2026 Biophysics Summer REU

Mentor: Hugo Sanabria, Ph.D., physics and astronomy, medical biophysics graduate program

Significance: The actin cytoskeleton plays a major role in determining the mechanical strength of cells, especially in structures such as dendritic spines, where actin is constantly remodeled. These dynamic changes create a complex environment with both viscous and elastic behavior, yet the mechanical pathways that govern how actin networks respond to stress are still not well understood. Recent evidence suggests that actin networks can exhibit structural memory, where previous mechanical or biochemical states influence future organization and responsiveness. This phenomenon is thought to be essential for maintaining dendritic spine morphology and supporting synaptic plasticity, which underlies learning and memory in neurons. Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) is a key regulator of actin dynamics through its ability to bind and crosslink filaments, potentially reinforcing or modulating this memory effect. The participant will employ experimental and imaging-based approaches to investigate how CaMKII affects the mechanical properties and structural memory of actin networks, thereby contributing to a deeper understanding of how molecular interactions influence cellular structure and function.

Research plan: The student will examine how actin filaments and actin-binding proteins affect the mechanical behavior of complex fluids using passive and active microrheology. They will prepare samples containing actin networks mixed with microspheres and use particle tracking to measure the motion of the beads and extract their viscoelastic properties. In active microrheology, the student will use an optical tweezer system to apply small forces to individual beads and analyze their responses. By comparing actin alone with networks cross-linked by proteins such as CaMKII, α-actinin, and fascin, the goal is to determine how each protein alters stiffness and particle mobility.

Equipment/techniques participants will learn and use: Optical tweezers, laser alignment, TIRF microscopy, particle-tracking analysis, LabVIEW, microrheology, actin solutions, microfluidics.

Mentor: Delphine Dean, Ph.D., bioengineering

Significance: Recent research suggests that low levels of radiation are not necessarily harmful to cells. However, the underlying physical, chemical and biological pathways that take place during low-dose irradiation remain largely unstudied. The participant will use combinations of experimental approaches to characterize the effect of ionizing radiation on cells and subcellular components contributing to the understanding of how low levels of radiation affect individual biological machinery in cells.

Research plan: The selected participant will study the interaction between low levels of monochromatic soft X-ray radiation and biological tissues. The participating students will grow breast cells and characterize their properties in response to radiation and radiosensitizing materials using various biological assays. The goal is to precisely quantify the radiation that cell cultures receive and use well-defined protocols to understand how low levels of radiation affect individual biological machinery in cells and cell cultures.

Equipment/techniques participants will learn and use: Mini-X-ray tubes, solid-state X-ray detectors, single-photon counters, spectral analysis, statistical analysis software, cell culture, optical microscopy and image analysis, cell proliferation and cycle analysis, cell function, and differentiation assays.

Mentors: David Dunlap, Ph.D., and Laura Finzi, Ph.D., physics and astronomy, medical biophysics graduate program

Significance: Liquid-liquid phase separation is a viable, less energetically costly alternative to membrane-enclosed compartments and is emerging as the underlying mechanism for the regulation of many cellular processes. LLPS gives origin to “(biomolecular)condensates,” separate liquid droplets, containing specific subsets of proteins or nucleic acids-protein complexes. Understanding how the viscoelastic properties of such droplets affect the dynamic properties of the molecules therein, modulate exchange of material with the exterior and drive cellular processes, such as transcription, is important to understand cellular regulation.

Research plan: The selected participant will prepare condensates of relevant DNA sequences and proteins with or without a fluorescent label, measure their viscoelastic properties using single particle tracking and the force involved in the compaction of DNA within the condensate. Then, transcription through condensates by single RNA polymerase motors will be measured and data analyzed to understand the role of condensates in gene regulation.

Equipment/techniques participants will learn and use: We will use atomic force microscopy, magnetic and/or optical tweezers and single molecule fluorescence microscopy. These are powerful and complementary single-molecule techniques that, avoiding the in-bulk ensemble averaging, reveal subpopulations of behavior that are responsible for emerging cellular behavior.

Mentors: Meredith Morris (cell biology, imaging), Ph.D., genetics and biochemistry, and James Morris (genetics), Ph.D., genetics and biochemistry

Significance: Analysis of the genome of the so called “brain-eating amoeba,” Naegleria folweri, has revealed the conservation of many of the proteins involved in the biosynthesis of peroxisomes, essential organelles that play a role in the metabolism of fatty acids and detoxification of reactive oxygen species. However, homologs to two key proteins involved in protein import into the organelle, PEX 13 and PEX 14, are not obvious, suggesting that the pathogen uses mechanisms different from other organisms that could be targeted for drug development. Participants will use informatic and newly developed genetic tools to identify the proteins that serve the functions of PEX 13 and 14. Findings from this research will lead to new candidates for therapeutic intervention.

