Biophysics

Faculty of the Committee on Higher Degrees in Biophysics

James M. Hogle, Edward S. Harkness Professor of Biological Chemistry and Molecular Pharmacology (Medical School) (Chair)
Howard C. Berg, Professor of Molecular and Cellular Biology and Professor of Physics
Stephen C. Blacklow, Assistant Professor of Pathology (Medical School)
George M. Church, Professor of Genetics (Medical School)
Thomas E. Ellenberger, Hsien Wu and Daisy Yen Wu Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
David R. Liu, Assistant Professor of Chemistry and Chemical Biology
Markus Meister, Jeff C. Tarr Professor of Molecular and Cellular Biology
Eugene I. Shakhnovich, Professor of Chemistry and Chemical Biology
Gregory L. Verdine, Harvard College Professor and Professor of Chemistry
Gerhard Wagner, Elkan Blout Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Christopher T. Walsh, Hamilton Kuhn Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Don C. Wiley, John L. Loeb Professor of Biochemistry and Biophysics, Tutor in Biochemical Sciences (on leave 2001-02)

Other Faculty Offering Instruction in Biophysics

John A. Assad, Assistant Professor of Neurobiology (Medical School)
Frederick Ausubel, Professor of Genetics (Medical School)
William H. Bossert, David B. Arnold, Jr. Professor of Science
Daniel Branton, Higgins Research Professor of Biology
Lewis C. Cantley, Professor of Cell Biology (Medical School)
David E. Clapham, Professor of Neurobiology (Medical School)
Jonathan B. Cohen, Professor of Neurobiology (Medical School)
R. John Collier, Maude and Lillian Presley Professor of Microbiology and Molecular Genetics (Medical School)
Bruce F. Demple, Professor of Toxicology (Public Health)
John E. Dowling, Harvard College Professor and Gordon and Llura Gund Professor of Neurosciences (on leave fall term)
Michael J. Eck, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Raymond L. Erikson, American Cancer Society Professor of Cellular and Developmental Biology
Christin A. Frederick, Associate Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Walter Gilbert, Carl M. Loeb University Professor (on leave 2001-02)
David E. Golan, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Jene A. Golovchenko, Gordon McKay Professor of Applied Physics and Professor of Physics (on leave spring term)
Edward E. Harlow, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Stephen C. Harrison, Higgins Professor of Biochemistry
J. Woodland Hastings, Paul C. Mangelsdorf Professor of Natural Sciences
Martin Karplus, Theodore William Richards Research Professor of Chemistry
Tomas Kirchhausen, Professor of Cell Biology (Medical School)
Nancy Kleckner, Herchel Smith Professor of Molecular Biology
Roberto G. Kolter, Professor of Microbiology and Molecular Genetics (Medical School)
David R. Liu, Assistant Professor of Chemistry and Chemical Biology
Jun S. Liu, Professor of Statistics
Tom Maniatis, Thomas H. Lee Professor of Molecular and Cellular Biology
Keith W. Miller, Mallinckrodt Professor of Pharmacology (Medical School)
Timothy J. Mitchison, Hasib Sabbagh Professor of Cell Biology (Medical School)
Venkatesh N. Murthy, Assistant Professor of Molecular and Cellular Biology, Tutor in Biochemical Sciences
Mara Prentiss, Professor of Physics (on leave spring term)
Tom Rapoport, Professor of Cell Biology (Medical School)
Frederick P. Roth, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Gary B. Ruvkun, Professor of Genetics (Medical School)
Bruce J. Schnapp, Associate Professor of Cell Biology (Medical School)
Stuart L. Schreiber, Morris Loeb Professor of Chemistry and Chemical Biology
Brian Seed, Professor of Genetics (Medical School)
Steven E. Shoelson, Associate Professor of Medicine (Medical School)
Pamela A. Silver, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Jack Szostak, Professor of Genetics (Medical School)
John R. Wakeley, Assistant Professor of Biology
Thomas Walz, Assistant Professor of Cell Biology (Medical School)
George M. Whitesides, Mallinckrodt Professor of Chemistry and Chemical Biology
Wing H. Wong, Professor of Statistics (FAS) and Professor of Computational Biology (Public Health)
Xiaoliang Sunney Xie, Professor of Chemistry and Chemical Biology
Gary I. Yellen, Professor of Neurobiology (Medical School)
Xiaowei Zhuang, Assistant Professor of Chemistry and Chemical Biology and of Physics

Biophysics students should consult course listings from the departments of Biology, Chemistry and Chemical Biology, Physics, Molecular and Cellular Biology (formerly) Biochemistry and Molecular Biology, Applied Mathematics, the Division of Engineering and Applied Sciences, and the Division of Medical Sciences.

