Faculty and Projects

CAFE/IMR | Chemistry & Biochemistry | Mathematics
Microbiology | Physics | Public Health | Statistics | TCORS

Center for Advanced Semiconductor Fabrication Research and Education/Institute for Materials Research (CAFE/IMR)

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Shamsul Arafin (Electrical & Computer Engineering)
Optics and Photonics Research
The Optics and Photonics Research Lab (OPREL) led by Prof. Shamsul Arafin focuses on fundamental and applied science of exotic and novel materials and next-generation classical and quantum light sources. Projects range from device design, material growth, material characterization, device fabrication in the cleanroom and device testing. During the 10-week program, a REU student will conduct an experimental research project primarily with the instrumentation of an optical test setup. The student will have an opportunity to participate in professional development activities that will prepare them for graduate school and research-related careers, network with peers and take part in various social events.

Jinwoo Hwang (Materials Science & Engineering)
Scanning Transmission Electron Microscopy
This project requires a researcher who is able to perform machine learning analysis of electron microscopy images. We expect the analysis will provide the detailed information on the atomic structure within the semiconductor materials.

Sanjay Krishna (Electrical & Computer Engineering)
Infrared Detection and Imaging
Dr. Krishna’s lab is part of the research theme on photonic devices and integration.  The student can work on testing and analysis of the integrated devices that we are developing as a part of the Intel Café project.

Siddharth Rajan (Electrical & Computer Engineering)
High-Performance Semiconductor Heterostructure Materials and Devices
Our group works at the interface of applied physics, materials science, and electrical engineering to develop next-generation electronics and photonics. The project will involve using a combination of simulation and experiment to engineer devices based on wide bandgap semiconductors. Potential devices include energy-efficient transistors for next-generation power electronics, radiation-tolerant electronics for space applications, and advanced ferroelectric-based logic/memory devices.

Wolfgang Windl (Materials Science & Engineering)
Computational Materials Science

Fengyuan Yang (Physics)
Complex Materials and Magnetism
The Yang lab is working on advancing semiconductor device fabrication of wide bandgap devices for power management and non-volatile memory applications creating pathways for multifunctional GaN integration on a Si platform. An undergraduate student would work on deposition of perovskite high-K dielectric and ferroelectric oxide layer on GaN and related nitrides, and characterize the structural and dielectric/ferroelectric properties of those perovskite films.

 

Chemistry & Biochemistry

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Analytical Chemistry

Premashis Manna
Molecular Biophysics and Protein Engineering
Manna Laboratory primarily works on developing analytical techniques and engineering proteins with significant applications in climate change-related areas. The students in the lab will have the opportunity to build optical microscopies and characterize light-harvesting antenna complexes, plastic-degrading enzymes, and fluorescent proteins found in jellyfish that have implications in photosynthesis, greener solutions for plastic waste management, and biosensing, respectively.

Biochemistry

Christopher Jaroniec
Structural and Dynamic Studies of Protein and Protein-DNA Assemblies
Our research is aimed at understanding mechanism and function in large protein and protein-nucleic acid complexes and assemblies of fundamental importance in biology via atomistic level characterization of biomacromolecular structure, conformational dynamics and interactions. We employ an interdisciplinary approach, which includes multidimensional nuclear magnetic resonance (NMR) in the solid-state and in solution, high-resolution cryo-electron microscopy, atomic force microscopy, scanning tunneling electron microscopy as well as complementary biophysical, chemical, molecular biology and computational tools. Major current research directions include: (i) elucidation of the structural basis of strain and cross-seeding barrier phenomena in mammalian prion protein amyloids, (ii) characterization of chromatin structure, dynamics and interactions with particular focus on the role of dynamic histone protein tail domains in mediating chromatin compaction and interactions with regulatory proteins, (iii) characterization of DNA base pairing and hydrogen bonding in large protein-DNA complexes and (iv) development of paramagnetic solid-state NMR methods for rapid protein structure determination.

Karin Musier-Forsyth
Molecular Biology & Enzymes
Projects in the Musier-Forsyth lab are focused on characterizing protein-RNA interactions involved in HIV-1 replication and fidelity mechanisms in protein synthesis. Undergraduate students will learn techniques such as protein and RNA purification, enzyme kinetic assays, RNA structure-probing, and characterizing RNA-protein binding interactions.

