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, Herchel Smith Professor of Physics and Professor of Molecular and Cellular Biology
Stephen C. Blacklow, Associate Professor of Pathology (Medical School)
George M. Church, Professor of Genetics (Medical School)
Stephen C. Harrison, Giovanni Armenise - Harvard Professor of Basic Biomedical Science and Professor of Pediatrics (Medical School)
David R. Liu, Professor of Chemistry and Chemical Biology, Harvard College Professor (on leave 2007-08)
Markus Meister, Jeff C. Tarr Professor of Molecular and Cellular Biology
Aravinthan D. T. Samuel, Associate Professor of Physics
Eugene I. Shakhnovich, Professor of Chemistry and Chemical Biology
Gerhard Wagner, Elkan Blout Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Xiaowei Zhuang, Professor of Chemistry and Chemical Biology and of Physics

Other Faculty Offering Instruction in Biophysics

John A. Assad, Professor of Neurobiology (Medical School)
Frederick Ausubel, Professor of Genetics (Medical School)
William H. Bossert, David B. Arnold, Jr. Professor of Science
Martha L. Bulyk, Associate Professor of Medicine and Health Sciences and Technology and of Pathology (Medical School)
Lewis C. Cantley, William Bosworth Castle Professor of Medicine and Professor of Systems Biology (Medical School)
James J. Chou, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
David E. Clapham, Arlo R. Castaneda Professor of Cardiovascular Research (Medical School)
Jon Clardy, Professor of Biological Chemistry and Molecular Pharmacology (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)
David P. Corey, Professor of Neurobiology (Medical School)
Bruce F. Demple, Professor of Toxicology (Public Health)
John E. Dowling, Gordon and Llura Gund Professor of Neurosciences (FAS) and Professor of Ophthalmology (Medical School)
Michael J. Eck, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Florian Engert, Associate Professor of Molecular and Cellular Biology
Raymond L. Erikson, American Cancer Society Professor of Cellular and Developmental Biology
Rachelle Gaudet, Associate Professor of Molecular and Cellular Biology
David E. Golan, Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Jene A. Golovchenko, Rumford Professor of Physics and Gordon McKay Professor of Applied Physics
Edward E. Harlow, Virginia and D.K. Ludwig Professor of Cancer Research and Teaching (Medical School)
J. Woodland Hastings, Paul C. Mangelsdorf Professor of Natural Sciences (on leave spring term)
Donald E. Ingber, Judah Folkman Professor of Vascular Biology (Medical School)
David Jeruzalmi, Associate Professor of Molecular and Cellular Biology
Tomas Kirchhausen, Professor of Cell Biology (Medical School)
Roy Kishony, Associate Professor of Systems Biology (Medical School)
Nancy Kleckner, Herchel Smith Professor of Molecular Biology (on leave spring term)
Roberto G. Kolter, Professor of Microbiology and Molecular Genetics (Medical School)
Galit Lahav, Assistant Professor of Systems Biology (Medical School)
Jun S. Liu, Professor of Statistics (on leave spring term)
Gavin MacBeath, Associate Professor of Chemistry and Chemical Biology
Thomas Maniatis, Jeremy R. Knowles Professor of Molecular and Cellular Biology
Jarrod Marto, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Keith W. Miller, Mallinckrodt Professor of Pharmacology (Medical School)
Timothy J. Mitchison, Hasib Sabbagh Professor of Systems Biology (Medical School)
Andrew W. Murray, Herchel Smith Professor of Molecular Genetics
Venkatesh N. Murthy, Professor of Molecular and Cellular Biology, Tutor in Biochemical Sciences
Erin K. O’Shea, Professor of Molecular and Cellular Biology and of Chemistry and Chemical Biology
David Pellman, Associate Professor of Pediatrics (Medical School)
Mara Prentiss, Mallinckrodt Professor of Physics
Tom Rapoport, Professor of Cell Biology (Medical School)
Frederick P. Roth, Associate Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Gary B. Ruvkun, Professor of Genetics (Medical School)
Bernardo L. Sabatini, Associate Professor of Neurobiology (Medical School)
Stuart L. Schreiber, Morris Loeb Professor of Chemistry
Brian Seed, Professor of Genetics and Professor of Health Sciences and Technology (Medical School)
Jagesh V. Shah, Assistant Professor of Systems Biology, of Medicine, and of Health Sciences and Technology (Medical School)
William Shih, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Steven E. Shoelson, Professor of Medicine (Medical School)
Pamela A. Silver, Professor of Systems Biology (Medical School)
Timothy A. Springer, Latham Family Professor of Pathology (Medical School)
Shamil R. Sunyaev, Assistant Professor of Medicine and Health Sciences and Technology (Medical School)
Jack Szostak, Professor of Genetics (Medical School)
Antoine van Oijen, Assistant Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Gregory L. Verdine, Erving Professor of Chemistry
John R. Wakeley, Professor of Organismic and Evolutionary Biology
Christopher T. Walsh, Hamilton Kuhn Professor of Biological Chemistry and Molecular Pharmacology (Medical School)
Ronald L. Walsworth, Senior Lecturer on Physics
Thomas Walz, Professor of Cell Biology (Medical School)
George M. Whitesides, Woodford L. and Ann A. Flowers University Professor
Kai Wucherpfennig, Professor of Neurology (Medical School)
Xiaoliang Sunney Xie, Professor of Chemistry and Chemical Biology (on leave 2007-08)
Gary I. Yellen, Professor of Neurobiology (Medical School)