Research plan: Two participants will collaborate on this project to identify the PEX 13 and 14 homologs. One student, working primarily with Meredith Morris, will generate candidate gene lists through informatics approaches and generate DNA constructs to express tagged versions of the proteins in Naegleria for co-localization and co-fractionation studies with markers of peroxisomes. The other student, working with James Morris, will generate molecular tools for affinity purification of peroxisomes from amoebae and then complete the isolation of these organelles for proteomic analysis. We anticipate establishing a comprehensive list of peroxisome-associated proteins, including the PEX 13 and 14 functional homologs identified by their partner.

Equipment/techniques participants will learn and use: Gene cloning, immunofluorescence, cytometry, cell fractionation approaches, protein purification, and cell husbandry.

Mentor: Sheng Liu, Ph.D., biophysics

Significance: A spatial light modulator is widely used in microscopy for aberration correction and structured illumination. In my research, one application of SLM is generating a donut excitation beam in a custom-built single-particle tracking microscope. The developed SPT microscope will be used for studying protein interactions at the cell membrane. These interactions are critical in triggering various cellular signaling pathways that regulate essential cell functions. Mutations of these membrane proteins are frequently associated with various diseases.

Research plan: The student will design and build a calibration path for an SLM using the methods in this paper: M. Siemons, et. al., “High precision wavefront control in point spread function engineering for single emitter localization,” Opt. Express, 2018. The student will also use the calibrated SLM to generate a donut beam pattern and quantify the beam shape.

Equipment/techniques participants will learn and use: A spatial light modulator, lasers, cameras, optical system design and alignment, instrument control, simulation of optical systems, programming in Julia, and CAD design in Inventor.

Mentor: David Jacobson, Ph.D., chemistry

Significance: Membrane proteins perform essential functions in metabolism, transport, and signaling, yet understanding how they fold into their functional structures remains a major challenge in biology. The topology of a membrane protein—the orientation of its helices relative to the membrane—is crucial for its function and is thought to be governed by electrostatic interactions between charged amino acid residues and lipid headgroups, as described by the "positive-inside rule." However, the energetic basis of topology formation has never been directly measured. This project will use the lactose permease as a model system because it is known to adopt different topological orientations depending on lipid composition. By quantifying how lipid-protein interactions influence the stability of different protein regions, this work will provide fundamental insights into membrane protein folding mechanisms with implications for understanding protein homeostasis, cellular quality control, and rational design of membrane proteins.

Research plan: Under the mentorship of a graduate student engaged in larger-scale studies of LacY, the student will use atomic force microscopy-based single-molecule force spectroscopy to probe the mechanical stability of different regions of LacY reconstituted into supported lipid bilayers of controlled composition. The student will prepare supported lipid bilayers on mica substrates composed of either anionic phosphatidylglycerol or mixed POPG/POPE lipids, deposit LacY-containing proteoliposomes onto these substrates, and conduct SMFS unfolding experiments using chemically modified cantilevers and site-specific protein attachment chemistry. By analyzing force-extension curves from proteins in different lipid environments, the student will identify regions of the protein that exhibit lipid-dependent stability changes. These measurements will provide quantitative data on how electrostatic interactions with lipid headgroups influence membrane protein topology formation.

Equipment/techniques participants will learn and use: Expression and purification of proteins; chemical functionalization of surfaces; mechanical unfolding experiments using an atomic force microscope ; analysis of single-molecule data using biophysical theory; computer coding in Igor Pro, Matlab, and/or Python.

Mentor: Andrew Jezewski, Ph.D., genetics and biochemistry

Significance: Cryptococcus neoformans is a deadly fungal pathogen responsible for over 180,000 deaths annually from cryptococcal meningitis, particularly in immunocompromised individuals. Its survival in the human host hinges on tolerating elevated CO2 levels, which trigger profound metabolic shifts involving several metabolic enzymes. However, the biophysical underpinnings, such as enzyme conformational dynamics, binding affinities, and localization under CO2 stress remain unexplored.

Research plan: This project will investigate how CO2 modulates the expression, localization, structural and functional properties of metabolic enzymes required for CO2 tolerance and virulence in C. neoformans, bridging cellular biology and biochemistry with biophysical tools to uncover mechanisms that could inspire structure guided antifungal drug target development. REU participants will measure enzyme localization and post-translational modifications of target enzymes via blotting techniques and purify enzymes under varying CO2 conditions to assess their biochemical properties using techniques that include enzyme activity assays and mass-photometry.

Equipment/techniques participants will learn and use: Microscopy, fungal genetics, protein purification, enzyme kinetics, mass-photometry, and standard molecular and cell biology techniques.

Mentors: Stephen Dolan, Ph.D., Department of Genetics and Biochemistry, and Laura Finzi, Ph.D., Department of Physics and Astronomy

Significance: Microbial communities constantly engage in competition and communication, shaping their physiology through chemical, metabolic, and ecological interactions. In chronic infection environments, these interkingdom interactions influence microbial survival, stress tolerance, and the evolution of traits linked to persistence. A central challenge in microbiology is understanding how bacteria sense chemical signals produced by neighboring species and reconfigure their regulatory and metabolic machinery in response. Our recent work highlights a newly identified stress-response module involving the transcription factor DnoR and its associated detoxifying enzyme DnoP, which together form part of a bacterial defense system activated during antagonistic encounters with fungal competitors. Despite their importance, the molecular mechanisms governing DnoR–DnoP function, activation, and downstream physiological remodeling remain poorly understood. This project integrates genetic, biochemical, and single-molecule biophysics approaches to illuminate how microbial interactions drive adaptive responses in complex communities.