For Undergraduates and Graduates

Biophysics 101. Genomics and Computational Biology
Catalog Number: 6896
George M. Church (Medical School)
Half course (fall term). Tu., 12–2; Tu., 5:30–7:30 p.m. and nine additional sections to be arranged. EXAM GROUP: 14, 15
Assesses the relationships between sequence, structure and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive functional-genomics analyses. Topics include algorithmic, statistical, database, and simulation approaches and practical applications to biotechnology, drug discovery and genetic engineering. Future opportunities and current limitations will be critically assessed. Problem sets and a course project emphasize creative, hands-on analyses using these concepts.
Prerequisite: Basic understanding of molecular biology, statistics, and computers.

Biophysics 164r (formerly Biophysics 151r). Molecular Biophysics and Biophysical Chemistry: Theory and Simulation of Macromolecules
Catalog Number: 7317 Enrollment: Limited to 18.
Eugene I. Shakhnovich
Half course (spring term). Tu., Th., 1–2:30. EXAM GROUP: 15, 16
Introduction to the principles of macromolecular structure, folding and dynamics, with emphasis on structure-function relationship. Principles of protein folding and molecular evolution. Molecular dynamics and other simulation approach to protein dynamics, enzymatic function and folding. Empirical and knowledge-based energy functions for structure prediction and design. Examples include: prediction of protein structure using ab initio and and bioinformatics approaches, theory of random and designed heteropolymers with application to protein folding and design, molecular recognition, rational drug design.
Note: Offered in alternate years. It is suggested that students enroll in Chemistry 164 when this course is bracketed. Cannot be taken for credit by students who have completed Chemistry 164.
Prerequisite: Biological Sciences 11 or 54 and one of the following: Chemistry 160, MCB 61, Physics 143, or permission of instructor.

Cross-listed Courses

Applied Mathematics 147. Non-linear Dynamical Systems
Biology 152. Population Genetics
Chemistry 160. Physical Chemistry
Chemistry 163. Molecular Biophysics and Biophysical Chemistry: Structure and Conformational Dynamics of Bio-macromolecules
[Chemistry 170. Chemical Biology]
Engineering Sciences 145. Introduction to Systems Analysis with Physiological Applications
Engineering Sciences 148. Neural Signal Processing
[MCB 112. Structure and Function of Proteins and Nucleic Acids]
[MCB 114. Structure and Function of Membrane Proteins]
MCB 129. Molecular Genetics of Neuronal Development
[MCB 138. Function of Neural Systems]
MCB 140. Introduction to Biophysics
MCB 141. Molecular and Developmental Neurobiology
MCB 150. Developmental Genetics and Genomics
*MCB 155. Molecular Mechanisms of Gene Control
MCB 169. Molecular and Cellular Immunology
MCB 176. Biochemistry of Membranes
[MCB 177. Macromolecular Assemblies in Genetic Processes]
Mathematics 115. Methods of Analysis and Applications

Primarily for Graduates

Biophysics 242r (formerly Biophysics 242). Special Topics in Biophysics
Catalog Number: 6011
Members of the Committee
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
This year the focus will be on Information Theory and Neural Systems. The course is directed by Dr. Garrett B. Stanley and will examine information theory and its application to the analysis of neural spike trains.

