Biophysics Graduate Program

BIOETHICS

MESSAGE FROM THE DIRECTOR

Candice Klug, PhD Professor of Biophysics Director, Graduate Program in Biophysics

 

Candice Klug, PhD

Professor of Biophysics
Director, Graduate Program in Biophysics

 

“Thank you for your interest in Biophysics at MCW! Our graduate program focuses on two magnetic resonance techniques with clinical and biomedical applications: we are the birthplace of functional magnetic resonance and pioneers in the development of electron paramagnetic resonance spectroscopy instrumentation and applications. Our program faculty are enthusiastic about their research, and our environment may be the ideal place to fulfill your graduate career goals—explore more about what our program has to offer below.”

candice@mcw.edu
(414) 955-4015

  • About
  • Current Students
  • Curriculum
  • Admissions
  • Tuition & Fees
  • Faculty

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

Current Students

 

 

Zachary Boyd

Zachary Boyd
  • zboyd@mcw.edu
  • Mentor: Dr. Eric Paulson
  • Year Entered MCW: 2017
  • Previous Education:
  • Research Interest:

Ethan Duwell

Ethan Duwell
  • eduwell@mcw.edu
  • Mentor: Dr. Edgar DeYoe
  • Year Entered MCW: 2015
  • Previous Education: St. Olaf College (Northfield, MN), BA, Chemistry and Philosophy (2013)
  • Research Interest: My research interests include visual attention, conscious awareness, and conscious experience. I am currently pursuing these interests in the DeYoe lab, where we study visual attention both behaviorally and neurophysiologically via functional magnetic resonance imaging (fMRI). The DeYoe lab develops novel fMRI paradigms to map brain patterns of attention-related activity and then uses mathematical models to explore the effects of attention on visual processing and other behaviors. The overall goal is to understand the brain mechanisms responsible for visual perception, attention, and awareness, ultimately providing tools for diagnosis and treatment of brain-related vision and attention deficits.

Alex Helfand

Alex Helfand
  • ahelfand@mcw.edu
  • Mentor: Dr. Jeffrey Binder
  • Year Entered MCW: 2016
  • Previous Education: Boston University (Boston, MA), BA, Psychology (2012); MS, Medical Science (2014)
  • Research Interest: I am interested in the neural networks that mediate behavior, especially the processing of external stimuli in order to plan and execute a response. I am particularly interested in the neural networks mediating motivated behaviors and reward valuation. I am also interested in studying the biological bases for human communication (verbal and written).

 Samantha Kohn

Samantha Kohn
  • skohn@mcw.edu
  • Mentor: Dr. Jimmy Feix
  • Year Entered MCW: 2014
  • Previous Education: Carroll University (Waukesha, WI), BS, Chemistry (2013)
  • Research Interest: The Feix lab focuses on the structure, conformational dynamics, and membrane interactions of ExoU, a key virulence factor of Pseudomonas aeruginosa that is strongly correlated with a poor clinical outcome. ExoU is a 74 kDa phospholipase that requires noncovalent interaction with ubiquitin for activity. Membrane binding of ExoU is enhanced by the phospholipid inositol-(4,5)-bisphosphate; however, the liposome binding mechanism, the liposome binding domain(s), and the role of ubiquitin in liposome binding remain unknown.  We are investigating these molecular processes using a combination of biochemical and biophysical methods.

Seung Yi Lee

Seung Yi Lee
  • selee@mcw.edu
  • Mentor: Dr. Matthew Budde
  • Year Entered MCW: 2016
  • Previous Education: The Catholic University of Korea (Seoul, South Korea), BS, Chemistry (2012); Pennsylvania State University (University Park, PA), MS, Chemistry (2015)
  • Research Interest: My research is to identify MRI biomarkers to diagnose spinal cord injury severity. The research utilizes animal models to screen for and develop novel MRI-based methods to detect injury.

Sean McGarry

Sean McGarry
  • smcgarry@mcw.edu
  • Mentor: Dr. Peter LaViolette
  • Year Entered MCW: 2015
  • Previous Education: Milwaukee School of Engineering (Milwaukee, WI), BS, Biomedical Engineering (2015)
  • Research Interest: My research interests involve structural imaging in brain cancer. I actively work in radiomics, a field of study dedicated to extracting quantitative imaging features from a medical image to produce a mineable database of radiological features with clinical relevance. Radiomic features are hypothesized to capture phenotypic differences within a tumor and have prognostic power. Through the combination of magnetic resonance imaging and ex vivo histology, cellular and genetic information regarding the patients tumor can be linked to macroscopic in vivo images. 

Nikolai Mickevicius

Nikolai Mickevicius
  • nmickevicius@mcw.edu
  • Mentor: Dr. Eric Paulson
  • Year Entered MCW: 2013
  • Previous Education: Milwaukee School of Engineering (Milwaukee, WI), BS, Biomedical Engineering (2013)
  • Research Interest: My main area of interest is in developing real-time simultaneous multislice MRI pulse sequences and image reconstruction algorithms for managing patient motion during MRI-guided radiation therapy treatment fractions. 

