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Course Criteria
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3.00 Credits
(Same as APPPHYS 292.) For advanced undergraduates or beginning graduate students. Quantitative models used in molecular biophysics. The relation of structure to function. Chemical equilibria, cooperativity, and control: elementary statistical mechanics, affinity plots, allostery, models of hemoglobin-oxygen binding, bacterial chemotaxis. Macromolecular conformations: polymer chain models, protein folding, taxonomy of globular proteins, general principles of sequence selection. Chemical kinetics. Multiple barriers: COmyoglobin kinetics, ion diffusion through channels and ion selectivity, spectroscopy of ion channels-acetylcholine receptor. Supramolecular kinetics: conversion of chemical energy to mechanical force, myosin and kinesin, actin polymers. Nerve impulse propagation: membrane potentials, voltage sensitive ion gates, Hodgkin-Huxley equations, propagation of the nerve impulse. 3 units, alternate years, not given this year
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3.00 Credits
Lecture/lab emphasizing analog and digital electronics for lab research. RC and diode circuits. Transistors. Feedback and operational amplifiers. Active filters and circuits. Pulsed circuits, voltage regulators, and power circuits. Precision circuits, low-noise measurement, and noise reduction techniques. Circuit simulation tools. Principles of synchronous demodulation and applications of lock-in amplifiers. Combinatorial and synchronous digital circuits. Design using programmable logic. Analog/digital conversion. Microprocessors and real time programming. Current lab interface protocols. Techniques commonly used for lab measurements. Development of student lab projects during the last three weeks of 208. Limited enrollment. Prerequisites: undergraduate device and circuit exposure. 3 units, Win (Fox, J)
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3.00 Credits
Lecture/lab emphasizing analog and digital electronics for lab research. RC and diode circuits. Transistors. Feedback and operational amplifiers. Active filters and circuits. Pulsed circuits, voltage regulators, and power circuits. Precision circuits, low-noise measurement, and noise reduction techniques. Circuit simulation tools. Principles of synchronous demodulation and applications of lock-in amplifiers. Combinatorial and synchronous digital circuits. Design using programmable logic. Analog/digital conversion. Microprocessors and real time programming. Current lab interface protocols. Techniques commonly used for lab measurements. Development of student lab projects during the last three weeks of 208. Limited enrollment. Prerequisites: undergraduate device and circuit exposure. 3 units, Spr (Fox, J), alternate years, not given next year
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3.00 Credits
(Same as STATS 214.) Topics include: random numbers, and their generation and application; disordered systems, quenching, and annealing; percolation and fractal structures; universality, the renormalization group, and limit theorems; path integrals, partition functions, and Wiener measure; random matrices; and optical estimation. Prerequisite: introductory course in statistical mechanics or analysis. 3 units, Spr (Diaconis, P; Fisher, D; Holmes, S), alternate years, not given next year
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3.00 Credits
Research and classical concepts in photon science. Photon-electron interactions; x-ray absorption and Compton scattering. X-ray spectroscopy; EXAFS, SEXAFS, edge structure, magnetic circular dichroism, and linear dichroism. Photoemission spectroscopy and many-electron effects: angle-resolved and integrated photoemission, resonance photoemission, spin-polarized photoemission. Photoelectron diffraction and holography. X-ray interactions with condensed matter: diffraction and scattering. Photon sources: synchrotron, wigglers, and undulators. Photon and electron detectors and analyzers. Prerequisite: familiarity with quantum mechanics. 3 units, alternate years, not given this year
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3.00 Credits
Recursive filtering, parameter estimation, and feedback control methods based on linear and nonlinear state-space modeling. Topics in: dynamical systems theory; practical overview of stochastic differential equations; model reduction; and tradeoffs among performance, complexity, and robustness. Numerical implementations in MATLAB. Contemporary applications in systems biology and quantum precision measurement. Prerequisites: linear algebra and ordinary differential equations. 3 units, not given this year
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3.00 Credits
Interaction of x-rays and neutrons with matter. Modern sources of radiation: synchrotrons, x-ray free electron lasers, and spallation neutron sources. Scattering formulae. Determination of molecular, crystal, and magnetic structures, and their associated charge, lattice, and magnetic excitations. Applications from condensed matter physics, materials science, biophysics, medicine, and the arts. Examples include thermal and quantum phase transitions, excitations and competing phases in high-temperature superconductors, materials under extreme pressure, structure of nanoparticles, proteins and water, computer-aided tomography, and nondestructive testing of art objects. 3 units, alternate years, not given this year
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3.00 Credits
Technology issues for a secure energy future; role of solid state physics in energy technologies. Topics include the physics principles behind future technologies related to solar energy and solar cells, solid state lighting, superconductivity, solid state fuel cells and batteries, electrical energy storage, materials under extreme condition, nanomaterials. 3 units, Win (Shen, Z), alternate years, not given next year
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3.00 Credits
(Same as BIO 223.) Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics. 3 units, alternate years, not given this year
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3.00 Credits
Structure of quantum theory emphasizing states, measurements, and probabilistic modeling. Generalized quantum measurement theory; parallels between classical and quantum probability; conditional expectation in the Schr dinger and Heisenberg pictures; covariance with respect to symmetry groups; reference frames and superselection rules. Classical versus quantum correlations; nonlocal aspects of quantum probability; axiomatic approaches to interpretation. Prerequisites: undergraduate quantum mechanics, linear algebra, and basic probability and statistics. 3 units, Aut (Mabuchi, H)
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