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Research

Biophysics Summer REU

physics-bio-reu-lead.jpgExplore nature’s machinery through the prism of physics, biology, chemistry and engineering! The Research Experience for Undergraduates Program in Biophysics is funded by the National Science Foundation to support 10 highly qualified students to undertake interdisciplinary, supervised research projects at Clemson University, for a period of 10 weeks each summer. The summer 2022 REU program runs from May 23 – July 29, 2022. Move-in is at least one day before the start date, and move-out is one day after the end date.

Program participants work with faculty members, postdocs, graduate students, other undergrads and each other on collaborative research projects about nature’s machinery. Participants are paired in teams of two to carry out independent but highly collaborative research under the guidance of two faculty mentors, each from a different discipline. The projects are designed to give participants a sense of the contributions that physical scientists can make to biological problems and the contributions that biologists can make to physical problems. The focus is on cross-disciplinary training.

The program includes a weeklong biophysics boot camp, a biophysics seminar series, a research tools workshop, a professional development workshop, a journal club, off-campus field trips and social activities. Program participants regularly present their research to and hear about the research conducted by, their peers. By the end of the program, participants present their projects at a University-wide summer research symposium, draft a research article manuscript, and are encouraged to present their work at relevant scientific conferences. Participants also participate in outreach activities throughout the summer.

This program is highly interdisciplinary and collaborative. Students in the program will get the opportunity to work with faculty and students from the Department of Biological Sciences, the Department of Genetics and Biochemistry, bioengineering, the Department of Physics and Astronomy, the Department of Chemistry and the Department of Materials Science and Engineering. Additionally, students will interact with participants in the other summer REU sites on campus.

 

You Can Join the Summer REU

Eligibility

No research experience is necessary to apply, but a participant must meet the following requirements:

  • Have completed at least two semesters of college-level physical science/engineering or biological science/engineering by the start of the program in May 2022.
  • Be enrolled as an undergraduate at a two- or four-year institute of higher learning at the time of application.
  • Have an expected graduation date (earning a bachelor’s or associate’s degree) on or after December 2022. Students who have completed their bachelor’s degree are not eligible.
  • Have an overall GPA of 3.2 or greater.
  • Major in natural science (biological or physical science) or engineering.
  • Attend all 10 weeks of the program (May 23 – July 29, 2022).
  • Be a U.S. citizen or permanent resident.
  • Provide a ranked list of five preferred mentors (mentor list is below in the Projects area).

Stipend and Housing

Student in lab at microscope.Participants receive a stipend of $5,750 for the 10-week program.

Participants receive on-campus housing in a residence hall with other REU students and a meal plan/supplemental compensation for meals. Accommodations will be made for students living locally. Participants receive reimbursement for travel expenses for their move to and from Clemson.

How to Apply

As part of the application process, students will need to submit a transcript, CV and contact information for two faculty to write letters of recommendation, as well as a statement of purpose and statements summarizing research experience, if any. No research experience is necessary to apply. Instructions for submitting these materials will be provided within the online application.

Application deadline: Feb. 3, 2022

Application: NSF Education and Training Application

Questions? For questions regarding the Clemson University Biophysics REU program, contact
Celeste Hackett, undergraduate student services coordinator, at 864-656-3418. Or, email her using the button, below. 

Projects and Mentors

The Clemson REU Program: Nature’s machinery through the prism of physics, biology, chemistry and engineering has mentors in physics, chemistry, materials science, bioengineering, genetics and biochemistry, and biology. All mentors have extensive experience in supervising undergraduate research students. Participants will work in pairs within a dynamic research team led by two principal investigators to:

  • Design and conduct experiments.

  • Use modern research equipment.

  • Learn applied and theoretical methods.

  • Analyze data and draw conclusions.

  • Present results in multiple formats.

  • Enjoy an engaging, academically stimulating and highly collaborative interdisciplinary research environment.