Biophysics students should consult course listings from the departments of Life Sciences, Chemistry and Chemical Biology, Physics, Molecular and Cellular Biology, the Division of Engineering and Applied Sciences (Applied Mathematics, Applied Physics, Computer Sciences, Engineering Sciences), Systems Biology, 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 (spring term). Section I: Tu., Th., 10–11:30; Section ll: Tu., Th., 2–3:30. EXAM GROUP: 12, 13
Focuses on modern technologies with exponential growth and their impact on global quality of life through weekly updated Wiki class project (in-depth case studies on personal genomics and/or biofuels). Integrating knowledge, tools for research, and commercial decision-making concerning new aspects of bioengineering, personalized medicine, genetically modified organisms, and stem cells. Interplays of biophysical, ecological, economic, and social/ethical modeling will be explored through multi-disciplinary teams of students, and individual brief reports.
Note: Expected to be given in 2008–09.

Biophysics 170. Quantitative Genomics
Catalog Number: 3598
Shamil R. Sunyaev (Medical School), Isaac S. Kohane (Medical School), Leonid Mirny and members of the Committee
Half course (fall term). M., W., 2:30–4. EXAM GROUP: 7, 8
Introduction to genomics with in-depth study of four areas: models of evolution and population genetics; comparative genomics: analysis and comparison; structural genomics: protein structure, evolution and interactions; functional genomics, gene expression, structure and dynamics of regulatory networks.
Note: Offered jointly with the Medical School as HT 508.

Cross-listed Courses

Applied Mathematics 105a. Complex and Fourier Analysis
Applied Mathematics 105b. Ordinary and Partial Differential Equations
Applied Mathematics 115. Mathematical Modeling
Applied Mathematics 147. Nonlinear Dynamical Systems
Chemistry 160. Physical Chemistry
Chemistry 161. Statistical Thermodynamics
Chemistry 163. Frontiers in Biophysics
*Chemistry 165. Experimental Physical Chemistry
Engineering Sciences 145. Physiological Systems Analysis
[Engineering Sciences 148. Neural Signal Processing]
Engineering Sciences 156. Signals and Systems
[Mathematics 115. Methods of Analysis]
MCB 105. Systems Neuroscience
MCB 111 (formerly MCB 211). Mathematics in Biology
MCB 115. Cellular Basis of Neuronal Function
[MCB 117. Experimental Neuroscience]
*MCB 129. Molecular Genetics of Neural Development and Behavior
MCB 140. Introduction to Biophysics
MCB 150. Developmental Genetics and Genomics
*MCB 155. Molecular Mechanisms of Gene Control
MCB 156. Structural Biology of the Flow of Information in the Cell
MCB 169. Molecular and Cellular Immunology
MCB 176. Biochemistry of Membranes
[OEB 152. Population Genetics]

Primarily for Graduates

[Biophysics 204. Structural Biology From Molecules to Cells]
Catalog Number: 1728
Stephen C. Harrison (Medical School)
Half course (spring term). Hours to be arranged.
Imaging of molecules and of molecular localization in cells, including x-ray and electron crystallography, electron microscopy of single molecules, and high-resolution light microscopy. Lectures and student presentations of selected papers from the literature.
Note: Expected to be given in 2008–09.