Dehua Pei
Cell Penetration and Drug Delivery
Investigating how biomolecules cross the cell membrane and developing cell-permeable peptides and proteins as research tools, therapeutics, and agricultural products.

Inorganic Chemistry

Christine Thomas
Catalysis
Research in the Thomas laboratory focuses on the design of functional catalysts using Earth-abundant transition metals for the development of more sustainable and environmentally friendly technology. The summer project will involve the synthesis and characterization of new transition metal complexes and their use as catalysts for the activation of readily available small molecules (e.g. carbon dioxide, nitrogen, ammonia) and/or organic transformations. Over the course of the summer project, students will learn how to synthesize and manipulate air and moisture-sensitive inorganic and organometallic complexes using glovebox and Schlenk techniques, as well as a variety of spectroscopic and analytical methods such as NMR, IR, and UV-Vis spectroscopies and cyclic voltammetry.

Shiyu Zhang
Inorganic Synthesis and Energy
We are a group of chemists utilizing synthetic inorganic chemistry to tackle unmet challenges at the frontiers of energy storage and energy conversion. Group members can expect to gain experience in the synthesis of organic, inorganic, and organometallic compounds, characterization of air-sensitive/temperature-sensitive complexes, spectroscopy, electrochemistry, and battery fabrication techniques.

Organic Chemistry

Christopher Hadad
Computational Chemistry, Synthesis and Enzymology
The Hadad research team uses computational modeling, organic synthesis and biochemical evaluations to design, synthesize and evaluate the efficacy of novel drug-like compounds for the treatment of organophosphorus poisoning. An undergraduate student could be involved in one of these approaches as part of our research team, perhaps doing computational modeling for the design of novel therapeutics or the synthesis, characterization and biochemical evaluation of individual compounds for in vitro studies.

Physical Chemistry

William “Memo” Carpenter
Spectroscopy of Single Biomolecules and Biological Nanoparticles
The Carpenter Group focuses on fundamental relationships between the chemical and physical properties of nanoparticles made from biological building blocks. For example, we are interested in systems like drug delivery nanoparticles, and how their molecular properties could be understood and improved upon for more effective drug delivery. A key feature of these objects is that they are highly heterogeneous in their properties: each nanoparticle is different in terms of aspects like their size, stoichiometry, and molecular arrangement. An undergraduate researcher in this lab would make new fluorescence measurements to assess variability between single biological nanoparticles, and contribute to designing and constructing laser experiments for sensitive detection.

Christopher Jaroniec – see Biochemistry above
Structural and Dynamic Studies of Protein and Protein-DNA Assemblies

Alexander Sokolov
Computational Chemistry and Theory
Summer projects in the Sokolov group will focus on computer simulations of excited states and spectra of molecules and materials with complicated electronic structure. Students will use state-of-the-art quantum chemical methods to understand properties of molecules and materials important in photochemistry and catalysis. Students will also use computer programming to analyze the results of calculations and will have an opportunity to participate in the development of new theoretical methods.

 

Mathematics

For additional information on research in Mathematics, see:

Maria Han Viega
Mathematics of Machine Learning: Exploring How Neural Networks Learn
Machine learning has found its way to many fields, both in industry and academia, but some aspects of the theory remain far from the mainstream. The neural tangent kernel (NTK) describes the training evolution of a deep neural network using gradient descent, and establishes connections between NNs and kernel methods. In fact, in the infinite-width limit, a closed form solution of the trained neural network can be obtained. In this project, we will explore the limits of this theory empirically, for example; how far are finite dimensional NNs from the stationary NTK regime and what can be learned about the training dynamics. Prior familiarity with linear algebra, multivariate calculus, basic probability and some familiarity with programming in python are recommended pre-requisites for the project.

Ghaith Hiary
Computational Number Theory
Prime numbers are the building blocks of all the natural numbers using multiplication. A highly successful approach to understanding the primes is to study properties of functions constructed using the primes. The most famous example is the Riemann zeta function. This leads to the Riemann zeros and then to the Riemann hypothesis (RH), which tells us that the primes should in a sense be randomly behaved. In this project, we will consider the Riemann zeros as well as zeros of closely related L-functions. Prior familiarity with elementary number theory and some mathematical software such as Mathematica are the main prerequisites for the project. A course in mathematical analysis would also be useful.

