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BIOPHYS 227: Functional MRI Methods (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; neuroscience recommended.
Terms: Win | Units: 3
Instructors: ; Glover, G. (PI)

BIOPHYS 232: Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIO 232, GENE 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, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.
Terms: Spr | Units: 4
Instructors: ; Block, S. (PI); Ehrhardt, D. (PI); Greenleaf, W. (PI); Schnitzer, M. (PI); Hogan, D. (TA)

BIOPHYS 241: Biological Macromolecules (BIOC 241, GENE 241, SBIO 241)

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.
Terms: Spr | Units: 3-5
Instructors: ; Das, R. (PI); Fordyce, P. (PI); Harbury, P. (PI); Yeh, E. (PI); Barrett, S. (GP); Habebo, T. (GP); Latorraca, N. (GP)

BIOPHYS 242: Methods in Molecular Biophysics (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.
Terms: Win | Units: 3
Instructors: ; Puglisi, J. (PI); Weis, W. (PI)

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.
Terms: Aut | Units: 1 | Repeatable for credit
Instructors: ; Weis, W. (PI)

BIOPHYS 300: Graduate Research

Investigations sponsored by individual faculty members. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit
Instructors: ; Altman, R. (PI); Barron, A. (PI); Block, S. (PI); Boxer, S. (PI); Brunger, A. (PI); Bryant, Z. (PI); Butte, M. (PI); Cegelski, L. (PI); Chen, X. (PI); Chu, G. (PI); Cochran, J. (PI); Cui, B. (PI); Das, R. (PI); Davis, M. (PI); Doniach, S. (PI); Dror, R. (PI); Dunn, A. (PI); Feng, L. (PI); Ferrell, J. (PI); Fisher, D. (PI); Frydman, J. (PI); Garcia, C. (PI); Glover, G. (PI); Goodman, M. (PI); Greenleaf, W. (PI); Hanawalt, P. (PI); Harbury, P. (PI); Herschlag, D. (PI); Hodgson, K. (PI); Huang, K. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Liphardt, J. (PI); Long, S. (PI); Maduke, M. (PI); Meyer, T. (PI); Moerner, W. (PI); Pande, V. (PI); Pelc, N. (PI); Prakash, M. (PI); Pruitt, B. (PI); Puglisi, J. (PI); Quake, S. (PI); Rao, J. (PI); Riedel-Kruse, I. (PI); Schnitzer, M. (PI); Skotheim, J. (PI); Smith, S. (PI); Solomon, E. (PI); Spakowitz, A. (PI); Spudich, J. (PI); Tang, S. (PI); Theriot, J. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Habebo, T. (GP); Mesa, J. (GP)

BIOPHYS 311: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 211, BIOE 311, DBIO 211)

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.
Terms: Win | Units: 2-3
Instructors: ; Riedel-Kruse, I. (PI)

BIOPHYS 342A: Mechanobiology and Biofabrication Methods (ME 342A)

Review of current cell mechanobiology topics and methods for controlling and assessing the biomechanics of living systems. Practice and theory of design and fabrication of devices for cell mechanobiology. Limited enrollment. NOTE: Compressed schedule starts 7/21 with Tu/Th lecture 10-12 in Weeks 1 and 3, and labs 9-5 (with lunch break) in Weeks 2 and 4.
| Units: 3

BIOPHYS 399: Directed Reading in Biophysics

Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit
Instructors: ; Altman, R. (PI); Barron, A. (PI); Block, S. (PI); Boxer, S. (PI); Brandman, O. (PI); Brunger, A. (PI); Bryant, Z. (PI); Butte, M. (PI); Cegelski, L. (PI); Chaudhuri, O. (PI); Chen, X. (PI); Chu, G. (PI); Cochran, J. (PI); Cui, B. (PI); Das, R. (PI); Davis, M. (PI); Doniach, S. (PI); Dror, R. (PI); Dunn, A. (PI); Feng, L. (PI); Ferrell, J. (PI); Fisher, D. (PI); Frydman, J. (PI); Garcia, C. (PI); Glover, G. (PI); Goodman, M. (PI); Greenleaf, W. (PI); Hanawalt, P. (PI); Harbury, P. (PI); Herschlag, D. (PI); Hodgson, K. (PI); Huang, K. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Liphardt, J. (PI); Long, S. (PI); Maduke, M. (PI); Meyer, T. (PI); Moerner, W. (PI); Pande, V. (PI); Pelc, N. (PI); Prakash, M. (PI); Pruitt, B. (PI); Puglisi, J. (PI); Quake, S. (PI); Rao, J. (PI); Riedel-Kruse, I. (PI); Salzman, J. (PI); Schnitzer, M. (PI); Skotheim, J. (PI); Smith, S. (PI); Solomon, E. (PI); Spakowitz, A. (PI); Spudich, J. (PI); Tang, S. (PI); Theriot, J. (PI); Wandless, T. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Habebo, T. (GP); Mesa, J. (GP)

