Prerequisite of 2 other courses

An introduction to bioengineering that includes lectures and hands-on laboratory for design projects. The principles of problem definition, engineering inventiveness, team design, prototyping, and testing, as well as information access, engineering standards, communication, ethics, and social responsibility will be emphasized. P/NP grades only. Prerequisites: none. (W)

Introduction to MATLAB is designed to give students fluency in MATLAB, including popular toolboxes. Consists of interactive lectures with a computer running MATLAB for each student. Topics: variables, operations, and plotting; visualization and programming; and solving equations and curve fitting. Prerequisites: bioengineering: biosystems majors only or consent of department. (F)

The First-year Student Seminar Program is designed to provide new students with the opportunity to explore an intellectual topic with a faculty member in a small seminar setting. First-year student seminars are offered in all campus departments and undergraduate colleges, and topics vary from quarter to quarter. Enrollment is limited to fifteen to twenty students, with preference given to entering first-year students. (F,W,S)

Seminar discussing the interface between and opportunities for bioengineering and medicine. Students will interact with clinical faculty and bioengineering faculty to discuss current topics and problems where engineering solutions could improve the practice of medicine. Intended for first-year and transfer students in the Department of Bioengineering. Prerequisites: bioengineering majors only or consent of department.

An enrichment program available to a limited number of lower-division undergraduate students, which provides work experience with industry, government offices, and hospitals. The internship is coordinated through UC San Diego’s Academic Internship Program under the supervision of a faculty member and an industrial, government, or hospital employee. Prerequisites: lower-division standing, completion of thirty units of UC San Diego undergraduate study, a minimum UC San Diego GPA of 3.0, and a completed and approved Special Studies form. (F,W,S)

Directed group study on a topic or in a field not included in the regular department curriculum. (P/NP grades only.) Prerequisites: lower-division standing, completion of thirty units of undergraduate study at UC San Diego with a UC San Diego GPA of at least 3.0 and consent of a bioengineering faculty member; completed and approved Special Studies form.

Independent reading or research by arrangement with a bioengineering faculty member. (P/NP grades only.) Prerequisites: lower-division standing, completion of thirty units of undergraduate study at UC San Diego with a UC San Diego GPA of at least 3.0 and consent of a bioengineering faculty member; completed and approved Special Studies form.

Independent study or research under direction of a member of the faculty. Prerequisites: student must be of first-year standing and a Regents Scholar; approved Special Studies form.

Prerequisite of 9 other courses

The class provides foundation in probability and statistics. Topics include probability spaces, random variables, independence, common distributions, CLT, estimator accuracy, maximum likelihood, and hypothesis testing. Written problems are provided for each topic. Applications are discussed in regard to bioengineering problems. Prerequisites: BENG 1, MATH 18 or MATH 31AH or MATH 20F, MATH 20C or MATH 31BH; bioengineering majors only or consent of department. (S)

Prerequisite of 2 other courses

Introduction to molecular structures. Macromolecules and assemblies-proteins, nucleic acids, and metabolites. Principles of design of simple and complex components of organelles, cells, and tissues. Prerequisites: BENG 120 or consent of department. (S)

Prerequisite of 1 other course

Mass transfer in solids, liquids, and gases with application to biological systems. Free and facilitated diffusion. Convective mass transfer. Diffusion-reaction phenomena. Active transport. Biological mass transfer coefficients. Steady and unsteady state. Flux-force relationships. (Credit not allowed for both CENG 101C and BENG 103B.) Prerequisites: CENG 101A or MAE 101A or BENG 112A, or consent of department. (S)

Prerequisite of 2 other courses

Statics, dynamics, and solid mechanics of hard and soft musculoskeletal tissues. Forces, moments, static equilibrium, kinematics, kinetics applied to human mechanics, and movement. Stress, strain, and material properties of musculoskeletal tissues. Problem solving and design in biomechanics. Prerequisites: MATH 20D, MATH 20E or MATH 31CH, MATH 18 or MATH 31AH; PHYS 2C, or consent of department. (F)

Prerequisite of 3 other courses

Tensor analysis. Stress, strain, equilibrium, and constitutive law for soft biological tissues. Applications of solid mechanics to mammalian tissue physiology. Viscoelasticity. Finite elasticity. Problem solving and design in soft tissue biomechanics. Prerequisites: BENG 110 or consent of department. (W)

Prerequisite of 2 other courses

Fluid hydrostatics and flow dynamics. Flow kinematics and conservation laws applied to the circulation. Viscous biofluids. Biopolymers, cell mechanics, and mechanobiology. Problem solving and design in biofluid and cell mechanics. Prerequisites: BENG 112A or consent of department. (S)

Development of design project in biomechanics. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in biomechanics. Prerequisites: concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 5 other courses