Cross-listed Courses

Applied Mathematics 201. Complex Function Theory with Applications
[Applied Mathematics 202. Partial Differential and Integral Equations]
BCMP 201. Proteins: Structure, Function and Catalysis
[BCMP 228. Macromolecular Crystallography and NMR]
Cell Biology 201. Molecular Biology of the Cell
[Cell Biology 211b. Growth Factors and Signal Transduction]
Chemistry 240. Statistical Mechanics
Chemistry 242. Quantum Mechanics I
Chemistry 245. Single-molecule Biophysics
Genetics 201. Principles of Genetics
[MCB 212. Topics in Biophysics]
Neurobiology 200. Introduction to Neurobiology
Neurobiology 204. Neurophysiology of Central Circuits

Graduate Courses of Reading and Research

*Biophysics 300r. Introduction to Laboratory Research
Catalog Number: 7509
James M. Hogle (Medical School) 2943 and Members of the Committee
Half course (fall term; repeated spring term). M., W., F., 4:30–5:30.
Introductory lectures by faculty members associated with the Biophysics program. Lectures are accompanied by three periods of instruction in laboratories of structural molecular biology, cell and membrane biophysics, molecular genetics and development, physical biochemistry, neurobiology and bioinformatics. Students normally spend each laboratory period in a different field. It is possible to undertake a suitable problem in mathematical biophysics in place of one of the three fields.

*Biophysics 302. Molecular Biology
Catalog Number: 8772
Walter Gilbert 1306 (on leave 2001-02)

*Biophysics 303. NMR Studies of Macromolecular Structure and Function
Catalog Number: 6135
Gerhard Wagner (Medical School) 2626

*Biophysics 309. Motile Behavior of Bacteria
Catalog Number: 2070
Howard C. Berg 1377

*Biophysics 310. Structural Molecular Biology
Catalog Number: 7980
Don C. Wiley 3598 (on leave 2001-02)

*Biophysics 311. Digital Computer Applications in Biophysics
Catalog Number: 7606
William H. Bossert 1049

*Biophysics 314. Structure of Viruses and Viral Proteins
Catalog Number: 0687
James M. Hogle (Medical School) 2943

*Biophysics 315. Structural Molecular Biology
Catalog Number: 2805
Stephen C. Harrison 3597

*Biophysics 317. Biophysical Aspects of the Visual System
Catalog Number: 4770
John E. Dowling 3545 (on leave fall term)

*Biophysics 318. Mechanisms of Circadian Rhythms, Bioluminescence
Catalog Number: 4699
J. Woodland Hastings 1311

*Biophysics 321. Molecular and Mechanical Analysis of Chromosomes
Catalog Number: 7297
Nancy Kleckner 4697

*Biophysics 322. Theoretical Studies of the Structure, Functions, and Dynamics of Molecules of Biological Interest
Catalog Number: 6525
Martin Karplus 1361

*Biophysics 323. Molecular Oncology
Catalog Number: 8284
Edward E. Harlow (Medical School) 2863

*Biophysics 327. Molecular Genetics
Catalog Number: 4202
Frederick Ausubel (Medical School) 4639

*Biophysics 328. X-Ray Crystallographic Studies of Macromolecular Structures
Catalog Number: 4010
Christin A. Frederick (Medical School) 2614

*Biophysics 329. Computational and Functional Genomics
Catalog Number: 4437
George M. Church (Medical School) 1608

*Biophysics 332. Function of Neuronal Circuits
Catalog Number: 5444
Markus Meister 3007

*Biophysics 333. Topics in Biophysics and Molecular Biology
Catalog Number: 0196
Brian Seed (Medical School) 7619

*Biophysics 335. Gene Expression
Catalog Number: 3602
Tom Maniatis 7231

*Biophysics 337. Membrane Structure and Function
Catalog Number: 1800
Keith W. Miller (Medical School) 4124

*Biophysics 338. Redox Signaling and Repair of Oxidative DNA Damage
Catalog Number: 4755
Bruce F. Demple (Public Health) 7853

*Biophysics 340. Membrane Organization and Protein-Protein Interactions in the Membrane Skeleton
Catalog Number: 7506
Daniel Branton 4139

*Biophysics 341. Structure and Function of Ligand-Gated Ion Channels
Catalog Number: 7567
Jonathan B. Cohen (Medical School) 1120

*Biophysics 343. Theory of Protein Folding and Design
Catalog Number: 6947
Eugene I. Shakhnovich 3147

*Biophysics 344. Directed Evolution and Design of Simple Cellular Systems
Catalog Number: 6277
Jack Szostak (Medical School) 7096

*Biophysics 346. Biofilm Dynamics
Catalog Number: 5538
Roberto G. Kolter (Medical School) 7727

*Biophysics 347. Membrane Dynamics; Membrane Structure
Catalog Number: 5516
David E. Golan (Medical School) 1558