  • Active Matter Driven by Molecular Motor Proteins

    Mentors: Joshua Alper, physics and astronomy, and Olga Kuksenok, materials science and engineering.

    Introduction: Engineered active polymer gels have the potential to revolutionize the next generation of smart biomedical devices and tissue-engineering scaffolds. The cytoskeleton is essentially a naturally occurring active gel found in nearly every eukaryotic cell. It is capable of forming structures, changing shape, and driving oscillations both spontaneously and in response to external cues. Recently, there has been increased interest in building active materials from cytoskeletal filaments and motors and using viscoelastic material theory and computational models to describe their properties. However, these studies only hint of what is possible with biomimetic active gels engineered from components of the cytoskeleton.

    Research Plan: Two participants will collaborate to study motor protein-driven active gels. One participant, primarily engaged in experimental research in the Alper Lab, will reconstitute active polymeric gels using microtubules, crosslinking microtubule-associated proteins (Ase1 and inactive motors), and motor proteins (axonemal dyneins). The participant will measure the passive and active properties of the gels using high-resolution microscopy and force spectroscopy (optical tweezers). The other participant, primarily doing theoretical and computational work in the Kuksenok Lab, will model the passive and active properties of these gels. This participant will adapt existing models developed and validated for similar systems to predict and explain the behaviors of these active biological gels. Together, the participants will design, build, model, and engineer nature’s machinery to generate active gels with novel properties. The participants will make significant contributions to this exciting field of active nano-biological materials by expanding the molecular constituents used in the design of these gels.

    Equipment/techniques participants will learn and use: fluorescence microscope; optical tweezers; general biochemical and biophysical equipment including centrifuges, gel electrophoresis, and spectrophotometers; high-performance computer cluster.

  • Dielectrophoretic Forces in the Diagnosis of Parasitic Disease

    Mentors: Rodrigo Martinez-Duarte, mechanical engineering, and James Morris, genetics and biochemistry.

    Introduction: Diagnosis of infection by the kinetoplastid parasites, including Trypanosoma brucei, Leishmania spp., and Trypanosoma cruzi, remains challenging, in part, due to the technical challenges associated with performing microscopy-based tests in remote settings. Dielectrophoresis forces, which result from exposing the parasites to an electric field gradient, can selectively concentrate parasites in specific locations within a microfluidic chip and greatly facilitate their detection. However, the response of kinetoplastids to the DEP force likely depends on the properties of the parasite, which can change due to growth, environmental conditions, and exposure to sub-curative doses of different anti-parasitic agents.

    Research Plan: Two participants will collaborate to study how growth, environmental factors, and exposure to drugs affect the DEP behavior of T. brucei. One participant primarily engaged in mechanical and biological engineering research in the Martinez-Duarte Lab will develop an experimental platform to study the response of parasites to various electric fields. This participant will use hydrodynamic and electrical forces to manipulate parasites of interest inside microfluidic systems selectively. The other participant, primarily doing molecular parasitology research in the Morris Lab, will use molecular genetics approaches to generate parasites that express distinct fluorescent markers. This participant will clone fluorescent protein genes into trypanosome expression vectors, transfect them into parasites, and score the expression of these proteins by flow cytometry and microscopy. Together, the participants will determine whether DEP can distinguish between subtle differences in trypanosomes. Ultimately this research will lead to better diagnostic techniques for parasitic disease with the potential to impact the lives of millions of people worldwide.

    Equipment/techniques participants will learn and use: Molecular cloning, in vitro parasite culture, transfection approaches, flow cytometry, microfluidics, dielectrophoresis.

  • The Effects of Radiation on Cells and Tissues

    Mentors: Endre Takacs, physics and astronomy, and Delphine Dean, bioengineering.

