• Bioengineering
• Chemistry
• Computer Science
• Engineering
• Integrative Biology
• Mathematics
• Molecular and Cell Biology
• Physics
• Psychology
• Public Health
• Statistics
• Vision Science

We advise our students to match their curricula of study to their individual backgrounds and research interests. Therefore, Biophysics students often take a variety of coursework in different fields. The following courses have been recommended as being particularly helpful to many students.

Bioengineering 131/231
Introduction to Computational Biology
Topics include computational approaches and techniques to gene structure and finding, sequence alignment using dynamic programming, protein folding and structure prediction, protein drug interactions, genetic and biochemical pathways and networks, and microarray analysis. Various case studies in these areas are reviewed and web-based computational biology tools will be used by students. Computational biology research connections to biotechnology will be explored.

Bioengineering 142
Programming and Algorithm Design for Computational Biology & Genomics Applications
This course will introduce students to structured software development and select principles of computer science with applications in computational biology and allied disciplines. The principle language used for instruction will be Java with a course module on Perl. Examples and tutorials will draw from problems in computational biology. The course will require one significant programming project, preferably biologically oriented.

Bioengineering 143/243
Computational Methods in Biology
Topics include thermodynamics, statistical mechanics, classical mechanics, and quantum mechanics that connect most directly to modern simulation methodology. Various case studies in the areas of classical dynamical simulations, ab initio dynamics, and Monte Carlo techniques will be covered. The areas of mathematical optimization and "non-algorithmic" computation such as neural networks and Hidden Markov Models will also be considered.

Bioengineering 144
Introduction to Protein Bioinformatics
This course will introduce students to the fundamentals of molecular biology and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods and practical hands-on experience with protein sequence analysis methods applied to real data.

Bioengineering 164
Optics and Microscopy
Prerequisites: Physics 7A-7B-7C, or 8A-8B or equivalent introductory physics course. Description: This course teaches fundamental principles of optics and examines contemporary methods of optical microscopy for cells and molecules. Students will learn how to design simple optical systems, calculate system performance, and apply imaging techniques including transmission, reflection, phase, and fluorescence microscopy to investigate biological samples. The capabilities of optical microscopy will be compared with complementary techniques including electron microscopy, coherence tomography, and atomic force microscopy.

Chemistry 208
Structure Analysis by X-Ray Diffraction
The theory and practice of modern, single-crystal X-ray diffraction. Groups of four students determine the crystal and molecular structure of newly synthesized materials from the College of Chemistry. The laboratory work involves the mounting of crystals and initial evaluation by X-ray diffraction film techniques, the collection of intensity data by automated diffractometer procedures, and structure analysis and refinement.

Chemistry 220A
Thermodynamics and Statistical Mechanics
A rigorous presentation of classical thermodynamics followed by an introduction to statistical mechanics with the application to real systems.

Chemistry 220B
Advanced Statistical Mechanics
Static and dynamic linear response, response functions, density and polarization fluctuations, polymers, biopolymers, membranes, 'exotic' phase transitions.

Chemistry C230
Protein Chemistry, Enzymology, and Bio-organic Chemistry
Topics include: protein structure, denaturation, and folding; RNA catalysis; protein-protein and protein-nucleic acid interactions; enzyme kinetics and solving "hard" enzyme mechanisms; catalytic antibodies.

Chemistry 231A-231C
Advanced Biophysical Chemistry
Survey of physico-chemical approaches to structural and dynamic aspects of RNA, DNA and proteins, bioenergetics, membrane organization and membrane protein structure. 231B emphasizes the crystallography of biomacromolecules. 231C emphasizes nuclear magnetic resonance of biomacromolecules.

Chemistry 298
Seminars for Graduate Students
In addition to the weekly Graduate Research Conference and weekly seminars on topics of interest in biophysical, organic, physical, nuclear and inorganic chemistry, there are group seminars on specific fields of research.

Computer Science 294
Algorithms for Computational Biology
Topics vary each semester.

Electrical Engineering 210A-210B
Applied Electromagnetic Theory
Advanced treatment of classical electromagnetic theory and its application to engineering problems. Static electric and magnetic fields. Maxwell's equations and special theory of relativity. Methods of analyzing field problems arising from wave guides, antennas, and wave scatterings.

Electrical Engineering 219
Circuit Theory and Computer-Aided Analysis
Device modeling, formulation of network equations. Causality, reciprocity, losslessness, passivity, stability, gain-bandwidth. Algorithms for computing linear, piecewise-linear, and nonlinear resistive and dynamic circuits. Sparse matrices. Explicit, implicit and stiff integration formulas and circuit interpretations. Sensitivity analysis. Non-linear distortion.

