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Undergraduate Research Opportunities

Biomedical Engineering Computer Science & Engineering Electrical & Systems Engineering Energy, Environmental & Chemical Engineering Mechanical Engineering & Materials Science

Biomedical Engineering

Quantifying sensitivity and gait with intervertebral disc injury

Faculty: Lori Setton

Intervertebral disc degeneration is a cause of chronic back pain and disability, which affects millions of Americans every year and contributes to increased healthcare costs. Disc degeneration is characterized by structural changes in disc height and decreased proteoglycan and water content. Causes of disc degeneration include aging, repetitive loading of the spine, or an injury to the intervertebral disc. Our laboratory seeks to identify mechanisms that contribute to pain following injury to the intervertebral disc and to develop novel strategies to inhibit the progression of symptoms and pathology.

The objective of the project is to advance systems to measure sensitivity and behavior in preclinical models of intervertebral disc injury. Using mechanical measures of gait and locomotion, and instruments to record touch force, we hope to relate sensitivity and behavior parameters to the development of anatomic pathology in the intervertebral disc after injury. The student will work with instrumentation and non-invasive assessments of these measures in the rodent, and learn methods for calibration, error analysis, coding, optical image analysis and more. Additionally, the student will have the opportunity to generate new ideas for sensors of behavioral metrics that would be useful in characterizing musculoskeletal injury patterns more broadly.

Regulation of matrix-induced mechanisms of nucleus pulposus cell phenotype

Faculty: Lori Setton

Degenerative disc diseases contribute to dysfunction and painful symptoms in large numbers of affected patients. The IVD consists of a dense extracellular matrix (ECM) rich in collagens, proteoglycans, and laminin isoforms. Cells of the nucleus pulposus (NP) reside in the inner portion of the IVD and contribute to matrix synthesis during development and maintenance during aging. With aging and degeneration, however, cell density decreases and existing cells are unable to replace and repair the native extracellular matrix. Our laboratory seeks to develop new strategies that can support the maintenance of healthy disc cells and healthy extracellular matrix production for regeneration of the IVD.

Little is known of how aging-related changes in physical cues of matrix stiffness regulate cell morphology and subsequent biological activity. We believe that cytoskeletal remodeling occurs with changes in matrix stiffness and that these changes activate nuclear factors that regulate relevant signaling pathways. The objective of this research experience is to determine if manipulation of cytoskeletal-associated transcription factors can influence moleculr marker expression and bioactivity for human NP cells in environment of varying stiffness. The student will be involved in primary cell isolation, developing reporter constructs to characterize NP cell response to substrates, and evaluate cell activity using immunofluorescence, flow cytometry, confocal microscopy, and qRT-PCR.

Skills required: basic wet lab skills; experience in tissue culture and viral vector work a plus

Switching anti-amyloid activity in Parkinson's disease by phosphorylation

Faculty: Jan Bieschke

Aggregation of the protein alpha-synuclein into insoluble fibrillar amyloid structures is at the heart of Parkinson's disease pathology. We found that the microtubule-associated protein Ezrin, which is important for neuronal growth and plasticity, inhibits fibril formation of alpha-synuclein by a unique new mechanism. The function and conformation of Ezrin is switched through phosphorylation. Since the anti-amyloid activity of Ezrin depends on a specific structure of a linker region within the protein, we hypothesize that phosphorylation will switch its activity. Phosphorylation of Ezrin would be a possible target for therapeutic intervention in Parkinson's disease. The project will test the anti-amyloid activities of phosphorylation mutants of Ezrin.

Experimental techniques will include protein expression and purification, aggregation studies using ThT fluorescence, ultracentrifugation, SDS Page and CD spectroscopy. Students applying for the program should have some biochemical lab skills including basic sample preparation and pipetting skills and be interested in a quantitative understanding of disease processes.

Skills required: basic biochemical lab skills

Enrichment and aggregation of Amyloid-beta on neuronal membranes

Faculty: Jan Bieschke

Amyloid-beta (Abeta) is the peptide that is deposited extracellularly in the brains of Alzheimer patients in the form of fibrillar macromolecular structures. Fibril formation is well understood in vitro but not in vivo. In vivo the total concentration of Abeta is much lower than would be needed for fibril formation. It is known that Abeta gets internalized into neurons and it is suspected that this process is connected to fibril formation in vivo. We found that binding to cellular membranes concentrates Abeta more than 100-fold compared to the cell media. The project is aimed to study this effect in neuronal model cells by biochemical and biophysical methods, and to determine how if and how the concentration of Abeta on the membrane leads to fibril formation and neurotoxicity.

Experimental techniques will include aggregation studies using ThT fluorescence, fluorescence microscopy, and cell culture techniques. Students applying for the program should have some biochemical lab skills including basic sample preparation and pipetting skills and be interested in a quantitative understanding of disease processes.

Skills required: basic biochemical lab skills

Binding of Ezrin to helical oligomers in Parkinson's disease

Faculty: Jan Bieschke

Aggregation of the natively unstructured protein alpha-synuclein has been directly linked to Parkinson's disease pathology. Helical oligomers were recently identified as crucial species on the aggregation pathway. We have discovered a new, very potent inhibitor of alpha-synuclein aggregation, Ezrin. This protein most likely interacts with the helical oligomer species and may form helix bundles with this crucial aggregation intermediate, which could be the model for a new therapeutic mechanism in Parkinson's disease. In the project the student will prepare helical oligomers alpha-synuclein and characterize their interaction with Ezrin by biophysical and biochemical techniques.

Experimental techniques will include protein expression and purification, aggregation studies using ThT fluorescence, electron microscopy, Western blotting, and fluorescence spectroscopy. Students applying for the program should have some biochemical lab skills including basic sample preparation and pipetting skills and be interested in a quantitative understanding of disease processes.

