Bioengineering (BE) Graduate Courses (2018-19)
BE/Bi 101. Order of Magnitude Biology. 6 units (3-0-3): third term. 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. Not offered 2018-19. Instructors: Bois, Phillips.
BE/Bi 103. Data Analysis in the Biological Sciences. 12 units (1-3-8): first term. This course covers a basic set of tools needed to analyze quantitative data in biological systems, both natural and engineered. Students analyze real data in class and in homework. Python is used as the programming language of instruction. Topics include regression, parameter estimation, outlier detection and correction, error estimation, image processing and quantification, de-noising, hypothesis testing, and data display and presentation. Instructor: Bois.
BE/Bi 106. Comparative Biomechanics. 9 units (3-0-6): second term. Have you ever wondered how a penguin swims or why a maple seed spins to the ground? How a flea can jump as high as a kangaroo? If spider silk is really stronger than steel? This class will offer answers to these and other questions related to the physical design of plants and animals. The course will provide a basic introduction to how engineering principles from the fields of solid and fluid mechanics may be applied to the study of biological systems. The course emphasizes the organismal level of complexity, although topics will relate to molecular, cell, and tissue mechanics. The class is explicitly comparative in nature and will not cover medically-related biomechanics. Topics include the physical properties of biological materials, viscoelasticity, muscle mechanics, biological pumps, and animal locomotion. Instructor: Dickinson.
BE 107. Exploring Biological Principles Through Bio-Inspired Design. 9 units (3-5-1): third term. 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. Instructor: Dickinson.
ChE/BE/MedE 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.
Bi/BE 115. Programmable Viruses and Applications to Biological Systems. 9 units (3-2-4): second term. The course will introduce the chemistry and biology of viruses, emphasizing their engineerable properties for use in basic research and translational applications. Topics include: viruses by the numbers, mammalian and non-mammalian (plant, bacteria) viruses, enveloped vs. non-enveloped viruses, host-virus interactions, viral life cycles (replication vs. dormancy), the immune response to viruses, zoonosis, diverse mechanisms of entry and replication, the application of viruses as gene-delivery vehicles (with a focus on adeno associated viruses or AAVs, lentiviruses, and rabies), how to engineer viral properties for applications in basic research and gene therapy. The lectures will be complemented by short lab exercises in AAV preparation, bioinformatics, and structure visualization (e.g. by Rosetta computational modeling). Offered 2019-20. Instructors: Gradinaru, Van Valen.
Ph/APh/EE/BE 118 abc. Physics of Measurement. 9 units (3-0-6): first, second terms. 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 term will include examples from optical methods, high-frequency and fast temporal measurements, biological interfaces, signal transduction, biosensing, and measurements at the quantum limit. Part c not offered in 2018-19. Instructor: Roukes.
Bi/BE 129. The Biology and Treatment of Cancer. 9 units (3-0-6): second term. The first part of the course will concern the basic biology of cancer, covering oncogenes, tumor suppressors, tumor cell biology, metastasis, tumor angiogenesis, and other topics. The second part will concern newer information on cancer genetics and other topics, taught from the primary research literature. The last part of the course will concern treatments, including chemotherapy, anti-angiogenic therapy, and immunotherapy. Textbook: The Biology of Cancer, 2nd edition, by Robert Weinberg. Given in alternate years; offered 2018-19. Instructors: Zinn, Campbell.
BE 150. Design Principles of Genetic Circuits. 9 units (3-0-6): third term. 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 153. Case Studies in Systems Physiology. 9 units (3-0-6): third term. 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. 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 2018-19. Instructor: Lester.
BE 159. Signal Transduction and Mechanics in Morphogenesis. 9 units (3-0-6): second term. 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. 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: Bois.
ChE/BE 163. Introduction to Biomolecular Engineering. 12 units (3-0-9): first term. 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 (Python is the language of instruction). Instructors: Arnold, Pierce.