Daniel Olson

Daniel Olson
  • dolson@mcw.edu
  • Mentor: Dr. L. Tugan Muftuler
  • Year Entered MCW: 2013
  • Previous Education: Marquette University, BS (Milwaukee, WI), Biomechanical Engineering and Physics (2013)
  • Research Interest: My research is in diffusion-weighted imaging with emphasis on diffusion kurtosis tensor imaging (DKTI). We have applied DKTI to quantify the extent and severity of acute physiological changes following sport-related concussion. 

Jaiqing (Tony) Tong

Jaiqing (Tony) Tong
  • jtong@mcw.edu
  • Mentor: Dr. Jeffrey Binder
  • Year Entered MCW: 2016
  • Previous Education: Fenyang Collage, Shanxi Medical University (Taiyuan, China), BS, Clinical Laboratory Technician (2012); School of Basic Medicine, Shanxi Medical University (Taiyuan, China), MS, Physiology (2015)
  • Research Interest: My research explores how neurons code the information of language learning. 

Zhan Xu

Zhan Xu
  • zhanxu@mcw.edu
  • Mentor: Dr. Shi-Jiang Li
  • Year Entered MCW: 2012
  • Previous Education: Beijing Jiaotong University (Beijing, China), BS, Biomedical Engineering (2007)
  • Research Interest: My research focuses on improving the BOLD (blood-oxygen-level dependent) contrast in the fMRI application, as well as on improving the repeatability of the fMRI signal. To improve the contrast-to-noise ratio and repeatability, the most accepted approach is to increase acquisition duration. However, this method is not efficient enough, and motion artifacts usually become more severe during longer periods of data acquisition. As such, I am developing a new method, named the spatial compensated intro-shot turbo keyhole (SCITH) method. This multi-echo imaging technique aims to improve contrast within the same scan duration as is used in the current fMRI acquisition approach. The SCITH method is developed first at the 3T platform, but it can easily be transferred to the 7T platform. The conventional multi-echo approach is hard to implement due to the fast T2* decay at a strong magnetic field of 7T, but the SCITH method is capable of reducing the echo time interval between echoes as low as 6 ms that break the readout time limitation.

Magnetic Resonance Imaging (fMRI)

 

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

  • Functional MRI Contrast Mechanisms and Applications
  • Functional MRI Journal Club
  • Nuclear Magnetic Resonance
  • Seminar

During a student's first two years, courses in biophysics, biostatistics and a biomedical science are taken in combination to complement the student's strengths and interests and as needed for their research direction. 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 University of Wisconsin-Milwaukee.

A written comprehensive qualifying exam and oral dissertation proposal defense are expected to be completed by the middle of the third year of the program. A final dissertation defense is expected to occur by the fifth year of study.

 

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Magnetic Resonance Imaging Courses

Biophysics 03230: Nuclear Magnetic Resonance (3 credits)

This course is designed as an introduction to nuclear magnetic resonance spectroscopy (MRS). Emphasis will be placed on modern MRS techniques and their application to structural determinations of biomolecules. Imaging-guided in vivo spectroscopy and its applications to biomedicine will also be introduced.

 

Biophysics 03239: Functional MRI Contrast Mechanisms and Applications (3 credits)

The use of MRI to evaluate tissue function will be described. The course will be dedicated to discussing fMRI methods that use both endogenous contrast (labeled water, deoxygenated blood) and exogenous (injectable) MR contrast agents to image tissue function. The theory and physiology necessary for understanding MR contrast mechanisms, together with the practical knowledge necessary for performing MR experiments, will be discussed. Demonstrations of fMRI experiments will be included.

 

Biophysics 03240: Fourier Transforms (3 credits)

This course provides basic knowledge for students who will continue to study EPR or NMR. Material will cover the theory of Fourier transforms, digital transforms, NMR images, reconstruction, pulse spectroscopy methods and electrical signal processing. An understanding of calculus and tensor vectors is recommended.

 

Biophysics 03238: Magnetic Resonance Imaging (3 credits)

This course focuses on the physics of modern MRI. It will take a classical approach to spin physics and will focus on pulse sequences, k-space analysis and hardware. An understanding of calculus is required.

Biophysics 03240: Fourier Transforms is required prior to taking this course.

 

Biophysics 03295: Readings and Research (1 to 9 credits)
 

Biophysics 03298: Biophysics MRI Journal Club (1 credit)

Selected papers in theory, practice and application of MRI will be read and discussed in separate sessions.

 

Biophysics 03300: Seminar (1 credit)

Weekly invited seminar speakers present their research on molecular biophysics or MRI topics.

