University of Virginia
The Rotunda at U.Va.
2005-2006
GRADUATE RECORD
Graduate School of Arts and Sciences
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Faculty
Course Descriptions

Program in Biophysics

UVa Health Systems
P.O. Box 800738
Charlottesville, VA 22908-0738
(434) 924-1757
medgpo22@virginia.edu
www.healthsystem.virginia.edu/internet/biophysics

Requirements

The Interdisciplinary Program in Biophysics at the University of Virginia comprises the research and teaching facilities of some 30 faculty members in the College of Arts and Sciences, the School of Engineering and Applied Science, and the School of Medicine. The graduate teaching program is designed to allow a maximum degree of flexibility so that students with varying backgrounds can be prepared to investigate the broad range of problems encompassed by biophysics.

Admission Students with a bachelor’s degree in science or engineering will be considered for admission. A strong undergraduate background in physics, chemistry, and mathematics is desirable. Students lacking particular prerequisites may take appropriate courses during their first year of graduate study.

Financial Support Financial support is available to all students in the program. Biophysics fellowships are granted to first- and second-year students on a competitive basis. Research assistantships are available to graduate students at all levels. Several departments which have faculty members active in the biophysics program administer fellowships and teaching assistantships for which biophysics students may qualify.

Supervision An entering biophysics student is assigned an advisory committee which guides the student in choosing course work and rotations. Later, when the student chooses a thesis mentor, a thesis committee is chosen upon mutual consent of the mentor, student, and committee member. This committee meets at regular intervals to review the progress of the student’s research, and acts as a thesis defense committee.

Course of Study and Degree Requirements

The program maintains a maximum degree of flexibility in order to meet the needs and wishes of each individual student. Students will be advised to take courses in biology, chemistry, physics, mathematics, or other appropriate areas to supplement their training and to prepare them for their field of special interest. Specifically designed biophysics courses, seminars, and journal clubs are also offered. No language requirement is specified. Each student will be expected to demonstrate an advanced understanding of his or her chosen field. In addition the student must meet the University residency and credit requirement as listed in this Graduate Record. The student will meet periodically with their advisory committee during the course of their research work. Finally, the student must submit and successfully defend a dissertation describing original research in a field of biophysics.


Course Descriptions

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BIOP 506 - (4) (Y)
Experimental Approaches in Molecular Biophysics
A survey course of modern biophysical methods, including diffraction, spectroscopy, electrophysiology, and microscopy. The course is taught collaboratively by a large fraction of the Biophysics Program faculty. Besides getting an introduction into the various aspects of molecular biophysics, it offers the students an opportunity to get to know many of the program faculty and their research.

BIOP 507 - (3) (Y)
Thermodynamics and Kinetics of Biological Systems
This course introduces students to key theoretical concepts in modern biophysics. Statistical thermodynamics, electrostatics and electrochemistry, biochemical kinetics, and molecular driving forces will be discussed at an intermediate to advanced level.

BIOP 751 - (1-5) (Y)
Directed Reading
Designed on an individual basis, students who have deficiencies in particular areas pertaining to biophysics will be advised by a faculty member to read texts in that area and will discuss the contents with the faculty mentor on a regular basis.

BIOP 801 - (1) (S)
Special Topics in Biophysics
A seminar series comprised of 45-minute informal talks given by students, faculty, and guest speakers.

BIOP 802 - (3) (SI)
Advanced Protein Crystallography
An in-depth assessment of the current methodology in macromolecular crystallography. In addition to formal lectures, a number of hands-on sessions introduce students to experimental aspects of crystallization and sample preparation, data collection, as well as selected problems in computing. The lectures cover selected aspects of crystal symmetry, diffraction theory including diffraction by helical structures and fiber diffraction, methods of data collection and structure solution, with emphasis on the contemporary approaches utilizing synchrotron radiation and exploiting anomalous scattering. Refinement and model assessment and selected papers are discussed.

BIOP 803 - (3) (Y)
Magnetic Resonance Spectroscopy of Macromollecules
The course focuses on the application of NMR spectroscopy to protein structure determination. Topics include classical and quantum description of NMR, density matrix theory and relaxation mechanisms, multi-dimensional homo/heteronuclear NMR, pulse sequence design, structure calculation from NMR data, molecular dynamics calculations. Two additional lectures each are devoted to solid-state NMR and EPR.