Structural and design principles of carbon compounds. Structure and stereochemistry. Functional groups and chemical transformations. Structure and design principles of biomolecules. Molecules of life and their organization. Prerequisites: CHEM 6A and 6B; majors only or consent of department. (W)

Prerequisite of 3 other courses

Systems and control theory applied to bioengineering. Modeling, linearization, transfer functions, Laplace transforms, closed-loop systems, design and simulation of controllers. Dynamic behavior and controls of first and second order processes. PID controllers. Stability. Bode design. Features of biological controls systems. A simulation project using MATLAB and an oral presentation are required. Credit not allowed for both ECE 101 and BENG 122A. Prerequisites: MAE 140 or BENG 134 or consent of department. (F)

Prerequisite of 3 other courses

Dynamic simulation of biochemical reaction networks, including reconstruction of networks, mathematical description of kinetics of biochemical reactions, dynamic simulation of systems of biochemical reactions, and use of simulators for data interpretation and prediction in biology. Emphasis on a design project. Prerequisites: MATH 18 or MATH 31AH, MATH 20D, BENG 120, or CHEM 40B; majors only or consent of department. (W)

Computational modeling of molecular bioengineering phenomena: excitable cells, regulatory networks, and transport. Application of ordinary, stochastic, and partial differential equations. Introduction to data analysis techniques: power spectra, wavelets, and nonlinear time series analysis. Prerequisites: BENG 122A or BENG 123 or consent of department. (S)

Prerequisite of 1 other course

Development of design project in bioinformatics bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in bioinformatics bioengineering. Prerequisites: BENG 126A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Development of design project in molecular systems bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in molecular systems bioengineering. Prerequisites: BENG 127A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Development of design project in genetic circuits bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in genetic circuits bioengineering. Prerequisites: BENG 128A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Development of design project in cell systems bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in cell systems bioengineering. Prerequisites: BENG 129A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

An introduction to physical principles that govern biological matter and processes, with engineering examples. Thermodynamic principles, structural basis of life, molecular reactions and kinetics, and models to illustrate biological phenomena. Prerequisites: CHEM 6B, MATH 20A, 20B, 20D, PHYS 2A, 2B, 2C; majors only or consent of department. (W)

Prerequisite of 2 other courses

Principles of digital computing, including number representation and arithmetic operations. Accuracy, stability, and convergence. Algorithms for solving linear systems of equations, interpolation, numerical differentiation, and integration and ordinary differential equations. Prerequisites: MATH 20D and 18 or consent of department. (S)

Prerequisite of 7 other courses

A combined lecture and laboratory course that provides an introductory treatment of probability theory, including distribution functions, moments, and random variables. Practical applications include estimation of means and variances, hypothesis testing, sampling theory, and linear regression. Prerequisites: MATH 20D and MATH 18 or MATH 31AH; BENG 100 or consent of department. (F)

Prerequisite of 1 other course

Discrete systems: linearity, convolution, impulse, and step responses. Linear systems properties. Difference equations. Fourier Series. Continuous FS. Discrete FS. Periodic signals, filtering, and FT. Discrete FT examples. Frequency response of linear systems. Sampling. Relationship between FT, DFT. Laplace Transform. LT and inverse LT. Prerequisites: ECE 45 and BENG 133 or consent of department. (F) Not offered until fall 2016.

Prerequisite of 1 other course

Development of design project in molecular bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in molecular bioengineering. Prerequisites: BENG 139A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 4 other courses

Introductory mammalian physiology for bioengineering students, with emphasis on control mechanisms and engineering principles. Basic cell functions; biological control systems; muscle; neural; endocrine, and circulatory systems. Not intended for premedical bioengineering students. Credit not allowed for both BIPN 100 and BENG 140A. Prerequisites: CHEM 6A-B, PHYS 2A-B-C, BILD 1, or BENG 102; majors only or consent of department. (W)

Prerequisite of 2 other courses

Introductory mammalian physiology for bioengineering students, with emphasis on control mechanisms and engineering principles. Digestive, respiratory, renal, and reproductive systems; regulation of metabolism, and defense mechanisms. (Credit not allowed for both BIPN 102 and BENG 140B.) Prerequisites: BENG 140A; majors only or consent of instructor. (S)

Introduction to optics. Light propagation in tissue. Propagation modeling. Optical components. Laser concepts. Optical coherence tomography. Microscopic scattering. Tissue optics. Microscopy. Confocal microscopy. Polarization in tissue. Absorption, diffuse reflection, light scattering spectroscopy. Raman, fluorescence lifetime imaging. Photo-acoustic imaging. Prerequisites: BENG 100 or consent of department. (F)

