BBE Graduate Courses (2018-19)
MedE 100 abc. Medical Engineering Seminar. 1 unit: first, second, third terms. All PhD degree candidates in Medical Engineering are required to attend all MedE seminars. If there is no MedE seminar during a week, then the students should go to any other graduate-level seminar that week. Students should broaden their knowledge of the engineering principles and sciences of medical engineering. Students are expected to learn the forefronts of the research and development of medical materials, technologies, devices and systems from the seminars. Graded pass/fail. Instructors: Gao, Tai and Wang.
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.
MedE 101. Introduction to Clinical Physiology and Pathophysiology for Engineers. 9 units (3-0-6): First term. The goal of this course is to introduce engineering scientists to medical physiological systems: with a special emphasis on the clinical relevance. The design of the course is to present two related lectures each week: An overview of the physiology of a system followed by examples of current clinical medical challenges and research highlighting diagnostic and therapeutic modalities. The final three weeks of the course will be a mini-work shop where the class explores challenging problems in medical physiology. The course ultimately seeks to promote a bridge between relevant clinical problems and engineering scientists who desire to solve them. Graded pass/fail. Instructor: Petrasek.
CNS/SS/Psy/Bi 102 ab. Brains, Minds, and Society. 9 units (3-0-6): second, third terms. Introduction to the computations made by the brain during economic and social decision making and their neural substrates. First quarter: Reinforcement learning. Unconscious and conscious processing. Emotion. Behavioral economics. Goal-directed and habit learning. Facial processing in social neuroscience. Second quarter: History and mechanisms of reinforcement. Associative learning. Mentalizing and strategic thinking. Neural basis of prosociality. Exploration-exploitation tradeoff. Functions of basal ganglia. Instructors: O'Doherty/Adolphs, Camerer.
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.
Bi/Ge/ESE 105. Evolution. 12 units (3-4-5): second term. The theory of evolution is arguably biology's greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Given in alternate years; not offered 2018-19. Instructors: Phillips, Orphan.
E/ME/MedE 105 ab. Design for Freedom from Disability. 9 units (3-0-6): terms to be arranged. This Product Design class focuses on people with Disabilities and is done in collaboration with Rancho Los Amigos National Rehabilitation Center. Students visit the Center to define products based upon actual stated and observed needs. Designs and testing are done in collaboration with Rancho associates. Speakers include people with assistive needs, therapists and researchers. Classes teach normative design methodologies as adapted for this special area. Instructor: TBD.
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.
Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8): first term. Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, and the intermediary metabolism that provides energy to an organism. Instructors: Parker, Virgil.
Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8): second term. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and protein synthesis. Instructors: Campbell, Parker.
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 114. Immunology. 9 units (3-0-6): second term. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, gene rearrangement of lymphocyte receptors, cytokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. The course will present an integrated view of how the immune system interacts with viral and bacterial pathogens and commensal bacteria. Given in alternate years; offered 2018-19. Instructors: Mazmanian, Bjorkman.
EE/MedE 114 ab. Analog Circuit Design. 12 units (4-0-8): second, third terms. Analysis and design of analog circuits at the transistor level. Emphasis on design-oriented analysis, quantitative performance measures, and practical circuit limitations. Circuit performance evaluated by hand calculations and computer simulations. Recommended for juniors, seniors, and graduate students. Topics include: review of physics of bipolar and MOS transistors, low-frequency behavior of single-stage and multistage amplifiers, current sources, active loads, differential amplifiers, operational amplifiers, high-frequency circuit analysis using time- and transfer constants, high-frequency response of amplifiers, feedback in electronic circuits, stability of feedback amplifiers, and noise in electronic circuits, and supply and temperature independent biasing. A number of the following topics will be covered each year: trans-linear circuits, switched capacitor circuits, data conversion circuits (A/D and D/A), continuous-time Gm.C filters, phase locked loops, oscillators, and modulators. Offered 2018-19. Instructor: Hajimiri.
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.
EE/MedE 115. Micro-/Nano-scales Electro-Optics. 9 units (3-0-6): first term. The course will cover various electro-optical phenomena and devices in the micro-/nano-scales. We will discuss basic properties of light, imaging, aberrations, eyes, detectors, lasers, micro-optical components and systems, scalar diffraction theory, interference/interferometers, holography, dielectric/plasmonic waveguides, and various Raman techniques. Topics may vary. Not offered 2018-19.
