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Bioengineering

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 and an overview of the courses offered in the Bioengineering option. Required for BE undergraduates. Graded pass/fail. Instructor: Staff. 

Bi/BE 24. Scientific Communication for Biological Scientists and Engineers. 6 units (3-0-3).  For course description, see Biology.

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 co-advised 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); third 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. Not offered 2017–18.

BE/Bi 103. Data Analysis in the Biological Sciences. 12 units (1-3-8); 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 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); third 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. 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. Instructor: Dickinson.

ChE/BE/MedE 112. Design, Invention, and Fundamentals of Microfluidic Systems. 9 units (3-0-6). For course description, see Chemical Engineering.

Ph/APh/EE/BE 118 ab. Physics of Measurement. 9 units (3-0-6). For course description, see Physics.

Ph/APh/EE/BE 118 c. Physics of Measurement. 9 units (3-0-6). For course description, see Physics.

BE 150. Design Principles of Genetic Circuits. 9 units (3-0-6); third term. Prerequisites: Bi 1, Bi 8, or equivalent; Ma 2 or equivalent, or instructor’s permission. 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. 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). For course description, see Biology.

BE 159. Signal Transduction and Mechanics in Morphogenesis. 9 units (3-0-6); second term. Prerequisites: Bi 8, Bi 9, ACM 95/100 ab, 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 2 ab and ACM 95/100 ab, 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. 

ChE/BE 163. Introduction to Biomolecular Engineering. 12 units (3-0-9). For course description, see Chemical Engineering.

EE/BE/MedE 166. Optical Methods for Biomedical Imaging and Diagnosis. 9 units (3-1-5). For course description, see Electrical Engineering.

BE 167. Research Topics in Bioengineering. 1 unit; first term. Introduction to current research topics in Caltech bioengineering labs. Graded pass/fail. Instructor: Staff.

Bi/BE 177. Principles of Modern Microscopy. 9 units (3-0-6). For course description, see Biology.

Bi/BE 182. Animal Development and Genomic Regulatory Network Design. 9 units (3-0-6). For course description, see Biology.

Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics. 9 units (3-0-6). For course description, see Biology.

EE/BE/MedE 185. MEMS Technology and Devices. 9 units (3-0-6). For course description, see Electrical Engineering.

ChE/BE/MedE 188. Molecular Imaging. 9 units (3-0-6). For course description, see Chemical Engineering.

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. Prerequisites: ACM 95/100 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/ 453 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. 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; a (3-6-3) second term; b  (2-8-2) third term. Prerequisites: none. 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. 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. Prerequisites: none. 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 “boot camp” starting two weeks before the start of the fall term, in which students spend all day working on the course. Graded pass/fail. Instructor: Bois.

Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4). For course description, see Biology.

Bi/CNS/BE/NB 230. Optogenetic and CLARITY Methods in Experimental Neuroscience. 9 units (3-2-4). For course description, see Biology. 

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). For course description, see Aerospace.

MedE/BE/Ae 243. Biological Flows: Transport and Circulatory Systems. 9 units (3-0-6). For course description, see Medical Engineering.

BE 262. Physical Biology Bootcamp. 12 units (2-10-0); summer term. Prerequisites: Enrollment limited to incoming Biology, Biochemistry and Molecular Biophysics, Bioengineering, and Neurobiology graduate students, or instructor’s permission. 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.