigen. Use of this functionalized platform will eliminate steps in analysis workflow involving equipment largely limited to the sophisticated clinical laboratory setting and numerous sample preparation reagents, departing from traditional fluorescent methods of cell surface characterization.

Tiffany Jansen - Astronomy, Physics

Jansen, Tiffany

Tiffany Jansen is a senior studying Physics and Astronomy. She became involved in astronomical research by joining the Pre-Major in Astronomy Program, which aims to give college freshmen hands-on research experience in astronomy. Through this program she began her research career observing stellar flares on M-dwarf stars using Kepler data. Wanting to get more involved in the exoplanet field, Tiffany joined Eric Agol’s research team in her sophomore year, where she began her research on spectroastrometry as a detection method for exomoons. At this time Tiffany also began working as a telescope engineering assistant for the Telescope Engineering Group at the University of Washington, assessing the quality of integral parts for the Sloan Digital Sky Survey’s 2.5-m telescope. As a member and treasurer of the University’s astronomy club the League of Astronomers, Tiffany has spent a total of six nights observing on the 1.8-m telescope at the Dominion Astrophysical Observatory for the club’s research project on the metallicity of open star clusters. Tiffany also provides service to the Astronomy Department by serving as a liaison between the department and the undergraduates as the Astronomy Undergraduate Representative. In the summer after her junior year, Tiffany continued her research on exomoons with a grant from the Washington NASA Space Grant Consortium. In the following summer she applied her work to NASA’s Haystacks Project at the Goddard Center for Astrobiology, adding exomoons to the high fidelity planetary system models for simulating exoplanet observations. With the Washington Research Foundation fellowship, she will use these models to determine the feasibility of detecting and characterizing exomoons with next generation space telescopes. Tiffany plans to pursue a Ph.D. in astronomy with a focus in exoplanet detection and characterization.

Mentor: Eric Agol, Astronomy

Project Title: Determining the Feasibility of Detecting a Habitable Exomoon in the Presence of Exozodiacal Dust

Abstract: Although nearly two thousand exoplanets have been discovered and confirmed to date, exomoons have yet to be detected orbiting these planets. The detection of an exomoon would give insight into planetary formation and possibly increase the habitable real estate in a planetary system. Current telescopes are not capable of spatially resolving an exoplanet and its exomoon, or of separating the two blended spectra in a combined light measurement. However, previous work has shown that there is a wavelength dependent photometric centroid shift between a planet and its moon due to the weighted nature of the center of light. This spectroastrometric shift is highest in bands where the planet is dim and the moon is relatively bright, which can happen if it differs compositionally from its planet. As part of the “Finding the Needles in the Haystacks” project, we generated a realistic spatial/spectral model of an Earth-like exomoon orbiting a warm Jupiter in the habitable zone of a Sun-like star, including plausible exozodiacal dust structure. Preliminary results show that the presence of an Earth-like exomoon can produce centroid shifts greater than a milliarcsecond at some wavelengths, enabling the detection of the Earth-like exomoon even in the presence of dust. However, extracting the spectrum of the Earth-like exomoon proved challenging, even when employing a simple telescope simulation devoid of coronagraphic effects, and further work will be needed to determine if it is possible even with 12-meter-class space telescopes.

Malte Lange - Biochemistry

Lange, Malte 2

Malte Lange is a fourth year biochemistry student at the University of Washington. In the summer of 2014, he became a member of the Li group as an Amgen Scholar. His current research project focuses on improving battery technology by improving the robustness of the battery structure. Using simplified models of quantum dots, he hopes to understand the mechanism of fracturing which limits current battery technology and then potentially provide alternative solutions. Upon completing his degree in biochemistry, he plans to attend graduate school to study theoretical chemistry with potential applications in protein structure, function, and design. In his free time he enjoys playing soccer, climbing, and attending concerts. He is thankful to the whole Li group, especially his PI, Xiaosong Li, and his mentor David Lingerfelt, for supporting his research and academic efforts. He would also like to thank the WRF foundation for their generous support of his research.

