98-99 University Bulletin Entry for:

Biophysics and Structural Biology

(file last updated: [8/10/1998 - 15:21:22])


Graduate Program in Biophysicsand Structural Biology

The interdepartmental graduateprogram in biophysics and structural biology, leading to the degreeof doctor of philosophy, is designed to develop the student'scapacity for independent research. The program is focused on theapplication of the physical sciences to important problems inmolecular and cellular biology. It offers opportunities for studyand research in a variety of fields, including protein crystallographyand magnetic resonance spectroscopy, molecular microscopy, biophysicalchemistry, neuroscience, sensory transduction, and chemo-mechanicalenergy transduction. Applicants are expected to have strong backgroundsin physical sciences with undergraduate concentrations in anyrelated 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 complementthe student's previous academic work, with the goal of providinga broad background in the physics and chemistry of biologicalprocesses.

Research for the Ph.D. dissertationis 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 facultyresearch interests and recent publications from the program orview this information on the World Wide Web at: www.bio.brandeis.edu/pages/faculty/BioPhysicsFaculty.html.

How to Be Admitted tothe Graduate Program

The general requirements foradmission to the Graduate School are given in an earlier sectionof this Bulletin. Applications should include, in additionto letters of reference, a personal statement describing the reasonsfor the applicant's interest in the field and previous researchexperience, if any. Applicants are required to take the GraduateRecord Examination and are encouraged to visit Brandeis for interviews,if possible.

Faculty Advisory Committee

Jeff Gelles, Chair

(Biochemistry, Center for ComplexSystems)

Carolyn Cohen

(Biology, Rosenstiel Center)

David DeRosier

(Biology, Rosenstiel Center)

Seth Fraden

(Physics, Center for ComplexSystems)

Judith Herzfeld


John Lisman

(Biology, Center for ComplexSystems)

Christopher Miller


Gregory Petsko

(Biochemistry and Chemistry,Rosenstiel Center)

Thomas Pochapsky


Dagmar Ringe

(Biochemistry and Chemistry,Rosenstiel Center)

Requirements for the Degreeof Master of Science

Program of Study

The graduate program does notnormally admit students to pursue the M.S. degree. In specialcases, however, the M.S. degree may be awarded upon completionof an approved program of study consisting of at least six graduate-levelcourses in biology, physics, biochemistry, or chemistry with agrade of B- or better. Generally, the courses include BIOP 200b,BIOP 300a, and BIOP 300b.

Residence Requirement

The minimum residence requirementis 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 oforiginal research carried out under the supervision of the researchadvisor.

Requirements for the Degreeof Doctor of Philosophy

Program of Study

The graduate program in biophysicsand structural biology is designed to accomodate students withprevious academic concentrations in a wide range of fields, includingbiology, physical chemistry, engineering, and physics. Consequently,the course requirements for the Ph.D. degree are tailored to theneeds of the particular student. In consultation with each enteringstudent, the program chair formulates a program of study for thestudent based on the student's previous academic accomplishmentsand scientific interests. Successful completion of the courseslisted in the program of study fulfills the course requirementsfor the Ph.D. degree. Ordinarily, the required program of studyconsists of seven one-semester courses, of which six are completedin the student's first year. The first year courses generallyinclude the proseminar (BIOP 200b) and two courses of laboratoryrotations (BIOP 300a,b). In addition to the courses listed inthe program of study, the noncredit course CONT 300b (EthicalPractice in Health-Related Sciences) is required of all first-yearstudents.

Residence Requirement

The minimum residence requirementis three years.

Language Requirement

There is no foreign languagerequirement. However, students must demonstrate proficiency incomputer programming as a requirement for the Ph.D. degree.

Financial Support

Students may receive financialsupport (tuition and stipend) throughout their participation inthe Ph.D. program. This support is provided by a combination ofUniversity funds, training grants, and faculty research grants.


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

Qualifying Examinations

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

Dissertation and Defense

The dissertation must reportthe results of an original scientific investigation into an approvedsubject and must demonstrate the competence of the Ph.D. candidatein independent research. The dissertation research must be presentedand defended in a Final Oral Examination.

Courses of Instruction

(200 and above) Primarilyfor Graduate Students

BIOP 200b Seminar in BiophysicalResearch

Introduces students to quantitativeapproaches to biological problems through critical evaluationof the biophysical literature. Gives students practice in attackingproblems in a wide range of areas through the use of physicaland mathematical reasoning. Each week, one or two papers suitedto quantitative analysis are chosen and prepared by students.Discussion aims at identifying the core ideas of the papers andat transforming these ideas into quantitative, testable predictions.Topics include macromolecular structure and function, spectroscopicmethods of structure determination, thermodynamics of ligand-macromoleculeinteractions, stochastic approaches to electrophysiology, andelectrostatics of macromolecular surfaces, among others. In consultationwith the instructor, each student develops a research propositionbased on independent reading and prepares a research plan in theform of a mock-thesis proposal. Open to graduate students in othersciences with permission of the instructor. Usually offered everyyear.


BIOP 300a and b Introductionto Research in Biophysics

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


Students register for DissertationResearch in the 400 series with a faculty member in the programin which they are doing their research.

CONT 300b Ethical Practicein Health-Related Sciences

Required of all first-yeargraduate students in health-related science programs. Not forcredit.

Scientists are becoming increasinglyaware of the importance of addressing ethical issues and valuesassociated with scientific research. This course, taught by Universityfaculty from several graduate disciplines, covers major ethicalissues germane to the broader scientific enterprise, includingareas or applications from a number of fields of study. Lecturesand relevant case studies are complemented by two public lecturesduring the course. Usually offered every year.

Ms. Ringe

Cross-Listed Courses

BCHM 104b

Physical Chemistry of Macromolecules

BCHM 128b

Statistical Biophysics andBiochemistry

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 Transcriptionand Transcriptional Regulation

BIOL 102b

Structural Molecular Biology

BIOL 103b

Mechanisms of Cell Functions

BIOL 104a

Structural Approaches to CellBiology

CHEM 111a

Computational Chemistry

CHEM 132b

Advanced Organic Chemistry:Spectroscopy

CHEM 141b


CHEM 229b

Special Topics in InorganicChemistry: Introduction to X-Ray Structure Determination

NBIO 140b

Introductory Neuroscience

NBIO 144b

The Neurobiology of Memory

NBIO 145b

Integrative Neuroscience