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
George M. Church, Professor of Genetics (Medical School)
Thomas E. Ellenberger, Associate Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Mara Prentiss, Professor of Physics
Stuart L. Schreiber, Morris Loeb Professor of Chemistry and Chemical Biology (on leave 1999-00)
Eugene I. Shakhnovich, Professor of Chemistry and Chemical Biology
Gregory L. Verdine, 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 fall term)

Other Faculty Offering Instruction in Biophysics

John A. Assad, Assistant Professor of Neurobiology (Medical School)
Frederick Ausubel, Professor of Genetics (Medical School)
Stephen C. Blacklow, Assistant Professor of Pathology (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)
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 the Maria Moors Cabot Professor of Natural Sciences
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, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Walter Gilbert, Carl M. Loeb University Professor (on leave spring term)
David E. Golan, Associate Professor of Medicine and Associate Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Edward E. Harlow, Professor of Genetics and American Cancer Society Research Professor of Molecular Genetics (Medical School)
Stephen C. Harrison, Higgins Professor of Biochemistry
J. Woodland Hastings, Paul C. Mangelsdorf Professor of Natural Sciences (on leave spring term)
Tomas Kirchhausen, Associate Professor of Cell Biology (Medical School)
Nancy Kleckner, Professor of Biochemistry and Molecular Biology
Roberto G. Kolter, Professor of Microbiology and Molecular Genetics (Medical School)
Stuart A. Lipton, Associate Professor of Surgery (Neuroscience) (Medical School)
Tom Maniatis, Thomas H. Lee Professor of Molecular and Cellular Biology
Markus Meister, Jeff C. Tarr Professor of Molecular and Cellular Biology
Matthew S. Meselson, Thomas Dudley Cabot Professor of the Natural Sciences
Keith W. Miller, Mallinckrodt Professor of Pharmacology (Medical School)
Timothy J. Mitchison, Professor of Cell Biology (Medical School)
Ernest G. Peralta, Professor of Molecular and Cellular Biology
Tom Rapoport, Professor of Cell Biology (Medical School)
Gary B. Ruvkun, Professor of Genetics (Medical School)
Bruce J. Schnapp, Associate Professor of Cell Biology (Medical School)
Brian Seed, Professor of Genetics (Medical School)
Pamela A. Silver, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Jack L. Strominger, Higgins Professor of Biochemistry
Jack Szostak, Professor of Genetics (Medical School)
James C. Wang, Mallinckrodt Professor of Biochemistry and Molecular Biology
George M. Whitesides, Mallinckrodt Professor of Chemistry
Gary I. Yellen, Professor of Neurobiology (Medical School)

Biophysics students should consult course listings from the departments of Biology, Chemistry, Physics, Molecular and Cellular Biology (formerly) Biochemistry and Molecular Biology, 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., Th., 11:30–1. EXAM GROUP: 13, 14
This course will assess 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 will 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 will emphasize creative, hands-on analyses using these concepts.
Note: Course will be offered in alternate years.
Prerequisite: Basic understanding of molecular biology, statistics, and computers.

[Biophysics 164r (formerly Biophysics 151r). Molecular Biophysics and Biophysical Chemistry: Simulation of Macromolecules]
Catalog Number: 7317 Enrollment: Limited to 18.
Eugene I. Shakhnovich and Oren M. Becker (Tel Aviv University)
Half course (fall term). Hours to be arranged.
Introduction to the principles and methods used for the simulation of macromolecules of biological interest. Protein conformation and dynamics are emphasized. Empirical energy and molecular dynamics calculations as well as other approaches are described. Specific problems are discussed to illustrate the methodology. Examples include the cooperative mechanism of hemoglobin, protein folding predictions, the nature of reaction rate enhancement in enzyme catalysis, motional properties of proteins, simulations of free energy changes in mutations, molecular recognition, and the properties of binding sites. The laboratory introduces students to molecular graphics and to simulation methodology. During reading period, each student carries out an original research project that makes use of the techniques.
Note: Expected to be given in 2000–01. 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 and one of the following: Chemistry 160, Biochemistry 61, Physics 143, or permission of instructor.