Skills required: basic biochemical lab skills

Computations in an olfactory neural circuit

Faculty: Barani Raman

We use simple invertebrate models (fruit flies and locusts) to study how odors are transduced and represented by sensory neurons in the insect antenna, how this sensory input is transformed by central circuits in the insect brain, and finally how dynamical neural activity drive appropriate behavioral output. To achieve this goal, we use a variety of electrophysiological, imaging, genetic and computational tools. An ideal summer project will involve training in one or more of these tools with the objective of answering a well-defined research question in olfaction.

Skills required: Intellectual curiosity and willingness to work hard. Prior wet-lab skills and/or computational modeling/analysis will be handy.

Open source ensemble clustering

Faculty: Kristen Naegle

Ensemble clustering is the approach of finding many alternate solutions to a clustering problem. We have ongoing work to establish a suite of open source ensemble approaches and establish methods for comparing solutions and extracting final solutions. A WUSEF summer student would join this effort and be responsible for the development of a particular piece of the research and code development.

Skills required: Competent in programming (Python preferred, but not necessary), linear algebra, and statistics

Delivery of gold nanoparticles to the brain by focused ultrasound technique

Faculty: Hong Chen

Gold nanoparticles have many potential therapeutic and diagnostic applications outside the brain. However, the blood brain barrier (BBB) limits their delivery to the brain. The goal of this project is to develop focused ultrasound technique for noninvasive, localized and safe delivery of gold nanoparticles across the BBB. A summer student will be involved in the animal experiment, acquire brain images, and data analysis.

Skills required: Wet lab skills

Brain stimulation with transcranial ultrasound

Faculty: Hong Chen

Ultrasound has recently been shown to be capable of noninvasively stimulating brain activity. The goal of this project is to develop a protocol for transcranial ultrasound brain stimulation in mice. A summer student will be involved in experiment design and data analysis.

Skills required: Wet lab skills

Computer Science & Engineering

Alignment-free algorithms for analyzing massive genomic sequence data with variation

Faculty: Jeremy Buhler

Modern DNA sequencers can sample tens of billions of bases from a genome, metagenome, or other set of DNA sequences in a single day. We often want to ask questions questions about how different data sets of this type relate to each other, e.g. by computing the evolutionary distances between organisms or identifying families of sequences common to multiple sets of sequences. But the sheer size of the data to be analyzed makes it very expensive to apply traditional approaches that assemble and align long sequences from these data sets in order to compare them.

In this project, we will explore effective alignment-free algorithms to answer questions about the relationships among large DNA or protein data sets. Unlike previous work, we will focus on alignment-free methods that are tolerant of variations among sequences due to mutation and sequencing error. Increased variation tolerance will open up new opportunities for the use of alignment-free methods in computational biology.

Skills required: ability to write code in C or C++, and familiarity with basic algorithms and data structures (sorting, hashing, trees). Some background in molecular biology is desirable but not strictly required.

Accelerating Computations on GPUs with MERCATOR

Faculty: Roger Chamberlain and Jeremy Buhler

In this project, students will implement algorithms on NVIDIA GPUs using MERCATOR, a novel framework being developed by our group to help build complex GPU apps efficiently. Potential application domains include bioinformatics (e.g. biological sequence comparison and mapping tools) and machine learning and data mining (e.g. decision forest methods, correlation clustering). We'll focus on methods that are both algorithmically non-trivial and potentially parallelizable on a GPU.

Skills required: C++ and facility with basic algorithms and data structures (sorting, hashing, graph, traveral, possibly dynamic programming). Prior experience programming with CUDA is a strong plus. Familiarity with a scripting language such as Python or Perl is a plus.

Data-centric Approaches to Modeling Individual Behavior in Large-scale Online Social Systems

Faculty: Sanmay Das

REU students will work on different aspects of a project that attempts to unify micro-modeling of agent behavior based on data and large-scale modeling of social systems in which these agents interact. We have developed a model that uses positive or negative pairwise interaction data to estimate a maximum likelihood model of point-of-view. We would now like to develop algorithms that can use prior information and other side information (for example, mined from the natural language aspects of what the user writes on a website) to build much richer models of opinion that can be applied to web-scale data such as that on Wikipedia, Reddit, or Yelp. Building such models will allow us to study the dynamics of opinion formation and change on the social network.

Skills required: mathematical maturity for the theoretical project (familiarity with game theory and/or machine learning is a plus); proficiency with Java, C/C++, or Python for the simulation project.

Big data analysis for active drug discovery

Faculty: Roman Garnett and Benjamin Moseley

REU participants will design intelligent policies for actively querying a large, real-world database of compounds to quickly detect potential drugs. The database contains 120 different biological targets of relevance to humans and a background set of 1 million putative inactive compounds gathered from the ZINC database. Along with these, a baseline implementation of a state-of-the-art virtual screening system will be made available for comparison. There are several numerous outstanding questions for students to pursue. (1): Previous work on active search assumed that the result of each experiment ("is this compound a potential drug?") would be made immediately available before selecting the next. Modern high-throughput screening devices, however, can process many compounds at once. How can active search policies be best adapted to the batch setting? (2): Previous work on active search showed that myopic polices can perform arbitrarily bad compared to the theoretically optimal policy. Is that still true in the batch setting? (3): Can we design feasible non-myopic search policies in the batch setting? (4): Can the search process by enhanced by encouraging diversity among the compounds in each batch?

Skills required: Familiarity with MATLAB and machine learning and mathematical maturity. Familiarity with chemistry/biology a plus but not required.

Intelligently segmenting the long tail

Faculty: Brendan Juba

Students will run a study using these new algorithms to investigate the quality of models produced and overall proportion of the population covered by the discovered segments on some real world domain, as compared to standard clustering techniques. For example, we might consider the domain of providing personalized medicine: For a complex, heterogeneous disease like cancer, we might seek to use patient records to pick out subpopulations for which we can effectively model the risk factors or progression of the disease. Along the way, participants will learn to use standard data science tools such as Python, R, and/or MATLAB, and will gain experience in handling real datasets. Students will also be encouraged to experiment with variants of the proposed algorithms to try to improve the quality of models and/or coverage of the population achieved.

