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Office: 1215 Welch Road, Modular A, Room 87 & 89
Mail Code: 94305-5417
Phone: (650) 723-7576; (650) 498-8179
Email: biophysics@med.stanford.edu
Web Site: http://med.stanford.edu/biophysics

Courses offered by the Biophysics Program are listed under the subject code BIOPHYS on the Stanford Bulletin's ExploreCourses web site.

The Biophysics Program offers instruction and research opportunities leading to the Ph.D. in Biophysics. Students admitted to the program may perform their graduate research in any appropriate department.

The Stanford Biophysics Program is an interdisciplinary, interdepartmental training program leading to the Ph.D. Degree in biophysics. The program centers on understanding biological function in terms of physical and chemical principles. The Program comprises faculty from 16 departments in the Schools of Humanities and Sciences, Medicine, Engineering, and the Stanford Synchrotron Radiation Laboratory. Research in the Program involves two overlapping branches of biophysics: the application of physical and chemical principles and methods to solving biological problems, and the development of new methods.

The Biophysics Program aims to train students in quantitative approaches to biological problems, while also developing their perspective in choosing forefront biological problems. A balanced academic program is tailored to the diverse backgrounds of the students. The program requires graduate-level coursework in physical and biological sciences, participation in seminar series, and most importantly achievement of a high level of proficiency in independent research.

Learning Outcomes (Graduate)

The Ph.D. is conferred upon candidates who have demonstrated substantial scholarship and the ability to conduct independent research and analysis in Biophysics. Through completion of advanced course work and rigorous skills training, the doctoral program prepares students to make original contributions to the knowledge of Biophysics and to interpret and present the results of such research.

 

 

Graduate Program in Biophysics

For information on the University's basic requirements for the Ph.D. degree, see the "Graduate Degrees" section of this bulletin.

A small number of qualified applicants are admitted to the program each year. Applicants should present strong undergraduate backgrounds in the physical sciences and mathematics. The graduate course program, beyond the stated requirements, is worked out for each student individually with the help of appropriate advisers from the Committee on Biophysics.

The requirements and recommendations for applying to the Ph.D. Program in Biophysics include:

Units
CHEM 131Organic Polyfunctional Compounds3
CHEM 171Physical Chemistry I4
CHEM 173Physical Chemistry II3
CHEM 175Physical Chemistry III3
BIOC 200Applied Biochemistry2

Ph.D. students in the Program in Biophysics are required to complete the following course requirements:

Units
BIOPHYS 241Biological Macromolecules3-5
or BIOE 300A Molecular and Cellular Bioengineering
BIOPHYS 242Methods in Molecular Biophysics (offered every other year)3
BIOPHYS 250Seminar in Biophysics1
MED 255The Responsible Conduct of Research1
AND, 4 graduate level courses in physical or biological science, with
at least 1 course in physical science
at least 1 course in literature-based biological science
  1. Training in a major with connections to biophysics such as physics, chemistry, or biology, with a quantitative background equivalent to that of an undergraduate physics or chemistry major at Stanford.
  2. Opportunities for teaching are available during the first nine quarters, at the discretion of the advising committee.
  3. The student must prepare a dissertation proposal defining the research to be undertaken, including methods of procedure. This proposal should be submitted by Autumn Quarter of the second year, and it must be approved by a committee of at least three members, including the principal research adviser and at least one member from the Biophysics Program. The candidate must defend the dissertation proposal in an oral examination. The dissertation reading committee normally evolves from the dissertation proposal review committee.
  4. The student must present a Ph.D. dissertation as the result of independent investigation that expresses a contribution to knowledge in the field of biophysics.
  5. The student must pass the University oral exam, taken only after the student has substantially completed the dissertation research. The examination is preceded by a public seminar in which the research is presented by the candidate.

Emeritus:

  • Harden M. McConnell (Chemistry)
  • Stephen J. Smith (Molecular & Cellular Physiology)

Director:

  • KC Huang (Bioengineering)

Professors:

  • Russ Altman (Bioengineering, Genetics, Medicine - Biomedical Informatics)
  • Steve M. Block (Applied Physics, Biology)
  • Steven Boxer (Chemistry)
  • Axel Brunger (Molecular & Cellular Physiology)
  • Gilbert Chu (Oncology, Biochemistry)
  • Steven Chu (Physics, Molecular & Cellular Physiology)
  • Mark Davis (Microbiology & Immunology)
  • Sebastian Doniach (Physics, Applied Physics)
  • James Ferrell (Chemical & Systems Biology, Biochemistry)
  • Daniel Fisher (Applied Physics)
  • Judith Frydman (Biology, Genetics)
  • Chris Garcia (Molecular & Cellular Physiology, Structural Biology)
  • Miriam Goodman (Molecular & Cellular Physiology)
  • Philip C. Hanawalt (Biology, Dermatology)
  • Daniel Herschlag (Biochemistry)
  • Keith O. Hodgson (Chemistry)
  • Theodore Jardetzky (Structural Biology)
  • Peter S. Kim (Biochemistry)
  • Brian Kobilka (Molecular & Cellular Physiology)
  • Eric Kool (Chemistry)
  • Ron Kopito (Biology)
  • Roger D. Kornberg (Structural Biology)
  • Craig Levin (Radiology)
  • Michael Levitt (Structural Biology)
  • Richard Lewis (Molecular & Cellular Physiology)
  • Sharon Long (Biology)
  • Tobias Meyer (Chemical & Systems Biology)
  • W. E. Moerner (Chemistry)
  • Vijay Pande (Chemistry)
  • Norbert Pelc (Bioengineering, Radiology)
  • Joseph D. Puglisi (Structural Biology)
  • Stephen Quake (Bioengineering, Applied Physics)
  • Edward I. Solomon (Chemistry)
  • James A. Spudich (Biochemistry)
  • Julie Theriot (Biochemistry, Microbiology & Immunology)
  • Thomas Wandless (Chemical & Systems Biology)
  • William I. Weis (Structural Biology, Molecular & Cellular Physiology)
  • Richard Zare (Chemistry)

Associate Professors:

  • Annelise Barron (Bioengineering)
  • Zev Bryant (Bioengineering)
  • Jennifer Cochran (Bioengineering)
  • Bianxiao Cui (Chemistry)
  • Rhiju Das (Biochemistry)
  • Ron Dror (Computer Science)
  • Pehr Harbury (Biochemistry)
  • KC Huang (Bioengineering)
  • Jan Liphardt (Bioengineering)
  • Merritt Maduke (Molecular & Cellular Physiology)
  • Beth Pruitt (Mechanical Engineering)
  • Jianghong Rao (Radiology)
  • Mark Schnitzer (Biology, Applied Physics)
  • Andrew Spakowitz (Chemical Engineering)

Assistant Professors:

  • Onn Brandman (Biochemistry)
  • Manish Butte (Pediatrics)
  • Lynette Cegelski (Chemistry)
  • Ovijit Chaudhuri (Mechanical Engineering)
  • Adam de la Zerda (Structural Biology)
  • Alexander Dunn (Chemical Engineering)
  • Liang Feng (Molecular & Cellular Physiology)
  • Polly Fordyce (Genetics)
  • William Greenleaf (Genetics)
  • Anshul Kundaje (Genetics, Computer Science)
  • Jin Billy Li (Genetics)
  • Lingyin Li (Biochemistry)
  • Manu Prakash (Bioengineering)
  • Ingmar H. Riedel-Kruse (Bioengineering)
  • Julia Salzman (Biochemistry)
  • Jan Skotheim (Biology)
  • Sindy Tang (Mechanical Engineering)
  • Mary Teruel (Chemical & Systems Biology)
  • Bo Wang (Bioengineering)

Courses

BIOPHYS 196. INTERACTIVE MEDIA AND GAMES. 1 Unit.

Interactive media and games increasingly pervade and shape our society. In addition to their dominant roles in entertainment, video games play growing roles in education, arts, and science. This seminar series brings together a diverse set of experts to provide interdisciplinary perspectives on these media regarding their history, technologies, scholarly research, industry, artistic value, and potential future.
Same as: BIOE 196

BIOPHYS 227. Functional MRI Methods. 3 Units.

Basics of functional magnetic resonance neuroimaging, including data acquisition, analysis, and experimental design. Journal club sections. Cognitive neuroscience and clinical applications. Prerequisites: basic physics, mathematics; neuroscience recommended.
Same as: RAD 227

BIOPHYS 232. Advanced Imaging Lab in Biophysics. 4 Units.

Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.
Same as: APPPHYS 232, BIO 132, BIO 232, GENE 232

BIOPHYS 241. Biological Macromolecules. 3-5 Units.

The physical and chemical basis of macromolecular function. Topics include: forces that stabilize macromolecular structure and their complexes; thermodynamics and statistical mechanics of macromolecular folding, binding, and allostery; diffusional processes; kinetics of enzymatic processes; the relationship of these principles to practical application in experimental design and interpretation. The class emphasizes interactive learning, and is divided equally among lectures, in-class group problem solving, and discussion of current and classical literature. Enrollment limited to 50. Prerequisites: Background in biochemistry and physical chemistry recommended but material available for those with deficiency in these areas; undergraduates with consent of instructor only.
Same as: BIOC 241, BIOE 241, SBIO 241

BIOPHYS 242. Methods in Molecular Biophysics. 3 Units.

