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Bulletin Archive

This archived information is dated to the 2008-09 academic year only and may no longer be current.

For currently applicable policies and information, see the current Stanford Bulletin.

Graduate courses in Biophysics

Primarily for graduate students; undergraduates may enroll with consent of instructor.

BIOPHYS 227. Functional MRI Methods

(Same as RAD 227.) 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. Recommended: neuroscience.

3 units, not given this year

BIOPHYS 228. Computational Structural Biology

(Same as SBIO 228.) Interatomic forces and interactions such as electrostatics and hydrophobicity, and protein structure in terms of amino acid properties, local chain conformation, secondary structure, domains, and families of folds. How protein motion can be simulated. Bioinformatics introduced in terms of methods that compare proteins via their amino acid sequences and their three-dimensional structures. Structure prediction via simple comparative modeling. How to detect and model remote homologues. Predicting the structure of a protein from knowledge of its amino acid sequence. Via Internet.

3 units, Aut (Levitt, M), Spr (Levitt, M)

BIOPHYS 232. Advanced Imaging Lab in Biophysics

(Same as BIO 132, BIO 232, MCP 232.) 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, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.

4 units, Spr (Block, S; Schnitzer, M; Smith, S; Stearns, T)

BIOPHYS 241. Biological Macromolecules

(Same as BIOC 241, SBIO 241.) The physical and chemical basis of macromolecular function. Forces that stabilize biopolymers with three-dimensional structures and their functional implications. Thermodynamics, molecular forces, and kinetics of enzymatic and diffusional processes, and relationship to their practical application in experimental design and interpretation. Biological function and the level of individual molecular interactions and at the level of complex processes. Case studies. Prerequisites: introductory biochemistry and physical chemistry or consent of instructor.

3-5 units, Aut (Herschlag, D; Puglisi, J; Garcia, K; Ferrell, J; Block, S; Weis, W)

BIOPHYS 242. Methods in Molecular Biophysics

(Same as SBIO 242.) 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.

3 units, Win (Weis, W; Puglisi, J), alternate years, not given next year

BIOPHYS 250. Seminar in Biophysics

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

1 unit, Aut (Weis, W), Win (Weis, W)

BIOPHYS 297. Bio-Inorganic Chemistry

(Same as CHEM 297.) 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.

3 units, alternate years, not given this year

BIOPHYS 300. Graduate Research

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

1-18 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

BIOPHYS 399. Directed Reading in Biophysics

Prerequisite: consent of instructor.

1-18 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

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