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BIOPHYS 196: INTERACTIVE MEDIA AND GAMES (BIOE 196)

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.
Terms: Aut, Win, Spr | Units: 1 | Repeatable 3 times (up to 3 units total)
Instructors: ; Riedel-Kruse, I. (PI)

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, BIOE 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: ; Bryant, Z. (PI); Das, R. (PI); Ferrell, J. (PI); Harbury, P. (PI); Huang, P. (PI); Pinney, M. (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 244: Mechanotransduction in Cells and Tissues (BIOE 283, ME 244)

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.
Terms: Aut | Units: 3
Instructors: ; Chaudhuri, O. (PI); Nam, S. (TA)

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 279: Computational Biology: Structure and Organization of Biomolecules and Cells (BIOE 279, BIOMEDIN 279, CME 279, CS 279)

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.
Terms: Aut | Units: 3
Instructors: ; Dror, R. (PI); Bedi, R. (GP); El-Gabalawy, O. (TA); Fernandes, D. (GP); Ma, A. (TA); Paggi, J. (GP); Sanborn, A. (GP); Ujihara, G. (GP)

BIOPHYS 294: Cellular Biophysics (APPPHYS 294, BIO 294)

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.
Last offered: Autumn 2015 | 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.
Last offered: Winter 2016 | Units: 3

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: ; Airan, R. (PI); Altman, R. (PI); Barron, A. (PI); Bintu, L. (PI); Block, S. (PI); Boettiger, A. (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); Chu, S. (PI); Cochran, J. (PI); Cui, B. (PI); Dabiri, J. (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); Fordyce, P. (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); Huang, P. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Kundaje, A. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Li, J. (PI); Li, L. (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); Teruel, M. (PI); Theriot, J. (PI); Ting, A. (PI); Wagner, A. (PI); Wandless, T. (PI); Wang, B. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Geiselhart, K. (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 42, or equivalent.
Terms: Spr | Units: 2-3
Instructors: ; Riedel-Kruse, I. (PI); Kim, H. (TA)

BIOPHYS 315: Methods in Computational Biology (APPPHYS 315)

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.
Terms: Spr | Units: 3
Instructors: ; Doniach, S. (PI)

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

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.
Terms: Win, Sum | Units: 3
Instructors: ; Pruitt, B. (PI); Denisin, S. (TA); Wilson, R. (TA)

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

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).
Terms: Win | Units: 3
Instructors: ; Dror, R. (PI); El-Gabalawy, O. (GP); Ma, A. (GP); Ujihara, G. (GP)

BIOPHYS 392: Topics in Molecular Biophysics: Biophysics of Functional RNA (APPPHYS 392)

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.
Last offered: Autumn 2015 | Units: 3

BIOPHYS 393: Biophysics of Solvation (APPPHYS 393)

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.
Last offered: Spring 2016 | Units: 3

BIOPHYS 399: Directed Reading in Biophysics

Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum | Units: 1-18 | Repeatable for credit
Instructors: ; Airan, R. (PI); Altman, R. (PI); Barron, A. (PI); Bintu, L. (PI); Block, S. (PI); Boettiger, A. (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); Chu, S. (PI); Cochran, J. (PI); Cui, B. (PI); Dabiri, J. (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); Fordyce, P. (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); Huang, P. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Kundaje, A. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Li, J. (PI); Li, L. (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); Teruel, M. (PI); Theriot, J. (PI); Ting, A. (PI); Wandless, T. (PI); Wang, B. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Geiselhart, K. (GP)

BIOPHYS 801: TGR Project

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit
Instructors: ; Airan, R. (PI); Altman, R. (PI); Barron, A. (PI); Bintu, L. (PI); Block, S. (PI); Boettiger, A. (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); Chu, S. (PI); Cochran, J. (PI); Cui, B. (PI); Dabiri, J. (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); Fordyce, P. (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); Huang, P. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Kundaje, A. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Li, J. (PI); Li, L. (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); Teruel, M. (PI); Theriot, J. (PI); Ting, A. (PI); Wandless, T. (PI); Wang, B. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Geiselhart, K. (GP)

BIOPHYS 802: TGR Dissertation

Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit
Instructors: ; Airan, R. (PI); Altman, R. (PI); Barron, A. (PI); Bintu, L. (PI); Block, S. (PI); Boettiger, A. (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); Chu, S. (PI); Cochran, J. (PI); Cui, B. (PI); Dabiri, J. (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); Fordyce, P. (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); Huang, P. (PI); Jardetzky, T. (PI); Khosla, C. (PI); Kim, P. (PI); Kobilka, B. (PI); Kool, E. (PI); Kopito, R. (PI); Kornberg, R. (PI); Kundaje, A. (PI); Levin, C. (PI); Levitt, M. (PI); Lewis, R. (PI); Li, J. (PI); Li, L. (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); Teruel, M. (PI); Theriot, J. (PI); Ting, A. (PI); Wandless, T. (PI); Wang, B. (PI); Weis, W. (PI); Zare, R. (PI); de la Zerda, A. (PI); Frank, D. (GP); Geiselhart, K. (GP)
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