Summer 2025 Project Descriptions
(in alphabetical order by PI last name)
Flynt Lab: Research in the Flynt lab broadly investigates the role of RNA biology in post-transcriptional gene regulation. Projects are focused on the biogenesis and function of non-coding, small regulatory RNAs. These molecules are most famously known as the effectors of RNAi and fall into distinct classes that vary by maturation pathway and function. To study these molecules the Flynt lab takes a multidisciplinary approach that combines genetics, biochemistry, and bioinformatics. A major emphasis in the Flynt lab is using transcriptomics to gain insights into the production and function of small RNAs. This includes developing software to analyze high throughput data that leverages artificial intelligence and other methods to characterize classes of RNAs and novel processing events. The Flynt lab’s goal is to translate these insights into genetic technology for clinical and biotechnology applications. To this end, projects involve collaboration with diverse disciplines such as material scientists and cancer biologists. Students in the Flynt lab will gain expertise in computing biological data in high performance cluster environments, recombinant DNA technologies, using animal models for genetic experiments, and advanced microscopy.
Hua Lab: The Vision Laboratory offers undergraduate researchers an opportunity to explore the fundamental biomechanical and hemodynamic principles shaping the behavior of the optic nerve head under diverse physiological and pathological conditions. Projects include investigating the effects of elevated intracranial pressure on the optic nerve head during spaceflight, studying the delicate balance between intraocular and intracranial pressures in glaucoma, and examining how the elongation of the eye in myopia influences the structural and functional integrity of ocular tissues. Participants will also develop and validate computational models to understand the mechanical interactions between blast waves and ocular tissues, providing insights into trauma mechanics. By combining cutting-edge experimental techniques with computational modeling, this program seeks to uncover the fundamental nanoscale and biomechanical processes that drive ocular function and adaptation, equipping students with a strong foundation in nanoengineering and its applications to complex biological systems.
Li Lab: The Li lab is dedicated to unraveling sequence-structure-dynamics-function relationship of membrane proteins using cutting-edge computational chemistry and biology approaches. Our primary focus lies in investigating how missense mutations in ion channels can instigate protein dysfunction, ultimately contributing to the development of various diseases. The profound impact of disease-associated mutations in ion channels usually hinges on the dynamic structural transitions occurring within these proteins. To gain a comprehensive understanding of the pathophysiological consequences driven by these mutations, it is imperative to scrutinize the atomic-level alterations they induce in structural dynamics. The REU student will learn to employ a combination of bioinformatics and molecular dynamics (MD) simulations to probe the effects of specific mutations on the structural transitions within ion channels. Beginning with a literature meta-analysis and in-depth protein sequence analysis, the REU student will skillfully map the most up-to-date genetic data, pinpointing critical mutation hotspots. Subsequently, they will adeptly construct all-atom simulation systems for both the wild-type protein and its mutant counterparts using advanced molecular modeling techniques. Extensive MD simulations will be meticulously executed to shed light on how these mutations influence pivotal channel functions. Analyzing these MD trajectories will offer insights into the molecular mechanisms underlying mutation-driven phenotypes, thereby providing a foundation for designing drugs tailored to treat these diseases.
Maniruzzaman Lab: Work in PharmE3D Lab led by Dr Maniruzzaman, focuses on 3D/4D printing of biologics and mRNA, Artificial Intelligence (AI)/Machine Learning (ML) powered drug development, and medical robotics. Additional projects focus on 3D bioprinting of scaffolds and smart medical implants as well as pharmaceutical process engineering and continuous manufacturing to make medicines for efficient and affordable. We have several ongoing projects in the lab in one of the following areas: (i) next generation platform technologies (i.e., SMART, MAGiC and MeET) for the delivery of biologics, vaccines and mRNA therapeutics; (ii) microbial based drug delivery systems (bugs as drugs) – novel delivery platform with bioengineered microbes which can produce therapeutics on demand; (iii) 3D/4D bioprinting of novel biomaterials for tissue engineering applications; (iv) continuous manufacturing and process engineering of pharmaceuticals/ medical devices and innovative 3D printing technologies for pharmaceutical dosage forms; and (v) AI/ML powered self-driving labs for accelerating drug discovery, development and delivery processes.
