A graduate program in Biophysics and Structural Biology

Last updated: August 28, 2009 at 11:14 a.m.

Objectives

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 the physical sciences with undergraduate majors in any related field, such as biology, biochemistry, chemistry, engineering, mathematics, or physics. The course requirements for the PhD 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 PhD dissertation is carried out under the personal supervision of a faculty adviser; advisers 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 at: 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

Dorothee Kern, Chair
 (Biochemistry)

Jeff Gelles
 (Biochemistry)

Michael Hagan
(Physics)

Jané Kondev
 (Physics)

Christopher Miller
 (Biochemistry)

Requirements for the Degree of Master of Science

Program of Study
 This graduate program does not normally admit students to pursue the MS degree. In special cases, however, the MS degree may be awarded upon completion of an approved program of study consisting of at least six graduate-level courses in biology, physics, biochemistry, quantitative biology, 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.

Thesis
 To qualify for the MS, a student must submit a thesis reporting a substantial piece of original research carried out under the supervision of a research adviser or advisers. The master’s thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

Requirements for the Degree of Doctor of Philosophy

Program of Study
 The PhD program in biophysics and structural biology is designed to accommodate students with previous academic majors in a wide range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. Consequently, the course requirements for the PhD 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 PhD. 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 include BIOP 200b and two courses of laboratory rotations (BIOP 300a,b). In addition to the seven courses, the noncredit course CONT 300b (Ethical Practice in Health-Related Sciences) is required of all first-year students. All students beyond the first year must register for BIOP 401d. Students in their third and higher years of study will have yearly progress meetings with a faculty committee of three for the purpose of maintaining a satisfactory trajectory toward completion of the thesis defense.

Teaching Requirement
 As part of their PhD 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 PhD program. This support is provided by a combination of university funds, training grants, and faculty research grants.

Qualifying Examinations
 To qualify for the PhD degree, each student must write and defend in oral examinations two 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 PhD candidate in independent research. The dissertation research must be presented and defended in a final oral examination.

Requirements for the Degree of Doctor of Philosophy in Biophysics and Structural Biology with Specialization in Quantitative Biology

Program of Study
 Students wishing to obtain this specialization must first gain approval of the graduate program chair or quantitative biology liaison. This should be done as early as possible; ideally, during the first year of graduate studies. In order to receive the PhD in biophysics and structural biology with additional specialization in quantitative biology, candidates must complete the requirements for the PhD described above and the course requirements for the quantitative biology specialization that are described in the quantitative biology section of this Bulletin.

Any alteration to the quantitative biology course requirements must be approved by the graduate program chair and by the quantitative biology program faculty advisory committee.

Courses of Instruction

(200 and above) Primarily for Graduate Students

BIOP 200b Reading in Macromolecular Structure-Function Analysis
Required for first-year biochemistry and biophysics and structural biology graduate students.
Introduces students to chemical 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 biochemistry and biophysics. 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 author's conclusions are well justified by the experimental results. Usually offered every year.
Mr. Petsko

BIOP 300a Introduction to Research in Biophysics
Students must consult with the program chair prior to enrolling in these courses.
Students carry out four nine-week projects in the research laboratories of biological and physical science faculty members.
Staff

BIOP 300b Introduction to Research in Biophysics
A continuation of BIOP 300a.
Staff

BIOP 401d Biophysical Research Problems
Independent research for the MS or PhD degrees. All graduate students beyond the first year must register for this course. Usually offered every semester.
Staff

Required First-Year Graduate Health-Related Science Programs Course

CONT 300b Ethical Practice in Health-Related Sciences
Required of all first-year graduate students in health-related science programs. Not for credit.
Ethics is an essential aspect of 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. Usually offered every year.
Mr. Simister

Cross-Listed in Biophysics & Structural Biology

BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents.
Describes the principles of biological catalysts and the chemical logic of metabolic pathways. Discusses representative enzymes from each reaction class, with an emphasis on understanding how mechanisms are derived from experimental evidence. Topics include serine proteases, phosphatases, isomerases, carboxylases, and dehydrogenases. Usually offered every year.
Mr. Petsko

