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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 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 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 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)
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