Bi 116. Microbial Genetics. 9 units (3-0-6): second term. A course on microbial genetics, emphasizing the history of the discipline as well as modern approaches. Students will be exposed to different ways of manipulating microbial genomes (primarily bacterial, but we will also cover archaea and microbial eukaryotes). The power of microbial genetics to shed light on diverse process will be discussed in a variety of contexts, ranging from environmental science to the mammalian microbiome. Given in alternate years; offered 2019-20. Instructors: Mazmanian, Newman.
MS/ME/MedE 116. Mechanical Behavior of Materials. 9 units (3-0-6): second term. Introduction to the mechanical behavior of solids, emphasizing the relationships between microstructure, architecture, defects, and mechanical properties. Elastic, inelastic, and plastic properties of crystalline and amorphous materials. Relations between stress and strains for different types of materials. Introduction to dislocation theory, motion and forces on dislocations, strengthening mechanisms in crystalline solids. Nanomaterials: properties, fabrication, and mechanics. Architected solids: fabrication, deformation, failure, and energy absorption. Biomaterials: mechanical properties of composites, multi-scale microstructure, biological vs. synthetic, shear lag model. Fracture in brittle solids and linear elastic fracture mechanics. Instructor: Greer.
Bi 117. Developmental Biology. 9 units (3-0-6): second term. A survey of the development of multicellular organisms. Topics will include the beginning of a new organism (fertilization), the creation of multicellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), induction of the nervous system (neurulation), and creation of specific organs (organogenesis). Emphasis will be placed on the molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development, covering both classical and modern approaches to studying these processes. Instructor: Bronner.
Bi 118. Morphogenesis of Developmental Systems. 9 units (3-0-6): second term. Lectures on and discussion of how cells, tissues, and organs take shape: the influence of force on cell shape change; cell migration including chemotaxis and collective cell movement; adhesion/deadhesion during migration; the relationship between cell migration and metastasis; and a review/overview of general signaling principles and embryonic development of invertebrate and vertebrate animals. Students will choose term project involving writing a grant proposal or quantitative analysis of available datasets relating to lecture topics. Given in alternate years; offered 2018-19. Instructor: Stathopoulos.
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 122. Genetics. 9 units (3-0-6): first term. Lecture and discussion course covering basic principles of genetics. Not open to freshmen. Instructor: Hay.
EE/MedE 124. Mixed-mode Integrated Circuits. 9 units (3-0-6): first term. Introduction to selected topics in mixed-signal circuits and systems in highly scaled CMOS technologies. Design challenges and limitations in current and future technologies will be discussed through topics such as clocking (PLLs and DLLs), clock distribution networks, sampling circuits, high-speed transceivers, timing recovery techniques, equalization, monitor circuits, power delivery, and converters (A/D and D/A). A design project is an integral part of the course. Instructor: Emami.
EE/CS/MedE 125. Digital Electronics and Design with FPGAs and VHDL. 9 units (3-6-0): third term. Study of programmable logic devices (CPLDs and FPGAs). Detailed study of the VHDL language, with basic and advanced applications. Review and discussion of digital design principles for combinational-logic, combinational-arithmetic, sequential, and state-machine circuits. Detailed tutorials for synthesis and simulation tools using FPGAs and VHDL. Wide selection of complete, real-world fundamental advanced projects, including theory, design, simulation, and physical implementation. All designs are implemented using state-of-the-art development boards. Instructor: Pedroni.
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.
Ch/BMB 129. Introduction to Biophotonics. 9 units (3-0-6): first term. This course will cover basic optics and introduce modern optical spectroscopy principles and microscopy techniques. Topics include molecular spectroscopy; linear and nonlinear florescence microscopy; Raman spectroscopy; coherent microscopy; single-molecule spectroscopy; and super-resolution imaging. Instructor: Wei.
CNS/Psy/Bi 131. The Psychology of Learning and Motivation. 9 units (3-0-6): second term. This course will serve as an introduction to basic concepts, findings, and theory from the field of behavioral psychology, covering areas such as principles of classical conditioning, blocking and conditioned inhibition, models of classical conditioning, instrumental conditioning, reinforcement schedules, punishment and avoidance learning. The course will track the development of ideas from the beginnings of behavioral psychology in the early 20th century to contemporary learning theory. Not offered 2018-19. Instructor: O'Doherty.