Mentor: Xiaosong Li, Chemistry

Project Title: Lithium Ion Intercalation into ZnO Lattice

Abstract: The diffusion of ions into a nano-scale ZnO lattice has gained attention in the past decade as a possible solution to the rapid fracturing of ZnO electrodes in bulk batteries and as an alternative to conventional LiCoO2 and LiFePO4 materials which are expensive to manufacture and environmentally hazardous. Experiments have shown that bulk (i.e. not nano-structured) ZnO electrodes fracture in discrete segments (a leapfrog effect) after only a few charge/discharge cycles, diminishing the effective charging/discharging capacity. Current efforts are aimed at using nano-scale lattices which fall within the size range of the cracking separations and thus are not susceptible to leapfrog fracturing. Using an optimized quantum dot structure and conventional ab initio electron structure theory methods, the effects of lithium ion intercalation into a Zn33O33 quantum dot lattice were investigated. The main research questions were (1) where are the potential energy valleys in which lithium ions can settle (2) what effect does lattice expansion have on the energy of a lithium-ion charged quantum dot and (3) how does doping the dot with iron affect the energy? Using a rigid and a relaxed scan of a lithium ion entering and exiting through the C3V axis of the quantum dot, the potential energy landscape was mapped, illustrating the presence of multiple potential valleys in which ions could settle. We used single point calculations to determine the optimal expansion factor after observing expansion in previous molecular dynamics simulations. Currently preliminary results indicate a possible trend regarding iron positioning within the lattice and we hope to improve our data by introducing a larger Zn84O84 dot. Hopefully our findings will demonstrate that nano-scale iron doped ZnO lattices are not subject to leapfrog fracturing and may therefore be cheap and viable options as battery electrodes.

Jeffrey Lee - Neurobiology, Philosophy

Lee, Jeffrey

Jeffrey Lee initially became interested in circadian rhythms during a research project for his Honors Chemistry class. He was assigned to pick one subject of interest related to chemistry and write about it. He chose to study vitamin D, and throughout his research he realized how powerful this little molecule really is: it acts on several hundred different genes in the body! Since he also takes vitamin D on a daily basis, he asked a very fundamental question: is there a difference between taking vitamin D in the morning or nighttime? He reasoned that, since vitamin D is manufactured in our skin through exposure to the sun, taking vitamin D at night could, as a daytime signal, disrupt our daily rhythms. This question remained on his mind and led him to discover the field of chronobiology, whereupon he joined the de la Iglesia lab. Jeffrey’s project focuses on the circadian system. Circadian rhythms can be entrained by external time signals called Zeitgebers. Although the light-dark cycle is the most prominent Zeitgeber, there are several others, including environmental temperature cycles and temporally restricted food access. Jeffrey’s research focuses on how cyclic fear stimuli can have the capability to entrain circadian rhythms in mice. After determining this, he can begin genetic manipulations to determine the molecular and anatomical basis for fear entrainment.
After he graduates, Jeffrey plans to pursue an MD in primary care, where he can share the importance of preventive medicine in improving health. Outside of school, he is an avid photographer and pianist. He would like to thank the Washington Research Foundation for its generous support of his research, and he would like to thank his mentors, Dr. de la Iglesia and Dr. Miri Ben-Hamo, for their effective guidance in his research.

Mentor: Horacio de la Iglesia, Biology

Project Title: Fear Entrains Circadian Rhythms

Abstract: Circadian rhythms are vital to maintaining proper mental health. Stress, fear, and anxiety have been shown to affect circadian rhythms. However, it is unknown whether or not fear has the ability to entrain the circadian system. Our laboratory, in collaboration with others, has shown that nocturnal cyclic fear stimuli are sufficient to induce a shift of the natural nocturnal activity and feeding of rats to daytime activity. Because these behavioral rhythms are sustained with the same timing under constant conditions, they reflect the output of an endogenous circadian clock that is entrained to the fear stimuli. For the current proposal, we aim to translate these findings to mice, in order to begin genetic manipulations to determine the molecular and anatomical basis for fear entrainment.

