2000-01 Bulletin Entry for:

Biophysics and Structural Biology


Graduate Program in Biophysics and Structural Biology

The interdepartmental graduate program in biophysics and structural biology, leading to the degree of doctor of philosophy, is designed to develop the student's capacity for independent research. The program is focused on the application of the physical sciences to important problems in molecular and cellular biology. It offers opportunities for study and research in a variety of fields, including protein crystallography and magnetic resonance spectroscopy, molecular microscopy, biophysical chemistry, neuroscience, sensory transduction, and chemo-mechanical energy transduction. Applicants are expected to have strong backgrounds in physical sciences with undergraduate concentrations in any related field, such as biology, biochemistry, chemistry, engineering, mathematics, or physics. The course requirements for the Ph.D. degree are formulated individually for each student to complement the student's previous academic work, with the goal of providing a broad background in the physics and chemistry of biological processes.

Research for the Ph.D. dissertation is carried out under the personal supervision of a faculty advisor; advisors can be from any department within the School of Science. Prospective applicants should obtain the complete list of faculty research interests and recent publications from the program or view this information on the World Wide Web at: http://www.bio.brandeis.edu/biophysics

How to Be Admitted to the Graduate Program

The general requirements for admission to the Graduate School are given in an earlier section of this Bulletin. Applications should include, in addition to letters of reference, a personal statement describing the reasons for the applicant's interest in the field and previous research experience, if any. Applicants are required to take the Graduate Record Examination and are encouraged to visit Brandeis for interviews, if possible.

Faculty Advisory Committee

Jeff Gelles, Chair

(Biochemistry, Center for Complex Systems)

Carolyn Cohen

(Biology, Rosenstiel Center)

David DeRosier

(Biology, Rosenstiel Center)

Seth Fraden


Judith Herzfeld


John Lisman

(Biology, Center for Complex Systems)

Christopher Miller

(Biochemistry, Center for Complex Systems)

Gregory Petsko

(Biochemistry and Chemistry, Rosenstiel Center)

Thomas Pochapsky


Dagmar Ringe

(Biochemistry and Chemistry, Rosenstiel Center)

Requirements for the Degree of Master of Science

Program of Study

The graduate program does not normally admit students to pursue the M.S. degree. In special cases, however, the M.S. degree may be awarded upon completion of an approved program of study consisting of at least six graduate-level courses in biology, physics, biochemistry, or chemistry with a grade of B- or better. Generally, the courses include BIOP 200b, BIOP 300a, and BIOP 300b.

Residence Requirement

The minimum residence requirement is one year.

Language Requirement

There is no language requirement.


To qualify for the M.S. degree, a student must submit a thesis reporting a substantial piece of original research carried out under the supervision of the research advisor.

Requirements for the Degree of Doctor of Philosophy

Program of Study

The graduate program in biophysics and structural biology is designed to accommodate students with previous academic concentrations in a wide range of fields, including biology, physical chemistry, engineering, and physics. Consequently, the course requirements for the Ph.D. degree are tailored to the needs of the particular student. In consultation with each entering student, the program chair formulates a program of study for the student based on the student's previous academic accomplishments and scientific interests. Successful completion of the courses listed in the program of study fulfills the course requirements for the Ph.D. degree. Ordinarily, the required program of study consists of seven one-semester courses, of which six are completed in the student's first year. The first year courses generally include the proseminar (BIOP 200b) and two courses of laboratory rotations (BIOP 300a,b). In addition to the courses listed in the program of study, the noncredit course CONT 300b (Ethical Practice in Health-Related Sciences) is required of all first-year students.

Residence Requirement

The minimum residence requirement is three years.

Language Requirement

There is no language requirement.

Financial Support

Students may receive financial support (tuition and stipend) throughout their participation in the Ph.D. program. This support is provided by a combination of University funds, training grants, and faculty research grants.


As part of their Ph.D. training, students are required to participate as teaching assistants for a total of two semesters.

Qualifying Examinations

To qualify for the Ph.D. degree, each student must write and defend in oral examinations three propositions related to research in biophysics or structural biology. The subject of the second proposition must be outside the immediate area of the student's dissertation research.

Dissertation and Defense

The dissertation must report the results of an original scientific investigation into an approved subject and must demonstrate the competence of the Ph.D. candidate in independent research. The dissertation research must be presented and defended in a Final Oral Examination.

Courses of Instruction

(200 and above) Primarily for Graduate Students

BIOP 200b Seminar in Biophysical Research

Introduces students to quantitative approaches to biological problems through critical evaluation of the biophysical literature. Gives students practice in attacking problems in a wide range of areas through the use of physical and mathematical reasoning. Each week, one or two papers suited to quantitative analysis are chosen and prepared by students. Discussion aims at identifying the core ideas of the papers and at transforming these ideas into quantitative, testable predictions. Topics include macromolecular structure and function, spectroscopic methods of structure determination, thermodynamics of ligand-macromolecule interactions, stochastic approaches to electrophysiology, and electrostatics of macromolecular surfaces, among others. In consultation with the instructor, each student develops a research proposition based on independent reading and prepares a research plan in the form of a mock-thesis proposal. Open to graduate students in other sciences with permission of the instructor. Usually offered every year.


BIOP 300a and b Introduction to Research in Biophysics

Students carry out projects in the research laboratories of faculty members. Projects and faculty are selected from the departments of biochemistry, biology, chemistry, and physics. Offered every year.


Students register for Dissertation Research in the 400 series courses within the department of the faculty member with whom they are doing their research.

CONT 300b Ethical Practice in Health-Related Sciences

Required of all first-year graduate students in health-related science programs. Not for credit.

Scientists are becoming increasingly aware of the importance of addressing ethical issues and values associated with scientific research. This course, taught by University faculty from several graduate disciplines, covers major ethical issues germane to the broader scientific enterprise, including areas or applications from a number of fields of study. Lectures and relevant case studies are complemented by two public lectures during the course. Usually offered every year.

Mr. Fulton

Cross-Listed Courses

BCHM 104b

Physical Chemistry of Macromolecules

BCHM 128b

Statistical Biophysics and Biochemistry

BIBC 105b

Molecular Biology

Courses of Related Interest

BCHM 171b

Protein X-Ray Crystallography

BCHM 219b

Enzyme Mechanisms

BCHM 224a

Microtubule-Based Mechanoenzymes

BCHM 233b

Mechanisms of Transcription and Transcriptional Regulation

BIOL 102b

Structural Molecular Biology

BIOL 103b

Mechanisms of Cell Functions

BIOL 104a

Structural Approaches to Cell Biology

CHEM 111a

Computational Chemistry

CHEM 132b

Advanced Organic Chemistry: Spectroscopy

CHEM 141b


CHEM 229b

Special Topics in Inorganic Chemistry: Introduction to X-Ray Structure Determination

CHEM 235b

Advanced NMR Spectroscopy

NBIO 140b

Introductory Neuroscience

NBIO 144b

The Neurobiology of Memory

NBIO 145b

Integrative Neuroscience