 

Microbiology

For additional information on research in Microbiology, see:

Kurt Fredrick
Protein Synthesis in Bacteria
The Fredrick lab studies mechanistic aspects of ribosome assembly and function. Summer students would learn molecular and biochemical techniques such as gene cloning, mutagenesis, protein purification and enzyme assays.

Justin North
Biofuels
The North Lab studies the production of renewable fuels and chemicals by bacteria. Bacteria can convert greenhouse gases like carbon dioxide into needed fuel and plastic alternatives that reduce our dependence on fossil fuels. Students in the lab will learn to grow photosynthetic bacteria engineered for ethylene, propylene, or hydrogen biofuel production. They will also learn and apply genetic techniques to help further engineer these bacteria with new or enhanced capabilities. This results in bacteria with increased biofuel production, which students quantify by chromatography and mass spectroscopy techniques to identify which engineered bacteria strains are best suited for industrial-scale biofuel production.

Krithika Rajaram
Malaria Parasite Biology
The Rajaram lab studies how Plasmodium falciparum, the parasite behind the most severe form of malaria, adapts to survive and thrive in human red blood cells. We are especially interested in two unique structures inside the parasite—a highly unusual mitochondrion and a plastid called the apicoplast. These organelles are essential for the parasite’s survival, and we are working to understand how they are built, what proteins they contain, and how they keep the parasite alive. Students will learn to use genetic tools like CRISPR/Cas9, along with microscopy and enzyme assays, to study the roles of important proteins within the organelles.

Chad Rappleye
Fungal Respiratory Pathogens
The Rappleye lab investigates how respiratory pathogens cause disease with a specific focus on fungal pathogens like Histoplasma capsulatum. We use molecular genetic approaches to facilitate functional tests of factors used by Histoplasma to survive and proliferate within host cells. We model infections using cultured macrophage cells and employ cellular and biochemical studies to understand fungal virulence factors. In addition, we are using screening of small molecules to identify potential antifungal compounds as therapeutics for fungal disease. Students will be involved in projects to create mutants in Histoplasma using CRISPR/Cas9 methodology as well as analyze mutants by cellular/microscopy and biochemical tests.

Matt Sullivan
Viral Discovery, Virocells, and Phage Therapy
The Sullivan lab studies viruses of microbes and has a long and strong history of training undergraduate researchers. We have established quantitative viral metagenomic sample-to-sequence pipeline and community-available informatics platforms to analyze such data, expanded our understanding of the global virosphere, and developed approaches to link and explore virus-host interactions. While our research initially focused on ocean viral ecology and evolution, we now apply these approaches to soils, humans, and extreme environments to understand their diversity and impacts, as well as establish them as practical tools for treating disease (e.g., phage therapy). Potential projects include: (1) generating single gene knockouts in Pseudomonas simiae and putida to identify the function of bacterial genes in phage infection; and (2) host-range testing of Pseudomonas simiae and Pseudomonas putida phages.

Darryl Wesener
Microbiome Glycobiology
The Wesener Research Group is interested in the microbial community that inhabits the human gut, our gut microbiota. We hypothesize that bacterially-derived carbohydrates are critical in directing community assembly and function, and interacting with immunoregulatory proteins. Students in the Wesener Group will apply approaches from microbiology, biochemistry, chemistry, and computation to projects that may include bacterial polysaccharide isolation and characterization, polysaccharide utilization assays with anaerobic human gut microbes, or heterologous protein expression to identify novel enzyme activities.

 

Physics

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Daniel Brandenburg
Nuclear Physics of Heavy Ion Collisions
My research focuses on ultra-relativistic heavy-ion collisions to study nuclear matter under extreme temperature and density. These collisions recreate the quark-gluon plasma (QGP), a state of matter from the early universe where quarks and gluons are no longer confined within hadrons. When heavy nuclei collide, they form a hot, dense fireball of quarks and gluons that momentarily exists in the QGP phase before cooling rapidly. Since the QGP cannot be observed directly, we reconstruct its properties from the particles produced as it cools. I also study so-called Ultra-relativistic heavy-ion collisions – those where the colliding nuclei just miss one another. These Ultra-relativistic heavy-ion collisions are still interesting because they generate the strongest electromagnetic fields in the universe. I use these fields as intense photon sources to study the gluon structure and dynamics inside large nuclei. These photon interactions also provide opportunities to search for physics beyond the Standard Model. Additionally, my research contributes to the next-generation nuclear physics experiment in the US: the Electron Ion Collider (EIC). The EIC will collide high-energy electrons with heavy nuclei, offering unprecedented precision to map the structure of nuclear matter. My group is actively involved in developing the EIC’s physics program and building its first detector, as part of the EPIC collaboration.