Bi 145 a. Tissue and Organ Physiology. 9 units (3-0-6): first term. Reviews of anatomy and histology, as well as in-depth discussion of cellular physiology. Building from cell function to tissues, the course explores human physiology in an organ-based fashion. First term topics include endocrine physiology, the autonomic nervous system, urinary physiology, and the cardiovascular system. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.
Bi 145 b. Tissue and Organ Physiology. 9 units (3-0-6): second term. Building on the foundations of Bi 145a, Bi 145b will continue the exploration of human physiology incorporating anatomy and cellular physiology. Topics include muscle physiology, the skeletal system, digestive and hepatic physiology, nutrition, the respiratory system and reproductive physiology. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective. Instructor: Tydell.
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.
Bi/CNS/NB/Psy 150. Introduction to Neuroscience. 10 units (4-0-6): third term. General principles of the function and organization of nervous systems, providing both an overview of the subject and a foundation for advanced courses. Topics include the physical and chemical bases for action potentials, synaptic transmission, and sensory transduction; anatomy; development; sensory and motor pathways; memory and learning at the molecular, cellular, and systems level; and the neuroscience of brain diseases. Instructors: Adolphs, Lester.
Bi/CNS/NB 152. Neural Circuits and Physiology of Appetite and Body Homeostasis. 6 units (2-0-4): third term. An advanced course of lectures, readings, and student presentations focusing on neural basis of appetites such as hunger and thirst. This course will cover the mechanisms that control appetites both at peripheral and central level. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on the logic of how the body and the brain cooperate to maintain homeostasis. Given in alternate years; offered 2018-19. Instructor: Oka.
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/CNS/NB 154. Principles of Neuroscience. 9 units (3-0-6): first term. This course aims to distill the fundamental tenets of brain science, unlike the voluminous textbook with a similar title. What are the essential facts and ways of understanding in this discipline? How does neuroscience connect to other parts of life science, physics, and mathematics? Lectures and guided reading will touch on a broad range of phenomena from evolution, development, biophysics, computation, behavior, and psychology. Students will benefit from prior exposure to at least some of these domains. Given in alternate years; offered 2018-19. Instructor: Meister.
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.
Bi/CNS/NB 157. Comparative Nervous Systems. 9 units (2-3-4): third term. An introduction to the comparative study of the gross and microscopic structure of nervous systems. Emphasis on the vertebrate nervous system; also, the highly developed central nervous systems found in arthropods and cephalopods. Variation in nervous system structure with function and with behavioral and ecological specializations and the evolution of the vertebrate brain. Letter grades only. Given in alternate years; offered 2018-19. Instructor: Allman.
Bi/CNS 158. Vertebrate Evolution. 9 units (3-0-6): third term. An integrative approach to the study of vertebrate evolution combining comparative anatomical, behavioral, embryological, genetic, paleontological, and physiological findings. Special emphasis will be given to: (1) the modification of developmental programs in evolution; (2) homeostatic systems for temperature regulation; (3) changes in the life cycle governing longevity and death; (4) the evolution of brain and behavior. Letter grades only. Given in alternate years; not offered 2018-19. Instructor: Allman.
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.
Bi 160. Molecular Basis of Animal Evolution. 6 units (2-2-2): third term. We share the planet with well over 1.5 million other animal species. This course covers how the staggering diversity of the animal kingdom came about through underlying molecular evolutionary phenomena, including gene and protein sequence evolution, gene family and genome evolution, the evolution of developmental processes, neural circuit evolution and behavior, and molecular mechanisms that physiologically adapt animals to their environment. Molecular processes involved in speciation will be explained, together with an analysis of constraints and catalysts on the production of selectable variation that have shaped the evolution of animal life. Participants will undertake a laboratory project on evolutionary genomics, involving fieldwork, genome sequencing and comparative genome analysis. The course focuses on the >99.9% of animals that lack backbones. Instructor: Parker.
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.