Albert Ng - Neurobiology, Anthropology

Ng, Albert

Albert started his undergraduate research career as an undergraduate research assistant and lab technician in the Kim Lab in the Department of Psychology. From 2012-2014 he worked on several projects investigating the neural-cognitive effects of stress on the hippocampus and sub-hippocampal structures, and the corresponding innate fear responses in rats. This research sparked his interest in neurobiology and ultimately led him to pursue this field for his undergraduate degree. During this time he was also the Assistant Director for the Associated Students of the University of Washington Student Health Consortium promoting physical health and mental wellness through advocacy programs aimed towards improving the holistic health for all persons at UW. He was also an appointed committee member on the Hall Health Advisory Board, advising the University of Washington Medical Center and Neighborhood Clinics on student, faculty, and community based health services and education.

In 2014 he was admitted into the Computational Neuroscience Training Program and joined the Buffalo Laboratory in the Department of Physiology and Biophysics as an undergraduate research assistant. Under the joint mentorship of Elizabeth Buffalo, Ph.D. and Adrienne Fairhall, Ph.D., he is investigating activity of neural networks underlying learning and memory in non-human primates by studying hippocampal place cell firing patterns and analyzing unique behavioral events of navigation through virtual reality foraging tasks.

In 2015, he also joined the Opp Lab in the Department of Anesthesiology and Pain Medicine at Harborview Medical Center as part of the Innovations in Pain Research Program. Under the mentorship of Mark Opp, Ph.D., he focuses on exploring the neuronal basis for the interaction between the sleep and pain pathways. By using immunohistochemical microscopy and histological techniques, he will be investigating the localization of microglia and astrocytes in areas of the brain that are highly involved in sleep and pain regulation to identify mechanisms by which immune response alters sleep.

Albert hopes to combine his passions for health advocacy and research in pursuit of a Medical Scientist Training Program (MD/Ph.D.) with a focus on neurobiology and behavioral science. He is very thankful for the generous support and encouragement from the Washington Research Foundation Fellowship, the Scan|Design Foundation, the Washington Research Foundation Innovation Undergraduate Fellows in Neuroengineering, and the University of Washington Computational Neuroscience Training Grant.

Mentor: Elizabeth Buffalo, Physiology, Biophysics

Project Title: Understanding Neural Encoding of Space and Navigation in the Rhesus Macaque during a Virtual Foraging Task.

Abstract: There have been major advancements in the use of Virtual Reality (VR) technologies in military, medical, and educational applications over the past decade. However, it is not well understood how representations of spatial memory are encoded by the bi-modal, visual and audio sensory stimulation inherent to VR interactions. Previous studies have identified the hippocampus and entorhinal cortex as structures involved in the formation of spatial memory. Using VR, non-human primates will utilize a joystick to move a first-person avatar and perform a foraging task wherein they must collect virtual objects to obtain food rewards. We hypothesize that monkeys will use a demonstrable strategy to optimize behavior in our VR task and propose experiments and computational methods to identify unique strategies wherein memory and route planning are being used. Furthermore, we hypothesize that hippocampal neurons and hippocampal networks in animals performing our VR task will represent complex spaces, as well as encode representations of memory and planning elicited by our task. Thus, chronically implanted multi-electrode arrays in the hippocampus are used to study local field potentials, single units, and network activity in animals performing our task. Preliminary results indicate that the two monkeys fully trained on this task utilize unique strategies to obtain food rewards. Furthermore, individual strategies suggest that memory and other factors may play a role in route planning. We have also successfully recorded more than 6 months of neurophysiological data from 32 channels on three electrode arrays chronically implanted across the hippocampus of one monkey performing the VR task. Because Alzheimer’s pathology affects medial temporal structures and is characterized by deficits in memory, spatiotemporal reasoning, route finding, and better understanding of spatial representations in medial temporal areas would help create VR with potentially therapeutic effects in patients with memory deficits.

