BE 1. Frontiers in Bioengineering. 1 unit; second term. A weekly seminar series by Caltech faculty providing an introduction to research directions in the field of bioengineering. Graded pass/fail. Instructor: Pierce.

FS/BE 5. Freshman Seminar: Introduction to Biomechanics. 6 units (2-0-4); third term. Prerequisite: None. This course is an introduction to the application of engineering principles from solid and fluid mechanics to the study of biological systems. The course emphasizes the organismal, rather than the molecular, level of complexity. It draws on a wide array of biological phenomena from animals and plants, and is not intended as a technical introduction to medically related biomechanics. Topics include scaling and heuristic modeling of biological systems; fundamental properties of biological solids and fluids; viscoelasticity; drag and locomotion; biological pumps; and biology-inspired engineering. Textbook: Life's Devices: The Physical World of Animals and Plants by Steven Vogel. Limited enrollment: 10 (by lottery). Given in alternate years; not offered 2012-2013. Freshman Seminar course. Instructor: Dabiri

BE 98. Undergraduate Research in Bioengineering. Variable units, as arranged with the advising faculty member; first, second, third terms. Undergraduate research with a written report at the end of each term; supervised by a Caltech faculty member, or coadvised by a Caltech faculty member and an external researcher. Graded pass/fail. Instructor: Staff.

BE 141. Biomaterials: Science and Engineering. 9 units (3-0-6); second term. Prerequisites: Ph 2 ab or Ph 12 abc, Ch 1 ab, Ch 3 a, or instructor's permission. MS 115 ab recommended. Lectures and experiments demonstrating the bulk and surface properties of materials; review of the major classes of materials-metals, ceramics, polymers-with a view to their relevance to the biomedical field. Special materials and processes of relevance will also be discussed, e.g., hydrogels, fabrics, thin films, bioresorbable and bioerodible materials, cardiac jelly, etc. Proteins, cells, tissues and their interactions with materials; key concepts in reactions between host materials and implants, including inflammation, coagulation, and tumorigenesis. Testing and degradation of biomaterials, material applications in medicine and dentistry, especially orthopedic, cardiovascular, ophthalmologic, oral and maxillofacial implants, and artificial organs. Instructor: Ravi.

BE 150. Systems Biology. 9 units (3-0-6); second term. Prerequisite: None. Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives. Instructors: Elowitz, Murray.

BE 151. Bioengineering Principles and Practice in Molecular Biology. 9 units (3-0-6); first term. Prerequisite: None. This course will explore the bioengineering principles and developments that drive new avenues of research in molecular biology. We will review the basic principles of current research approaches, dissect the protocols, equipment and chemistry that enable these approaches, and discuss how they impose the existing limitations on performance. Students will be expected to engage in more reading on one of the approaches and develop strategies for implementing improvements. A written and oral presentation of the area under study will be required. Areas to be investigated will be drawn from DNA sequencing, RNA analysis, genomic approaches, flow cytometry, and array technologies. Instructor: Lansford.

BE/Bi 152. Bioengineering Principles and Practice in Cell Physiology. 9 units (3-0-6); second term. This course will explore our current knowledge based on the fundamental properties of nerves and synapses, and present the bioengineering principles and developments that drive new avenues of research in cell physiology. We will present the tools used for making current research measurements, dissect the protocols, equipment, and physics that enable the approaches, and discuss the current limitations that limit performance. Students will be expected to engage in one of the technologies and develop a greater understanding in both written and oral presentations the the class. Areas to be investigated will be drawn from electrophysiology, single channel recording, imaging with indicator dyes, and screening technologies. Not offered 2012-2013.

BE 153. Case Studies in Systems Physiology. 9 units (3-0-6); third term. Prerequisites: Bi 8, Bi 9, or equivalent. This course will explore the process of creating and validating theoretical models in systems biology and physiology. It will examine several macroscopic physiological systems in detail, including examples from immunology, endocrinology, cardiovascular physiology, and others. Emphasis will be placed on understanding how macroscopic behavior emerges from the interaction of individual components. Instructor: Petrasek.

BE 157. Modeling Spatiotemporal Pattern Formation in Complex Biological Systems. 9 units (3-0-6); second term. Prerequisites: Bi 8, Bi 9, ACM 95 abc, and Ph 2 b or Ph 12 c or Ch 25. This course describes how to use statistical mechanics and nonlinear dynamics to model selforganized spatiotemporal pattern formation and transition kinetics in complex biological systems. These phenomena include Turing patterns in morphogenesis, oscillations by excitation-relaxation dynamics in cell signaling networks, and the propagation of traveling waves observed in action potentials and collective cell migration. This course emphasizes the construction of phenomenological models for stochastic nonlinear behavior in biological systems, including derivation of the corresponding Turing analysis, Langevin equation, Fokker-Planck equation, and Kramer theory. Instructor: Guo.

