### Courses

**APPPHYS 10AX. The Expressive Vessel: An Immersive Introduction to Clay. 2 Units.**

Students learn to make and to analyze functional ceramic forms with a focus on wheel-thrown pottery. Studio time dedicated to the acquisition and refinement of shaping, marking/glazing and finishing skills; supplementary lectures and discussions to explore contemporary studio ceramics and major historical traditions. No prior experience necessary; instructors will tailor assignments for students at all levels of ability.

**APPPHYS 77N. Functional Materials and Devices. 3 Units.**

Preference to freshmen. Exploration via case studies how functional materials have been developed and incorporated into modern devices. Particular emphasis is on magnetic and dielectric materials and devices. Recommended: high school physics course including electricity and magnetism.

**APPPHYS 79N. Energy Options for the 21st Century. 3 Units.**

Preference to freshmen. Choices for meeting the future energy needs of the U.S. and the world. Basic physics of energy sources, technologies that might be employed, and related public policy issues. Trade-offs and societal impacts of different energy sources. Policy options for making rational choices for a sustainable world energy economy.

**APPPHYS 100. The Questions of Clay: Craft, Creativity and Scientific Process. 5 Units.**

Students will create individual studio portfolios of ceramic work and pursue technical investigations of clay properties and the firing process using modern scientific equipment. Emphasis on development of creative process; parallels between science and traditional craft; integration of creative expression with scientific method and analysis. Prior ceramics experience desirable but not necessary. Limited enrollment. Prerequisite: any level of background in physics.

**APPPHYS 201. Electrons and Photons. 4 Units.**

Applied Physics Core course appropriate for graduate students and advanced undergraduate students with prior knowledge of elementary quantum mechanics, electricity and magnetism, and special relativity. Interaction of electrons with intense electromagnetic fields from microwaves to x- ray, including electron accelerators, x-ray lasers and synchrotron light sources, attosecond laser-atom interactions, and x-ray matter interactions. Mechanisms of radiation, free-electron lasing, and advanced techniques for generating ultrashort brilliant pulses. Characterization of electronic properties of advanced materials, prospects for single-molecule structure determination using x-ray lasers, and imaging attosecond molecular dynamics.

Same as: PHOTON 201

**APPPHYS 203. Atoms, Fields and Photons. 4 Units.**

Applied Physics Core course appropriate for graduate students and advanced undergraduate students with prior knowledge of elementary quantum mechanics, electricity and magnetism, and ordinary differential equations. Structure of single- and multi-electron atoms and molecules, and cold collisions. Phenomenology and quantitative modeling of atoms in strong fields, with modern applications. Introduction to quantum optical theory of atom-photon interactions, including quantum trajectory theory, mechanical effects of light on atoms, and fundamentals of laser spectroscopy and coherent control.

**APPPHYS 204. Quantum Materials. 4 Units.**

Applied Physics Core course appropriate for graduate students and advanced undergraduate students with prior knowledge of elementary quantum mechanics. Introduction to materials and topics of current interest. Topics include superconductivity, magnetism, charge and spin density waves, frustration, classical and quantum phase transitions, multiferroics, and interfaces. Prerequisite: elementary course in quantum mechanics.

**APPPHYS 205. Introduction to Biophysics. 3-4 Units.**

Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.

Same as: BIO 126, BIO 226

**APPPHYS 206. Dynamical Systems: Linear, Non-Linear, and Stochastic. 4 Units.**

Introduction to dynamical systems including linear,nnonlinear, stochastic and spatiotemporal models. Emphasis on asymptoticnand multi-scale analysis as well as fundamental concepts of stability,nbifurcation and oscillation. Prerequisites: linear algebra and anfamiliarity with ordinary and partial differential equations; basicnprobability.

**APPPHYS 207. Laboratory Electronics. 4 Units.**

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. Analog signal processing techniques and modulation/demodulation. Principles of synchronous detection and applications of lock-in amplifiers. Common laboratory measurements and techniques illustrated via topical applications. Prerequisites: undergraduate device and circuit exposure.

**APPPHYS 208. Laboratory Electronics. 4 Units.**

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.

**APPPHYS 215. Numerical Methods for Physicists and Engineers. 4 Units.**

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.

**APPPHYS 217. Estimation and Control Methods for Applied Physics. 4 Units.**

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.

**APPPHYS 219. Solid State Physics Problems in Energy Technology. 3 Units.**

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.

**APPPHYS 220. Applied Electrodynamics. 3 Units.**

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.

**APPPHYS 223B. Nonlinear Dynamics: This Side of Chaos. 3 Units.**

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.

**APPPHYS 225. Probability and Quantum Mechanics. 3 Units.**

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 super-selection 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.