Amisha Parikh - Biochemistry

Parikh, Amisha

Since a young age, Amisha Parikh has been riveted by the power of the brain. At the start of college, she knew she wanted to get involved in research related to neurological or mental disorders. She joined Dr. Nicholas Poolos’ Cellular
Neurophysiology Lab at Harborview Medical Center during her freshman year and has been working there since. In this lab, Amisha is studying the activation of c-Jun N-terminal kinase (JNK) during various time stages in the development of chronic epilepsy. Understanding the timeline of JNK activation can create effective targets for medicine through anti-epileptic drugs and other therapeutic options. A greater knowledge of JNK’s role in epilepsy can assist with subsequent research in the field of neurology. She hopes that, through this knowledge, they can explore avenues to alleviate the pain for those suffering with debilitating brain disorders.
Amisha is currently double majoring in biochemistry and neurobiology and aspires to be a neurologist. She hopes to take the critical thinking skills learned in the lab into the clinical setting and professionally contribute to the ongoing discussion about mental and neurological disorders. She wants to advocate a strong connection between the medical and research communities, supporting and working alongside researchers for the benefit of her patients.
When not in the lab or class, Amisha spends her time volunteering, dancing (as part of the UW Bollywood Kahaani dance team), reading, running, and baking. She wishes to express her sincere gratitude to her family, peers, mentors, colleagues, and the Washington Research Foundation for supporting her along this journey. Her passion for neurology continues to grow as she learns more in this field, and being a part of this research project has helped her advance towards becoming the scholar, individual, and eventually the physician that she dreams to be.

Mentor: Nicholas Poolos, Neurology

Project Title: Examining the Activation of c-Jun N-terminal Kinase (JNK) during the Development of Chronic Epilepsy

Abstract: There is evidence of dysregulation of phosphorylation signaling in epilepsy and previous researchers at the Poolos lab have discovered an increase in activation of c-Jun N-terminal kinase (JNK), seen by increased phosphorylated JNK, in animals experiencing seizures. This is a novel connection and my project aims to understand the timeline of JNK activity during the development of epilepsy. We hypothesize that JNK activity will precede epilepsy onset and may be a cause of chronic epilepsy. In order to study epilepsy, we administer research-bred rats a pilocarpine injection. Shortly after, the rat is in status epilepticus (SE), a state of continuous seizures. After one hour, the animal is given a phenobarbital injection to halt SE. Seizures begin around one week post-SE and achieve steady-state frequency around six weeks. I am in the process of analyzing brain tissue samples taken after one hour, one day, and one week post-SE using western blotting to obtain a relationship between JNK levels from pilocarpine-treated rats to control rats. There are three JNK isoforms, and I have discovered a significant increase in activation of JNK isoform 2 one hour post-SE (130 ± 10%, p0.5, n=9). It is vital to gather data one day and one week post-SE to see whether activation of any JNK isoform precedes seizure onset and is potentially causative of epilepsy. If we do see activation of an isoform, we can explore ways to prevent the onset of epilepsy or lessen its severity after a brain injury. Thus, by understanding JNK activation, we can look at avenues that can potentially serve as treatments for epilepsy.

Wen Lin Tan - Physics, Applied & Computational Mathematical Sciences

Tan, Wen Lin

The potentials of quantum mechanics are endless. One of them is quantum computing and information. Wen Lin became interested in quantum computing and information after she took her first quantum mechanics class. She later joined the UW Trapped Ion Quantum Computing group as an undergraduate assistant under the Principal Investigator (PI) Professor Blinov in Spring 2014. Barium-Ytterbium ion chains are used as the basis of quantum computers by confining the ion chains in an ion trap using electromagnetic fields. Wen Lin’s current project focuses on generating a quartic anharmonic trap from a harmonic trap to produce equal ion-ion spacing in ion chains for uniquely addressing each individual ion and scaling the system for useful quantum operations. She plans on pursuing a Ph.D. in a related field so that she can continue her research as an experimental physicist. With the generous support from the WRF Fellowship, Wen Lin can focus more on research and learn valuable skills for her goals.