Research plan: Participants will investigate how chemical cues from competing microbes activate the DnoR–DnoP regulatory pathway and reshape cellular stress responses. Students will use CRISPR-based genetics to generate mutants in DnoR, DnoP, and related stress-response genes, and will characterize their behavior in microbial co-culture systems that mimic competitive ecological environments. Through fluorescent reporter assays, enzyme activity measurements, and time-lapse imaging, participants will quantify changes in redox balance, membrane integrity, and growth phenotypes. In collaboration with the Finzi Lab, students will apply single-molecule microscopy and biophysical assays to measure DnoR-DNA binding dynamics and determine how environmental stressors influence transcriptional regulation at the molecular level. Together, these experiments will help define how interkingdom chemical interactions drive adaptive remodeling in bacteria and reveal the mechanistic roles of DnoR and DnoP in these processes.

Equipment/techniques participants will learn and use: Time-lapse fluorescent microscopy, microbial culture and co-culture assays, CRISPR-based gene editing, enzyme and stress-response assays, quantitative image analysis, protein-DNA interaction assays, single-molecule biophysics, and core molecular microbiology methods.

Mentor: Feng Ding, Ph.D., Department of Physics and Astronomy

Significance: Deposition of amyloid aggregates is a hallmark of Alzheimer’s disease and many other neurodegenerative disorders. Experimental and clinical evidence point to aggregation of beta-amyloid and related peptides, especially their small oligomeric intermediates, as a key driver of cytotoxicity. However, many antibody-based strategies aimed at clearing amyloid plaques have not yielded effective cures, underscoring critical gaps in our molecular understanding of how proteins misfold and assemble into toxic species. This project will focus on uncovering the molecular mechanisms of amyloid aggregation and how endogenous proteins, peptide inhibitors, and engineered nanomaterials can alter aggregation pathways and mitigate toxicity.

Research plan: The student will work in the Ding Lab to perform multiscale molecular dynamics simulations of amyloid-forming peptides and their interactions with candidate anti-amyloid agents. Using coarse-grained and all-atom models on the Palmetto supercomputer, the participant will (i) characterize early aggregation pathways and oligomer structures, (ii) probe how molecular chaperones, designed peptide inhibitors, and nanoparticles modulate these pathways, and (iii) identify structural and energetic signatures associated with reduced aggregation or destabilization of toxic oligomers. Simulation results will be analyzed to generate mechanistic hypotheses that can be compared with ongoing experimental studies in collaborating labs, ultimately guiding strategies to mitigate amyloid aggregation and toxicity.

Equipment/techniques participants will learn and use: Linux systems, Palmetto supercomputer programming, molecular dynamics simulations (coarse-grained and all-atom), basic scripting for job submission and data analysis, and quantitative analysis and visualization of biomolecular simulation trajectories.

Mentor: Ramakrishna Podila, Ph.D., Department Physics and Astronomy

Significance: Biomarker panel measurements, rather than single-marker detection, are rapidly becoming the gold standard for diagnosing complex diseases such as chronic kidney disease. However, current multimarker biosensing platforms require large instrumentation and often lack real-time signal integration. Graphene field-effect transistors combined with size-tunable colloidal quantum dots offer a unique opportunity to overcome this challenge. Our previous studies (e.g., biosensors 15 (5), 269) have shown that photoluminescence quenching and recovery in graphene–QD hybrids enable femtomolar detection sensitivity without lifetime changes. By leveraging this physical mechanism, multiple biomolecular interactions can be simultaneously resolved both electrically and optically, establishing a pathway toward compact, multiplexed biosensing systems suitable for future wearable applications.

Research plan: The selected participant will fabricate a multimarker biosensor by integrating graphene-based FET channels with differently sized CdSe quantum dots, each functionalized with a disease-relevant antibody (e.g., NGAL, KIM-1, and cystatin C). Due to quantum confinement, each QD size emits a distinct fluorescence color, providing a color-coded optical signature for each biomarker. Electrical readouts combined with color-coded optical spectrum will be employed for ultrasensitive multimarker detection in a single-shot. The student will (1) synthesize and functionalize size-controlled QDs, (2) assemble QD–GFET hybrid sensors, (3) perform fluorescence and electrical measurements for multimarker detection, and (4) evaluate strategies for transitioning this platform toward wearable sensing architectures such as flexible GFET arrays integrated with microfluidic sampling, inspired by emerging technologies in 2D-material wearables.

Equipment/techniques participants will learn and use: Graphene field-effect transistor fabrication and operation, colloidal QD synthesis and surface functionalization, fluorescence microscopy and spectroscopy, electrical transport measurements, surface biofunctionalization protocols, device integration on flexible substrates, and statistical analysis of multimarker biosensing data.