Biophysics 205. Computational and Functional Genomics
Catalog Number: 6777 Enrollment: Limited to 20.
Frederick P. Roth (Medical School), Martha L. Bulyk (Medical School), and Shamil R. Sunyaev (Medical School)
Half course (spring term). M., W., 3–4:30. EXAM GROUP: 8, 9
Experimental functional genomics, computational prediction of gene function, and properties and models of complex biological systems. The course will primarily involve critical reading and discussion rather then lectures.
Prerequisite: Molecular Biology (MCB 52 or equivalent), solid understanding of basic probability and statistics.

Biophysics 242r. Special Topics in Biophysics
Catalog Number: 6011
James M. Hogle (Medical School), Kenneth B. Crozier, and Marko Loncar
Half course (spring term). M., W., 11:30–1.
This year’s topic will focus on Nanophotonics and its applications in Physics and Biology.

Cross-listed Courses

Applied Mathematics 201. Physical Mathematics I
Applied Mathematics 202. Physical Mathematics II
BCMP 200. Molecular Biology
BCMP 201. Proteins: Structure, Function and Catalysis
[BCMP 228. Macromolecular NMR]
Cell Biology 201. Molecular Biology of the Cell
Chemical Biology 2100 (formerly Biophysics 201). Organic Chemistry for Biologists
*Chemistry 242. Quantum Mechanics I
*Chemistry 270. Chemical Biology
[*Chemistry 280 (formerly Chemistry 180). Macromolecular Structure and Function]
Genetics 201. Principles of Genetics
[MCB 212. Topics in Biophysics]
Microbiology 200. Molecular Microbiology and Pathogenesis
*Microbiology 205. Mechanisms of Microbial Pathogenesis
Neurobiology 200. Introduction to Neurobiology
Neurobiology 204. Neurophysiology of Central Circuits
*Neurobiology 221. Molecular Neurobiology
[Statistics 215. Fundamentals of Computational Biology]
Systems Biology 200 (formerly Systems Biology 101). A Systems Approach to Biology

Graduate Courses of Reading and Research

*Biophysics 300. 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., at 4:30.
Introductory lectures by associated Biophysics faculty members. Lectures accompanied by three periods of instruction in laboratories of structural biology, cell and membrane biophysics, molecular genetics and development, neurobiology, bioinformatics, and physical biochemistry.

*Biophysics 301. Quantitative Proteomics of Cancer Progression
Catalog Number: 1302
Jarrod Marto (Medical School) 5326

*Biophysics 302. Quantitative Analysis of Regulatory Networks - (New Course)
Catalog Number: 4405
Erin K. O’Shea 5239

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

*Biophysics 304. Basic Mechanisms of T cell Mediated Autoimmune Diseases
Catalog Number: 5921
Kai Wucherpfennig (Medical School) 2481

*Biophysics 305. Experimental Atomic Physics, Biophysics, and Soft Matter Physics
Catalog Number: 8626
Ronald L. Walsworth 2263

*Biophysics 306. Quantitative Models of Cellular Behavior to Investigate Protein Function
Catalog Number: 4339
Jagesh V. Shah (Medical School) 5248

*Biophysics 307. Dynamics of Network Motifs in Single Living Human Cells
Catalog Number: 9749
Galit Lahav (Medical School) 5247

*Biophysics 308. System-level Genetic Networks - (New Course)
Catalog Number: 1036
Roy Kishony (Medical School) 5501

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

*Biophysics 310. Sensory Information in Neuronal Processes - (New Course)
Catalog Number: 6651
Naoshige Uchida 5745