Ralf Bundschuh
Bioinformatics and Statistical Physics
The Bundschuh lab studies the interactions between nucleic acid molecules (DNA and RNA) and proteins using computational methods from Statistical Physics and biological sequence analysis. High throughput sequencing has made it possible to obtain exquisitely detailed information on nucleic acids protein interactions but it requires the analysis of large data sets in order to extract biological knowledge from the sequencing data. Students will learn how to perform such data analysis on one (or more) of several experimental collaborators’ data sets and hopefully discover new insights into the Biology involving nucleic acid protein interactions.

Jackie Chini
Physics Education Research
Dr. Chini’s research group studies access and inclusion in physics, mainly at the undergraduate level and beyond. Our group uses both qualitative and quantitative research methods and applies frameworks from sociology, psychology, disability studies and education to address challenges in physics. Research projects can be tailored to students interests and are ideal for students with a background in physics and interests in fields such as sociology, psychology, education, and/or statistics.

Michael Poirier
Chromatin Biophysics and Single-Molecule Spectroscopy
The Poirier lab investigates the physical properties of the human genome and how these properties regulates gene expression. Undergraduate Students will participate in studies that could include the preparation of DNA-protein complexes that mimic how genomic DNA is organized in chromatin, preparation and application of DNA origami nano devices for studying chromatin structural dynamics, and application of single molecule fluorescence and force measurements to characterize chromatin structure dynamics and function.

 

Public Health

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Epidemiology

Robert Hood
Environmental Exposures and Maternal & Child Health
Dr. Hood’s research focuses on the health impacts of environmental exposures on reproductive health specifically, maternal and child health and development. He utilizes a variety of methodologies to study the link between the environment and human health including big data and omics (such as metabolomics and epigenomics). Dr. Hood works with a variety of studies including a cohort of individuals exposed to a brominated flame retardant, several IVF based cohorts, and several pregnancy cohorts as well as studies utilizing publicly available data. For summer projects, students may gain skills in 1) community engagement, 2) searching, reading, and summarizing scientific literature, 3) data management and analysis, and 4) scientific writing and presenting.

 

Statistics

For additional information on research in Statistics, see:

Steephanson Anthonymuthu
Intervention Efficacy Methods for Non-Normal Outcomes
The efficacy of an intervention, such as a vaccine, can be established through the estimation of several numerical measures. Analyzing normal and continuous data for vaccine efficacy is much flexible and many tools are available to measure the efficacy. In response to the growing interest in measures of disease severity when the outcome variable is binary/ordinal, especially when observations are clustered or measured longitudinally or zero inflated, non-parametric method can be employed for efficacy methods with some limitations. Also, much convenient parametric method with latent variables approaches via generalized linear mixed models (GLMM) for vaccine efficacy under different design settings can be discussed in this project. The student will learn about selection criteria in mixed-models and perform simulation studies in R to explore their performance under different settings. Students with some experience coding in R are encouraged to apply.

Dena Asta
Analyzing and Visualizing Graph Laplacians Across Diverse Network Models
The research project focuses on analyzing and visualizing the spectral properties of the graph Laplacian across various network types. The graph Laplacian, a cornerstone in spectral graph theory, encodes critical structural and functional information about networks. By studying its eigenvalues and eigenvectors, we gain insights into properties such as connectivity, clustering, and diffusion dynamics. The project will explore graph Laplacians for networks generated from negatively curved, flat, and positively curved latent spaces as well as Erdős–Rényi random graphs, Watts–Strogatz small-world networks, and lattice graphs. One of the goals of this project will be to identify patterns and key differences in spectral properties across network models, linking findings to network topology, curvature, and randomness. Another goal will be to develop interactive and aesthetically appealing visualizations to represent the spectral analysis of the different networks. This project blends computational mathematics, statistical analysis, and creative visualization, equipping participants with interdisciplinary skills. The results will deepen our understanding of graph spectra and provide tools for studying complex networks in applications such as social science, biology, and physics.

