University Bulletin 2001-02 Biophysics and Structural Biology University Bulletin 2001-02
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:

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)

David DeRosier

(Biology, Rosenstiel Center)

Nikolaus Grigorieff

(Biochemistry, Rosenstiel Center)

Dorothee Kern

(Biochemistry, Center for Complex Systems)

Christopher Miller

(Biochemistry, Center for Complex Systems)

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.

Teaching Requirements

As part of their Ph.D. training, students are required to assist with the teaching of two one-semester courses.

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 Biophysics and Structural Biology Proseminar

Intended for first-year biophysics and structural biology graduate students, but open to other graduate students with permission of the instructor.

Introduces students to quantitative and physical approaches to biological problems through critical evaluation of the original literature. Students analyze scientific papers on a wide range of topics in the fields of biophysics and structural biology. Discussion focuses on understanding of the scientific motivation for and experimental design of the studies. Particular emphasis is placed on making an independent determination of whether the authors' conclusions are well justified by the experimental results. In consultation with the instructor, each student also develops a research proposition based on independent reading and prepares a research plan in the form of a mock-grant proposal. Usually offered every year.

Messrs. Gelles and Miller

BIOP 300a and b Introduction to Research in Biophysics

Students must consult with the program chair prior to enrolling in these courses.

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. Usually offered every year.

Mr. Gelles and Staff

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. Lowenstein

Cross-Listed Courses

BCHM 102a

Physical Biochemistry

BCHM 104b

Physical Chemistry of Macromolecules

BIOL 105b (Formerly BIBC 105b)

Molecular Biology

Courses of Related Interest

BCHM 171b

Protein X-Ray Crystallography

BCHM 219b

Enzyme Mechanisms

BCHM 224a

Microtubule-Based Mechanoenzymes

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

Principles of Neuroscience

NBIO 145b

Systems Neuroscience