2014-15 Catalog | Caltech Academic Catalog

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. Required for BE undergraduates. Graded pass/fail.

Instructor: Staff

FS/BE 5

Freshman Seminar: Introduction to Biomechanics

6 units (2-0-4) | third term

Freshmen only; limited enrollment. 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. Given in alternate years; not offered 2014-15.

Bi/BE 24

Technical Communication for Biological Scientists and Engineers

6 units (3-0-3) | first term

This course offers instruction and practice in writing and speaking relevant to professional biological scientists and engineers working in research, teaching, and/or medical careers. Students will write a paper for a scientific or engineering journal, either based on their previous research or written as a review paper of current work in their field. A Caltech faculty member, a postdoctoral scholar, or technical staff member serves as a technical mentor for each student, to provide feedback on the content and style of the paper. Oral presentations will be based on writing produced in the course, with feedback from instructors and peers. Fulfills the Institute scientific writing requirement.

Instructor: Staff

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/Bi 101

Order of Magnitude Biology

6 units (3-0-3) | second term

Prerequisites: none.

In this course, students will develop skills in the art of educated guesswork and apply them to the biological sciences. Building from a few key numbers in biology, students will "size up" biological systems by making inferences and generating hypotheses about phenomena such as the rates and energy budgets of key biological processes. The course will cover the breadth of biological scales: molecular, cellular, organismal, communal, and planetary. Undergraduate and graduate students of all levels are welcome.

Instructors: Bois, Phillips

BE/Bi 103

Data Analysis in the Biological Sciences

9 units (1-3-5) | first term

Prerequisites: CS 1 or equivalent; Bi 1, Bi 1x, Bi 8, or equivalent, or instructor's permission.

This course covers a basic set of tools needed to analyze quantitative data in biological systems, both natural and engineered. Students will analyze real data in class and in homework. Python will be used as the programming language of instruction. Topics will include regression, parameter estimation, outlier detection and correction, error estimation, image processing and quantifcation, denoising, hypothesis testing, and data display and presentation.

Instructor: Bois

BE/Bi/MedE 106

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. Not offered 2014-15.

BE 107

Exploring Biological Principles Through Bio-Inspired Design

9 units (1-0-8) | third term

Prerequisites: None.

Students will formulate and implement an engineering project designed to explore a biological principle or property that is exhibited in nature. Students will work in small teams in which they build a hardware platform that is motivated by a biological example in which a given approach or architecture is used to implement a given behavior. Alternatively, the team will construct new experimental instruments in order to test for the presence of an engineering principle in a biological system. Example topics include bio-inspired control of motion (from bacteria to insects), processing of sensory information (molecules to neurons), and robustness/fault-tolerance. Each project will involve proposing a specific mechanism to be explored, designing an engineering system that can be used to demonstrate and evaluate the mechanism, and building a computer-controlled, electro-mechanical system in the lab that implements or characterizes the proposed mechanism, behavior or architecture.

Instructors: Dickinson, Murray

ChE/BE 112

Design, Invention, and Fundamentals of Microfluidic Systems

9 units (3-0-6) | second term

This course combines three parts. First, it will cover fundamental aspects of kinetics, mass-transport, and fluid physics that are relevant to microfluidic systems. Second, it will provide an understanding of how new technologies are invented and reduced to practice. Finally, students in the course will work together to design microfluidic systems that address challenges in Global Health, with an emphasis on students' inventive contributions and creativity. Students will be encouraged and helped, but not required, to develop their inventions further by working with OTT and entrepreneurial resources on campus. Participants in this course benefit from enrollment of students with diverse backgrounds and interests. For chemical engineers, suggested but not required courses are ChE 101 (Chemical Reaction Engineering) and ChE 103abc (Transport Phenomena). Students are encouraged to contact the instructor to discuss enrollment.

Instructor: Ismagilov

Ph/APh/EE/BE 118 abc

Physics of Measurement

9 units (3-0-6) | first, second, third terms

Prerequisites: Ph127, APh 105, or equivalent, or permission from instructor.

This course focuses on exploring the fundamental underpinnings of experimental measurements from the perspectives of responsivity, noise, backaction, and information. Its overarching goal is to enable students to critically evaluate real measurement systems, and to determine the ultimate fundamental and practical limits to information that can be extracted from them. Topics will include physical signal transduction and responsivity, fundamental noise processes, modulation, frequency conversion, synchronous detection, signal-sampling techniques, digitization, signal transforms, spectral analyses, and correlations. The first term will cover the essential fundamental underpinnings, while topics in second and third terms will include examples from optical methods, high-frequency and fast temporal measurements, biological interfaces, signal transduction, biosensing, and measurements at the quantum limit.

Instructors: Roukes, Yeh

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 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. Not offered 2014-15.

Instructor: Staff

BE 150

Systems Biology

9 units (3-0-6) | third term

Prerequisites: 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: Bois, Elowitz

BE 151

Bioengineering Principles and Practice in Molecular Biology

9 units (3-0-6) | first term

Prerequisites: 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. Not offered 2014-15.

BE/Bi 152

Bioengineering Principles and Practice in Cell Physiology

9 units (3-0-6) | second term

Prerequisites: None.

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 2014-15.