Electrical Engineering 220
Nonlinear Circuits
Algebraic and dynamic n-ports. Potential and state functions. Volterra series. Frequency-power formulas. Qualitative properties: Equilibrium states, stability, oscillations, subharmonic, almost-periodic, and chaotic phenomenon. Frequency entrainment. Harmonic balance, describing functions and bifurcation. Applications to oscillators, multivibrators, mixers, modulators and harmonic generators.

Electrical Engineering 221A
Linear System Theory
Basic system concepts: state-space and I/O representation. Properties of linear systems. Controllability, observability, minimality, state and output-feedback. Stability. Observers. Characteristic polynomial. Nyquist test.

Electrical Engineering 221B
Multuivariable Feedback Systems
MIMO feedback systems. Matrix fraction description. Stabilization, tracking, disturbance rejection. Two degrees of freedom design. Robustness. Large scale interconnected systems. Linear Quadratic Optimal Control.

Electrical Engineering 222
Nonlinear Systems-Analysis, Stability and Control
Basic graduate course in non-linear systems. Second Order systems. Numerical solution methods, the describing function method, linearizaion. Stability-direct and indirect methods of Lyapunov. Application to the Lure problem- Popov, circle criterion. Input-Output stability. Additonal topics include: bifurcations of dynamical systems, introduction to the "geometric" theory of control for nonlinear systems, passivity concepts and dissipative dynamical systems.

Electrical Engineering 223
Stochastic Systems: Estimation and Control
Parameter and state estimation. System identification. Nonlinear filtering. Stochastic control. Adaptive control.

Electrical Engineering 225B
Multidimensional Signal Processing
Multidimensional signal and system analysis, design and representation. Implicit and explicit sampling schemes. Fourier analysis, stability issues, design and implementation of FIR and IIR filters. Additional topics depend on instructor and may include: Signal reconstruction from partial information, Array processing, beam forming and spectral estimation. Image processing, enhancement, restoration, compression and coding, sampling, interpolation and reconstruction of time-varying imagery.

Electrical Engineering 229
Information Theory and Coding
Fundamental bounds of Shannon theory and their application. Source and channel coding theorems, Galois field theory, algebraic error-correction codes. Private and public-key cryptographic systems.

Engineering 253A-253B
Physics of Medical Imaging
A: Interaction of radiation with matter, radiation detection, medical image formation, radiographic instrumentation, image quality, design of imaging systems. B: Dual-energy radiography, quantitative techniques, tomographic reconstruction, radiologic informatics, picture archiving and communication systems, image processing, medical image database design.

Integrative Biology 202
Quantitative Systematics
An examination of the theoretical background and application of quantitative methods in systematics, including measures of similarity and difference, cluster analysis, ordination techniques, cladistic methods, and information retrieval.

Integrative Biology 202L
Quantitative Systematics Laboratory
A discussion of recent papers and a laboratory devoted to the application of quantitative systematic methods. Each student will undertake a project using methods discussed.

Mathematics 127
Mathematical and Computational Methods in Molecular Biology
Introduction to mathematical and computational problems arising in the context of molecular biology. Theory and applications of combinatorics, probability, statistics, geometry, and topology to problems ranging from sequence determination to structure analysis.

Mathematics 290
Hidden Markov Models in Comparative Genomics
Topics in foundations of mathematics, theory of numbers, numerical calculations, analysis, geometry, topology, algebra, and their applications, by means of lectures and informal conferences; work based largely on original memoirs.

Molecular and Cell Biology 137
Computer Simulation in Biology
Modeling and computer simulation of dynamic biological processes using special graphical interfaces requiring very little mathematical or computer experience. First half is realistic models from current literature to teach concepts and technique; second is workshop for student-selected individual projects.

Molecular and Cell Biology 200
Advanced Biochemistry and Molecular Biology
Recent advances in the study of structural, functional, and genetic characteristics of prokaryotic and eukaryotic cells and their viruses, macromolecular syntheses, regulation of gene expression, chromosome organization and cell differentiation.

Molecular and Cell Biology 205
The Chemistry, Biochemistry, and Physical Chemistry of Nucleic Acids
Primary, secondary, tertiary structures of nucleic acids, and methods used for structural analysis. Thermodynamics and kinetics of structural transitions. Theories of ligand interactions with nucleic acids, and analysis of those interactions and their effects on nucleic acid structure, reactivity, and stability.

Molecular and Cell Biology 206
Physical Biochemistry
Application of modern physical concepts and experimental methods to the analysis of the structure, function, and interaction of large molecules of biological interest.

Molecular and Cell Biology 211
Structural Biology and Physical Biochemistry
This course will teach principles of protein and nucleic acid structure and outline basic experimental methods for conformation studies. The classical problems of structural biology, as well as new approaches and methods, will be emphasized.