    Introduction: High-dose radiation treatment is commonly used to kill diseased cells within the target tissue, but healthy cells near to the target also get exposed to low doses of radiation. Recently, there has been some evidence that suggests various tissues react to low doses of radiation, potentially altering their underlying physical, chemical, and biological pathways during irradiation. However, precisely how tissues respond to low-dose radiation and whether we can create materials to make cells more or less radio-sensitive remains unknown.

    Research Plan: Two participants will collaborate to study the interaction between low levels of monochromatic soft X-ray radiation and biological tissues. One student, primarily working on tissue engineering in the Dean Lab, will grow breast cells and characterize their properties in response to radiation and radiosensitizing materials using various biological assays. The other student, primarily performing medical physics research in the Takacs Lab, will characterize the low dose X-rays and model their effects on tissue. Together, the participants will 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 software, statistical analysis software, cell culturing, optical microscopy and image analysis, cell proliferation and cell cycle analysis, cell function and differentiation assays.

  • The Role of Defects in Nanomaterial-Biomolecular Interactions

    Mentors: Ramakrishna Podila, physics and astronomy, and Terri Bruce, bioengineering.

    Introduction: Nanomaterials have many exciting potential biological and biomedical applications, including in diagnostic and therapeutic devices. Nanomaterials are more chemically reactive than their bulk counterparts because they possess a high density of naturally occurring structural defects (e.g., atomic vacancies). The altered chemical reactivity of nanomaterials leads to pronounced interactions with biomolecules and increases their ability to efficiently cross physiological barriers (e.g., blood-brain barrier). In this scenario, it is critical to understand the interactions between biomolecules and defects within nanomaterials to both predict the fate of nanomaterials and develop safe nanomaterials by design. 

    Research Plan: Two participants will collaborate to study how defects in graphene affect protein interactions from the individual protein level to the complex biological milieu. One participant, primarily doing nanotechnological research in the Podila Lab, will use defected graphene sheets to study the interactions between defects and individual proteins (e.g., fibrinogen) using a comprehensive array of techniques, including high-resolution transmission electron microscopy, Raman spectroscopy, and atomic force microscopy. This participant will also determine the impact of defects on the formation and composition of protein corona through detailed proteomics studies on pristine and defected graphene incubated in fetal bovine serum. The other participant, primarily doing cell biological and biochemical research in the Bruce Lab, will evaluate the physiological responses to defected graphene with and without protein corona using cell viability and oxidative stress assays, flow cytometry, and hyperspectral microscopy. Together, the participants will explore how defects in nanomaterials influence their interactions with biomolecules. Ultimately this research will be used to guide the development of novel biomedical devices.

    Equipment/techniques participants will learn and use: Electron microscopy, Raman and X-ray photoelectron spectroscopy, atomic force microscopy, proteomics, mammalian cell culture, flow cytometry, ELISA and LDH cytotoxicity assay.

  • Small GTPases That Organize Septins Essential for the Pathogenesis of Cryptococcus Neoformans

    Mentors: Feng Ding, physics and astronomy and Lukasz Kozubowski, genetics and biochemistry.

    Introduction: Cryptococcus neoformans is a major opportunistic fungal pathogen worldwide and a leading cause of death in AIDS patients. Like all microbial pathogens, C. neoformans must cope with stress in the adverse environment of the host, and thus inhibiting its stress response pathways is a promising therapeutic strategy. Recently, proper organization and dynamics of septin filaments, which act in cell division and morphogenesis, have been identified as essential to the C. neoformans stress response, and Cdc42, a small GTPase, has been identified to play a significant role in septin organization. However, the mechanisms by which Cdc42 organizes septin assembly and dynamics and its connections to the stress response in C. neoformans remain unknown. 

