IDP-Biophysics Graduate ProgramAbout the Biophysics Graduate Program


The Biophysics Graduate Program features two primary areas of research: Magnetic Resonance Imaging and Molecular Biophysics. Our program is designed to assist young scientists in developing the research skills they need to thrive in academic and clinical settings. Our program offers an informal atmosphere where students are able to work closely with faculty members, as well as other graduate students and postdoctoral fellows.

Magnetic Resonance Imaging

The Magnetic Resonance Imaging track places particular emphasis on magnetic resonance imaging (MRI). A particularly active area of research is functional MRI (fMRI) of the human brain (e.g., neuroscience, contrast mechanisms, technical development), which  is the measurement of the indirect consequences of locally increased neural activity—increased blood flow and increased blood oxygenation, both confined to the region near the neural activation. Our fMRI program emphasizes the following:

  • The development and application of faster imaging methods, with a principal application of mapping human brain function (fMRI);
  • The quantitation of clinically relevant imaging parameters such as differential relaxation times in cancerous and normal brain tissues, which can aid in the diagnosis of cancerous tissue; and
  • The development of more rigorous mathematical and statistical techniques for modeling and analyzing MRI and fMRI experiments. Fourier image reconstruction and computing of statistical activations are integral parts of MRI/fMRI.

Research also focuses on the basic physics and mechanisms of MRI. Designing improved hardware, experimental protocols and post-processing algorithms is key to achieving the goals of this program.

Research directions that stem from these goals include:

  • Creating new, faster imaging techniques and hardware
  • Understanding the precise interaction between basic neural events, their physiological consequences (e.g., blood oxygenation changes) and the nuclear magnetic resonance (NMR) signal
  • Developing new mathematical and statistical models for Fourier image reconstruction and the precise quantification of activations in structure-function relationships

Instrumentation for fMRI research is maintained by the Center for Imaging Research

Magnetic Resonance Imaging Faculty

Jeffrey R. Binder, MD
Professor, Neurology

Matthew Budde, MD
Assistant Professor, Neurosurgery

Joseph Carroll, PhD, FAVRO
Professor, Ophthalmology

Edgar A. DeYoe, PhD
Professor, Radiology

Andrew S. Greene, PhD
Professor, Physiology

Kevin M. Koch, PhD
Associate Professor, Radiology

Peter LaViolette, PhD
Assistant Professor, Radiology

Shi-Jiang Li, PhD
Professor, Biophysics

L. Tugan Muftuler, PhD
Associate Professor, Neurosurgery

Andrew S. Nencka, PhD
Assistant Professor, Radiology

Eric Paulson, PhD
Assistant Professor, Radiation Oncology

Merav Sabri, PhD
Assistant Professor, Neurology

Kathleen M. Schmainda, PhD
Professor, Radiology

Molecular Biophysics


The Molecular Biophysics track encompasses the investigation, detection and use of free radicals and paramagnetic metal ions in biological systems. Free radicals are involved in many disease processes but are also an integral part of cellular communication. They can be used to label proteins and map out protein structure, providing information on protein dynamics and conformational changes that cannot be obtained from crystal structure data. In addition, free-radical labels can be used to probe the dynamics of biological membranes. Paramagnetic metal ions are central to most biological processes and electron transfer systems. A major technique used in the above studies is electron paramagnetic resonance (EPR) spectroscopy.

The Department of Biophysics houses the National Biomedical EPR Center, one of the few national centers for EPR-related research, as well as the Free Radical Research Center and the Redox Biology Center. Students interested in the biomedical application of EPR spectroscopy to the study of biology, biochemistry and structural biology should enter our program through the Interdisciplinary Program (IDP) in Biomedical Sciences. Students with more of a physical background who are interested in specializing in EPR instrumentation should apply directly to the Biophysics Graduate Program. 

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  Free Radicals

Generally, free radicals have a bad reputation because their production is associated with many diseases such as atherosclerosis and Lou Gehrig's disease, and they are also largely responsible for the unhealthy effects of air pollution. Most people are surprised to learn that many free radicals are stable molecules and that biological systems purposely make free radicals as paracrine hormones. The free radical nitric oxide (NO) is involved in the control of blood pressure, memory and inflammation, and is a major focus of research in the Department of Biophysics. Free radicals have been used for many years to probe metal-ion-containing sites of proteins such as hemoglobin. 

  Spin Labels

Free radicals can be introduced at any site in a protein or peptide by a technique known as site-directed spin labeling. Free radicals are excellent reporters of their environment and, therefore, can be used to investigate protein structure and dynamics. Site-directed spin-labeling studies of bacterial pores (used to control the flow of chemicals into and out of cells), as well as other proteins, peptides and lipid membranes, are conducted in the Department of Biophysics. 

  Metal Ions

Paramagnetic metals are involved in all aspects of biology. For example, ribonucleotide reductase, an enzyme, contains both a tyrosyl free radical and a mu-oxo dinuclear iron center. An antitumor agent, iron bleomycin, damages DNA by free-radical chemistry. And, superoxide dismutase, a free-radical-scavenging enzyme, contains an active-site copper that may be important in Lou Gehrig's disease. 

Molecular Biophysics Faculty

William E. Antholine, PhD
Associate Professor, Biophysics

Jimmy B. Feix, PhD
Professor, Biophysics

Neil Hogg, PhD
Professor, Biophysics

Balaraman Kalyanaraman, PhD
Professor and Chair, Biophysics 

Candice S. Klug, PhD
Professor, Biophysics

Michael Lerch, PhD
Assistant Professor, Biophysics

W. Karol Subczynski, PhD, DSc
Professor, Biophysics

Jeannette Vasquez-Vivar, PhD
Professor, Biophysics