Pl/CNS/NB/Bi/Psy 161. Consciousness. 9 units (3-0-6): second term. One of the last great challenges to our understanding of the world concerns conscious experience. What exactly is it? How is it caused or constituted? And how does it connect with the rest of our science? This course will cover philosophy of mind, cognitive psychology, and cognitive neuroscience in a mixture of lectures and in-class discussion. There are no formal pre-requisites, but background in philosophy (equivalent to PI41, PI110) and in neuroscience (equivalent to BI/CNS 150) is strongly recommended and students with such background will be preferentially considered. Limited to 20. Instructors: Eberhardt, Adolphs.
Bi/CNS/NB 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-4-6): second term. A laboratory-based introduction to experimental methods used for electrophysiological studies of the central nervous system. Through the term, students investigate the physiological response properties of neurons in vertebrate and invertebrate brains, using extra- and intracellular recording techniques. Students are instructed in all aspects of experimental procedures, including proper surgical techniques, electrode fabrication, and data analysis. The class also includes a brain dissection and independent student projects that utilize modern digital neuroscience resources. Instructor: Bremner.
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.
Bi/CNS/NB 164. Tools of Neurobiology. 9 units (3-0-6): first term. Offers a broad survey of methods and approaches to understanding in modern neurobiology. The focus is on understanding the tools of the discipline, and their use will be illustrated with current research results. Topics include: molecular genetics, disease models, transgenic and knock-in technology, virus tools, tracing methods, gene profiling, light and electron microscopy, optogenetics, optical and electrical recording, neural coding, quantitative behavior, modeling and theory. Instructor: Meister.
Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1): first term. The course will serve to introduce graduate students to 1) the process of writing fellowships to train students in preparing effective funding applications; 2) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities as well as projects in other fields; and 3) presentation of research and asking questions in research presentations. The first half of the class will involve training in grant writing by drafting an NSF-GRFP proposal. The second half of the class will involve giving chalk talk research presentations. Students can apply from all departments; priority will be given to those in microbiology. Enrollment is limited to instructor approval. Instructor: Hoy.
ESE/Bi 166. Microbial Physiology. 9 units (3-1-5); first term: Recommended prerequisite: one year of general biology. A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration. Instructor: Leadbetter.
BE 167. Research Topics in Bioengineering. 1 unit: first term. Introduction to current research topics in Caltech bioengineering labs. Graded pass/fail. Instructor: Staff.
ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6): second term. A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Given in alternate years; offered 2018-19. Instructor: Newman.
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.
BMB/Bi/Ch 170. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-0-6): first term. Detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Not offered 2018-19.
BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6): second term. Basic principles of modern biophysical and structural methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, NMR spectroscopy, single molecule techniques, circular dichroism, surface plasmon resonance, mass spectrometry, and molecular dynamics and systems biological simulations. Instructor: Jensen.
BMB/Bi/Ch 174. Molecular Machines in the Cell. 9 units (3-0-6); third term: Prerequisites: Bi/Ch 110 and BMB/Bi/Ch 173. Discussion of macromolecular machines and pathways that illustrate the principles and biophysical methods taught in BMB/Bi/Ch 170, 173, and 178. Development of skills in literature analysis, information synthesis, and proposal writing. Instructors: Clemons, Shan, and various guest lecturers (subject to change each year).
EE/CS/MedE 175. Digital Circuits Analysis and Design with Complete VHDL and RTL Approach. 9 units (3-6-0): third term. A careful balance between synthesis and analysis in the development of digital circuits plus a truly complete coverage of the VHDL language. The RTL (register transfer level) approach. Study of FPGA devices and comparison to ASIC alternatives. Tutorials of software and hardware tools employed in the course. VHDL infrastructure, including lexical elements, data types, operators, attributes, and complex data structures. Detailed review of combinational circuits followed by full VHDL coverage for combinational circuits plus recommended design practices. Detailed review of sequential circuits followed by full VHDL coverage for sequential circuits plus recommended design practices. Detailed review of state machines followed by full VHDL coverage and recommended design practices. Construction of VHDL libraries. Hierarchical design and practice on the hard task of project splitting. Automated simulation using VHDL testbenches. Designs are implemented in state-of-the-art FPGA boards. Not Offered 2018-19. Instructor: Pedroni.
