CAFE/Semiconductors | Chemistry & Biochemistry | Mathematics
Microbiology | Physics | Public Health | Statistics | Tobacco Regulatory Science
**This page is under construction.**
CAFE (Semiconductor Fabrication Research)
For additional information see:
- Institute for Materials Research
- Center for Advanced Semiconductor Fabrication Research and Education (CAFE)
- News release about establishment of CAFE (2022)
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.
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
Chemistry & Biochemistry
For additional information on research in Chemistry & Biochemistry, see:
Bioanalytical Mass Spectrometry and Paper-Based Microfluidics
Research in the Badu group focuses on bioanalytical method development to enable ultra-sensitive chemical detection in underserved communities. Specific experiments involve the development of paper-based microfluidic devices for finger prick blood collection, in-chip immunoassay to simultaneously capture multiple disease biomarkers, room temperature storage of the captured proteins, and direct on-chip analysis by a portable mass spectrometer. Participating students will develop expertise in paper-based immunoassays, paper device fabrication using wax-printing and laser cutting technology, and mass spectrometry analyses.
Raman Spectroscopic Imaging and Trace Detection
The Schultz lab is interested in developing Raman spectroscopy for the identification of chemical species. Applications range from identifying chemicals in living plants to identifying chemical changes in cells and tissue resulting from exposure to radiation. We are also interested in understanding spatially resolved chemical profiles related to biological activity and are actively developing new methods to image molecular properties.
Molecular Biology & Enzymes
The Jackman lab investigates the biochemical mechanisms of enzymes that catalyze key reactions during the maturation of the critical non-coding RNA molecule, tRNA. We study enzyme that utilize unusual chemistry for biological reactions, and use the tools of mechanistic enzymology (kinetics, protein engineering, biophysical structural approaches) combined with the power of model organism genetics to make new discoveries about the molecular mechanisms and biological functions of these unusual enzymes in living cells.
Christopher Jaroniec – Structural and Dynamic Studies of Protein and Protein-DNA Assemblies – see below in Physical Chemistry
The Magliery lab does work in protein folding and protein engineering. We study the sequence basis of protein stability and other physical properties using high-throughput, statistical, and rational approaches. Summer students could participate in fundamental studies in protein stability or in applied protein engineering for diagnostic or therapeutic purposes, such as antibody fragment engineering.
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.
Peptide Chemical Biology
The student will be involved in the synthesis, purification, and biochemical/cellular characterization of peptides for cell penetration and/or protein binding.
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 both the activation of naturally abundant small molecules (e.g. carbon dioxide, water, oxygen) 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.
Inorganic Materials and Catalysis
Research in the Wade Lab combines molecular inorganic/organometallic chemistry and materials science. Current projects involve the design of bio-inspired metal-organic frameworks (MOFs) for direct air capture of CO2 capture, small molecule activation, and catalytic C–H functionalization of organic molecules. Students will gain experience in the synthesis and characterization of new transition metal complexes and MOFs. Synthesis plays a central role in our research program, and a variety of solution and solid-state characterization techniques are used to elucidate the structure and properties of newly synthesized materials. These include X-ray diffraction, gas porosimetry, thermogravimetric analysis, cyclic voltammetry, and NMR, IR, and UV-Vis spectroscopies.
Solar Energy and Batteries
The research in Yiying Wu’s group focuses on functional materials for energy conversion and storage. The projects include developing solid and liquid electrolytes for Li and K batteries, photoelectrochemistry of semiconductors for solar fuels, and organic-inorganic hybrid materials for quantum materials and spintronics. The students will participate in the design and synthesis of these materials, their structural characterization, and measurements of their properties.
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.
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.
Research in the McGrier group focuses on utilizing novel synthetic methods to create functional porous and polymeric materials that can be useful for energy storage, chemical sensing, and catalytic applications. Research in the group relies mostly on organic synthesis with a strong focus on utilizing organic spectroscopy (i.e., NMR, IR, and UV-Vis), powder x-ray diffraction, and molecular modeling to characterize and understand the electronic and catalytic properties of our materials.
Material Science and NMR
Undergraduate students working with Professor Grandinetti will apply multi-dimensional NMR spectroscopy and machine learning to extract structural distributions in glasses. These distributions reveal details on modifier cation clustering, ionic transport, the mixed alkali effect, chemical strengthening, and phase separation in glasses. Such insights help glass scientists and engineers working on the next generation of specialty glasses, impacting diverse applications such as handheld electronic devices, displays, optical fibers, glass substrates for lighting, bio-glass implants, and nuclear waste storage.
Computational Chemistry and Theory
The Herbert group works on the development of novel quantum chemistry methods, algorithms, and software. Summer projects include exploration of non-covalent interactions in ligand-protein binding with application to developing high-throughput methods for computational drug discovery.
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.