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

*Biophysics 312. Multiphoton Microscopy in Imaging Alzheimer’s Disease - (New Course)
Catalog Number: 5860
James M. Hogle (Medical School) 2943, and Brian Bacskai

*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 (Medical School) 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 321. Molecular and Mechanical Analysis of Chromosomes
Catalog Number: 7297
Nancy Kleckner 4697 (on leave spring term)

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

*Biophysics 343. Theoretical Protein Science, Bioinformatics, Computational Chemistry
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 353. Molecular Genetics of Development
Catalog Number: 5016
Gary B. Ruvkun (Medical School) 1366

*Biophysics 354. Structural Biology and Cancer Drug Discovery
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 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. Systems 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. Imaging, Optics, and Biology
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. Probing Polymers with Nanospores, Experimental Condensed Matter Physics
Catalog Number: 1400
Jene A. Golovchenko 1986

*Biophysics 369. Organic Chemistry and Chemical Biology of Molecular Evolution
Catalog Number: 6337
David R. Liu 2717 (on leave 2007-08)

*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 (on leave 2007-08)

*Biophysics 376. Functional and Computational Genomics Studies of Transcription Factors and Cis Regulatory Elements
Catalog Number: 2254
Martha L. Bulyk (Medical School) 4259

*Biophysics 377. Statistical Theory and Inference for Stochastic Processes: With Applications to Bioinformatics
Catalog Number: 4768
Jun S. Liu 3760 (on leave spring term)

*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
James M. Hogle (Medical School) 2943 and Leonid Mirny 5773

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

*Biophysics 382. Regulation of Synaptic Transmission and Dendritic Function in the Mammalian Brain
Catalog Number: 6116
Bernardo L. Sabatini (Medical School) 4300

*Biophysics 384. NMR Spectroscopy on Membrane-associated Proteins and Peptides
Catalog Number: 4531
James J. Chou (Medical School) 4950

*Biophysics 385. Small Molecule Signaling, Biosynthesis, and Drug Discovery
Catalog Number: 8378
Jon Clardy (Medical School) 4667

*Biophysics 386. Synaptic Plasticity and Neuronal Networks
Catalog Number: 3012
Florian Engert 4290

*Biophysics 387. Structural Studies of the Stereochemistry of Signaling and Transport through Biological Membranes
Catalog Number: 6869
Rachelle Gaudet 4413

*Biophysics 388. Structural Studies of Nucleo-Protein Assemblies
Catalog Number: 1543
David Jeruzalmi 4528

*Biophysics 389. Chemical Biology and Systems Biology
Catalog Number: 4245
Gavin MacBeath 4347

*Biophysics 390. Regulation of Mitosis
Catalog Number: 2157
Andrew W. Murray 3765

*Biophysics 391. Computational Methods in Genetics, Genomics and Proteomics
Catalog Number: 7043
Shamil R. Sunyaev (Medical School) 4671

*Biophysics 392. Biophysics of Mechanosensation
Catalog Number: 2687
David P. Corey (Medical School) 1345

*Biophysics 393. The Mechanics and Regulation of Mitosis
Catalog Number: 6759
David Pellman (Medical School) 3702

*Biophysics 394. Experimental Biophysics
Catalog Number: 7138
Mara Prentiss 2741

*Biophysics 395. Biophysics of Cell Adhesion and Vascular Shear Flow
Catalog Number: 3918
Timothy A. Springer (Medical School) 6145

*Biophysics 396. Behavioral Neuroscience and Neurophysiology
Catalog Number: 0966
Aravinthan D. T. Samuel 4625

*Biophysics 397. Research in Integrin Signaling, Cytoskeleton, and Control of Angiogenesis
Catalog Number: 2982
Donald E. Ingber (Medical School) 2832

*Biophysics 398. Single-Molecule Novel Fluorescence and Nano-Manipulation Studies of Protein-Protein and Protein-Nucleic Acid Interactions
Catalog Number: 2547
Antoine van Oijen (Medical School) 5084

*Biophysics 399. Biomolecular Nanotechnology
Catalog Number: 8294
William Shih (Medical School) 5256