Skills required: mathematical maturity for the theoretical project (familiarity with game theory and/or machine learning is a plus); proficiency with Java, C/C++, or Python for the simulation project.

Executing big data applications on heterogeneous architectures

Faculty: Roger Chamberlain

Students will implement a set of big data applications in the Auto-Pipe and ScalaPipe development environments, assessing (via measurement and modeling) the performance of these applications on a variety of heterogeneous computer architectures. The two development environments support streaming data computation on traditional multicores, graphics engines, and reconfigurable logic. Targeted applications include astrophysics [Tyson 2008], computational biology [Jacob 2008], and computational finance, each of which can be characterized by large data streams that must be considered in their entirety to answer the scientific question(s) of interest.

Skills required: C++ and facility with basic algorithms and data structures (sorting, hashing, graph, traveral, possibly dynamic programming). Familiarity with a scripting lanauage such as Python or Perl is a plus. Prior biology background is not required.

Systems-biology approaches to understanding gene expression regulation underlying complex traits

Faculty: Weixiong Zhang and Sharlee Climer

TWe focus on complex human diseases, such as psoriasis, an autoimmune skin disorder with no cure, and many types of cancer; most of these diseases are devastating or detrimental, leading to enormous economic and societal burden. Understanding the genetic and molecular bases of disease mechanisms is the key to developing effective diagnostic and therapeutic means for such diseases. The REU students will be involved in developing machine learning and data mining approaches for analyzing biological data to understand the causal relationships between genotypic variations, gene expression changes, and disease phenotype.

Skills required: Proficiency with Jave, C or Python

Combinatorial complexity, heterogeneity, and big data: The challenges of mining genetic code

Faculty: Weixiong Zhang and Sharlee Climer

Students will experience a full computational biology experience. First they will analyze genome-wide genetic datasets using novel computational tools under development in our lab. While searching for significant associations, they will gain appreciation for the challenges inherent with the analysis of big data. Students will periodically present their results and brainstorm and critique each other's projects. Once significant associations have been identified, the interns will use functional annotation and analysis tools and study relevant literature to explore the potential biological meaning underlying these associations. Finally, they will prepare manuscripts describing their results and critique each other's manuscripts, with the ultimate goal of producing publishable work.

Skills required: Proficiency with Jave, C or Python

Design and Implementation of Language Constructs for Parallel Programming

Faculty: I-Ting Angelina Lee

Cilk is a C/C++-based multithreaded language that provides a high-level language abstraction for parallel execution. When writing a parallel program in Cilk, the programmer expresses the logical parallelism of the computation, and an underlying runtime scheduler schedules computation in a way that respects the logical parallelism specified by the programmer while taking full advantage of the processors available at runtime. Reducer hyperobjects is a construct in Cilk that allows the program to perform parallel reduction. Students will work with the PI to design, implement, and evaluate different runtime strategies to support reducer hyperobjects efficiently.

Skills Required: Familiarity with C/C++; experience with parallel programming (in any language or any platform) is a plus but not required.

Comprehensive Static Instrumentation for Dynamic-Analysis Tools

Faculty: I-Ting Angelina Lee

Key to understanding and improving the behavior of any system is visibility --- the ability to know what is going on inside the system. Various dynamic-analysis tools, such as race detectors, memory checkers, call-graph generators, code-coverage analyzers, and performance profilers, rely on compiler instrumentation to gain visibility into the program behaviors during execution. With this approach, the tool writer modifies the compiler to insert instrumentation code into the program-under-test so that it can execute behind the scene while the program-under-test run. This approach, however, means that the development of new tools requires compiler work, which many potential tool writers are ill equipped to do, and thus raises the bar for building new and innovative tools. We are developing CSI, a comprehensive static instrumentation framework, which allows the tool writers to easily develop analysis tools that require compiler instrumentation without actually doing the compiler work themselves. In this project, students will work with the PIs to develop the CSI framework and implement dynamic analysis tools using the CSI framework.

Skills required: Familiarity with C/C++; basic understanding ofhow a compiler works (e.g. having taken a compiler course).

Leveraging Eye-Tracking for Modeling Knowledge Discovery and Decision-Making with Visualization

Faculty: Alvitta Ottley

When we read a body of text, process an image, or reason with a data visualization, our eyes constantly move. This pattern of movements can reveal important information about how we interpret visual designs and whether a specific visualization is effective at communicating data. The goal of this project is to explore how eye-movements can be leveraged to understand how people use different visualization to ultimately improve visualization design. The REU students will run a study to collect eye tracking and mouse interaction data as users interact with visualizations. The students will then analyze the data using a variety of visualization, machine learning, statistical analysis techniques.

Skills Required: Proficiency with web programming. Some background in Machine Learning or Statistics would be beneficial.

Implementation of Speech-based Biometric System

Faculty: Shantanu Chakrabartty

The main goal of this project is to implement and optimize a biometric system that can recognize target speakers based on their speech samples. For this project the student will implement a text-independent speaker recognition system using a C or C++ programming language. The student will start by understanding a MATLAB level implementation of an existing text-independent speaker recognition system which they then will be required to translate into C or C++. During the translation process, the student will be involved in optimizing the algorithm and code for a back-end support vector machine classification engine and an auditory feature extraction module. The final objective would be to make the software to be scalable such that any number of target speakers (to be recognized) could be added at a later stage and the software can be optimized for different hardware platforms.

Skills Required: Working knowledge of MATLAB, and proficiency in C or C++ is required. Prior experience in algorithm design and optimization will be beneficial.

Creating an Example-Rich Programming Environment

Faculty: Caitlin Kelleher

Looking Glass is a 3D programming environment designed for kids with an online community. With Looking Glass kids can program their own 3D animated stories, remix other programs, and then share their creations to the community. For this project we want to utilize the shared programs as examples to teach kids programming within Looking Glass. For this project you will work with the Looking Glass lab to make Looking Glass an example-rich programming environment. To make sure we pick exciting examples for each user, you will need to filter and download examples from the online community that are customized to each kid's preferences and expertise. Then, you'll design and implement several ways to incorporate the examples into Looking Glass and then user test these changes to verify their effectiveness at helping kids learn new programming concepts.

