APPPHYS 208: Laboratory Electronics
Lecture/lab emphasizing analog and digital electronics for lab research. Continuation of
APPPHYS 207 with emphasis on applications of digital techniques. Combinatorial and synchronous digital circuits. Design using programmable logic. Analog/digital conversion. Microprocessors and real time programming, concepts and methods of digital signal processing techniques. Current lab interface protocols. Techniques commonly used for lab measurements. Development of student lab projects during the last three weeks. Prerequisites: undergraduate device and circuit exposure. Recommended: previous enrollment in
APPPHYS 207.
Terms: Sum, alternate years, not given next year

Units: 4

Grading: Letter (ABCD/NP)
Instructors:
Fox, J. (PI)
APPPHYS 215: Numerical Methods for Physicists and Engineers
Fundamentals of numerical methods applied to physical systems. Derivatives and integrals; interpolation; quadrature; FFT; singular value decomposition; optimization; linear and nonlinear least squares fitting; error estimation; deterministic and stochastic differential equations; Monte Carlo methods. Lectures will be accompanied by guided project work enabling each student to make rapid progress on a project of relevance to their interests.
Terms: Spr, alternate years, not given next year

Units: 4

Grading: Letter or Credit/No Credit
Instructors:
Moler, K. (PI)
APPPHYS 217: Estimation and Control Methods for Applied Physics
Recursive filtering, parameter estimation, and feedback control methods based on linear and nonlinear statespace 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.
Terms: alternate years, given next year

Units: 4

Grading: Letter or Credit/No Credit
APPPHYS 219: Solid State Physics Problems in Energy Technology
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.
Terms: alternate years, given next year

Units: 3

Grading: Letter or Credit/No Credit
APPPHYS 220: Applied Electrodynamics
Techniques for general electrodynamics, illustrated by examples from geophysics, microwave engineering, optical devices, accelerators, antennas, and plasma physics. RF/microwave structure representations, scattering matrices, treatments for periodic systems. Perturbation and variational techniques applied to approximate solutions, fundamentals of numerical techniques. Analysis methods via expansions in terms of natural modes. Introduction to finite element methods via the application of variational techniques. Laboratory experiments including time domain and frequency domain methods. Solutions of inverse electrodynamic problems via perturbation techniques coupled with lab measurements (such as estimation of a physical structure via experimental measurements and formal models). Prerequisites:
PHYSICS 121,
MATH 106 and
MATH 132, or equivalent experience.
Terms: alternate years, given next year

Units: 3

Grading: Letter or Credit/No Credit
APPPHYS 223B: Nonlinear Dynamics: This Side of Chaos
Linear dynamics, periodic systems, Hamiltonian motion and phase space. The physics of nonlinear motion: thinking in phase space. Perturbation theory, periodic orbits, resonances, stability and instability. Integrability and symplectic integration. The KAM theorem and renormalization description of the transition to chaos. Dissipation and bifurcation. Application of methods to nanoscience, lasers and accelerators, condensed matter physics and biophysics. Prerequisites: differential equations and classical mechanics.
Terms: alternate years, given next year

Units: 3

Grading: Letter or Credit/No Credit
APPPHYS 225: Probability and Quantum Mechanics
Structure of quantum theory emphasizing states, measurements, and probabilistic modeling. Generalized quantum measurement theory; parallels between classical and quantum probability; conditional expectation in the Schrödinger 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.
Terms: Win, alternate years, not given next year

Units: 3

Grading: Letter or Credit/No Credit
Instructors:
Mabuchi, H. (PI)
APPPHYS 232: Advanced Imaging Lab in Biophysics (BIO 132, BIO 232, BIOPHYS 232, GENE 232)
Laboratory and lectures. Advanced microscopy and imaging, emphasizing handson experience with stateoftheart techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrastgenerating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include singlemolecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, twophoton microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.
Terms: Spr

Units: 4

Grading: Medical Option (MedLtrCR/NC)
APPPHYS 236: Biology by the Numbers (BIOC 236)
For PhD students and advanced undergraduates. Students will develop skills in quantitative reasoning over a wide range of biological problems. Topics: biological size scales ranging from proteins to ecosystems; biological times time scales ranging from enzymatic catalysis and DNA replication to evolution; biological energy, motion and force from molecular to organismic scales; mechanisms of environmental sensing ranging from bacterial chemotaxis to vision.
Terms: alternate years, given next year

Units: 3

Grading: Medical Option (MedLtrCR/NC)
APPPHYS 240: From Atom Smashers to Xray Lasers (PHOTON 240)
Physics and impact of particle beams and accelerators from their origins up to the present state of the art. Accelerator fundamentals, special topic lectures by expert scientists, laboratory accelerator experiment using state of the art accelerators at SLAC. nPrerequisites: Advanced undergraduate courses in Maxwell's equations, special relativity, mathematical physics, and introductory quantum mechanics.
Terms: alternate years, given next year

Units: 3

Grading: Letter or Credit/No Credit
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