Molecular and Cell Biology 214
Protein/Nucleic Acid Chemistry and Enzymology
Protein structure, denaturation and folding. Nucleic acid chemistry structure and cleavage. Protein-protein and protein-nucleic acid interactions. Enzyme kinetics and mechanism, catalytic antibodies.

Molecular and Cell Biology 218Q
Structural Biophysics
Structural Biology with emphasis on proteins and nucleic acids, cell membranes, cytoskeletal and motile systems, and the protein folding problem.

Molecular and Cell Biology 230
Molecular Cell Biology
Comprehensive survey and in-depth examination of various topics in cell biology, including: membrane structure, organelle biogenesis, protein targeting, and secretion; receptors, signal transduction mechanisms, growth control, cell cycle regulation, and stress responses; cytoskeletal organization and dynamics, cell polarity and shape change, motor proteins, organelle movement and cell motility.

Molecular and Cell Biology 242A
Advanced Topics in Genetics: The Genome
Advanced level of coverage of current research problems in genetics. Topics covered vary from year to year.

Molecular and Cell Biology C246/C146
Topics in Computational Biology & Genomics
Instruction and discussion of topics in genomics and computational biology. Working from evolutionary concepts, the course will cover principles and application of molecular sequence comparison, genome sequencing and functional annotation, and phylogenetic analysis. Also listed as Plant Biology C246 and Molecular and Cell Biology C246.

Molecular and Cell Biology 254
Immunobiology of Cancer
Recent advances in tumor immunology, with emphasis on the treatment and prevention of cancer. The course will examine the application of basic research in immune regulation to more applied studies in animal models and clinical trials.

Molecular and Cell Biology 260
Principles of Neuroscience
Comprehensive survey of current state of knowledge in molecular, cellular, developmental, integrative and behavioral aspects of neurobiology.

Molecular and Cell Biology 261
Advanced Cellular Neurobiology
Physico-chemical basis of membrane potentials, electrotonus, action potential generation and propagations, synaptic transmission, sensory receptor function, and volume conductor potentials.

Molecular and Cell Biology 262
Integrative Neurobiology
In-depth consideration of current research questions central to the understanding of the organization of nervous systems, and of the behavior mediated by these systems. When appropriate these questions are illustrated with examples drawn from both the vertebrate and invertebrate literature. Circuit, networks, or system analogs and analysis will be emphasized where these approaches lend clarity. Sensorimotor integration is discussed in small systems or neurons.

Molecular and Cell Biology / Plant and Microbial Biology C148
Microbial Genomics and Genetics
Course emphasizes bacterial and archaeal genetics and comparative genomics. Genetics and genomic methods used to dissect metabolic and development processes in bacteria, archaea, and selected microbial eukaryotes. Genetic mechanisms integrated with genomic information to address integration and diversity of microbial processes. Introduction to the use of computational tools for a comparative analysis of microbial genomes and determining relationships among bacteria, archaea, and microbial eukaryotes. Also listed as Molecular and Cell Biology C148.

Physics 177
Molecular Biophysics
Review of the structure of proteins, nucleic acids, carbohydrates, lipids, and the forces and interactions maintaining their structures in solution; thermodynamics and kinetics of protein folding; polymer chain statistics and helix-coil transitions in biopolymers; biopolymer dynamics; structural methods in biology: X-ray crystallography, NMR and fluorescence spectroscopy, electron and probe microscopy; single-molecule methods.

Physics 205A
Advanced Dynamics
Lagrange and Hamiltonian dynamics, variational methods, symmetry, kinematics and dynamics of rotation, canonical variables and transformations, perturbation theory, non-linear dynamics, KAM theory.

Physics 208A
Introduction to Quantum Electronics and Nonlinear Optics
Semiclassical theories of emission and absorption, theory and operation of common laser systems, wave propagation in anisotropic and nonlinear media, nonlinear optical phenomena such as second harmonic generation and parameter amplification.

Physics 210B
Classical Physics: Electromagnetism
Electrostatics and magnetostatics, Green functions, reciprocation theorem, two- and three-dimensional problems, use of orthogonal functions, conformal mapping, relaxation methods, multipole expansions of charge and current distributions, forces on multipoles in external fields. Quasistatic phenomena. Plane waves in material media, polarization, Fresnel equations, attenuation, dispersion. Wave equation with sources, retarded solution for potentials and fields. Cartesian and spherical multipoled expansions, vector spherical harmonics, examples of radiating systems, diffraction, optical theorem. Fields of charges in arbitrary motion, radiated power, relativistic (synchrotron) radiation, radiation in collisions.

Physics 212
Nonequilibrium Statistical Physics
Time dependent processes. Kinetic equations. Transport processes. Irreversibility. Theory of many-particle systems. Fluctuation phenomena.

Psychology 218
Research Reviews on the Biological Basis of Cognition and Learning
Discussion of recent papers on the comparative and physiological study of learning and cognition.