Skills required: Basic programming skills.

Locality-aware concurrency platforms

Faculty: Kunal Agrawal and I-Ting Angelina Lee

We are building a platform for writing cache efficient parallel programs. As part of that platform, we are designing compiler and runtime transformations that can convert divide and conquer programs that are written without considering cache-efficiency and transform them so into cache efficient ones. In order to develop these transformations, we plan to conduct an algorithmic study in order to understand the potential of these transformations to improve performance. Students will conduct experimental study by implementing various algorithms and work with the PIs to design compiler / runtime transformations.

Skills required: Familiarity with C/C++; mathematical maturity including an undergraduate algorithms course.

Designing a programmable RFID platform for Internet-of-things

Faculty: Shantanu Chakrabartty

The goal of this project is to implement a complete Gen-2 UHF RFID communication protocol stack on a Texas Instruments MSP microcontroller. The embedded platform can then be used to implement different types of passive IoT sensors and computing devices that are wirelessly powered using a commercial RFID reader. The student will have to first understand the architecture of the Intel WISP platform and then program an on-board MSP micro controller (in C and some machine code) to communicate with the reader.

Skills required: Proficiency in C and embedded programming. Some background on RFID tags would be beneficial.

Networking Applications of Unmanned Air Vehicles/Drones

Faculty: Raj Jain

This project uses small quadcopter drones for a novel networking application. The students make sensors using Arduino and Raspberry Pi and fly them on drones and measure the performance.

Skills required: Must have taken at least one introductory course on networking and be familiar with Internet protocols.

Service Differentiation in the Cloud

Faculty: Roch Guerin

The project's overall goal is to explore offering different levels of service guarantees in cloud systems. In a cloud system, most resources have been virtualized so that interactions between virtual resources and physical resources are often difficult to predict with the level of accuracy that tight service guarantees call for. In particular, support for latency sensitive applications is challenging in cloud systems. The project involves two possible targets, both of which would be carried out in collaboration with a Ph.D. student. The first involves implementing extensions to a thread-based system we have developed to offer latency guarantees to different virtual machines (VMs) in the Xen system. The work would target adding scheduling and/or traffic shaping mechanisms to protect service guarantees against misbehaving VMs. An alternative target is to implement a "scavenger" service for Xen, which would migrate docker containers running low-priority applications across idle VMs, basically harnessing unused computational cycles. The challenge here is to realize a lightweight implementation that also ensures that resources are resources are immediately freed when requested by their primary owner. In other words, the scavenging domains have no service guarantees, i.e., they can be preempted at any time, but at the same time, their ability to access unused resources should be transparent to the service guarantees of other users.

Skills required: Proficiency with C/C++ and java, good knowledge of the Linux operating system and if possible its networking stack. Familiarity with network protocols and virtualization platforms such as Xen, is a plus but not required. Above all, a willingness to learn new material and to dive into complex software systems.

Designing a real-time user-interface for Multi-RFID tags

Faculty: Shantanu Chakrabartty

The goal of this project is to design a software user- interface that can read and manipulate multiple RFID tags in real-time. The student will investigate different multi-tag configurations using different commercial-grade RFID tags and will also be working on a commercial RFID reader and its SDK to design a user- interface. The end goal will be explore different RFID algorithms based on the tag's received signal strength and its orientation with respect to each other and with respect to the reader's antenna.

Skills required: Proficiency in C++ or C#. Good background in operating systems architecture. Some background on RFID operation would be beneficial.

Electrical & Systems Engineering

Remote Health Monitoring

Faculty: Arye Nehorai

Remote health monitoring can provide useful physiological information in the home. This monitoring is useful for elderly or chronically ill patients who would like to avoid a long costly hospital stay. Wireless sensors are used to collect and transmit signals of interest and a processor is programmed to receive and automatically analyze the sensor signals. In this project, you are to choose appropriate sensors according to what you would like to detect and design algorithms to realize your detection. Examples are detection of a fall, monitoring cardiac signals to detect arrhythmias, brain signal monitoring (EEG), in-home ultrasound, etc.

Energy-Efficient Computing Platform for Insect-Scale Micro-Robots

Faculty: Xuan 'Silvia' Zhang

Recent research advancement has driven the miniaturization of autonomous robots to the micro scale, and promising prototypes are being developed to explore this exciting yet untrodden frontier. One of the key challenges in designing such micro-robotic systems is how to build an energy-efficient computing platform that is capable of meeting the real-time performance demand, yet compact enough to fit onto an insect-sized robot. Our lab is looking into a number of approaches across the implementation stack (circuits, architecture, systems, software) to tackle this challenge.

Skills required: basic knowledge of electronics circuits and embedded systems; computer programming ability (C or Python), experience with micro-controller and FPGA is a plus

Mathematical Modeling of Systemic Risk of the Financial Sector

Faculty: Zachary Feinstein

Various financial crises have highlighted the paramount importance of systemic risk in the financial sector, i.e. the risk that the financial system is susceptible to failures due to the characteristics of the system itself. During the recent credit crunch, for example, financial contagion led to government intervention to avoid a chain reaction of failing institutions impacting the global economy significantly. The tremendous cost of systemic risk requires the design and implementation of realistic models for the financial system during a crisis.

Skills required: Knowledge of mathematical optimization; computer programming ability (Matlab, R, or Python languages recommended); NO prior knowledge of finance is required

Extraordinary Enhancement of Optical Nonlinearity in Metamaterials

Faculty: Jung-Tsung Shen

Artificially engineered materials (also called metamaterials) are man-made materials with extraordinary optical properties that are not accessible by naturally occurring materials. This research project will expose interested undergraduate students to the forefront research in this exciting emerging field. Specifically, the students will be guided to design and model compact metamaterials with ultra-large optical nonlinearities, and to demonstrate various nonlinear optical phenomena, such as harmonic generation, frequency sum and difference, and optical logic gates.