*Biophysics 348. Protein Kinases, Reversible Protein Phosphorylation
Catalog Number: 4964
Raymond L. Erikson 7506

*Biophysics 349. Structural Biochemistry and Cell Biology of Intracellular Membrane Traffic
Catalog Number: 4487
Tomas Kirchhausen (Medical School) 1155

*Biophysics 351. Signal Transduction
Catalog Number: 3848
Lewis C. Cantley (Medical School) 1287

*Biophysics 352. Structure and Mechanism of DNA Replication and Repair Enzymes
Catalog Number: 2914
Thomas E. Ellenberger (Medical School) 1643

*Biophysics 353. Molecular Genetics of Development
Catalog Number: 5016
Gary B. Ruvkun (Medical School) 1366

*Biophysics 354. Structural and Chemical Biology
Catalog Number: 4420
Gregory L. Verdine 1980

*Biophysics 355. Chemical Genetics and Genomics
Catalog Number: 3035
Stuart L. Schreiber 2166

*Biophysics 356. Structure and Activity of Bacterial Toxins
Catalog Number: 6886
R. John Collier (Medical School) 7972

*Biophysics 359. Vesicular Transport; Molecular Motors
Catalog Number: 7012
Bruce J. Schnapp (Medical School) 2948

*Biophysics 360. Enzymatic Mechanisms and Antibiotic Biosynthesis
Catalog Number: 7053
Christopher T. Walsh (Medical School) 2036

*Biophysics 361. Rational Drug Design; Biomaterials Science; Biophysics
Catalog Number: 7080
George M. Whitesides 7447

*Biophysics 362. Molecular Physiology of Ion Channels
Catalog Number: 3784
Gary I. Yellen (Medical School) 3268

*Biophysics 363. Biophysics of Receptor-Ligand Interactions
Catalog Number: 8687
Stephen C. Blacklow (Medical School) 1462

*Biophysics 364. Structural Cell Biology
Catalog Number: 5528
Pamela A. Silver (Medical School) 1595

*Biophysics 365. Visual Processing in Primates
Catalog Number: 8145
John A. Assad (Medical School) 2985

*Biophysics 366. Intracellular Signal Transduction
Catalog Number: 2877
David E. Clapham (Medical School) 2987

*Biophysics 367. Structure Biology of Cytoplasmic Signal Transduction
Catalog Number: 5512
Michael J. Eck (Medical School) 1739

*Biophysics 368. Experimental Condensed Matter Physics
Catalog Number: 1400
Jene A. Golovchenko 1986 (on leave spring term)

*Biophysics 369. Organic Chemistry and Chemical Biology
Catalog Number: 6337
David R. Liu 2717

*Biophysics 370. Cytoskeleton Dynamics; Mitosis and Cell Locomotion; Small Molecule Inhibitors
Catalog Number: 8034
Timothy J. Mitchison (Medical School) 3713

*Biophysics 371. Mechanisms of Synaptic Transmission and Plasticity
Catalog Number: 2326
Venkatesh N. Murthy 2424

*Biophysics 372. Protein Transport Across the ER Membrane
Catalog Number: 6922
Tom Rapoport (Medical School) 1815

*Biophysics 373. Computational Molecular Biology
Catalog Number: 5267
Frederick P. Roth (Medical School) 3912

*Biophysics 374. High-Resolution Electron Microscopy
Catalog Number: 8225
Thomas Walz (Medical School) 3778

*Biophysics 375. Single-Molecule Biophysics
Catalog Number: 7900
Xiaoliang Sunney Xie 2290

*Biophysics 376. Computational Methods in the Study of DNA-Protein Interactions
Catalog Number: 2254
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*Biophysics 377. Stochastic Processes: Probability Theory and Statistical Inference
Catalog Number: 4768
Jun S. Liu 3760

*Biophysics 378. Structural and Cellular Biology of Insulin Signal Transduction
Catalog Number: 4856
Steven E. Shoelson (Medical School) 3951

*Biophysics 379. Theoretical Population Genetics
Catalog Number: 2274
John R. Wakeley 5680

*Biophysics 380. Microarray Data: Issues and Challenges
Catalog Number: 4402
Wing H. Wong 3759

*Biophysics 381. Single-Molecule Biophysics
Catalog Number: 3046
Xiaowei Zhuang 3991