 

Molecular Biophysics

 

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

 

  • Advanced Protein Chemistry or Free Radicals in Biology
  • Biochemistry of the Cell
  • Biophysical Techniques in Biochemistry
  • Cell Signaling
  • Electron Paramagnetic Resonance Spectroscopy (Theory and Practical Applications)
  • EPR Journal Club
  • Genetics
  • Molecular and Cellular Biology
  • Seminar
  • Techniques in Molecular and Cellular 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 qualifying exam and dissertation proposal defense are expected to be completed by the middle of the third year of the program. A final dissertation defense is expected to occur by the fifth year of study. 

  

Molecular Biophysics Courses

Biophysics 03222: Biophysical Techniques in Biochemistry (3 credits)

This course will introduce the basic theory and practical applications of an array of biophysical techniques commonly used in biochemical research. Optical and magnetic spectroscopies, x-ray crystallography and kinetics techniques are just a sampling of the topics covered in this comprehensive course.

 

Biophysics 03223: Electron Paramagnetic Resonance (3 credits)

The aim of the course is to introduce the theory and practical applications of modern EPR spectroscopy. Basic EPR theory, biological free-radical spectroscopy, relaxation and motional phenomena, spin labeling and transition-metal EPR are among the topics covered.

 

Biophysics 03251: Free Radicals in Biology (3 credits)

Topics to be discussed include the nature of free radicals; radical initiation, propagation and termination; free-radical reactions of biological interest; and the role of free radicals in physiological and pathological processes.

 

Biophysics 03295: Readings and Research (1 to 9 credits)
 

Biophysics 03298: Biophysics EPR Journal Club (1 credit)

Selected papers in theory, practice and application of EPR spectroscopy will be read and discussed in separate sessions.

 

Biophysics 03300: Seminar (1 credit)

Weekly invited seminar speakers present their research on molecular biophysics or MRI topics. 

Applying to the Program

 

Start Your Application Now

Degree Offered

The Biophysics Graduate Program offers a Doctor of Philosophy.

Program Admission Requirements

The Biophysics Graduate Program encourages applications from students with strong backgrounds in chemistry, biology, biochemistry, biomedical engineering, physics or mathematics and an enthusiasm for carrying out scientific research. The program consists of two major and largely independent tracks—Magnetic Resonance Imaging and Molecular Biophysics. 

The Magnetic Resonance Imaging section emphasizes research in the areas of cognitive neuroscience, signal processing, statistical analysis, image production, and hardware development. Students wishing to pursue this track should apply directly to the Biophysics Graduate Program or through the Neuroscience Doctoral Program (NDP). Applicants to this track are expected to have a high level of competence in physics and mathematics. However, the program has also admitted students with backgrounds in biology, psychology and medicine.

Students interested in Molecular Biophysics should pursue admission through the Interdisciplinary Program (IDP) in Biomedical Sciences . The faculty in this section use biophysical techniques to study structural biology, free radicals in biology and paramagnetic metal ions in biological systems. For example, current research includes studies on protein structure, functional dynamics and free radical spin trapping.

Quantitative and analytical GRE scores should be above average. Personal statements and letters of recommendation from professors or research supervisors who know you well are highly regarded in the admission process.

Program Director: Candice S. Klug, PhD
Recruitment Director: Neil Hogg, PhD

TUITION AND FEES INFORMATION

If you have questions regarding tuition or your account, please contact the Office of Student Accounts, at (414) 955-8172 or mcwtuition@mcw.edu.

PhD Students

All full-time PhD students receive a full tuition remission, health insurance and stipend.

2017-2018 Stipend: $29,136.00

The following fees are covered by the tuition remission:

  • All Students Fee (Fall & Spring Semesters Only): $40.00
  • Graduate Student Association (GSA) Fee: $35.00
  • Tuition Per Credit - Fall, Spring & Summer Semesters: $1,250.00

Masters, Certificate & Non-Degree Students

Students seeking financial aid for MPH, MS or MA degree programs, visit the Financial Aid Office website.

  • Tuition Per Credit - Fall, Spring & Summer Semesters: $1,010.00
  • Master’s in Medical Physiology Tuition: $42,000/year
  • Continuation: $225.00
  • Audit - Per Class: $100.00

Current MCW Employees

Tuition Course Approval Form - Human Resources (PDF)

Late Fees

There will be a $250 late registration fee for anyone not completing registration by the date indicated on the schedule each semester. There is also a $250 late payment fee for tuition not paid on time according to the Tuition Payments policy in the Student Handbook.

Late payment fee is in addition to any late registration fee.

Graduate School of Biomedical Sciences General CAMPUS CONTACT INFORMATION

Mailing Address:
MCW Graduate School
8701 Watertown Plank Road
Milwaukee, WI 53226


(414) 955-8218
(414) 955-6555 (fax)
gradschool@mcw.edu

Department of Biophysics

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