Skills required: a working knowledge of the Maxwell's equations and a passion for numerical techniques.

Energy, Environmental & Chemical Engineering

Development of new materials and new methods of synthesis of nanostructured materials for Li-ion batteries:

Faculty: Richard L. Axelbaum

Li-ion batteries are ubiquitous now but advances in performance and reduction in cost are needed to accelerate the electric vehicle industry. The undergraduate student will assist in identifying advanced material chemistries and novel routes to synthesis of these materials to enable advanced Li-ion battery technologies. The student will assist in the operation of the reactor for the synthesis of nanostructured powders and will learn how to manufacture a battery from the materials that have been synthesized. The student will also learn how to test the performance of a battery and will be responsible for testing the performance of the materials that have been synthesized and reporting the results.

Skills required: High grades in Chemistry and Thermodynamics

Physico-chemical Processes Impacting Arsenic Mobilization

Faculty: Young-Shin Jun

Managed aquifer recharge (MAR) is one water reuse technique with the potential to meet growing water demands. In MAR, reclaimed wastewater is injected into aquifer formations for later use. Although filtration and adsorption in the vadose zone and underlying aquifer can remove some contaminants from reclaimed water, unfavorable soil-water interactions can mobilize arsenic from arsenic-bearing aquifer formations. The student will conduct benchtop scale column experiments and analyze the water and solid chemistry to understand the physico-chemical reactions during MAR. The student will also analyze the environmental condition data from MAR field sites.

Skills required: coursework in general chemistry

Immobilizing Contaminants by Biomimetic Apatite Formation at Biological Interfaces

Faculty: Young-Shin Jun

Using phosphate minerals as sorbents or precipitating secondary phosphate minerals to co-precipitate contaminants can be effective remediation options for heavy metals and radioactive materials, such as uranium. In this study, by enabling co-precipitation during the apatite (calcium phosphate) formation at biological interfaces, we will evaluate the immobilization of contaminants from aqueous environments.

Skills required: coursework in general chemistry

Developing Stronger Seal Integrity during Geologic CO2 Sequestration

Faculty: Young-Shin Jun

To help resolve global climate-change problems, much effort has recently been devoted to developing methods for storing atmospheric CO2. One of the most promising methods is geologic CO2 sequestration. Among many aspects of geologic CO2 sequestration operations, the integrity of wellbore cement and caprock is one of the most crucial factors for safe operations, because the weakening of cement or caprock by chemical attacks can provide pathways for CO2 leakage by creating defects such as cracks and fractures. However, at this stage, the quantitative link between chemical reactions and mechanical alterations of the seal is still weak. In this study, the integrity of wellbore cement and caprocks will be investigated in the context of geologic CO2 sequestration. The student will conduct bench-scale experiments and learn how chemical reactions at water-rock interfaces at the molecular level is very useful in controlling macroscale changes of seals.

Skills required: coursework in general chemistry

Eliciting the Reaction Mechanisms during Organosolv Lignin Extractions

Faculty: Marcus Foston

Our project focuses on understanding the mechanisms, both chemical and physical, occurring to during organosolv extractions of lignin from biomass. Organosolv is a process which utilizes common organic solvents, normally ethanol, along with high temperatures and pressures to separate biomass into its components for downstream processing. Our work specifically focuses on understanding on the chemical reactions, which can lead to downgraded product streams.

Skills required: Chemistry lab skills and basic knowledge of Excel

Investigating Supported and Unsupported Palladium Nanocatalysts for Hydrogenolysis of Lignin

Faculty: Marcus Foston

Catalytic hydrogenolysis of aryl ether linkages has been reported as a promising approach to selectively depolymerize and transform lignin into aromatic compounds, since the C-O bond in aryl ethers are the most abundant linkages in the framework of lignin. However, there is a lack of knowledge and research on the difference between two major type of catalytic systems, using supported and unsupported nanocatalysts. Our project will synthesize PVP-Pd (unsupported nanocatalyts) and Pd/C (supported nanocatalysts) and characterize them using TEM, DLS, and BET. The as-synthesized catalysts will be applied to the hydrogenolysis of lignin, and the results will be compared using mostly GC-MS. Kinetic studies will also be conducted to determine reaction network model.

Skills required: Chemistry lab skills

Improve Aromatic Compounds Production Through Lignin Depolymerization via Novel Heterogeneous Catalyst

Faculty: Marcus Foston

Project 1 - Hydrogenolysis of lignin in supercritical methanol (sc-MeOH) over Cu-doped porous metal oxide catalyst (CuPMO) has been proved effectively breaking the aryl ether linkages in lignin and product aromatic compounds. However, hydrogenation (HYD) is an undesired side reaction that usually accompanies with HDG, which further reduces the depolymerized aromatic products and boards the product distribution. In order to preserve the resulted aromatic compounds from further reducing to aliphatics, dimethyl carbonate (DMC) can be used as an environmental friendly co-solvent for the reaction. The phenolic compounds can be trapped through O-methylation by DMC, which the resulted compounds are much less favored to be hydrogenated.

Project 2 - In order to reduce the oxygen content of lignin depolymerized aromatic compounds and further narrows the product distribution, hydrodeoxygenation catalyst (bimetallic FeMo phosphide) is studied to selectively remove methoxyl and aryl hydroxyl groups of lignin depolymerized products. This process will directly produce an organic liquid with increasing yield of benzyl compounds.

Skills required: Organic chemistry background is strongly recommended. Research involves using multiple organic analyzing tools, including GC-MS, GPC, NMR, FT-IR, UV-vis. Students have experience with these techniques are also strongly recommended.

Dynamic Regulatory Systems: (synthetic biology, metabolic engineering)

Faculty: Fuzhong Zhang

When engineering microbes produce biofuels or other value-added chemicals, it is essential to have high productivity and conversion yield to make such technology economically viable. One powerful strategy to increase productivity/yield is to design dynamic regulatory systems, by which a microbial cell regulates metabolic pathways according to its own metabolism dynamically. We aim to apply cellular biosensors and construct dynamic regulatory systems at several levels to regulate metabolic pathways and to understand how such systems work. We are also interested in developing dynamic systems to control other cellular behaviors.