Psychology 216B/ Vision Science 216
Color Vision
Selected topics from color vision mechanisms, specification, and discrimination, psychophysics and neurophysiology of color processing. Color and brightness perception. Stiles two-color increment threshold measures, interaction of color and form, color vision anomalies.

Public Health 240D
Biostatistical Methods: Applications of Statistics to Genetics and Molecular Biology
The explosion of genomic information has revolutionized the way biological and biomedical problems are defined, approached, and ultimately solved. This course surveys applications of probability and statistics to genetics and molecular biology, from early Mendelian experiments to modern day genomic research. Biological questions to be considered include, but are not limited to, modeling meiosis; genetic mapping; nucleotide and protein sequence analysis; molecular evolution; computational gene finding; protein structure predictions; genetic and biochemical pathways; DNA microarray experiments. Related statistical topics span the entire spectrum of the discipline and include stochastic processes (Markov processes, hidden Markov models, Markov chain Monte Carlo); experimental design; likelihood analysis; multiple hypothesis testing; linear models; model selection; classification; resampling. Introduction to basic notions in genetics and molecular biology and to statistical computing resources for the analysis of biological data, with emphasis on the R language and environment.

Statistics/Bioengineering 141
Statistics for Bioinformatics
Study of bioinformatics problems such as DNA pattern finding, gene expression data analysis, molecular evolution models, and biomolecular sequence database searching. Introduction of the necessary probability and statistics: events, (conditional) probability, random variables, estimation, testing, and linear regression. Also listed as Statistics C141.

Statistics 246
Statistics in Genetics
Modelling meiosis, linkage mapping, pedigree analysis, genetic epidemiology. Clone libraries, physical mapping of chromosomes. Radiation hybrid mapping. DNA and protein sequence analysis, molecular evolution, sequence alignment, database searching. Analysis of microarray expression data.

Vision Science 202
Visual Evoked Potentials
Basis of visual evoked potentials, including application to visual development and deprivations, objective testing, functional anatomy of the visual brain, instrumentation, and future developments. Contributions from positron emission tomography.

Vision Science 204
Optical Formation in the Eye
Lectures and laboratory demonstrations. Measurement of optical properties of simple and compound eyes Image quality and resolution. Optometric instrumentation.

Vision Science 206
The Oculomotor System
Lectures and laboratory demonstrations on mechanical, physiological, servo-analytical, and behavioral aspects of pupil, accommodation, and monocular and binocular eye movement responses.

Vision Science 207
Simulation of Visual System
Analysis of eye movement and sensory visual systems from a control and systems approach made available to non-engineers, using computer simulation techniques, and biologist-oriented display programs.

Vision Science 210
Instrumentation and Methodology in Vision Research
Basic concepts of radiometry, photometry and colorimetry. Optical bench systems, video and oscilloscope stimulus generation and calibrations Neurophysiological and biophysical techniques from measurement of eye movements, pupil, accommodation, ERG, EOG, VEP, single unit activity. Psychophysical methodology, signal detection, computer control of stimuli, data acquisition and processing. Clinical assessment of ocular components: eye examination and function. Clinical trials.

Vision Science 212A
Optics and Dioptrics of the Eye
Introduction for graduate students to basic principles of classic and modern geometric optics (thick lens systems, mirrors, prisms, apertures, and stops) and physical optics (interference, diffraction, and polarization) with emphasis on dioptrics of the human eye (including schematic eyes, aberrations, and entoptic phenomena).

Vision Science 212B
Visual Neurophysiology and Development
Visual pathways will be considered from retina to lateral geniculate to visual cortex. Basic organization at each stage will be covered. Primary focus will be studies of receptive field characteristics and associated visual function. Development and plasticity of the same visual pathways will also be covered. Evidence and implications will be explored from controlled rearing procedures and studies of abnormal visual exposure.

Vision Science 212C
Spatial Vision and Machine Vision
Introduction for graduate students to human spatial vision, contrast sensitivity, visual acuity and spatial localization. Machine vision analogues and models of visual processing of spatial information.

Vision Science 212E
Color Vision and Visual Sensitivity
Introduction for graduate students to sensory aspects of light and color vision including: psychophysical methods, spectral response of the eye, mechanisms of sensitivity control, dark adaptation, color discrimination, mechanisms of normal and defective color vision.

Vision Science 218
Spatial Aspects of Vision
Selected topics from spatial perception: Visual direction, egocentric and oculocentric localization. Pattern vision: feature detector and spatial frequency filter models, local and global frequency analysis, visual acuity and relation to contrast sensitivity. Spatial aspects of color vision.

Vision Science 220
Binocular Vision
Selected topics from stereopsis and binocular depth perception. Development of binocular vision, binocular interactions, binocular disparity, binocular space perception and anomalies of binocular vision.