Mishra Lab: Molecular interactions between biomolecules play a key role in governing life. Deciphering the underlying principles behind biomolecular interactions is crucial for understanding biological processes and developing therapeutics. The Biomolecular Simulation Lab (BioSim) focuses on studying biomolecular interactions, particularity protein-glycan interactions, using advanced computational methods such as atomistic simulations, enhanced-sampling, binding-free energy calculations, and machine learning (ML) approaches to translate findings into therapeutic advancements. The lab uses high-performance computing and GPU computing and enhances sampling methods to accelerate atomistic simulations, enabling us to study phenomena of microseconds timescales for biological systems up to a few million atoms. Under the guidance of Dr. Mishra, REU student will learn and apply molecular dynamics (MD) simulations to study nanoparticles at the atomic scale, an essential area in nanotechnology and biomedical research. The student will first gain experience in building atomic models of the nanoparticles, setting up coarse-grain MD simulations, and running molecular dynamics simulation in supercomputers. Through this project, student will develop skills in MD simulations (all-atom, coarse grain), studying the structure and properties of nanoparticles, and gain first-hand experience in high performance computing for research.
Prager Lab: Dr. Prager’s present research primarily involves the development of novel, cellulose-based materials for food packaging applications. Her research group has completed several unique studies exploiting the supercritical impregnation of food-grade wax-based solutes into paper substrates, providing a substantial hydrophobic improvement into the sticky hydrophobic range (contact angle > 140o). Various exploration areas within this project have focused on optimizing the quantity of alkyl ketene dimer (AKD) impregnated into the paper; performing cloud-point solubility measurements of AKD and vegetable wax for future impregnation efforts; developing thermodynamic solubility models from this work; measuring the surface energy changes resulting from the impregnation; understanding the morphology of the resulting paper; and taking mechanical measurements to test the robustness of the material. Her other main focus is on traditional paper coating methods using the nanoadditives cellulose nanocrystal (CNC) and cellulose nanofiber (CNF). Both these additives have shown substantial improvement in the thermal barrier achieved upon coating the formulation onto paper. Various optimization studies to assess the colloidal properties, and mechanical analyses, have also been performed with this work. She is presently investigating the interfacial kinetics of AKD attaching onto cellulose biopolymers using a quartz crystal microbalance (QCM-D), and is discovering unique characteristics at the molecular level.
Reinemann Lab: The Molecular Biophysics and Engineering Lab aims to understand the fundamental design rules of life by exploring how cells achieve complex tasks through the interaction of their structural systems. One key focus is studying the cytoskeleton, which provides structural support and enables vital activities like cell division and movement. The two main components of the cytoskeleton—actin filaments and microtubules (MTs)—are essential for cell growth and division, yet they are typically researched separately. In reality, actin and MTs interact at the nanoscale through motor proteins and crosslinkers, allowing communication between these systems that drives coordinated cellular behavior. The lab seeks to uncover how these separate cytoskeletal systems “talk” to each other and work together, and it also explores the idea that when cytoskeletal proteins work in groups, they can exhibit new behaviors that don’t simply add up from the behavior of individual proteins. The REU student in this lab, guided by Dr. Reinemann and a graduate student mentor, will help investigate these mechanisms by engineering and studying synthetic “nanocells.” These are nanoscale structures that mimic the organization of a cell’s cytoskeleton. In this project, the student will learn basic lab skills and build microscopy setups, starting with flow cells to study how actin and MT filaments assemble. Using fluorescence microscopy, they will confirm the formation of these filaments and then construct a custom nanocell. They will measure its mechanical properties using OT and a quartz crystal microbalance with dissipation monitoring (QCM-D) and analyze the data in Matlab. Through these experiments, the student will contribute to understanding how molecular-level interactions scale up to enable the complex processes essential for life.