Skills required: basic molecular cloning and microbiology cell culture skills.

Cyanobacteria for Biofuels (synthetic biology, metabolic engineering)

Faculty: Fuzhong Zhang

Cyanobacteria can thrive in low-nutrient, high-salinity water and use sunlight energy to fix CO2 into organic compounds. These microbes are ideal hosts for biofuel production. However, the available tools to engineer cyanobacteria are very limited. We aim to develop synthetic biology toolkits for use in these organisms, and introduce heterologous pathways for the production of advanced biofuel in cyanobacteria.

Skills required: basic molecular cloning and microbiology cell culture skills.

Advanced Biofuels (synthetic biology, metabolic engineering)

Faculty: Fuzhong Zhang

To meet the increasing demands of sustainable transportation energy, we aim to engineer microbes to produce advanced biofuels that could be readily used in current engines. One of the biggest challenges is to biosynthesize non-natural molecules that have structures exactly the same or highly similar to the fuels currently derived from petroleum. We are engineering enzymes and constructing novel metabolic pathways to produce these compounds. In addition, we are also developing synthetic biology tools to improve the titer, yield, and productivity of the advanced biofuels.

Skills required: basic molecular cloning and microbiology cell culture skills.

Development and Characterization of a Multiwavelength Integrated Photoacoustic-Nephelometer (IPN) for Climate Change

Faculty: Rajan K. Chakrabarty

The undergraduate student will be assisting in the design and build of a multi-wavelength IPN in my group. IPN is a state-of-the-art instrument that measures the radiative properties of atmospheric pollutants in real-time with precision and accuracy. A full-time staff scientist will be available to guide the student in the construction of the instrument. After the instrument is completed, it will be used to characterize black and brown carbon aerosols---the two major climate warming agents. In the long-term the IPN will be deployed for measuring wild fire emissions to assist NASA scientists in fine-tuning their satellite retrieval algorithms and climate models. Apart from the instrument development, the undergraduate student intern will learn about the role of aerosols (black and brown carbon) in global warming.

Skills required: coursework in "Transport Phenomena"; knowledge in optics and electronic instrumentation design

Mechanical Engineering & Materials Science

Arterial Mechanics and Hypertension

Faculty: Jessica Wagenseil

One out of three Americans has hypertension, or high blood pressure. Our lab studies the interplay between arterial mechanics, specifically compliance, and hypertension using mouse models of human disease. The student will measure arterial compliance and blood pressure in different mouse models after a variety of treatments, including drugs or exercise. The student will also use imaging to investigate the microstructure of the arterial wall and mechanical engineering principles to quantify material properties.

Skills Required: Ability to work with animal tissue, interest in experimental biomechanics, knowledge of Matlab is a plus.

The Role of Elastin in Tendon Mechanics

Faculty: Spencer Lake

We are using genetically modified mice to examine how elastin contributes to the mechanical properties of tendons. Using elastic/viscoelastic mechanical testing, transmission electron microscopy, and histological assessment, this project will identify mechanisms by which elastin interacts with collagen to provide functional properties in healthy, injured and healing tissues.

Skills Required: Ability to work with animal or human tissue; an interest in orthopedics and mechanics; Matlab experience; enthusiasm!

Material and Microstructural Properties of Ligaments using Polarized Light Imaging

Faculty: Spencer Lake

We use optical techniques that utilize polarized light imaging to measure location-specific mechanical and microstructural properties of connective tissues. Ongoing work will validate a reflected light polarization technique to evaluate intact elbow ligaments in anatomically relevant orientations and evaluate how collagen alignment changes under different joint angles and loading conditions.

Skills Required: Ability to work with animal or human tissue; an interest in orthopedics and mechanics; Matlab experience; enthusiasm!

Manipulating Droplet Impact Dynamics using Electric Fields

Faculty: Patricia Weisensee

Using a high speed camera (many thousand frames per second), this project studies the effect of an electric field on the dynamics of impacting droplets. Our goal is to manipulate the trajectory of bouncing droplets to increase heat transfer rates during spray cooling or to prevent ice formation on the surface. The undergraduate student will take part in the design process, setting up the experiment, and will be (partially) responsible for conducting the experiments and for experimental analysis using Matlab.

Skills Required: Matlab, handy in building things

Design of a Boiling Chamber

Faculty: Patricia Weisensee

In order to be able to characterize boiling heat transfer on nano-engineered surfaces, we first need to build a boiling chamber to run the experiments in. Goal is to be able to characterize boiling with both an optical high speed camera (many thousands of frames per second), as well as an Infrared (IR) high speed camera, state of the art in heat transfer characterization. The undergraduate student would help us in designing and constructing the boiling chamber. Depending on the length of the undergraduate research program the student can design, conduct, and analyze first experiments in the new chamber.

Skills Required: Hands-on with building and constructing experimental setups, optional: previous experience in cleanroom work

Design of a Condensation Vapor Chamber

Faculty: Patricia Weisensee

In order to be able to characterize condensation heat transfer on nano-engineered surfaces, we first need to build a condensation vapor chamber to run the experiments in. Goal is to be able to characterize condensation with both an optical high speed camera (many thousands of frames per second), as well as an Infrared (IR) high speed camera, a novelty in heat transfer characterization. The undergraduate student would help us in designing and constructing the condensation chamber. Depending on the length of the undergraduate research program the student can design, conduct, and analyze first experiments in the new chamber.

Skills Required: Hands-on for design and construction of experimental setups

Wicking Behavior or Low-surface Tension fluids

Faculty: Patricia Weisensee

As part of a larger project that aims at designing phase-change cooling for electronics systems (i.e. heat pipes), this sub-projects studies the wicking behavior of low-surface tensio fluids such as alcohols and refrigerants. Wicking is a capillary-driven flow of liquid through micro-porous solids, i.e. it generates a passivle flow and eliminates the need for a pump. However, wicking depends strongly on the surface tension and has been characterized mostly with water, which has a very high surface tension. Here we want to extend the characterization and optimization to other fluids with lower surface tension.