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a or equivalent.
Introduces quantitative approaches to analyzing macromolecular structure and function. Emphasizes the use of basic thermodynamics and single-molecule and ensemble kinetics to elucidate biochemical reaction mechanisms. Also discusses the physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids. Usually offered every year.
Staff

BCHM 103b Advanced Biochemistry: Cellular Information Transfer Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents.
Address fundamental issues of information transfer in biological systems at a molecular level. Topics may cover: DNA recombination and replication; transcription (DNA to RNA); processing/maturation of precursor RNA transcripts; and translation (RNA to protein). An emphasis will be placed through review of the scientific literature, our understanding of the basics of these events in different biological systems as well as how they are regulated. Usually offered every year.
Mr. Krummel

BCHM 104b Physical Chemistry of Macromolecules
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Prerequisites: CHEM 141a or equivalent and BCHM 100a or equivalent.
Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Describes overall structures of proteins, nucleic acids, and membranes in terms of the underlying molecular forces: electrostatics, hydrophobic interactions, and H-bonding. The energetics of macromolecular folding and of the linkage between ligand binding and conformational changes will also be discussed. Usually offered every year.
Mr. Theobald

PHYS 105a Biological Physics
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Physical forces in living matter are studied from the perspective offered by statistical mechanics, elasticity theory, and fluid dynamics. Quantitative models for biological structure and function are developed and used to discuss recent experiments in single-molecule biology. Usually offered every second year.
Mr. Kondev

QBIO 110a Numerical Modeling of Biological Systems
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Prerequisite: MATH 10a and b or equivalent.
Modern scientific computation applied to problems in molecular and cell biology. Covers techniques such as numerical integration of differential equations, molecular dynamics and Monte Carlo simulations. Applications range from enzymes and molecular motors to cells. Usually offered every year.
Mr. Hagan

QBIO 120b Quantitative Biology Instrumentation Laboratory
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Focuses on optical and other instruments commonly used in biomedical laboratories to make quantitative measurements in vivo and in vitro. Students disassemble and reconfigure modular instruments in laboratory exercises that critically evaluate instrument reliability and usability and investigate the origins of noise and systematic error in measurements. Usually offered every year.
Mr. Dogic

Courses of Related Interest

BCHM 170b Bioinformatics
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Prerequisites: Familiarity with computing is necessary and a basic biochemistry course is recommended. A joint offering between Brandeis University and Wellesley College.
Familiarizes students with the basic tools of bioinformatics and provides a practical guide to biological sequence analysis. Topics covered include an introduction to probability and statistics; sequence alignments; database searches; alignments and phylogenetic trees; sequence pattern discovery; structure determination by secondary structure prediction; and three-dimensional structure prediction by homology modeling. In all cases, the strengths and limitations of the methods will be discussed. Usually offered every third year.
Ms. Ringe

BCHM 171b Protein X-ray Crystallography
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A practical guide to the determination of three-dimensional structures of proteins and nucleic acids by X-ray diffraction. Students learn the theory behind diffraction from macromolecular crystals and carry out all the calculations necessary to solve a protein structure at high resolution. Usually offered every second year.
Mr. Miller and Mr. Oprian

BCHM 219b Enzyme Mechanisms
Staff

BCHM 223a Enzymology of Biofuels, Bioplastics, and Bioremediation
Mr. Oprian

BCHM 224a Single-Molecule Biochemistry and Biophysics
Mr. Gelles

BIOL 102b Structural Molecular Biology
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Prerequisites: BIOL 22a and b, or permission of the instructor.
Cells are filled with machines that carry materials about the cell, that chemically transform molecules, that transduce energy, and much more. Our understanding of how these machines work depends on understanding their structures. This introduction to the structural basis of molecular biology examines the designs of proteins, their folding and assembly, and the means whereby we visualize these structures. Usually offered every second year.
Ms. Kosinski-Collins

BIOL 103b Mechanisms of Cell Functions
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Prerequisite: BIOL 22b or permission of the instructor.
An advanced course focusing on a mechanistic understanding of cell biological processes and the methods by which these processes are elucidated. Papers are chosen to illustrate a variety of experimental approaches, including biochemistry, genetics, and microscopy. Topics include cell cycle, signal transduction, cytoskeleton and cell movement, membrane traffic, and intercellular transport. Usually offered every year.
Mr. Goode and Ms. Nicastro

