2007-08 Catalog

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.

Offered to graduate students in bioengineering. Seminar series and training discussions with visiting speakers.

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.

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.

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.

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.

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.

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.

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. Given in alternate years; offered 2007-08.

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.

Topics relevant to the general educational goals of the bioengineering option. Graded pass/fail.

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.

By arrangement with members of the staff, properly qualified graduate students are directed in bioengineering research.