Skills Required: Experience with optical imaging helpful or photography, but not required, Matlab helpful

High speed droplet impact on nano-engineered surfaces

Faculty: Patricia Weisensee

In this project we want to study the droplet dynamics during and after impact on nono-engineered surfaces with very high impact speeds (~100 m/s). So far, only droplet impact at moderate impact speeds (< 10 m/s) has been studied. However, for aviation safety, the characterization of high speed impact is critical, for example to understand icing behavior during flight. As part of this project the student will help design, build, and run experiments with high droplet impact speeds using ultra high speed imaging (~100,000 frames per second). Depending on the length of the undergraduate research program the student will then also help analyzing data and be involved in preparing project reports.

Skills Required: Experience with optical imaging helpful or photography, but not required, Matlab helpful

Development of ALD organic/inorganic films for nanoelectronic applications

Faculty: Parag Banerjee

The summer project in the Laboratory for Emerging and Applied Nanomaterials will involve working on atomic layer deposition (ALD) of organic/inorganic hybrid films with applications in nanoelectronics and photovoltaics. There are no deposition processes that have the flexibility and fidelity of ALD. By putting films down one monolayer at a time, films can be grown with atomic scale precision. Further, sequential deposition of heterogeneous molecules can produce synthetic materials not normally found in nature. This project will explore one such material – an organic ethylene unit stacked with an inorganic zinc oxide (ZnO) unit to produce a nanocomposite film called, 'zincone'. By varying the fraction of organic to inorganic component in the film, it is expected that properties such as electronic conductivity and optical transparency can be varied. The electronic properties will be ascertained using Hall measurements. The optical properties will be measured using UV-Vis spectroscopy. The interaction of varying composition and structure with properties in the zincones will be highlighted for the first time. The student trainee will interact with a graduate student on a daily basis for mentorship and guidance. He/she will learn about design of experiments, data analysis, semiconductor process science and electronic device characterization. The expected duration of this project is 8 weeks. The potential for high impact publications is significant.

Bioenabled and Bioinspired Composites with Gradient Mechanical Properties

Faculty: Srikanth Singamaneni

Highly complex and sophisticated materials at various length scales are commonplace in nature and they have inspired the mankind throughout the history. Learning from nature and applying nature's engineering principles in materials science and engineering is a promising approach to sustainable solutions for various critical challenges and applications. Amazingly, biomaterials are able to achieve complex multifunctionality (e.g., responsive, autonomous, self-healing, self-replicating) utilizing a limited materials/chemistry palette. The beak of a jumbo squid is a fascinating example of gradient (hard to soft) material found in nature. The gradient mechanical properties are achieved through a gradient in chemical composition, crosslinking and water content. Achieving synthetic materials with such large mechanical gradient remains a daunting challenge. In this project, we will employ bacterial nanocellulose (BNC) network as a mimic to the chitin matrix found in the squid beak. We propose to develop methods to achieve gradient crosslinking of the BNC matrix and correlate the gradient structure at the nanoscale to their bulk-scale mechanical properties. In the later stages of the project, the gradient BNC matrix will be infiltrated with silk-like proteins to achieve biocomposites with gradient composition and properties that closely mimic jumbo squid beak.

Skills required: Basic wet chemistry lab experience and bacterial cell culture experience preferred.

SERS based detection of motile organisms

Faculty: Srikanth Singamaneni

The potential health risks associated with pathogens in food, water, blood and skin are innumerable. The detection of bacteria is often associated with issues related to sampling. This project aims at achieving a selective enrichment of bacteria at the point of detection by using chemotactic attractants. The motile organism metabolizes the chemotactic attractant, allowing the organism to move into the motility medium where it interacts with proteins specific to the organism at the point of detection. The isolated bacteria are detected using surface enhanced Raman scattering (SERS). This novel integration of SERS and chemotaxis will have potential implications in the food pathogen detection.

Skills required: Basic wet chemistry lab experience

Computational prediction of two-dimensional materials for photovoltaic applications

Faculty: Rohan Mishra

The newly discovered class of two-dimensional materials such as graphene and MoS2, due to their ultrathin nature, have some of the highest power densities amongst existing solar cells. However, the power conversion efficiency of MoS2-based solar cells is low (~1%). Thus, there is a need for two-dimensional materials with higher power conversion efficiency. In this project, the student will learn to use first-principles calculations running on one of the most powerful supercomputers to search and predict new two-dimensional Bi-based materials that can serve as potential candidates for high power density solar cells.

Skills required: Introductory course in Materials Science, active interest in computational materials science, knowledge of working in an Unix environment is a plus, but not necessary.

Computational prediction of two-dimensional materials for electrocatalysis

Faculty: Rohan Mishra

It has been recently demonstrated by our collaborators that catalysts based on two-dimensional (2D) materials show 1000 times higher catalytic activity for carbon dioxide (CO2) reduction reaction, far exceeding the performance of state-of-the-art catalysts. However, those results are based on only a handful of compounds from the large composition space of existing 2D materials. In this project, the student will use first-principles density functional theory calculations running on one of the fastest supercomputers to rapidly screen 2D materials with potential to achieve high efficient and affordable new catalysts to guide their experimental synthesis.

Skills required:

MEMS 3610 or any other introductory Materials Science course. Familiarity with a programming language (C++, Python)

Lift on Helicopter Blades in Forward Flight

Faculty: Dave Peters

As helicopter blades rotate, they traverse varying Mach numbers and angles of attack on each revolution. Portions of the blade even go into and out of stall on each revolution. What are needed are mathematical models of the lift that these blades develop that are efficient enough to run in real time on flight simulators. We are working on such models and trying to modify the models to be more general and to match experimental data.