Smith Lab: The Smith lab utilizes controlled radical polymerization (CRP) to synthesize stimuli-responsive block copolymers (BCPs) for the targeted delivery of nucleic acid (NA) therapeutics. The intravenous delivery of small interfering RNA (siRNA) is hampered by the rapid degradation of naked nucleic acids during circulation. As CRP techniques and facile conjugation chemistries have developed over the past two decades, polymer chemists now have tremendous control over polymer properties, enabling the rational design of polymeric NA delivery vehicles. Reversible addition-fragmentation chain transfer (RAFT) polymerization is arguably the most suitable CRP technique for preparing delivery vehicles for use in biological fluids.[50] Moreover, there is increasing interest in the controlled polymerization of monomers with latent reactive functionality, e.g. 2-vinyl-4,4-dimethylazlactone (VDMA), to modify the polymer or BCP. Such modifications enable synthesis of polymers with wide-ranging functionality from a single precursor, eliminating complications in synthesizing polymers of disparate functionality while maintaining constant polymer lengths. The REU student will synthesize BCPs of poly(ethylene glycol) (PEG) and VDMA. The synthesized BCPs will undergo post-polymerization modification with 2-(dimethylamino)ethanol and N,N-dimethylethylenediamine to yield BCPs with hydrolyzable, “charge reversing” side chains and analogous BCPs with hydrolytically-stable side cationic chains. The UG will characterize the BCPs via 1H NMR spectroscopy and gel permeation chromatography to determine the composition, molecular weight, and polydispersity of the BCPs and utilize agarose gel electrophoresis, dynamic light scattering, and spectrophotometry to examine how BCPs form stable polyplexes with siRNA and protect the nucleic acid payload from nuclease degradation.
Tanner Lab: The Tanner lab seeks to solve outstanding bioengineering research questions using a chemistry framework, where an understanding of the molecular interactions within the delivery system allows the development of predictive frameworks and task-specific solvent design. Ionic liquids, consisting of a bulky, asymmetric cation and an anion, have attracted significant interest in a broad range of applications, including catalysis and energy applications, due to their favorable properties, including non-volatility, recyclability, and their inherent tuneability whereby the anion and cation can be altered to change the physicochemical properties of the material. A range of common cations and anions are shown in the picture to the right. By synthesizing the ionic liquids with biocompatible or bioinspired starting materials, they can be employed in biological contexts. Because changing the structure of the ionic components results in changes to their their biologically relevant properties, including interactions with bio-interfaces, biomolecules and pharmaceutical ingredients, they can be tuned to solve a variety of problems.
Werfel Lab: Cancer immunotherapies such as immune checkpoint inhibitors (ICIs) are revolutionizing cancer therapy. However, only a portion of patients benefit from ICIs and many patients cannot complete treatments due to severe, life-threatening side effects. Our lab develops polymeric nanoparticles which can encapsulate immunomodulatory agents and target the delivery of these agents to immune cells to boost immunogenicity and treatment responses. This work sits at the interface of nanotechnology and cancer immunology, leveraging approaches in nanoparticle synthesis, characterization, and drug delivery; nano-bio interactions; and cellular/molecular biology. The Werfel Lab will support one REU student to produce polymeric nanoparticles with “sheddable” coronas for improved targeting of tumor-specific innate immune cells. These nanoparticles will be composed of two BCPs – one with a glucopyranose-based corona which is shed in reducing environments (e.g. tumor microenvironment) to unveil a hidden targeting ligand, methacrylamidomannose for macrophage-specific targeting in tumors. The REU student will perform synthesis of the BCPs making up these nanoparticles, followed by characterization of the BCPs for molecular weight and composition via 1H-NMR, GPC, and FT-IR. Next, the student will confirm that the glucopyranse polymer block (linked via a disulfide bond) can be removed in reducing conditions using glutathione and measuring polymer degradation by 1H-NMR (to view compositional changes) and GPC (to view change in molecular weight). Lastly, the student will produce nanoparticles composed of both BCPs; characterize the size, morphology, and surface charge of the nanoparticles via light scattering and electron microscopy; and monitor the “shedding” of glucopyranose coronas by monitoring size and morphology changes upon addition of glutathione. These studies will position the REU student for a publication in a drug delivery-focused journal and position our research group to deliver tumor macrophage-specific therapies with improved therapeutic windows in future work.
Xu Lab: The PiezoX Lab, led by Dr. Xu, focuses on developing human-machine interaction systems using high-performance flexible piezoelectric materials. The interdisciplinary research in the lab covers the synthesis of piezoelectric composites and micro/nanoparticles, the design of bio-inspired structures, and the development of flexible devices for bio-sensing and energy harvesting. The REU student will contribute to one of our ongoing research projects: (i) flexible piezoelectric metamaterials synthesis, (ii) implantable energy-harvesting devices for cardiovascular medical devices, (iii) smart multi-directional load sensing system for orthopedics, (iv) wearable sensor array for Dysphagia. Under the guidance of Dr. Xu, the REU student will gain hands-on experience in designing, fabricating, and testing materials and device structures using various tools and techniques. The student will also investigate the relationship between material structures and their mechanical properties and apply the devices developed in the lab to address real-world challenges.