Ultrafast Laser Spectroscopy
The Kohler Group has projects for undergraduates interested in physical chemistry, materials chemistry and nanoscience. Specifically, the group uses time-resolved spectroscopy to study biological and bioinspired molecules and materials. The ubiquitous melanin pigments have desirable optoelectronic properties that are difficult to mimic because the atomistic structure of melanin is unknown. An undergraduate researcher is needed to study supramolecular structure formation in synthetic melanins using fluorescence. In a second project, an undergraduate researcher will measure the formation of reactive oxygen species (ROS) generated when DNA or melanin nanoparticles are irradiated by light.
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.
For additional information on research in Mathematics, see:
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 elementary methods to verify the RH for the first few Riemann zeros. 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.
Since the 1970’s financial mathematics has incorporated advanced tools from stochastic calculus to help investors make better decisions. Stochastic calculus is the study of functions of a random process, like that of the price of a share of stock. We can use stochastic calculus to help solve optimization problems when considering assets whose values are random processes. In this project, we will learn some of these tools and apply them to a novel problem. Some coursework in economics or finance and a mathematical background in probability, analysis, and differential equations is preferred. Past undergraduate students and a brief description of their projects can be found here.
For additional information on research in Microbiology, see:
Natural Products Drug Discovery
The Ju lab integrates genomic, metabolomic, biochemical, and genetic methods to accelerate discovery of new microbial natural products and the mechanisms of their biosynthesis. Summer students will employ a combination of these techniques to reveal new chemical diversity encoded within microbial genomes important for drug discovery.
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.
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.
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.
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.
For additional information on research in Physics, see:
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.
Atomic-Resolution Imaging of Surfaces
The Gupta lab specializes in scanning tunneling microscopy studies of material surfaces. Summer research projects will involve helping prepare nanomaterial surfaces for STM imaging, including 2D materials, semiconductors, and magnetic materials. Summer students will learn about ultrahigh vacuum equipment such as ion pumps, vacuum chambers and surface characterization methods such as Auger Electron Spectroscopy and Low Energy Electron Diffraction. Summer students will work as part of a team with 1-2 other graduate students and 1-2 undergraduate students.
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.
For additional information on research in Public Health, see:
Selection Criteria in Linear Mixed Models
Analyzing longitudinal or repeated measures data using linear mixed-effects models offers flexibility through the incorporation of random effects, at the cost of relying on the proper specification of these effects and their distribution. Such specification can be particularly challenging when dealing with non-normal characteristics like skewness and heavy tails. This project aims to explore the use of alternative definitions of the Bayesian Information Criterion on the selection of fixed effects, random effects, and the distribution of random variables. The student will learn about selection criteria in mixed-effects models and perform simulation studies in R to explore their performance under different settings.
Public Health Implications of Natural Disasters
Dr. Hufton’s research is focused on physical, mental, and cognitive health outcomes among populations affected by natural disasters and environmental hazards. She is particularly interested in how social determinants of health and repeated exposure to natural disasters affect the risk of disease, and how these associations vary by race, ethnicity and nativity. Current projects include evaluating the influence of natural disaster exposure on health outcomes in older Mexican Americans; and examining the temporal and spatial distribution of injuries related to natural hazards in Galveston, Texas. For a summer project, students may engage in data management, data analyses, literature reviews for manuscript development, and regular research team meetings.
Racial and Socio-Economic Disparities in Psychiatric Care and Outcomes
I study how ambient or macro-social phenomena (such as economic recessions) and policy or programmatic changes (e.g. new health or social policy, cash transfers) impact mental health outcomes in a population. I am particularly interested in how these exposures influence racial and socio-economic disparities in psychiatric services utilization, deaths of despair (suicides, overdose, alcohol use-related mortality). Some of my key research findings thus far include the following: (1) populations, on average, increase risk-averse behaviors during ‘difficult’ times (e.g. during economic recessions), but these aggregate trends mask increased adverse psychiatric outcomes among vulnerable groups (such as low-income children and racial minorities), (2) improved socio-economic status in vulnerable groups (e.g. American Indian/Alaska Native) corresponds with increased optimism about the future, and (3) populations under stress exhibit scapegoating behavior where they target racial minorities for socially sanctioned micro-aggressions (e.g. involuntary psychiatric commitments).
For additional information on research in Statistics, see:
Bayesian model selection
Linear models with categorical predictors are a common and popular modeling approach. However, in many cases, the relationship between the categorical predictor and the response variable can be more complex than traditional methods account for; specifically, we consider the context where latent groups are formed within the levels of a categorical predictor, and these groups govern the regression effects and/or error variance. With our R package slgf, we use Bayesian model selection methodology to detect these latent groups and quantify the posterior probability associated with candidate models. We have striven to make this package accessible to practitioners by allowing the user to specify a set of candidate models, the prior on regression effects, and the structure of the unequal error variance. Participating students will work to develop an R Shiny app to facilitate the user experience of this R package, focusing on creating effective data visualizations and procuring canonical data examples to serve as illustrations of the package’s utility. Students will also obtain a foundational understanding of Bayesian model selection and its computational challenges. Students with some experience coding in R are encouraged to apply.
Tobacco Center of Regulatory Science (Public Health/Medicine)
For additional information on research in the TCORS, see:
Ahmad El Hellani and Theodore Wagener
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
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.
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
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.