CHEM 129b Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
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Topics include basic diffraction and space group theory, practical manipulations of crystals and X-ray diffraction equipment, solving crystal structures, and interpretation of structural chemistry. Course features self-paced exercises on PCs. Usually offered every second year.
Mr. Foxman

CHEM 132b Advanced Organic Chemistry: Spectroscopy
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Application of spectroscopy to the elucidation of structure and stereochemistry of organic compounds, with emphasis on modern NMR and MS methods. Usually offered every year.
Mr. Xu

CHEM 143b Kinetics, Dynamics, and Transport
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Macroscopic kinetics: elementary reactions and rate laws. Kinetic study of reaction mechanisms: techniques for kinetic measurements, fast reactions, treatment of kinetic data. Microscopic kinetics: molecular dynamics, transition state theory, reactions in the gas phase and in solution. Catalytic and chain reactions, enzyme kinetics. Nonlinear dynamics: chemical oscillations and waves. Usually offered every other year.
Mr. Jordan

CHEM 144a Computational Chemistry
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Topics in computational chemistry: applications of quantum mechanics to structural and spectroscopic analysis of small molecules; molecular dynamics and Monte Carlo simulations of biomacromolecules. Standard computational programs are used by students to perform homework exercises. Usually offered every other year.
Mr. Jordan

CHEM 246b Advanced NMR Spectroscopy
A detailed discussion of modern NMR methods will be presented. The course is designed so as to be accessible to nonspecialists, but still provide a strong background in the theory and practice of modern NMR techniques. Topics include the theory of pulse and multidimensional NMR experiments, chemical shift, scalar and dipolar coupling, NOE, spin-operator formalism, heteronuclear and inverse-detection methods, Hartmann-Hahn and spin-locking experiments. Experimental considerations such as pulse sequence design, phase cycling, and gradient methods will be discussed. Guest lecturers will provide insight into particular topics such as solid-state NMR and NMR instrumental design. Usually offered every third year.
Mr. Pochapsky

NBIO 140b Principles of Neuroscience
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Prerequisite: BIOL 22b or permission of the instructor.
Examines the basic principles of neuroscience. Topics include resting potentials, action potentials, synaptic transmission, sensory systems, motor systems, learning, neural circuits underlying behavior, neurological diseases, and mental illness. Usually offered every year.
Ms. Marder

NBIO 145b Systems Neuroscience
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Prerequisite: NBIO 140b.
A fundamental question in neuroscience is how our brains extract and compute features and functions--such as direction of motion from visual stimuli--and how experience allows the microcircuits within our brains to become better tuned to such features. Understanding these processes requires insight into the cellular and network mechanisms that give rise to them. We will begin by examining the classical literature, and then we will move on to recent advances in understanding the cellular and network properties of brain microcircuits. The course emphasizes reading from original papers, and extensive class discussion. Usually offered every year.
Ms. Turrigiano

PHYS 104a Condensed Matter Physics
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Mechanical, thermal, and electronic properties of matter including fluids, solids, liquid crystals, and polymers. Simple models of matter are developed and used to discuss recent experimental findings. Usually offered every second year.
Ms. Chakraborty

PHYS 110a Mathematical Physics
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Prerequisite: PHYS 30a, PHYS 31a (formerly PHYS 30b), or permission of the instructor.
A selection of mathematical concepts and techniques useful for formulating and analyzing physical theories. Topics may include: complex analysis, Fourier and other integral transforms, special functions, ordinary and partial differential equations (including their theory and methods for solving them), group and representation theory, and differential geometry. Usually offered every year.
Mr. Blocker

PHYS 163a Statistical Physics and Thermodynamics
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The thermal properties of matter. Derivation of thermodynamics from statistical physics. Statistical theory of fluctuations. Usually offered every year.
Mr. Hagan

PHYS 169b Advanced Laboratory
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Experiments in a range of topics in physics, possibly including selections from the following: wave optics, light scattering, Nuclear Magnetic Resonance, numerical simulation and modeling, phase transitions, laser tweezers, chaotic dynamics, and optical microscopy. Students work in depth on three or four experiments during the term. This course is co-taught with PHYS 39a. Usually offered every year.
Mr. Fraden or Mr. Samadani