University of Virginia
The Rotunda at U.Va.
2003-2004
GRADUATE RECORD
Graduate School of Arts and Sciences
General Information  |  Programs and Degress Offered  |  Admission Information  |  Financial Assistance  |  Graduate Academic Regulations  |  Requirements for Specific Graduate Degrees  |  Departments and Programs  |  Faculty
Course Descriptions

Interdisciplinary Program in Biophysics

Requirements

The Interdisciplinary Program in Biophysics at the University of Virginia comprises the research and teaching facilities of some 35 faculty members in the College of Arts and Sciences, the School of Graduate 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 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. Financial support is available to all students in the program.

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.

Address
HS Box 800738
Charlottesville, VA 22908-0738
(434) 924-1757
medgpo22@virginia.edu
www.med.virginia.edu/biophysics


Course Descriptions

TOP

BIOP 506 - (4) (Y)
Experimental Approaches in Molecular Biophysics

A survey course of modern biophysical methods, including diffraction, spectroscopy, patch clamping, thermodynamics of molecular interactions, 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 702 - (3) (Y)
Analysis of Biophysical Data

Prerequisite: Calculus, some advanced chemistry, and permission of the instructor.
Explores methods of simulating biochemical/biophysical experiments using small laboratory computers. Uses FORTRAN 77 to write computer programs relevant to individual research, including the application of nonlinear least-squares and maximum likelihood parameter estimation procedures for the analysis of biophysical laboratory data.

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)
Macromolecular 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)
Macromolecular Magnetic Resonance Spectroscopy

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 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.

BIOC 704 - (3) (Y)
Statistical Thermodynamics of Biological Systems

An in-depth review of classical and statistical thermodynamics of molecular processes of biological relevance. The relationship of kinetic phenomena to thermodynamic transitions is discussed. The theoretical background is illustrated with practical biological examples.

Microbiology

MICR 803 - (5) (Y)
Fundamental Immunology
MICR 810 - (5) (Y)
Molecular Pathogenesis
MICR 811 - (5) (Y)
Gene Structure, Expression and Regulation

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.

Cell Biology

CELL 505 - (4) (Y)
Methods and Applications in Biotechnology
CELL 808 - (3) (Y)
Development of the Nervous System

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 514 - (3) (Y)
Mathematics of Derivative Securities
MATH 521 - (3) (Y)
Advanced Calculus and Applied Mathematics

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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