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.

Magnetic Resonance Imaging

The Magnetic Resonance Imaging track, particular emphasis is placed on MRI and magnetic resonance spectroscopy (MRS). Functional MRI (fMRI) of the human brain (e.g., neuroscience, contrast mechanisms, technical development) is an active area of research. Faculty teach students the basic physics and mechanisms of MRI. Research directions that stem from these basics include:

  • Creation of 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
  • Development of new mathematical and statistical models for Fourier image reconstruction and the precise quantification of activations in structure-function relationships
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  fMRI

Functional MRI 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. These two physiological changes affect the NMR signal slightly, since they change the microscopic distribution of the magnetic field in the brain. 

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.

Designing improved hardware, experimental protocols, and post-processing algorithms are key to achieving the goals of this program.

  fMRI Research Facilities

Facilities for fMRI research are maintained by the Center for Imaging Research (CIR); additional details are presented on the CIR webpages.

Computational facilities include several SGI workstations and a collection of Windows/Linux computers.

  Magnetic Resonance Imaging Faculty

Magnetic Resonance Imaging faculty are deeply involved in both the scientific application and development of MRI technology.

Jeffrey R. Binder, MD
Professor, Neurology

Matthew Budde, MD
Assistant Professor, Neurosurgery

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

Robert W. Prost, PhD
Associate Professor, Radiology
Chief, Section of MR Technical Advances

Merav Sabri, PhD
Assistant Professor, Neurology

Kathleen M. Schmainda, PhD
Professor, Radiology

  Student Expectations

In the Magnetic Resonance Imaging track, students will take the following core courses in the first two years of entering the program:

  • Instrumentation: Magnetic Resonance Imaging
  • Nuclear Magnetic Resonance
  • Magnetic Resonance Imaging
  • Functional MRI Contrast Mechanisms and Applications
  • Fourier Transforms
  • Functional MRI Journal Club

During a student's first two years, each semester consists of one course in biophysics, one in neuroscience, and one in a related area to compliment the student's strengths and interests. This allows students to gain experience in both technical and applied areas. Since students' time is not occupied by teaching requirements, they will be involved with a research area under the direction of a faculty member. Students typically coauthor several refereed journal publications prior to graduation. Directed studies and research courses are available to students, as are classes at two area universities: Marquette University and the University of Wisconsin-Milwaukee.

An oral dissertation proposal defense and a written comprehensive qualifying exam are expected to be completed by the end of the third year or at the beginning of the fourth year of the program. A final dissertation defense is expected to occur by the fifth year of study.

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). The Department of Biophysics houses one of the few national centers for EPR-related research (i.e., the National Biomedical EPR Center). Students with more of a physical background may specialize in EPR instrumentation. Additionally, the Department of Biophysics is home to the Free Radical Research Center.

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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

Advances in genetic engineering now make it possible to introduce free radicals at any site in a protein 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, are conducted in 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

W. Karol Subczynski, PhD, DSc 
Professor, Biophysics

Jeannette Vasquez-Vivar, PhD 
Professor, Biophysics

  Student Expectations

In the Molecular Biophysics track, students will take the following courses in the first two years of entering the program:

  • Graduate Biochemistry
  • Advanced Protein Chemistry
  • Biophysical Techniques in Biochemistry
  • Techniques in Molecular Genetics
  • Electron Paramagnetic Spectroscopy (Theory and Practical Applications)
  • Free Radicals in Biology

In addition to the introductory core classes listed above, students have the opportunity to take more advanced classes specific to their chosen area of research. A dissertation proposal defense and qualifying exam are expected to be completed by the end of the third year of the program. A final dissertation defense is expected to occur by the fifth year of study.

Contact Us

Department of Biophysics
Medical College of Wisconsin
8701 Watertown Plank Road
Milwaukee, WI 53226-0509

(414) 955-4000
(414) 955-6512 (fax)

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Medical College of Wisconsin
8701 Watertown Plank Road
Milwaukee, WI 53226
(414) 955-8296
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Page Updated 07/12/2016
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