**APPPHYS 232. Advanced Imaging Lab in Biophysics. 4 Units.**

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.

Same as: BIO 132, BIO 232, BIOPHYS 232, GENE 232

**APPPHYS 236. Biology by the Numbers. 3 Units.**

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.

Same as: BIOC 236

**APPPHYS 240. From Atom Smashers to X-ray Lasers. 3 Units.**

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.

Same as: PHOTON 240

**APPPHYS 270. Magnetism and Long Range Order in Solids. 3 Units.**

Cooperative effects in solids. Topics include the origin of magnetism in solids, crystal electric field effects and anisotropy, exchange, phase transitions and long-range order, ferromagnetism, antiferromagnetism, metamagnetism, density waves and superconductivity. Emphasis is on archetypal materials. Prerequisite: PHYSICS 172 or MATSCI 209, or equivalent introductory condensed matter physics course.

**APPPHYS 272. Solid State Physics. 3 Units.**

Introduction to the properties of solids. Crystal structures and bonding in materials. Momentum-space analysis and diffraction probes. Lattice dynamics, phonon theory and measurements, thermal properties. Electronic structure theory, classical and quantum; free, nearly-free, and tight-binding limits. Electron dynamics and basic transport properties; quantum oscillations. Properties and applications of semiconductors. Reduced-dimensional systems. Undergraduates should register for PHYSICS 172 and graduate students for APPPHYS 272. Prerequisites: PHYSICS 170 and PHYSICS 171, or equivalents.

Same as: PHYSICS 172

**APPPHYS 273. Solid State Physics II. 3 Units.**

Introduction to the many-body aspects of crystalline solids. Second quantization of phonons, anharmonic effects, polaritons, and scattering theory. Second quantization of Fermi fields. Electrons in the Hartree-Fock and random phase approximation; electron screening and plasmons. Magnetic exchange interactions. Electron-phonon interaction in ionic/covalent semiconductors and metals; effective attractive electron-electron interactions, Cooper pairing, and BCS description of the superconducting state. Prerequisite: APPPHYS 272 or PHYSICS 172.

**APPPHYS 280. Phenomenology of Superconductors. 3 Units.**

Phenomenology of superconductivity viewed as a macroscopic quantum phenomenon. Topics include the superconducting pair wave function, London and Ginzburg-Landau theories, the Josephson effect, type I type II superconductivity, and the response of superconductors to currents, magnetic fields, and RF electromagnetic radiation. Introduction to thermal fluctuation effects in superconductors and quantum superconductivity.

**APPPHYS 285. Physics of Disordered Systems. 3 Units.**

Topics include types of disorder, percolation, localization, glasses and spin glasses, fractals, self-organized criticality, aggregation, gelation, and other random processes leading to disordered media.

**APPPHYS 290. Directed Studies in Applied Physics. 1-15 Unit.**

Special studies under the direction of a faculty member for which academic credit may properly be allowed. May include lab work or directed reading.

**APPPHYS 291. Practical Training. 3 Units.**

Opportunity for practical training in industrial labs. Arranged by student with research adviser's approval. Summary of activities required.

**APPPHYS 293. Theoretical Neuroscience. 3 Units.**

Introduction to fundamental theoretical ideas that provide conceptual insights into how networks of neurons cooperatively mediate important brain functions. Topics include basic mathematical models of single neurons, neuronal computation through feedforward and recurrent network dynamics, principles of associative memory, applications of information theory to early sensory systems, correlations and neural population coding, network plasticity and the self-organization of stimulus selectivity, and supervised and unsupervised learning through multiple mechanisms of synaptic plasticity. Emphasis on developing mathematical and computational skills to analyze complex neural systems. Prerequisites: calculus, linear algebra, and basic probability theory, or consent of instructor.

**APPPHYS 294. Cellular Biophysics. 3 Units.**

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.

Same as: BIO 294, BIOPHYS 294

**APPPHYS 302. Experimental Techniques in Condensed Matter Physics. 4 Units.**

Cryogenics; low signal measurements and noise analysis; data collection and analysis; examples of current experiments. Prerequisites: PHYSICS 170, PHYSICS 171, and PHYSICS 172, or equivalents.

**APPPHYS 304. Lasers Laboratory. 4 Units.**

Theory and practice. Theoretical and descriptive background for lab experiments, detectors and noise, and lasers (helium neon, beams and resonators, argon ion, cw dye, titanium sapphire, semiconductor diode, and the Nd:YAG). Measurements of laser threshold, gain, saturation, and output power levels. Laser transverse and axial modes, linewidth and tuning, Q-switching and modelocking. Limited enrollment. Prerequisites: EE 236C and EE 332, or consent of instructor.

