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BE 152: Bioengineering Principles and Practice in Cell Physiology
9.00 Credits
California Institute of Technology
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 to the class. Areas to be investigated will be drawn from electrophysiology, single channel recording, imaging with indicator dyes, and screening technologies. Not offered 2012–13.
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BE 152 - Bioengineering Principles and Practice in Cell Physiology
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BE 153: Case Studies in Systems Physiology
9.00 Credits
California Institute of Technology
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.
Prerequisite:
Bi 8, Bi 9, or equivalent
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BE 153 - Case Studies in Systems Physiology
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BE 157: Modeling Spatiotemporal Pattern Formation in Complex Biological Systems
9.00 Credits
California Institute of Technology
This course describes how to use statistical mechanics and nonlinear dynamics to model self-organized 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.
Prerequisite:
Bi 8, Bi 9, ACM 95 abc, and Ph 2 b or Ph 12 c or Ch 25
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BE 157 - Modeling Spatiotemporal Pattern Formation in Complex Biological Systems
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BE 159: Signal Transduction and Biomechanics in Eukaryotic Cell Morphogenesis
9.00 Credits
California Institute of Technology
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.
Prerequisite:
Bi 8, Bi 9, ACM 95 abc.
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BE 159 - Signal Transduction and Biomechanics in Eukaryotic Cell Morphogenesis
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BE 161: Physical Biology of the Cell
12.00 Credits
California Institute of Technology
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.
Prerequisite:
Ph 2ab and ACM 95abc, or background in differential equations and statistical and quantum mechanics, or instructor’s written permission.
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BE 161 - Physical Biology of the Cell
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BE 162: Physical Biology Laboratory
12.00 Credits
California Institute of Technology
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 2012–13.
Prerequisite:
Concurrent enrollment in BE/APh 161; limited to juniors and seniors who have completed the required BE courses.
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BE 162 - Physical Biology Laboratory
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BE 163: Introduction to Biomolecular Engineering
9.00 Credits
California Institute of Technology
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.
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BE 163 - Introduction to Biomolecular Engineering
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BE 166: Optical Methods for Biomedical Imaging and Diagnosis
9.00 Credits
California Institute of Technology
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. Given in alternate years; offered 2012–13.
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BE 166 - Optical Methods for Biomedical Imaging and Diagnosis
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BE 167: Research Topics in Bioengineering
1.00 Credits
California Institute of Technology
Introduction to current research topics in Caltech bioengineering labs. Graded pass/fail. Instructor: Pierce.
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BE 167 - Research Topics in Bioengineering
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BE 168: Reading the Bioengineering Literature
4.00 Credits
California Institute of Technology
Participants will read, discuss, and critique papers on diverse topics within the bioengineering literature. Instructor: Winfree.
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