    Research Plan: Two participants will collaborate to study the role that Cdc42 and other small GTPases play in organizing C. neoformans septins. One participant, primarily engaged in cell biological and biochemical research in the Kozubowski Lab, will use an allele of the Cdc42 protein that we engineered to be light-sensitive to study its role in C. neoformans cells. The participant will investigate how Cdc42 and other small GTPases regulate septin complex assembly and dynamics using fluorescent and confocal microscopy. The other participant, primarily doing computational biophysics and protein engineering in the Ding Lab, will design and model additional light switchable proteins to be subsequently tested in C. neoformans. This participant will use discrete molecular dynamics and other computational techniques to predict and model the dynamics of these proteins in silico. Together, the participants will define the mechanisms responsible for C. neoformans cell division and survival in the host and could potentially reveal new targets for therapeutic interventions.

    Equipment/techniques participants will learn and use: molecular modeling, computational protein engineering, molecular dynamics simulations, fluorescent microscopy, confocal microscopy.

  • DNA Repair Mechanisms: From Single-Molecule to Cell-Based Assays

    Mentors: Jennifer Mason, genetics and biochemistry, and Hugo Sanabria, physics and astronomy.

    Introduction: While DNA is being copied during the process of replication, factors such as secondary DNA structure or exposure to DNA damaging agents such as sunlight result in replication slowing or stalling. The inability of cells to respond to situations that slow replication increases mutation and result in human diseases such as cancer. Cells contain DNA repair molecular motors whose function is to protect and repair DNA during replication, but these processes are poorly understood.

    Research Plan: Two participants will collaborate to study how DNA repair protein motors function in response to DNA damage during replication. One student, primarily working on molecular biology techniques in the Mason Lab, will grow human epithelial cells and characterize their response to DNA damage using various cell-based assays. The other participant, working in the Sanabria Lab will measure changes in the conformation of the DNA upon the enzymatic assay of the DNA repair proteins. To do so, this participant will use single-molecule fluorescence microscopy in confocal and TIRF modalities. Together, the students will identify how DNA repair proteins respond and act on damaged DNA during replication.

    Equipment/techniques participants will learn and use: cell culture, fluorescent microscopy, single-molecule spectroscopy, general biochemical and biophysical equipment, gel electrophoresis, spectrometers, protein chromatography.

  • Redox Chemistry Models for Alcohol-induced Cardiac Dysfunction

    Mentors: Will Richardson bioengineering, and Andy Tennyson, chemistry.

    Introduction: Chronic alcohol abuse is a substantial health problem that can cause cardiac dysfunction through altered tissue structural remodeling. This tissue remodeling results from pathological cell signaling governed, in part, by the redox chemical reactions involved in alcohol metabolism, amongst other biochemical and biophysical signals. Therefore, understanding how redox reactions modulate cell signaling behavior could help us develop new therapeutic approaches for alcohol abuse-related cardiac dysfunction. Unfortunately, these redox reactions interact within a large and complex network of signaling pathways, making it difficult to predict their effect.

    Research Plan: Two participants will collaborate to study how redox chemistry relates to alcohol-induced cell signaling pathway dysfunction in cardiac cells. One student, primarily performing biochemical and cell biological research in the Tennyson Lab, will synthesize and characterize novel organometallic complexes that interfere with the reactive oxygen species that contribute to redox stress. Once synthesized, the participant will treat cardiac cells in culture with these complexes and test their effect on various cell functions. The other participant, primarily performing systems biological modeling in the Richardson Lab, will use a computational model of cardiac cell signaling networks to identify the particular signaling molecules and pathways that are most strongly affected by ROS. This participant will also perform virtual drug screens to identify other novel therapeutic targets for future study. Together, the participants will help discover how oxidative stresses contribute to alcohol-induced tissue damage and new potential therapeutic compounds to prevent this damage in the first place.

    Equipment/techniques participants will learn and use: general biochemical and biophysical equipment including centrifuges, gel electrophoresis, and spectrophotometers; mammalian cell culture equipment; optical and fluorescent microscopy; network systems modeling; high-performance computer cluster.

Department of Physics and Astronomy
Department of Physics and Astronomy | 118 Kinard Laboratory, Clemson, SC 29634