**APPPHYS 305. Advanced Nonlinear Optics Laboratory. 4 Units.**

Core concepts and experiments in the nonlinear interaction of laser light with matter. Experiments on second harmonic generation and optical parametric oscillation culminate with assembly and use of an optical frequency comb for student-defined, open-ended experiments. Supercontinuum light generation, carrier-envelope phase stabilization, and metrology and spectroscopy. Prerequisites: APPPHYS 304, or consent of instructor.

**APPPHYS 315. Methods in Computational Biology. 3 Units.**

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.

**APPPHYS 324. Introduction to Accelerator Physics. 3 Units.**

Physics of particle beams in linear and circular accelerators. Transverse and longitudinal beam dynamics, equilibrium emittances in electron storage rings, high-brightness electron sources, RF acceleration and emittance preservation, bunch compression and associated collective effects, accelerator physics design for x-ray FELs, advanced accelerator concepts.

**APPPHYS 325. X-rays: Past, Present and Future. 3 Units.**

Introduction to the physics of bright x-ray sources. Topics include: physics and basic properties of short wavelength radiation, X-ray generation via incoherent Compton scattering and High Harmonic Generation (HHG), applications and impact of insertion devices in synchrotron radiation facilities and the development of x-ray free electron lasers. Includes selected laboratory tours of the Linac Coherent Light Source and/or measurements at SLAC. Prerequisite: graduate-level electrodynamics, or consent of instructor.

Same as: PHOTON 325

**APPPHYS 345. Advanced Numerical Methods for Data Analysis and Simulation. 3 Units.**

Gaussian and unit sphere quadrature, singular value decomposition and principal component analysis, Krylov methods, non-linear fitting and super-resolution, independent component analysis, 3d reconstruction, "shrink-wrap", hidden Markov methods, support vector machines, simulated annealing, molecular dynamics and parallel tempering, Markov state methods, Monte Carlo methods for constrained systems.

**APPPHYS 376. Literature of Ultracold Atomic Physics. 3 Units.**

Ultracold atomic gases in modern quantum optics, metrology, quantum information science, and quantum many-body physics. Review of basic concepts and survey of key literature in seminar format.

**APPPHYS 383. Introduction to Atomic Processes. 3 Units.**

Atomic spectroscopy, matrix elements using the Coulomb approximation, summary of Racah algebra, oscillator and line strengths, Einstein A coefficients. Radiative processes, Hamiltonian for two- and three-state systems, single- and multi-photon processes, linear and nonlinear susceptibilities, density matrix, brightness, detailed balance, and electromagnetically induced transparency. Inelastic collisions in the impact approximation, interaction potentials, Landau-Zener formulation. Continuum processes, Saha equilibrium, autoionization, and recombination.

**APPPHYS 387. Quantum Optics and Measurements. 3 Units.**

Basic concerns and fundamental postulates in quantum theory of measurements. Quantum non-demolition measurements, nonlinear measurements and continuous measurements. Non-local quantum correlation and Bell's inequality. Generation, detection, and application of single photons and entangled photon-pairs. Reservoir theory of an open dissipative system. Laser phase transition versus BCS transition in microcavities.

**APPPHYS 390. Dissertation Research. 1-15 Unit.**

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**APPPHYS 392. Topics in Molecular Biophysics: Biophysics of Functional RNA. 3 Units.**

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.

Same as: BIOPHYS 392

**APPPHYS 393. Biophysics of Solvation. 3 Units.**

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.

Same as: BIOPHYS 393

**APPPHYS 453A. Collective Instabilities in Accelerators. 3 Units.**

A beam in an accelerator can become unstable if its intensity is too high. Topics include the physical mechanism causing these instabilities; establishing the framework by introducing the concepts of wakefield and impedance; various instability mechanisms with a special emphasis on the underlying physical principles; new types of instabilities encountered in modern high performance accelerators such as the fast ion and the electron cloud instabilities. Course may be repeated when a different course is offered as a Special Topics.

Same as: PHOTON 453A

**APPPHYS 470. Condensed Matter Seminar. 1 Unit.**

Current research and literature; offered by faculty, students, and outside specialists. May be repeated for credit.

**APPPHYS 473B. Topics in Condensed Matter Physics: Quantum Matter Meets Quantum Optics. 3 Units.**

Graduate seminar to survey the contemporary literature on emerging topics in light-matter interactions, including novel optical spectroscopy approaches to the study of material properties and exotic optical properties of novel materials.

**APPPHYS 483. Optics and Electronics Seminar. 1 Unit.**

Current research topics in lasers, quantum electronics, optics, and photonics by faculty, students, and invited outside speakers. May be repeated for credit.

**APPPHYS 801. TGR Master's Project. 0 Units.**

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**APPPHYS 802. TGR PhD Dissertation. 0 Units.**

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