BE 167. Research Topics in Bioengineering. 1 unit: first term. Introduction to current research topics in Caltech bioengineering labs. Graded pass/fail. Instructor: Staff.
MedE/EE/BE 168 ab. Biomedical Optics: Principles and Imaging. 9 units (4-0-5): second and third terms. The second term covers the principles of optical photon transport in biological tissue. Topics include a brief introduction to biomedical optics, single-scatterer theories, Monte Carlo modeling of photon transport, convolution for broad-beam responses, radiative transfer equation and diffusion theory, hybrid Monte Carlo method and diffusion theory, and sensing of optical properties and spectroscopy. The third term covers optical imaging technologies. Topics include ballistic imaging (confocal microscopy, two-photon microscopy, etc.), optical coherence tomography, Mueller optical coherence tomography, diffuse optical tomography, photoacoustic tomography, and ultrasound-modulated optical tomography. Instructor: Wang.
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. Given in alternate years; offered 2018-19. Instructor: Collazo.
Bi/BE 182. Animal Development and Genomic Regulatory Network Design. 9 units (3-0-6): second term. This course is focused on the genomic control circuitry of the encoded programs that direct developmental processes. The initial module of the course is devoted to general principles of development, with emphasis on transcriptional regulatory control and general properties of gene regulatory networks (GRNs). The second module provides mechanistic analyses of spatial control functions in multiple embryonic systems, and the third treats the explanatory and predictive power of the GRNs that control body plan development in mammalian, sea urchin, and Drosophila systems. Grades or pass/fail. Given in alternate years; offered 2018-19 Instructors: Stathopoulos, Peter.
Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics. 9 units (3-0-6): second term. Biology is becoming an increasingly data-intensive science. Many of the data challenges in the biological sciences are distinct from other scientific disciplines because of the complexity involved. This course will introduce key computational, probabilistic, and statistical methods that are common in computational biology and bioinformatics. We will integrate these theoretical aspects to discuss solutions to common challenges that reoccur throughout bioinformatics including algorithms and heuristics for tackling DNA sequence alignments, phylogenetic reconstructions, evolutionary analysis, and population and human genetics. We will discuss these topics in conjunction with common applications including the analysis of high throughput DNA sequencing data sets and analysis of gene expression from RNA-Seq data sets. Instructors: Pachter, Thomson.
EE/BE/MedE 185. MEMS Technology and Devices. 9 units (3-0-6): third term. 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 2018-19.
ChE/BE/MedE 188. Molecular Imaging. 9 units (3-0-6): second term. This course will cover the basic principles of biological and medical imaging technologies including magnetic resonance, ultrasound, nuclear imaging, fluorescence, bioluminescence and photoacoustics, and the design of chemical and biological probes to obtain molecular information about living systems using these modalities. Topics will include nuclear spin behavior, sound wave propagation, radioactive decay, photon absorption and scattering, spatial encoding, image reconstruction, statistical analysis, and molecular contrast mechanisms. The design of molecular imaging agents for biomarker detection, cell tracking, and dynamic imaging of cellular signals will be analyzed in terms of detection limits, kinetics, and biological effects. Participants in the course will develop proposals for new molecular imaging agents for applications such as functional brain imaging, cancer diagnosis, and cell therapy. Instructor: Shapiro.
BE/EE/MedE 189 ab. Design and Construction of Biodevices. 12 units (3-6-3) a = first and third terms: 9 units (0-9-0) b = third term. 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. Instructors: Bois, Yang.
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term: (2-4-3) third term. 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: a (3-6-3) second term. 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 self-assembled DNA nanostructures, as well as quantitatively analyze the designs and the experimental data. Students will learn laboratory techniques including fluorescence spectroscopy and atomic force microscopy, and will use software tools and program in MATLAB or Mathematica. Part b is an open-ended design and build project. Enrollment in both parts a and b is limited to 12 students. Part b not offered 2018-19. 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.
BE 201. Reading the Bioengineering Literature. 4 units (1-0-3): second term. Participants will read, discuss, and critique papers on diverse topics within the bioengineering literature. Offered only for Bioengineering graduate students. Instructor: Winfree.
BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units: summer term. This course provides an intensive, hands-on, pragmatic introduction to computer programming aimed at biologists and bioengineers. No previous programming experience is assumed. Python is the language of instruction. Students will learn basic concepts such as data types, control structures, string processing, functions, input/output, etc., while writing code applied to biological problems. At the end of the course, students will be able to perform simple simulations, write scripts to run software packages and parse output, and analyze and plot data. This class is offered as a week-long summer "boot camp" the week after Commencement, in which students spend all day working on the course. Graded pass/fail. Instructor: Bois.
Bi/BE 222. The Structure of the Cytosol. 6 units (2-0-4): third term. The cytosol, and fluid spaces within the nucleus, were once envisioned as a concentrated soup of proteins, RNA, and small molecules, all diffusing, mixing freely, and interacting randomly. We now know that proteins in the cytosol frequently undergo only restricted diffusion and become concentrated in specialized portions of the cytosol to carry out particular cellular functions. This course consists of lectures, reading, student presentations, and discussion about newly recognized biochemical mechanisms that confer local structure and reaction specificity within the cytosol, including protein scaffolds and "liquid-liquid phase separations that form "membraneless compartments." Instructor: Kennedy.
Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4): second term. 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 as well as other techniques for optical sectioning such as light sheet fluorescence microscopy (also called single plane illumination microscopy, SPIM). During the class students will construct a light sheet microscope based on the openSPIM design. Alongside the building of a light sheet microscope, the course will consist of semi-independent modules organized around different imaging challenges using confocal microscopes. Early modules will include a lab using lenses to build a cloaking device. Most of the early modules will focus on three-dimensional reconstruction of fixed cells and tissues. Later modules will include time-lapse confocal analysis of living cells and embryos. Students will also utilize the microscopes in the Beckman Institute Biological Imaging Facility to learn more advanced techniques such as spectral unmixing and fluorescence correlation spectroscopy. Enrollment is limited. Given in alternate years; not offered 2018-19. Instructor: Collazo.
Bi/CNS/BE/NB 230. Optogenetic and CLARITY Methods in Experimental Neuroscience. 9 units (3-2-4): third term. The class covers the theoretical and practical aspects of using (1) optogenetic sensors and actuators to visualize and modulate the activity of neuronal ensembles; and (2) CLARITY approaches for anatomical mapping and phenotyping using tissue-hydrogel hybrids. The class offers weekly hands-on LAB exposure for opsin viral production and delivery to neurons, recording of light-modulated activity, and tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Lecture topics include: opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics), compatible readout modalities (electrophysiology, imaging); design and use of methods for tissue clearing (tissue stabilization by polymers/hydrogels and selective extractions, such as of lipids for increased tissue transparency and macromolecule access). Class will discuss applications of these methods to neuronal circuits (case studies based on recent literature). Given in alternate years; offered 2020-21. 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. 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 2018-19.
MedE/BE/Ae 243. Biological Flows: Transport and Circulatory Systems. 9 units (3-0-6): second term. 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: Roh.
BE 262. Physical Biology Bootcamp. 12 units (2-10-0): summer term. This course provides an intensive introduction to thinking like a quantitative biologist. Every student will build a microscope from scratch, use a confocal microscope to measure transcription in living fly embryos and perform a quantitative dissection of gene expression in bacteria. Students will then use Python to write computer code to analyze the results of all of these experiments. No previous experience in coding is presumed, though for those with previous coding experience, advanced projects will be available. In addition to the experimental thrusts, students will use "street fighting mathematics" to perform order of magnitude estimates on problems ranging from how many photons it takes to make a cyanobacterium to the forces that can be applied by cytoskeletal filaments. These modeling efforts will be complemented by the development of physical models of phenomena such as gene expression, phase separation in nuclei, and cytoskeletal polymerization. Graded pass/fail. Instructor: Phillips.