Experimental methods in molecular biophysics from theoretical and practical standpoints. Emphasis is on X-ray diffraction, nuclear magnetic resonance, and fluorescence spectcroscopy. Prerequisite: physical chemistry or consent of instructor.
Same as: SBIO 242

BIOPHYS 244. Mechanotransduction in Cells and Tissues. 3 Units.

Mechanical cues play a critical role in development, normal functioning of cells and tissues, and various diseases. This course will cover what is known about cellular mechanotransduction, or the processes by which living cells sense and respond to physical cues such as physiological forces or mechanical properties of the tissue microenvironment. Experimental techniques and current areas of active investigation will be highlighted.
Same as: BIOE 283, ME 244

BIOPHYS 250. Seminar in Biophysics. 1 Unit.

Required of Biophysics graduate students. Presentation of current research projects and results by faculty in the Biophysics program. May be repeated for credit.

BIOPHYS 279. Computational Biology: Structure and Organization of Biomolecules and Cells. 3 Units.

Computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules and cells. These computational methods play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course topics include protein structure prediction, protein design, drug screening, molecular simulation, cellular-level simulation, image analysis for microscopy, and methods for solving structures from crystallography and electron microscopy data. Prerequisites: elementary programming background (CS 106A or equivalent) and an introductory course in biology or biochemistry.
Same as: BIOE 279, BIOMEDIN 279, CME 279, CS 279

BIOPHYS 294. Cellular Biophysics. 3 Units.

Physical biology of dynamical and mechanical processes in cells. Emphasis is on qualitative understanding of biological functions through quantitative analysis and simple mathematical models. Sensory transduction, signaling, adaptation, switches, molecular motors, actin and microtubules, motility, and circadian clocks. Prerequisites: differential equations and introductory statistical mechanics.
Same as: APPPHYS 294, BIO 294

BIOPHYS 297. Bio-Inorganic Chemistry. 3 Units.

Overview of metal sites in biology. Metalloproteins as elaborated inorganic complexes, their basic coordination chemistry and bonding, unique features of the protein ligand, and the physical methods used to study active sites. Active site structures are correlated with function. Prerequisites: 153 and 173, or equivalents.
Same as: CHEM 297

BIOPHYS 300. Graduate Research. 1-18 Unit.

Investigations sponsored by individual faculty members. Prerequisite: consent of instructor.

BIOPHYS 311. Biophysics of Multi-cellular Systems and Amorphous Computing. 2-3 Units.

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 41, BIOE 42, or equivalent.
Same as: BIOE 211, BIOE 311, DBIO 211

BIOPHYS 315. Methods in Computational Biology. 3 Units.

Methods of bioinformatics and biomolecular modeling from the standpoint of biophysical chemistry. Methods of genome analysis; cluster analysis, phylogenetic trees, microarrays; protein, RNA and DNA structure and dynamics, structural and functional homology; protein-protein interactions and cellular networks; molecular dynamics methods using massively parallel algorithms.
Same as: APPPHYS 315

BIOPHYS 342A. Mechanobiology and Biofabrication Methods. 3 Units.

Cell mechanobiology topics including cell structure, mechanical models, and chemo-mechanical signaling. Review and apply methods for controlling and analyzing the biomechanics of cells using traction force microscopy, AFM, micropatterning and cell stimulation. Practice and theory for the design and application of methods for quantitative cell mechanobiology.
Same as: ME 342A

BIOPHYS 371. Computational Biology in Four Dimensions. 3 Units.

Cutting-edge research on computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules, cells, and everything in between. These techniques, which draw on approaches ranging from physics-based simulation to machine learning, play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course is devoted primarily to reading, presentation, discussion, and critique of papers describing important recent research developments. Prerequisite: CS 106A or equivalent, and an introductory course in biology or biochemistry. Recommended: some experience in mathematical modeling (does not need to be a formal course).
Same as: BIOMEDIN 371, CME 371, CS 371

BIOPHYS 392. Topics in Molecular Biophysics: Biophysics of Functional RNA. 3 Units.

Survey of methods used to relate RNA sequences to the structure and function of transcribed RNA molecules. Computation of contributions of the counter-ion cloud to the dependence of free energy on conformation of the folded RNA. The relation of structure to function of riboswitches and ribozymes.
Same as: APPPHYS 392

BIOPHYS 393. Biophysics of Solvation. 3 Units.

Statistical mechanics of water-protein or water-DNA (or RNA) interactions; effects of coulomb forces on molecular hydration shells and ion clouds; limitations of the Poisson-Boltzmann equations; DNA collapse, DNA-protein interactions; structure-function relationships in ion channels.
Same as: APPPHYS 393

BIOPHYS 399. Directed Reading in Biophysics. 1-18 Unit.

Prerequisite: consent of instructor.

BIOPHYS 801. TGR Project. 0 Units.

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BIOPHYS 802. TGR Dissertation. 0 Units.

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