BE/Bi 5. Introduction to Biomechanics. 9 units (3-0-6); third term. Introduction to the basic concepts of applying engineering principles of 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 plants and animals, and is not intended as a technical introduction to medically related biomechanics. Topics may include fundamental properties of solids and fluids, viscoelasticity, drag, biological pumps, locomotion, and muscle mechanics. Instructor: Dickinson.

BE 100 abc. Bioengineering Seminar. 1 unit; first, second, third terms. Offered to graduate students in bioengineering. Seminar series and training discussions with visiting speakers. Instructor: Staff.

BE 141. Biomaterials: Science and Engineering. 9 units (3-0-6); first 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: Staff.

APh/BE 161. Physical Biology of the Cell. 9 units (3-0-6); second term. 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.

APh/BE 162. Physical Biology Laboratory. 9 units (0-6-3); second term. Prerequisite: concurrent enrollment in APh/BE 161. This laboratory course accompanies APh/BE 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. Instructor: Phillips.

ChE/BE 163. Introduction to Biomolecular Engineering. 9 units (3-0-6); third term. Prerequisites: 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. Instructors: Arnold, Pierce.

APh/BE 165. Advanced Bioengineering Laboratory. 9 units (0-6-3); third term. Prerequisite: BE 201 or equivalent. Laboratory experiments at the interface of molecular biology and biophysics. Topics will vary from year to year and will be selected from the following list: use of atomic force microscopy to image and to manipulate proteins and DNA, use of fluorescent probes for single-molecule observation, physics of fluids in small devices, use of microfluidic devices for cell sorting and for stretching DNA, and application of optical tweezers to measure forces on single molecules. Not offered 2007–08.

EE/BE 166. Optical Methods for Biomedical Imaging and Diagnosis. 9 units (3-1-5); third 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. Topics in Bioengineering. 1 unit; first term.Introduction to the current research in bioengineering and related fields, focusing specifically on projects carried out by Caltech faculty. The course is intended for first-year graduate students in the BE option, but is open to all related options. The course will provide the students with background within the lecturer’s specific discipline. Instructor: Staff.

ChE/BE 169. Biomolecular Cell Engineering. 9 units (3-0-6); first term. Quantitative analysis of molecular mechanisms governing mammalian cell behavior. Topics include topology and dynamics of signaling and genetic regulatory networks, receptor-ligand trafficking, and biophysical models for cell adhesion and migration. Instructor: Asthagiri. Given in alternate years; offered 2007–08.

CNS/Bi/BE/Ph 178. Evolution and Biocomplexity. 9 units (3-0-6); first term. Prerequisites: Bi 2, preferably Bi 8, or instructor’s permission; programming skills. An introduction to Darwin’s theory of evolution from a theoretical, experimental, and computational point of view, with special emphasis on the mechanisms responsible for the evolution of complexity from simplicity. Experiments conducted with digital organisms. Topics covered include the principal ideas of Darwinism, measures of complexity, information content of genomes, the “natural” Maxwell Demon, Eigen’s theory of molecular evolution, evolution on neutral networks, "epistasis" and the evolution of recombination, and the evolution of mutation rate. Not offered 2007–08.

EE/BE 185. MEMS Technology and Devices. 9 units (3-0-6); first term. Prerequisites: APh/EE 9 ab, EE 187, 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. Not offered 2007–08.

BE 201 abc. Physiology for Bioengineering. 12 units (3-5-4); first, second, third terms. Part a: Cell physiology of eukaryotic cells, with an emphasis on the correlation of structure and function at the molecular, organelle, and cellular levels. Survey of physiological organization as cooperative assemblies of epithelial sheets, tissues, and organs. Part b provides a foundation in physiology for bioengineering students. Systematic approach to examination of the functions of major systems, and the regulatory mechanisms controlling normal function. Detailed examination of specific systems pertinent to major areas of bioengineering research, including membranes, channels and transport, the muscular system, the nervous system, the sensory system and its integration, and the cardiac system. Part c continues the approach of part b with a detailed examination of the circulatory, renal, respiratory, digestive, and hormonal/neurohormonal systems. Instructors: Guo, Gharib, Petrasek, 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. Not offered 2007–08.

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.

BE/CNS 248. Magnetic Resonance Imaging. 9 units (3-1-5); first term. Prerequisites: Undergraduate-level physics, biology, and/or engineering courses recommended; basic quantum mechanics, statistics, and signal processing are helpful. Physics, engineering, and computational aspects of MRI. Theory, engineering, and practice of MRI for biological and medical applications are covered in detail. Provides technical background necessary for a full understanding of the concepts underpinning the specific uses of MRI for functional brain imaging. Complements CNS/SS 251. Not offered 2007–08.

BE 250. 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.

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