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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 | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit
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 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Glover, G. (PI); Lan, P. (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: Win | Units: 3-5 | Grading: Medical Option (Med-Ltr-CR/NC)

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 | Grading: Medical Satisfactory/No Credit

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: Win | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Riedel-Kruse, I. (PI)

BIOPHYS 342A: Mechanobiology and Biofabrication Methods (BIOE 342A, 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: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

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 | Grading: Letter or Credit/No Credit

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.
Terms: Win, alternate years, not given next year | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Doniach, S. (PI)
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