Mentor: Boris Blinov, Physics

Project Title: Confining Barium-Ytterbium Ions Chain in a Quartic Anharmonic Oscillator for Quantum Computing

Abstract: Ion traps use electromagnetic fields to trap charged particles in vacuums. We use ion traps to trap ions, which can be used to implement qubits (quantum bits) for quantum operations. Barium and ytterbium are promising candidates because their photo-ionization and cooling laser optics and fiber optics are readily available. The micro-fabricated surface ion trap that I am using now traps long chains of ions which can potentially be scalable for running real and useful quantum algorithms and building a quantum computer. However, our current trap is a harmonic oscillator. As the number of ions increases, the ion chain will form a zigzag pattern which makes uniquely addressing an individual ion for quantum gates with a laser beam impossible. Therefore, my goal is to confine barium-ytterbium ion chains in a quartic anharmonic oscillator to solve the zigzag issue and have equal ion-ion spacing. My project will minimize quantum operation errors for quantum gates which are the fundamental components to run a quantum. I will first find the solutions for the DC electrode voltages numerically, using and improving the existing Boundary Element Method to generate a quartic anharmonic trap. Then, starting from the initial harmonic trap, I will use the solution to morph the real trap potential into the quartic one. The changes of ion-ion positions will be compared and verified using an EMCCD camera. Then, I will determine the resonant frequencies of the ion chains in both the original (harmonic) and the modified (anharmonic) traps. The resonant frequency stays the same for the harmonic trap, but decreases in the quartic anharmonic trap as more ions are added to the chain. In conclusion, the quartic anharmonic trap will have constant ion-ion spacing and overcome the zigzag issue which increases our ability to control qubits for quantum operations and to build a quantum computer.

Jingwen Xiao - Bioengineering

Xiao, Jingwen

Jingwen Xiao is a senior in Bioengineering, and she is working in the Molecular Biophotonics Lab in the Department of Mechanical Engineering. Her project is in collaboration with pathologists at the UW Medical Center, with the expected deliverable of a fast and inexpensive imaging system to accelerate the screening process of cancer biopsies. Jingwen is fortunate to be under direct guidance of Prof. Jonathan Liu, who graciously sets aside time to meet with her every week and provides instrumental support in her project. Conducting research gives Jingwen an incredible opportunity to explore the field of biomedical engineering and find her passion in biomedical imaging. She is sincerely grateful for the generous support of the Washington Research Foundation Fellowship to allow her to wholeheartedly delve into research and to encourage her to continue learning in graduate school. Beyond coursework and research, Jingwen loves volunteering and has a special affinity for animals. From an octopus feeder and interpreter at Seattle Aquarium, to a cat caretaker at animal shelters, to a fundraising assistant at the zoo – every role she has had brings her closer to the loving community that has become home for her as an international student.

Mentor: Jonathan Liu, Mechanical Engineering

Project Title: Development of a Widefield Imaging System Combining Deconvolution for Acceleration of Screening Cancer Biopsies

Abstract: Cancer is a leading cause of mortality worldwide, and the number of new cases is projected to reach 22 million in the next two decades. A tissue biopsy is the “gold standard” for cancer diagnosis and is also performed to examine whether all tumor growths have been surgically removed. However, conventional procedure requires intense labor and is often time-consuming and costly, as it involves extensive tissue sectioning and other processing for microscopic examination. In addition, the majority of the examined biopsy specimens turn out to be benign. These factors reveal the need to significantly accelerate the screening process and increase the efficient use of healthcare resources. Therefore, to reduce unnecessary processing time and costs, we propose a fast and inexpensive imaging system to screen the surface of thick tissues for abnormality, before full histological processing. Our system is designed to enable a wide field-of-view and integrate deconvolution algorithms, which restore diffracted light back to its original location, thus achieving high contrast and resolution. More specifically, the project will be carried out in three phases:
1) Design, construction, and optimization of an inverted fluorescence microscope;
2) Calibration of light diffraction and optimization of deconvolution algorithms;
3) System validation using fresh human tissues.
Success of such a system will directly translate into clinical settings and increase efficiency of biopsy procedures, which is beneficial to both patients and healthcare providers.