CNS/Bi/SS/Psy/NB 176. Cognition. 9 units (4-0-5): third term. The cornerstone of current progress in understanding the mind, the brain, and the relationship between the two is the study of human and animal cognition. This course will provide an in-depth survey and analysis of behavioral observations, theoretical accounts, computational models, patient data, electrophysiological studies, and brain-imaging results on mental capacities such as attention, memory, emotion, object representation, language, and cognitive development. Instructor: Shimojo.
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.
BMB/Ch 178. Macromolecular Function: Kinetics, Energetics, and Mechanisms. 9 units (3-0-6): first term. Discussion of the energetic principles and molecular mechanisms that underlie enzyme's catalytic proficiency and exquisite specificity. Principles of allosteric regulation, selectivity, enzyme evolution, and computational enzyme design. Practical kinetics sections discuss how to infer molecular mechanisms from rate/equilibrium measurements and their application to complex biological systems, including steady-state and pre-steady-state kinetics, kinetic simulations, and kinetics at the single molecule resolution. Instructor: Shan.
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.
Bi/CNS/NB 184. The Primate Visual System. 9 units (3-1-5): third term. This class focuses on the primate visual system, investigating it from an experimental, psychophysical, and computational perspective. The course will focus on two essential problems: 3-D vision and object recognition. We will examine how a visual stimulus is represented starting in the retina, and ending in the frontal lobe, with a special emphasis placed on mechanisms for high-level vision in the parietal and temporal lobes. An important aspect of the course is the lab component in which students design and analyze their own fMRI experiment. Given in alternate years; not offered 2018-19. Instructor: Tsao.
Bi/CNS/NB 185. Large Scale Brain Networks. 6 units (2-0-4): third term. This class will focus on understanding what is known about the large-scale organization of the brain, focusing on the mammalian brain. What large scale brain networks exist and what are their principles of function? How is information flexibly routed from one area to another? What is the function of thalamocortical loops? We will examine large scale networks revealed by anatomical tracing, functional connectivity studies, and mRNA expression analyses, and explore the brain circuits mediating complex behaviors such as attention, memory, sleep, multisensory integration, decision making, and object vision. While each of these topics could cover an entire course in itself, our focus will be on understanding the master plan--how the components of each of these systems are put together and function as a whole. A key question we will delve into, from both a biological and a theoretical perspective, is: how is information flexibly routed from one brain area to another? We will discuss the communication through coherence hypothesis, small world networks, and sparse coding. Given in alternate years, not offered 2018-19. Instructor: Tsao.
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.
CNS/Bi/EE/CS/NB 186. Vision: From Computational Theory to Neuronal Mechanisms. 12 units (4-4-4): second term. Lecture, laboratory, and project course aimed at understanding visual information processing, in both machines and the mammalian visual system. The course will emphasize an interdisciplinary approach aimed at understanding vision at several levels: computational theory, algorithms, psychophysics, and hardware (i.e., neuroanatomy and neurophysiology of the mammalian visual system). The course will focus on early vision processes, in particular motion analysis, binocular stereo, brightness, color and texture analysis, visual attention and boundary detection. Students will be required to hand in approximately three homework assignments as well as complete one project integrating aspects of mathematical analysis, modeling, physiology, psychophysics, and engineering. Given in alternate years; Not Offered 2018-19. Instructors: Meister, Perona, Shimojo.
CNS/Bi/Ph/CS/NB 187. Neural Computation. 9 units (3-0-6): first term. This course investigates computation by neurons. Of primary concern are models of neural computation and their neurological substrate, as well as the physics of collective computation. Thus, neurobiology is used as a motivating factor to introduce the relevant algorithms. Topics include rate-code neural networks, their differential equations, and equivalent circuits; stochastic models and their energy functions; associative memory; supervised and unsupervised learning; development; spike-based computing; single-cell computation; error and noise tolerance. Not Offered 2018-19. Instructor: Perona.
EE/MedE 187. VLSI and ULSI Technology. 9 units (3-0-6): third term. This course is designed to cover the state-of-the-art micro/nanotechnologies for the fabrication of ULSI including BJT, CMOS, and BiCMOS. Technologies include lithography, diffusion, ion implantation, oxidation, plasma deposition and etching, etc. Topics also include the use of chemistry, thermal dynamics, mechanics, and physics. Not offered 2018-19.
Bi 188. Human Genetics and Genomics. 6 units (2-0-4): third term. Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution. Given in alternate years; not offered 2018-19. Instructor: Wold.