Cross-listed Courses

Biology 152. Population Genetics
Biology 154. Theoretical Population and Community Ecology
Chemistry 160. Physical Chemistry
Chemistry 170. Chemical Biology
Engineering Sciences 145. Introduction to Systems Analysis with Physiological Applications
Engineering Sciences 148. Bioelectric Signals and Their Processing in Neural Networks
[Engineering Sciences 149. Muscles, Reflexes, and Locomotion]
MCB 112. Structure and Function of Proteins and Nucleic Acids
*MCB 113. Principles of Genetic Analysis
MCB 121. Animal Genetic Systems
[MCB 125. Introduction to Biophysics]
MCB 129. Molecular Genetics of Neuronal Development
MCB 138. Function of Neural Systems
*MCB 155. Molecular Mechanisms of Gene Control
MCB 169. Molecular and Cellular Immunology
[MCB 170. Molecular Mechanisms of Signal Transduction ]
MCB 176. Membrane Function
MCB 177. Macromolecular Assemblies in Genetic Processes
Mathematics 115. Methods of Analysis and Applications

Primarily for Graduates

Biophysics 242. Special Topics in Biophysics
Catalog Number: 6011
Members of the Committee
Half course (spring term). Tu., Th., 2:30–4. EXAM GROUP: 16, 17
Considers special topics in Biophysics. This year’s focus will be selected topics in neuroscience.

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
Chemistry 240. Statistical Mechanics
Chemistry 242. Quantum Mechanics
Genetics 201. Principles of Genetics
MCB 212. Topics in Biophysics
[*MCB 225. Topics in Neurobiology]
Microbiology 208. Microbial and Molecular Genetics

Graduate Courses of Reading and Research

*Biophysics 300r. Introduction to Laboratory Research
Catalog Number: 7509
James M. Hogle (Medical School) 2943 and staff
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, and physical biochemistry. 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 spring term)

*Biophysics 303. NMR Studies of Protein Structure and Mobility
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 fall term)

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

*Biophysics 312. Single Channel Analysis in Mammalian Central Neurons
Catalog Number: 6350
Stuart A. Lipton (Medical School) 1346

*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

*Biophysics 318. Mechanisms of Circadian Rhythms, Bioluminescence
Catalog Number: 4699
J. Woodland Hastings 1311 (on leave spring term)

*Biophysics 319. Molecular Immunology
Catalog Number: 3500
Jack L. Strominger 1193

*Biophysics 321. Molecular and Cellular Genetics
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. Chromosome and Genome Organization
Catalog Number: 4437
George M. Church (Medical School) 1608

*Biophysics 331. Macromolecular Assemblies in DNA Transactions
Catalog Number: 6708
James C. Wang 4870

*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 and Development; Molecular Evolution
Catalog Number: 3602
Tom Maniatis 7231

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

*Biophysics 338. Molecular Biology and Enzymology
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. Structure, Function and Evolution of RNA
Catalog Number: 6277
Jack Szostak (Medical School) 7096

*Biophysics 346. Protein Secretion; DNA Gyrase Inhibitors
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. Structures of DNA Repair Enzymes and Transcription Factors
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. Protein-Nucleic Acid Interactions
Catalog Number: 4420
Gregory L. Verdine 1980

*Biophysics 355. Intracellular Signal Transduction
Catalog Number: 3035
Stuart L. Schreiber 2166 (on leave 1999-00)

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

*Biophysics 357. Molecular Genetics and Molecular Evolution
Catalog Number: 6925
Matthew S. Meselson 1319

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

*Biophysics 360. Enzymatic Reaction and Signal Transduction Mechanisms
Catalog Number: 7053
Christopher T. Walsh (Medical School) 2036

*Biophysics 361. Molecular Pharmacology; Biosurface Chemistry; Virology
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
Half Course

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