BIOP 505 - (3) (Y)
Biophysical Literature
A journal club. Students present recent research papers in biophysics and/or report on progress of their own research projects. Students learn how to effectively read, critique, and present science research progress.

BIOP 897 - (3-12) (S-SS)
Non-Topical Research, Preparation for Master’s Research
Research for the master’s degree, taken before a thesis advisor has been chosen.

BIOP 898 - (3-12) (S-SS)
Non-Topical Research, Master’s Research
Research for the master’s degree, taken under the direction of a thesis advisor.

BIOP 995 - (3-12) (S)
Biophysics Research
Independent study, other than non-topical research, for course credits.

BIOP 997 - (3-12) (S-SS)
Non-Topical Research, Preparation for Doctoral Research
For doctoral research, taken before a dissertation director has been selected.

BIOP 999 - (3-12) (S-SS)
Non-Topical Research
For doctoral research, taken under the supervision of a dissertation director.

Non-Departmental Courses

Biophysics students may choose relevant courses from the following departments:

Biomedical Studies

BIMS 503 - (4) (Y)
Macromolecular Structure and Function
An introductory graduate course that integrates elements of biological regulation, enzyme function and kinetics, physical biochemistry, and structural biology.

BIMS 710 - (1) (Y)
Research Ethics
A discussion-based approach to ethical problems facing biomedical researchers.

BIMS 811 - (5) (Y)
Gene Structure, Regulation, and Expression

BIMS 812 - (5) (Y)
Cell Structure and Function
An analysis of current research on the interrelationships of structure and function in eukaryotic cells. Special emphasis is placed on cellular membranes, neuromuscular activities, and cellular interactions as they relate to development and cancer.

Biochemistry

BIOC 508 - (2) (Y)
Computer Analysis of DNA and Protein Sequences
The theory and practice of biological sequence analysis is covered. The course provides a quick introduction to the GCG package and other Web-based sequence analysis tools, and then goes into a detailed analysis of the algorithmic and statistical methods used for similarity searching, multiple-alignment, gene-finding, promoter recognition, RNA folding, and evolutionary tree construction.

Microbiology

MICR 803 - (5) (Y)
Fundamental Immunology

MICR 815 - (4) (Y)
Molecular Basis of Cancer

Pharmacology

PHAR 908 - (2) (E)
Biochemical Pharmacology

PHAR 910 - (2) (E)
Endocrine Pharmacology

Physiology

PHY 813 - (3) (Y)
Structure and Function of Biological Membranes
An in-depth assessment of the structure and function of biological membranes. The main topics are: (1) membrane and membrane protein structure, (2) lipid-protein interactions, (3) active transport and ion driven molecular motors, and (4) ion channels and their regulation. Emphasis is placed on biophysical approaches in these areas. The primary literature will be the main source of reading.

Chemistry

CHEM 521 - (3) (Y)
Advanced Physical Chemistry I

CHEM 522 - (3) (Y)
Advanced Physical Chemistry II

CHEM 821 - (3) (SI)
Principles of Quantum Mechanics

CHEM 822 - (3) (SI)
Chemical Applications of Quantum Mechanics

Physics

PHYS 725 - (3) (Y)
Mathematical Methods of Physics I

PHYS 751 - (3) (Y)
Quantum Theory I

PHYS 752 - (3) (Y)
Quantum Theory II

PHYS 831, 832 - (3) (Y)
Statistical Mechanics

Biology

BIOL 501 - (4) (Y)
Biochemistry

BIOL 503 - (4) (Y)
Molecular Genetics

BIOL 504 - (4) (IR)
Advanced Cell Biology

BIOL 817 - (4) (Y)
Neurophysiology

Mathematics

MATH 509 - (3) (Y)
Mathematical Probability

MATH 510 - (3) (Y)
Mathematical Statistics

MATH 511 - (3) (Y)
Stochastic Processes

MATH 521 - (3) (Y)
Advanced Calculus and Applied Mathematics

MATH 522 - (3) (Y)
Partial Differential Equations

Biomedical Engineering

BIOM 620, 621 - (3) (Y)
Application of Computers to Medicine and Biology

BIOM 701, 702 - (3) (E)
Fundamentals of Biophysical Sciences

BIOM 891, 892 - (2) (IR)
Advanced Topics in Biomedical Engineering

Chemical Engineering

CHE 615 - (3) (Y)
Advanced Thermodynamics

CHE 716 - (3) (SI)
Applied Statistical Mechanics


 
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