BIOPHYS 801: TGR Project

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit
Instructors: ; Altman, R. (PI); Barron, A. (PI); Block, S. (PI); Boxer, S. (PI); Brandman, O. (PI); Brunger, A. (PI); Bryant, Z. (PI); Butte, M. (PI); Cegelski, L. (PI); Chaudhuri, O. (PI); Chen, X. (PI); Chu, G. (PI); Cochran, J. (PI); Cui, B. (PI); Das, R. (PI); Davis, M. (PI); Doniach, S. (PI); Dror, R. (PI); Dunn, A. (PI); Feng, L. (PI); Ferrell, J. (PI); Fisher, D. (PI); Frydman, J. (PI); Garcia, C. (PI); Glover, G. (PI); Goodman, M. (PI); Greenleaf, W. (PI); Hanawalt, P. (PI); Harbury, P. (PI); Herschlag, D. (PI); Hodgson, K. (PI); Huang, K. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Liphardt, J. (PI); Long, S. (PI); Maduke, M. (PI); Meyer, T. (PI); Moerner, W. (PI); Pande, V. (PI); Pelc, N. (PI); Prakash, M. (PI); Pruitt, B. (PI); Puglisi, J. (PI); Quake, S. (PI); Rao, J. (PI); Riedel-Kruse, I. (PI); Salzman, J. (PI); Schnitzer, M. (PI); Skotheim, J. (PI); Smith, S. (PI); Solomon, E. (PI); Spakowitz, A. (PI); Spudich, J. (PI); Tang, S. (PI); Theriot, J. (PI); Wandless, T. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Habebo, T. (GP); Mesa, J. (GP)

BIOPHYS 802: TGR Dissertation

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit
Instructors: ; Altman, R. (PI); Barron, A. (PI); Block, S. (PI); Boxer, S. (PI); Brandman, O. (PI); Brunger, A. (PI); Bryant, Z. (PI); Butte, M. (PI); Cegelski, L. (PI); Chaudhuri, O. (PI); Chen, X. (PI); Chu, G. (PI); Cochran, J. (PI); Cui, B. (PI); Das, R. (PI); Davis, M. (PI); Doniach, S. (PI); Dror, R. (PI); Dunn, A. (PI); Feng, L. (PI); Ferrell, J. (PI); Fisher, D. (PI); Frydman, J. (PI); Garcia, C. (PI); Glover, G. (PI); Goodman, M. (PI); Greenleaf, W. (PI); Hanawalt, P. (PI); Harbury, P. (PI); Herschlag, D. (PI); Hodgson, K. (PI); Huang, K. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Liphardt, J. (PI); Long, S. (PI); Maduke, M. (PI); Meyer, T. (PI); Moerner, W. (PI); Pande, V. (PI); Pelc, N. (PI); Prakash, M. (PI); Pruitt, B. (PI); Puglisi, J. (PI); Quake, S. (PI); Rao, J. (PI); Riedel-Kruse, I. (PI); Salzman, J. (PI); Schnitzer, M. (PI); Skotheim, J. (PI); Smith, S. (PI); Solomon, E. (PI); Spakowitz, A. (PI); Spudich, J. (PI); Tang, S. (PI); Theriot, J. (PI); Wandless, T. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Habebo, T. (GP); Mesa, J. (GP)

BIOPHYS 228: Computational Structural Biology (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.
| Units: 3

BIOPHYS 297: Bio-Inorganic Chemistry (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.
| Units: 3

BIOPHYS 371: Computational Biology in Four Dimensions (BIOMEDIN 371, CME 371, CS 371)

Computational approaches to understanding the three-dimensional spatial organization of biological systems and how that organization evolves over time. The course will cover cutting-edge research in both physics-based simulation and computational analysis of experimental data, at scales ranging from individual molecules to entire cells. 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).
| Units: 3
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