Asuman Turkmen
Exploring Multi-Block Data Analysis: Integrating Omics Layers for Enhanced Insights
Multi-block data analysis has emerged as a pivotal approach for addressing complex datasets that integrate multiple sources of information. This methodology is particularly crucial in the era of high-throughput technologies, which generate extensive omics data encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. These layers provide complementary biological insights, necessitating advanced strategies for their integration. Similarly, in analytical chemistry, data obtained by multiple sources, such as data generated by two different spectroscopic techniques like mid-infrared (MIR) spectroscopy and Raman spectroscopy, is frequently encountered. Commonly used multi-block data integration methods, such as canonical correlation analysis, kernel learning, and partial least squares, are critical for extracting meaningful patterns, improving predictions, and identifying key variables that drive decision making for numerous disciplines. Students involved in this project will explore the recent promising multi-block methods through hands-on data applications by evaluating their performances in visualization, predictive modeling, and the identification of influential variables. This experience will enhance their analytical skills, foster critical thinking, and deepen their understanding of data integration techniques. Proficiency in R programming is advantageous, as it will serve as the primary tool for analysis throughout the project.

 

Tobacco Center of Regulatory Science (TCORS, Public Health/Medicine)

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Ahmad El Hellani and Theodore Wagener
Project 1
The El Hellani lab studies tobacco emissions in a controlled analytical lab setting using smoking machines. These machines are programmed based on standard puffing profiles or data collected from participants in clinical trials. Our work focuses on toxicity assessment of tobacco emissions and we manipulate tobacco ingredients to assess the impact of tobacco additives on emissions. An undergraduate student will have the chance to work in a transdisciplinary environment with access to state-of-the art tobacco research technologies and analytical instruments.

Brittney Keller-Hamilton and Marielle Brinkman
Project 2
Oral nicotine pouches (ONPs) have a lower toxicant burden than cigarettes and traditional smokeless tobacco products. Project 2 will identify characteristics of nicotine concentration, form, and isomer that best support cigarette smokers’ and smokeless tobacco users’ complete transition to lower-risk oral nicotine pouches. Project 2 will also evaluate changes to the human oral microbiome in response to switching from cigarettes/smokeless tobacco to oral nicotine pouches. Results will inform FDA regulations designed to reduce the disease burden of tobacco use by fostering complete switching to a less harmful product among established smokers and smokeless tobacco users who cannot or will not quit using nicotine.

Darren Mays
Project 3
The tobacco industry has long relied on specific marketing strategies to sell their products, and over time tobacco packaging has become an essential component of tobacco industry marketing. Increasingly, tobacco companies are shifting marketing investments to newer products, including oral nicotine pouches. Marketing for these products uses unique strategies, including communicating about dimensions of nicotine to consumers. This includes displaying nicotine concentration on oral nicotine pouch packaging, and using claims such as the products contain “tobacco free” nicotine. Project 3 will study how manipulating different dimensions of nicotine in oral nicotine pouch marketing affect how consumers engage with the marketing, their perceptions of oral nicotine pouches, their preferences for oral nicotine pouches relative to other tobacco products, and whether they decide to use them. Students involved in this project will have opportunities to assist with participant recruitment and screening, data collection including in-person laboratory visits with psychophysiological assessment, and working with resulting data.

Amy Ferketich and Megan Roberts
Project 4
The goals of Project 4 are to identify marketing exposures and product design characteristics across the nicotine dimensions that are appealing to adolescents and young adults and increase their risk of continued use, product escalation, and nicotine dependence. This project is a two-year, prospective observational study with a national sample of 2,000 youth and young adults. The methods involve administering surveys every six months and week-long ecological momentary assessments at baseline, one year, and two years. A focus of the analyses will also be on priority populations that have been historically targeted by the tobacco industry. Students working on this project will be involved with data collection and data cleaning. Their independent project may involve analyzing data from the National Youth Tobacco Survey to examine questions related to e-cigarettes or oral nicotine pouches.