BE 159. Signal Transduction and Biomechanics in Eukaryotic Cell Morphogenesis. 9 units (3-0-6); third term. Prerequisites: Bi 8, Bi 9, ACM 95 abc. This course examines the mechanical and biochemical pathways that govern eukaryotic cell morphogenesis. Topics include embryonic pattern formation, cell polarization and migration in tissue development and regeneration. Biomechanics will be treated at the molecular, cellular, and multicellular levels of organization. In addition to providing background material on cytoskeletal biomechanics and intra/intercellular signaling in cell-matrix and cell-cell interactions, the course will emphasize the interplay between mechanical and biochemical pathways in tissue morphogenesis and homeostasis. Current understanding of malignant transformation will be briefly described, as well. The course will briefly introduce appropriate modeling techniques and tools such as fabrication and optical approaches to the quantitative study of morphogenesis. Instructor: Guo.

BE/APh 161. Physical Biology of the Cell. 12 units (3-0-9); second term. Prerequisites: Ph 2ab and ACM 95abc, or background in differential equations and statistical and quantum mechanics, or instructor's written permission. Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. Topics include the force response of proteins and DNA, models of molecular motors, DNA packing in viruses and eukaryotes, mechanics of membranes, and membrane proteins and cell motility. Instructor: Phillips.

BE/APh 162. Physical Biology Laboratory. 12 units (0-6-6); second term. Prerequisites: concurrent enrollment in BE/APh 161; limited to juniors and seniors who have completed the required BE courses. This laboratory course accompanies BE/APh 161 and is built around experiments that amplify material covered in that course. Particular topics include background on techniques from molecular biology, mechanics of lipid bilayer vesicles, DNA packing in viruses, fluorescence microscopy of cells, experiments on cell motility, and the construction of genetic networks. Not offered 2012-2013.

ChE/BE 163. Introduction to Biomolecular Engineering. 9 units (3-0-6); first term. Prerequisite: Bi/Ch 110 or instructor's permission.The course introduces rational design and evolutionary methods for engineering functional protein and nucleic acid systems. Rational design topics include molecular modeling, positive and negative design paradigms, simulation and optimization of equilibrium and kinetic properties, design of catalysts, sensors, motors, and circuits. Evolutionary design topics include evolutionary mechanisms and tradeoffs, fitness landscapes, directed evolution of proteins, and metabolic pathways. Some assignments require programming (MATLAB or Python). Instructors: Arnold, Pierce.

EE/BE 166. Optical Methods for Biomedical Imaging and Diagnosis. 9 units (3-1-5); first term. Prerequisite: EE 151 or equivalent. Topics include Fourier optics, scattering theories, shot noise limit, energy transitions associated with fluorescence, phosphorescence, and Raman emissions. Study of coherent anti-Stokes Raman spectroscopy (CARS), second harmonic generation and near-field excitation. Scattering, absorption, fluorescence, and other optical properties of biological tissues and the changes in these properties during cancer progression, burn injury, etc. Specific optical technologies employed for biomedical research and clinical applications: optical coherence tomography, Raman spectroscopy, photon migration, acousto-optics (and opto-acoustics) imaging, two photon fluorescence microscopy, and second- and third-harmonic microscopy. Instructor: Yang.

BE 167. Research Topics in Bioengineering. 1 unit; first term. Introduction to current research in Caltech bioengineering labs. Graded Pass/Fail. Instructor: Pierce.

BE 168. Reading the Bioengineering Literature. 4 units (1-0-3); second term. Prerequisite: None. Participants will read, discuss, and critique papers on diverse topics within the bioengineering literature. Instructor: Winfree.

Bi/BE 177. Principles of Modern Microscopy. 9 units (3-0-6); second term. Lectures and discussions on the underlying principles behind digital, video, differential interference contrast, phase contrast, confocal, and two-photon microscopy. The course will begin with basic geometric optics, characteristics of lenses and microscopes, and principles of accurate imaging. Specific attention will be given to how different imaging elements such as filters, detectors, and objective lenses contribute to the final image. Course work will include critical evaluation of published images and design strategies for simple optical systems. Emphasis in the second half of the course will be placed on the analysis and presentation of two- and three-dimensional images. No prior knowledge of microscopy will be assumed. Instructor: Staff.

BE/APh/Ph 181. Biological Interfaces, Transduction, and Sensing. 9 units (3-0-6); third term. Prerequisites: APh 105, Ph129 or equivalent (students without a background in statistical physics are still encouraged to take the course-additional tutorial sessions will be arranged as needed). Basic physics and chemical physics of interfaces between the fundamental realm of biology-molecules and cells-and the physical world. The course centers on processes that are essential for transduction to energy domains in which modern sensors operate. Information transfer from the biological realm to optical, electronic, and mechanical domains will be considered. Particular attention will be paid to both the sensitivity and the kinetics of transduction processes, and to how fluctuations affect and ultimately impose fundamental limits on such interactions. Instructor: Roukes.