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.
Bi 189. The Cell Cycle. 6 units (2-0-4): third term. The course covers the mechanisms by which eukaryotic cells control their duplication. Emphasis will be placed on the biochemical processes that ensure that cells undergo the key events of the cell cycle in a properly regulated manner. Instructor: Dunphy.
Bi 190. Systems Genetics. 6 units (2-0-4): first term. Lectures covering how genetic and genomic analyses are used to understand biological systems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Given in alternate years; not offered 2018-19. Instructor: Sternberg.
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.
Bi 192. Introduction to Systems Biology. 6 units (2-0-4): first term. The course will explore what it means to analyze biology from a systems-level point of view. Given what biological systems must do and the constraints they face, what general properties must biological systems have? Students will explore design principles in biology, including plasticity, exploratory behavior, weak-linkage, constrains that deconstrain, robustness, optimality, and evolvability. The class will read the equivalent of 2-3 scientific papers every week. The format will be a seminar with active discussion from all students. Students from multiple backgrounds are welcome: non-biology or biology students interested in learning systems-level questions in biology. Limited enrollment. Instructor: Goentoro.
Bi/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6): first term. This course develops the mathematical methods needed for a quantitative understanding of biological phenomena, including data analysis, formulation of simple models, and the framing of quantitative questions. Topics include: probability and stochastic processes, linear algebra and transforms, dynamical systems, scientific programming. Given in alternate years; not offered 2018-19. Instructor: Meister.
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.
MedE 199. Special Topics in Medical Engineering. Units to be arranged, terms to be arranged: . Subject matter will change from term to term depending upon staff and student interest, but will generally center on the understanding and applying engineering for medical problems. Instructor: Staff.
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.
MedE 201 ab. Principles and Design of Medical Devices. 9 units (3-0-6): second and third term. This course provides a broad coverage on the frontiers of medical diagnostic and therapeutic technologies and devices based on multidisciplinary engineering principles. Topics include biomaterials and biomechanics; micro/nanofluidics; micro/nano biophotonics and medical imaging; medical electronics, wireless communications through the skin and tissue; electrograms and biotic/abiotic interface; biochips, microPCR and sequencer and biosensors; micro/nano implants. The course will focus on the scientific fundamentals specific to medical applications. However, both the lectures and assignments will also emphasize the design aspects of the topics as well as up-to-date literature study. Instructor: Gao and Tai.
BMB/Ch 202 abc. Biochemistry Seminar Course. 1 unit: first, second, third terms. A course that includes a seminar on selected topics from outside faculty on recent advances in biochemistry. Students will participate in the seminar along with a formal discussion section with visiting faculty. Students will meet with the Biochemistry seminar speaker in the discussion section for an hour, and then attend the Biochemistry seminar at 4 p.m. BMB Seminars take place 1-2 times per month (usually on Thursdays). Instructor: Staff.
MedE 202. Sensors in Medicine. 9 units (3-0-6): second term. Sensors play a very important role in all aspect of modern life. This course is an essential introduction to a variety of physical, chemical and biological sensors that are used in medicine and healthcare. The fundamental recognition mechanisms, transduction principles and materials considerations for designing powerful sensing and biosensing devices will be covered. We will also discuss the development of emerging electronic-skin, wearable and soft electronics toward personalized health monitoring. Participants in the course will develop proposals for novel sensing technologies to address the current medical needs. Instructor: Gao.
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.
MedE 205. New Frontiers in Medical Technologies. 6 units (2-0-4): third term. New Frontiers of Medical Technologies is an introductory graduate level course that describes space technologies, instruments, and engineering techniques with current and potential applications in medicine. These technologies have been originally and mainly developed for space exploration. Spinoff applications to medicine have been explored and proven with various degrees of success and maturity. This class introduces these topics, the basics of the technologies, their intended original space applications, and the medical applications. Topics include but are not limited to multimodal imaging, UV/Visible/NIR imaging, imaging spectrometry, sensors, robotics, and navigation. Graded pass/fail. Instructor: Nikzad.
Bi 206. Biochemical and Genetic Methods in Biological Research. 6 units (2-0-4): third term. This course will comprise discussions of selected methods in molecular biology and related fields. Given in alternate years; not offered 2018-19. Instructor: Varshavsky.