BE 153

Case Studies in Systems Physiology

9 units (3-0-6) | second 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

Bi/NB/BE 155

Neuropharmacology

6 units (3-0-3) | second term

Prerequisites: Bi/CNS/NB 150 or Bi/NB 202.

The neuroscience of drugs for therapy, for prevention, and for recreation. Students learn the prospects for new generations of medications in neurology, psychiatry, aging, and treatment of substance abuse. Topics: Types of drug molecules. Drug receptors. Electrophysiology. Drugs activate ion channels. Drugs block ion channels. Drugs activate and block G protein pathways. Drugs block neurotransmitter transporters. Pharmacokinetics. Recreational drugs. Nicotine Addiction. Opiate Addiction. Drugs for neurodegenerative diseases: Alzheimer's disease, Parkinson's disease. Drugs for epilepsy and migraine. Psychiatric diseases: nosology and drugs. The course is taught at the research level. Given in alternate years, offered beginning 2014-15.

Instructor: Lester

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 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. Not offered 2014-15.

BE 159

Signal Transduction and Mechanics in Morphogenesis

9 units (3-0-6) | second term

Prerequisites: Bi 8, Bi 9, ACM 95 abc, or instructor's permission.

This course examines the mechanical and biochemical pathways that govern morphogenesis. Topics include embryonic patterning, cell polarization, cell-cell communication, and cell migration in tissue development and regeneration. The course emphasizes the interplay between mechanical and biochemical pathways in morphogenesis.

Instructor: Bois

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 2014-15.

ChE/BE 163

Introduction to Biomolecular Engineering

12 units (3-0-9) | first term

Prerequisites: Bi/Ch 110 or instructor's permission and CS 1 or equivalent.

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, Bois

EE/BE/MedE 166

Optical Methods for Biomedical Imaging and Diagnosis

9 units (3-1-5) | third term

Prerequisites: 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. Given in alternate years; offered 2014-15.

Instructor: Yang

BE 167

Research Topics in Bioengineering

1 unit | first term

Introduction to current research topics in Caltech bioengineering labs. Graded pass/fail.

Instructor: Staff

BE 168

Reading the Bioengineering Literature

4 units (1-0-3) | second term

Prerequisites: None.

Participants will read, discuss, and critique papers on diverse topics within the bioengineering literature. Enrollment limited to 10 students; undergraduates with instructor's permission. Offered in alternate years; offered 2014-15.

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 and characteristics of lenses and microscopes. 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 and the analysis and presentation of two- and three-dimensional images. The role of light microscopy in the history of science will be an underlying theme. No prior knowledge of microscopy will be assumed.

Instructor: Collazo

EE/BE/MedE 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. Not offered 2014-15.

BE/EE/MedE 189 ab

Design and Construction of Biodevices

12 units (3-6-3 a); 9 units (0-9-0 b) | a = third term; b = first term

Prerequisites: ACM 95 ab (for BE/EE/MedE 189 a); BE/EE/MedE 189 a (for BE/EE/MedE 189 b).

Part a, 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. Part b is a student-initiated design project requiring instructor's permission for enrollment. Enrollment is limited to 24 students. BE/EE/MedE 189 a is an option requirement; BE/EE/MedE 189 b is not.

Instructor: Yang

BE/CS/CNS/Bi 191 ab

Biomolecular Computation

9 units (3-0-6 a), (2-4-3 b) | second, third terms

Prerequisites: 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/CS 196 ab

Design and Construction of Programmable Molecular Systems

12 units (3-6-3) second term; (2-8-2) third term | a = third term; b = not offered 2014-15

Prerequisites: ChE/BE 163 or BE/CS/CNS/Bi 191a, or instructor's permission.

This course will introduce students to the conceptual frameworks and tools of computer science as applied to molecular engineering, as well as to the practical realities of synthesizing and testing their designs in the laboratory. In part a, students will design and construct DNA logic circuits, biomolecular neural networks, and complex two-dimensional and three-dimensional nanostructures, as well as quantitatively analyze the designs and the experimental data. Students will learn laboratory techniques including gel electrophoresis, fluorescence spectroscopy, and atomic force microscopy, and will use software tools and program in Mathematica or Matlab. Part b is an open-ended, design-and-build project requiring instructor's permission for enrollment. Enrollment in both parts a and b is limited to 12 students.

Instructor: Qian

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. Bi/BE 177 may be taken concurrently with this course.

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, zebrafish, 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. Not offered 2014-15.

Instructor: Collazo

Bi/CNS/BE/NB 230

Optogenetic Methods in Experimental Neuroscience

9 units (3-1-5) | third term

Prerequisites: Graduate standing or Bi/CNS/NB 150 and instructor permission.

The class covers the theoretical and practical aspects of optogenetic control and complementary readout methods in molecular, cellular, and systems neuroscience. Topics include opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics, LEDs), compatible readout modalities (electrophysiology, imaging) and applications to neuronal circuits (case studies based on recent literature). The class offers hands-on lab exposure for opsin delivery to the mammalian brain and recording of brain activity modulated by light.

Instructor: Gradinaru

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) | third 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

MedE/BE/Ae 243

Biological Flows: Transport and Circulatory Systems

9 units (3-0-6) | second 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: Pahlevan

BE 262

Physical and Synthetic Biology Boot Camp

9 units (1-8-0) | third term

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. Not offered 2014-15.

Published Date: July 28, 2022