EE/BE 185. MEMS Technology and Devices. 9 units (3-0-6); third term. Prerequisites: APh/EE 9 ab, or instructor's permission. Micro-electro-mechanical systems (MEMS) have been broadly used for biochemical, medical, RF, and lab-on-a-chip applications. This course will cover both MEMS technologies (e.g., micro- and nanofabrication) and devices. For example, MEMS technologies include anisotropic wet etching, RIE, deep RIE, micro/nano molding and advanced packaging. This course will also cover various MEMS devices used in microsensors and actuators. Examples will include pressure sensors, accelerometers, gyros, FR filters, digital mirrors, microfluidics, micro total-analysis system, biomedical implants, etc. Instructor: Tai.

BE/EE 189 ab. Design and Construction of Biodevices. 12 units (3-6-3) second term; 9 units (0-9-0) third term. Prerequisites: ACM 95 ab (for BE/EE 189 a); BE/EE 189 a (for BE/EE 189 b). Second term, students will design and implement biosensing systems, including a pulse monitor, a pulse oximeter, and a real-time polymerase-chain-reaction incubator. Students will learn to program in LABVIEW. Third term is a student-initiated design project requiring instructor's permission for enrollment. Enrollment is limited to 24 students. BE/EE 189 a is an option requirement; third term is not. Instructor: C. Yang.

BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term; (2-4-3) third term. Prerequisite: None. Recommended: ChE/BE 163, CS 21, CS 129 ab, or equivalent. This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics. Instructor: Winfree.

BE 200. Research in Bioengineering. Units and term to be arranged. By arrangement with members of the staff, properly qualified graduate students are directed in bioengineering research.

Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4); second term. Prerequisites: Bi/BE 177 or a course in microscopy. May be taken concurrently. Discussion and laboratory-based course covering the practical use of the confocal microscope, with special attention to the dynamic analysis of living cells and embryos. Course will begin with basic optics, microscope design, Koehler illumination, and the principles of confocal microscopy. After introductory period, the course will consist of semi-independent weeklong modules organized around different imaging challenges. Early modules will focus on three-dimensional reconstruction of fixed cells and tissues, with particular attention being paid to accurately imaging very dim samples. Later modules will include time-lapse confocal analysis of living cells and embryos, including Drosophila, zebra fish, chicken, and s embryos. Dynamic analysis will emphasize the use of fluorescent proteins. No prior experience with confocal microscopy will be assumed; however, a basic working knowledge of microscopes is highly recommended. Preference is given to graduate students who will be using confocal microscopy in their research. Instructor: Staff.

BE 240. Special Topics in Bioengineering. Units and term to be arranged. Topics relevant to the general educational goals of the bioengineering option. Graded pass/fail.

Ae/BE 242. Biological Flows: Propulsion. 9 units (3-0-6); second term. Prerequisites: Ae/APh/CE/ME 101 abc or equivalent or ChE 103 a. Physical principles of unsteady fluid momentum transport: equations of motion, dimensional analysis, conservation laws. Unsteady vortex dynamics: vorticity generation and dynamics, vortex dipoles/rings, wake structure in unsteady flows. Life in moving fluids: unsteady drag, added-mass effects, virtual buoyancy, bounding and schooling, wake capture. Thrust generation by flapping, undulating, rowing, jetting. Low Reynolds number propulsion. Bioinspired design of propulsion devices. Instructor: Dabiri.

BE/Ae 243. Biological Flows: Transport and Circulatory Systems.9 units (3-0-6); third term. Prerequisites: Ae/APh/CE/ME 101 abc or equivalent or ChE 103 a. Internal flows: steady and pulsatile blood flow in compliant vessels, internal flows in organisms. Fluid dynamics of the human circulatory system: heart, veins, and arteries (microcirculation). Mass and momentum transport across membranes and endothelial layers. Fluid mechanics of the respiratory system. Renal circulation and circulatory system. Biological pumps. Instructor: Gharib. Not offered 2012-2013.

BE 262. Physical and Synthetic Biology Boot Camp. 9 units (1-8-0); summer. This course provides an intensive research introduction to current projects in physical and synthetic biology. Projects are based on current research directions in participating labs, including those of visiting biologists invited for the course. Representative classes of experiments include quantitative fluorescent microscopy of cell and organelle dynamics, single-cell measurement of genetic expression levels during development, and design and construction of biological circuits in microbes. Graded pass/fail. Instructor: Phillips. Not offered 2012-2013.

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