Bi 214. Stem Cells and Hematopoiesis. 9 units (3-0-6): third term. An advanced course with classes based on active discussion, lectures, and seminar presentations. Development from embryos and development from stem cells are distinct paradigms for understanding and manipulating the emergence of ordered biological complexity from simplicity. This course focuses on the distinguishing features of stem-cell based systems, ranging from the natural physiological stem cells that are responsible for life-long hematopoiesis in vertebrates (hematopoietic stem cells) to the artificial stem cells, ES and iPS cells, that have now been created for experimental manipulation. Key questions will be how the stem cells encode multipotency, how they can enter long-term self-renewal by separating themselves from the developmental clock that controls development of the rest of the organism, and how the self-renewal programs of different stem cell types can be dismantled again to allow differentiation. Does "stem-ness" have common elements in different systems? The course will also cover the lineage relationships among diverse differentiated cell types emerging from common stem cells, the role of cytokines and cytokine receptors in shaping differentiation output, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Instructor: Rothenberg.
Bi/CNS/NB 216. Behavior of Mammals. 6 units (2-0-4): first term. A course of lectures, readings, and discussions focused on the genetic, physiological, and ecological bases of behavior in mammals. A basic knowledge of neuroanatomy and neurophysiology is desirable. Given in alternate years; not offered 2018-19. Instructor: Allman.
Bi/CNS/NB 217. Central Mechanisms in Perception. 6 units (2-0-4): first term. Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Given in alternate years; offered 2018-19. Instructor: Allman.
Bi/CNS/NB 220. Genetic Dissection of Neural Circuit Function. 6 units (2-0-4): first term. This advanced course will discuss the emerging science of neural "circuit breaking" through the application of molecular genetic tools. These include optogenetic and pharmacogenetic manipulations of neuronal activity, genetically based tracing of neuronal connectivity, and genetically based indicators of neuronal activity. Both viral and transgenic approaches will be covered, and examples will be drawn from both the invertebrate and vertebrate literature. Interested CNS or other graduate students who have little or no familiarity with molecular biology will be supplied with the necessary background information. Lectures and student presentations from the current literature. Instructor: Anderson.
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.
BMB/Ch 230. Macromolecular Structure Determination with Modern X-ray Crystallography Methods. 12 units (2-4-6): third term. Advanced course in macromolecular crystallography integrating lecture and laboratory treatment of diffraction theory, crystallization (proteins, nucleic acids and macromolecular complexes), crystal characterization, X-ray sources and optics, crystal freezing, X-ray diffraction data collection (in-house and synchrotron), data reduction, multiple isomorphous replacement, single- and multi-wavelength anomalous diffraction phasing techniques, molecular replacement, electron density interpretation, structure refinement, structure validation, coordinate deposition and structure presentation. In the laboratory component, one or more proteins will be crystallized and the structure(s) determined by several methods, in parallel with lectures on the theory and discussions of the techniques. Instructor: Hoelz.
Ch/Bi 231. Advanced Topics in Biochemistry. 6 units (2-0-4): third term. Transcriptional regulation in eukaryotes. Topics: the subunit structure of eukaryotic RNA polymerases and their role in transcriptional reactions; the composition of eukaryotic promoters, including regulatory units; general and specific transcription factors; developmental regulatory circuits and factors; structural motifs involved in DNA binding and transcriptional initiation and control. Not offered 2018-19.
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.
Ge/Bi 244. Paleobiology Seminar. 6 units (3-0-3): third term. Critical reviews and discussion of classic investigations and current research in paleoecology, evolution, and biogeochemistry. Instructor: Kirschvink.
Ge/Bi/ESE 246. Molecular Geobiology Seminar. 6 units (2-0-4); second term: Recommended preparation: ESE/Bi 166. Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Instructor: Orphan.
CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4): second term. A general survey of the structure and function of the cerebral cortex. Topics include cortical anatomy, functional localization, and newer computational approaches to understanding cortical processing operations. Motor cortex, sensory cortex (visual, auditory, and somatosensory cortex), association cortex, and limbic cortex. Emphasis is on using animal models to understand human cortical function and includes correlations between animal studies and human neuropsychological and functional imaging literature. Given in alternate years; Offered 2018-19. Instructor: Andersen.