Skills required: Matlab and basic engineering mechanics

Interaction of Wakes from Helicopter Rotors

Faculty: Dave Peters

The wake from a helicopter rotor can impinge on a second rotor. This can happen for co-axial helicopters and it can also happen when the wake impinges on the tail rotor in a conventional helicopter. The rotor wake can also interact with any wings, stabilizers, or tail surfaces. The interaction changes the loads on the surface (or second rotor) as well has changing the loads on the primary rotor. We are working on models that can predict this interaction efficiently.

Skills required: Matlab and basic engineering mechanics

Improving Energy Efficiency of Rotorcraft

Faculty: Dave Peters

In forward flight, rotorcraft can use 6 to 8 times the minimum possible induced power. We are studying why this is, where the power goes, and if it might be possible to make design changes that could prevent all of this power from escaping into the kinetic energy of the wake.

Skills required: Matlab and basic engineering mechanics

Design and Testing of Robotic Flagella

Faculty: Phil Bayly

Flagella are thin sub-cellular structures that propel swimming cells or bacteria through fluid. Robotic flagella or "axobots" are mechatronic devices that replicate the motion of flagella at the laboratory scale. Students design, make (using a 3D printer), and test these robotic systems. Supported by NSF.

Required skills: Interest and ability in hands-on lab work, design, and building devices.

Measure the Mechanical Behavior of Direction-dependent Biomaterials

Faculty: Phil Bayly

We study the mechanics of traumatic brain injury (TBI) and use MRI to look at brain motion. We are interested in how soft biological material with fibrous structure (like brain tissue) deforms. We synthesize and perform mechanical testing of these biomaterials.

Required skills: physics and math coursework; interest and experience in experimental work; experience with Matlab is a plus.

Acoustic microfluidic technologies for energy and life sciences applications

Faculty: J. Mark Meacham

Our research is focused on use of acoustic microfluidic technologies to solve various problems in energy and the life sciences. Projects include 1) development of acoustic "tweezers" for isolation of individual swimming algal cells and measurement of their response to mechanical and chemical perturbation, 2) evaluation of an ultrasonic droplet generator for high-throughput whole blood separations, and 3) use of a similar droplet generator to tune the properties of Li-ion battery materials synthesized by spray pyrolysis. Students will participate in design, build and experimental testing of microfluidic devices and test fixtures.

Skills required: interest in and ability to perform hands-on lab work, design and build microfluidic devices. Basic machining, CAD (AutoCAD or SolidWorks) and MatLAB programming experience are preferred.

Changes in Lower Extremity Biomechanics with Fatigue

Faculty: Michael Harris (Physical Therapy)

The goal of this project is to quantify biomechanical changes in people with and without hip abnormalities when they get tired during exercise or sport. It's possible that these changes exacerbate problems in the hip and lead to early damage of joint cartilage. The study involves capturing the motion (similar to technology used for video games and animation) and ground reaction forces of adults while they perform running and cutting activities before and after becoming fatigued.

Skills required: An interest motion analysis and research with human subjects; an understanding of basic dynamics;

Statistical Shape Modeling of Hip Dysplasia in Adults

Faculty: Michael Harris (Physical Therapy)

Hip dysplasia is a disorder characterized by a shallow acetabulum (socket of the pelvis) that does not provide sufficient coverage and stability of the femoral head (the long bone of the leg). Surgical procedures have been established to treat hip dysplasia, but there is much to be learned about the variation in shape among dysplastic patients and how to optimize clinical care. This study will use statistical shape modeling to quantify where variation in dysplastic hip shape is most common compared to healthy hips. A summer student will be involved in making 3D subject-specific models from CT images to inform and develop the statistical shape models.

Skills required: an interest in medical imaging; familiarity with C++ and/or correspondence optimization is a plus but not required

Cancer Cell Motility in Engineered Tissue-like Environments

Faculty: Amit Pathak

Professor Pathak's research interests include biomechanics, biomaterials, mechanobiology of the cell, and interactions between cells and extracellular matrices. In particular, his research aims to understand how mechanical properties of the three-dimensional tumor microenvironment interactively regulate tumor cell invasion to drive cancer metastasis. His lab tackles this multi-variable problem through a multidisciplinary approach that includes fabrication of new matrix platforms, development of advanced measurement tools in cell biology, and construction of predictive computational models.

Skills required: wet lab experience (cell culture experience preferred)

Micromechanical characterization of Earth materials (i.e. rocks)

Faculty: Kathy Flores

The summer undergraduate research student will assist a graduate student studying the low temperature rheology of minerals found in the Earth's mantle, including olivine and quartz. Large-scale deformation studies of rocks are commonly conducted at high temperatures and under large confining pressures, simulating the conditions found in the mantle, in order to prevent cracking and promote plastic deformation. However, such bulk testing provides limited insight into the local deformation processes occurring at the atomic level, and repeated testing to achieve statistically significant results can be challenging. In this project, we apply nanoindentation methods to characterize the local plastic deformation behavior of rocks at low temperatures (e.g. room temperature). By pressing a small pyramidal indenter into the rock surface at positions of interest, we can probe variations in properties over micron length scales, while the undeformed material surrounding the indent provides a natural constraint against crack formation and growth. The student involved in this project will learn to prepare and test nanoindentation specimens and will assist with post-test microscopy.

Skills required: Experience with Matlab and/or finite element methods to model the nanoindentation process is desirable but not required.

Processing of bulk metallic glass matrix composites

Faculty: Kathy Flores

Metallic glasses are a class of metallic materials with a disordered atomic structure, which gives rise to exceptionally high strengths while enabling unique forming characteristics similar to those used for polymers. However, the room temperature tensile ductility of most metallic glasses is quite limited. In this project, the summer undergraduate student will produce and characterize a series of metallic glass alloys reinforced with ductile crystalline particles, with the goal of producing composite materials that combine high strength and ductility. The student involved in this project will learn to prepare and cast metallic alloys and characterize the materials using optical microscopy and thermal analysis methods. The student will also assist with electron microscopy characterization and, if warranted, mechanical testing of the materials.

Other Research Opportunities