Bi 250 a. Topics in Molecular and Cellular Biology. 9 units (3-0-6): first term. Lectures and literature-based discussions covering research methods, scientific concepts and logic, research strategies and general principles of modern biology. Students will learn to critique papers in a wide range of fields, including molecular biology, developmental biology, genetics and neuroscience. Graded pass/fail. Instructors: Aravin, Voorhees.
Bi 250 b. Topics in Systems Biology. 9 units (3-0-6): third term. The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale. Instructors: Elowitz, Bois.
Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6): third term. The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley's landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components. Instructor: Siapas.
Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit: . Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.
Bi 252. Responsible Conduct of Research. 4 units (2-0-2): third term. This lecture and discussion course covers relevant aspects of the responsible conduct of biomedical and biological research. Topics include guidelines and regulations, ethical and moral issues, research misconduct, data management and analysis, research with animal or human subjects, publication, conflicts of interest, mentoring, and professional advancement. This course is required of all trainees supported on the NIH training grants in cellular and molecular biology and neuroscience, and is recommended for other graduate students in labs in the Division of Biology and Biological Engineering labs. Undergraduate students require advance instructor's permission. Graded pass/fail. Instructors: Meyerowitz, Sternberg, Staff.
Bi 253. Reading, Writing, Reviewing, Experimental Design and Reproducibility. 6 units (2-0-4): second term. This course will consider scholarly communication in molecular and cellular biology, broadly defined. Students will learn about data standards, the minimal information required to describe an experiment and computer code. Discussion will include long term storage of data and informatics workflows. Appropriate citation of other article and resources will be considered. We will discuss evaluation of scientific premise, rigorous experimental design and interpretation, appropriate statistical power, authentication of key biological and chemical resources, data and material sharing, record keeping, and transparency in reporting data and observations. Students will learn to read papers critically and practice reviewing short articles from Micropublication: biology, which are short enough to allow a thorough analysis of methods necessary to ensure reproducibility. Graded Pass/Fail. Instructors: Sternberg, Hay, Staff.
SS/Psy/Bi/CNS 255. Topics in Emotion and Social Cognition. 9 units (3-0-6): third term. Emotions are at the forefront of most human endeavors. Emotions aid us in decision-making (gut feelings), help us remember, torment us, yet have ultimately helped us to survive. Over the past few decades, we have begun to characterize the neural systems that extend from primitive affective response such as fight or flight to the complex emotions experienced by humans including guilt, envy, empathy and social pain. This course will begin with an in-depth examination of the neurobiological systems that underlie negative and positive emotions and move onto weekly discussions, based on assigned journal articles that highlight both rudimentary and complex emotions. The final weeks will be devoted to exploring how the neurobiological systems are disrupted in affective disorders including anxiety, aggression and psychopathy. In addition to these discussions and readings, each student will be required to write a review paper or produce a short movie on a topic related to one of the emotions discussed in these seminars and its underlying neural mechanisms. Instructor: Mobbs.
CNS/Bi/NB 256. Decision Making. 6 units (2-0-4): third term. This special topics course will examine the neural mechanisms of reward, decision making, and reward-based learning. The course covers the anatomy and physiology of reward and action systems. Special emphasis will be placed on the representation of reward expectation; the interplay between reward, motivation, and attention; and the selection of actions. Links between concepts in economics and the neural mechanisms of decision making will be explored. Data from animal and human studies collected using behavioral, neurophysiological, and functional magnetic resonance techniques will be reviewed. Given in alternate years; Not offered 2018-19. Instructor: Andersen.
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.
Bi 270 abc. Special Topics in Biology. Units to be arranged each term: first, second, third. Students may register with permission of the responsible faculty member.
BMB 278. Fundamentals of Molecular Genetics. 9 units (3-0-6): third term. Principles and mechanisms of DNA repair and replication, transcription and splicing, and protein synthesis. Not offered 2018-19.
CNS/Bi 286 abc. Special Topics in Computation and Neural Systems. Units to be arranged: First, second, third terms. Students may register with permission of the responsible faculty member.
MedE 291. Research in Medical Engineering. Units to be arranged, first, second, third terms: . Qualified graduate students are advised in medical engineering research, with the arrangement of MedE staff.
Bi 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.
BMB 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.
NB 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.