Prerequisite of 1 other course

Development of design project in neural engineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in neural engineering. Prerequisites: BENG 147A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Development of design project in cardiac bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in cardiac bioengineering. Prerequisites: BENG 148A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Development of design project in vascular bioengineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in vascular bioengineering. Prerequisites: BENG 149A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 1 other course

Experimental study of real and simulated systems and their controls (examples will include electrical, biological, and biomechanical systems). Projects consist of identification, input-output analysis, design, and implementation of analog controls. Laboratory examples will include electrical circuit design and analysis, analysis of living tissues such as bone, analysis and manipulation of cells (bacteria in chemostat). Program or materials fees may apply. Prerequisites: BENG 102; bioengineering: biosystems majors only or consent of department. (W)

Prerequisite of 2 other courses

Introductory laboratory course in current principles and techniques of chemistry and molecular biology applicable to bioengineering. Quantitation of proteins and nucleic acids by spectrophotometric, immunological, and enzymatic methods. Separations and purification by centrifugation, chromatographic, and electrophoretic methods. Course materials fees may apply. Prerequisites: BICD 100, BENG 100, MAE 170; majors only or consent of department. (S)

Prerequisite of 1 other course

Engineering, biochemical, and physiological considerations in the design of bioreactor processes: enzyme kinetics, mass transfer limitations, microbial growth, and product formation kinetics. Fermentation reactor selection, design, scale-up, control. Quantitative bioengineering analysis and design of biochemical processes and experiments on biomolecules. Prerequisites: BENG 123 and BENG 160 or consent of department. (F)

Commercial production of biochemical commodity products. Application of genetic control systems and mutant populations. Recombinant DNA and eukaryotic proteins in E. coli and other host organisms. Product recovery operations, including the design of bioseparation processes of filtration, adsorption, chromatography, and crystallization. Bioprocess economics. Human recombinant erythropoietin as an example, from genomic cloning to CHO cell expression, to bioreactor manufacturing and purification of medical products for clinical application. Prerequisites: BENG 161A or consent of department. (W)

Laboratory practices and design principles for biotechnology. Culture of microorganisms and mammalian cells, recombinant DNA bioreactor design and operation. Design and implementation of biosensors. A team design-based term project and oral presentation required. Course materials fees may apply. Prerequisites: MAE 170 and BENG 160; majors only or consent of department. (F)

Engineering analysis of physico-chemical rate processes that affect, limit, and govern the function of cells and tissues. Cell migration, mitosis, apoptosis, and differentiation. Dynamic and structural interactions between mesenchyme and parenchyme. The role of the tissue microenvironment including cell-cell interactions, extracellular matrix, and growth factor communication. The design of functional tissue substitutes including cell and material sourcing, scale-up and manufacturability, efficacy and safety, regulatory, and ethical topics. Clinical applications. Prerequisites: BENG 103B or BENG 112B; senior standing or consent of department. (F)

Prerequisite of 1 other course

Basic molecular biology and recombinant DNA technologies. Structure and function of biomolecules that decode genomes and perform energy conversion, enzymatic catalysis, and active transport. Metabolism of macromolecules. Molecular diagnostics. Design, engineering, and manufacture of proteins, genomes, cells, and biomolecular therapies. Prerequisites: BILD 1 and BENG 100, or consent of department. (W)

Prerequisite of 1 other course

Development of design project in tissue engineering. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in tissue engineering. Prerequisites: BENG 169A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

A laboratory course demonstrating basic concepts of biomechanics, bioengineering design, and experimental procedures involving animal tissue. Sources of error and experimental limitations. Computer data acquisition, modeling, statistical analysis. Experiments on artery, muscle and heart mechanics, action potentials, viscoelasticity, electrocardiography, hemorheology. Course materials fees may apply. Prerequisites: MAE 170; junior or senior standing in the major or consent of instructor. (S)

Prerequisite of 1 other course

Development of design project in bioinstrumentation. Prerequisites: concurrent enrollment in BENG 187B; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (F)

Implementation of design project in bioinstrumentation. Prerequisites: BENG 179A; concurrent enrollment in BENG 187C; bioengineering or bioengineering: biotechnology majors only or consent of instructor. (W)

Prerequisite of 4 other courses

(Cross-listed as BIMM 181 and CSE 181.) This course covers the analysis of nucleic acid and protein sequences, with an emphasis on the application of algorithms to biological problems. Topics include sequence alignments, database searching, comparative genomics, and phylogenetic and clustering analyses. Pairwise alignment, multiple alignment, DNA sequencing, scoring functions, fast database search, comparative genomics, clustering, phylogenetic trees, gene finding/DNA statistics. Prerequisites: CSE 100; CSE 101; BIMM 100 or CHEM 114C; bioinformatics majors only. (W)

Prerequisite of 4 other courses

(Cross-listed as BIMM 182, CSE 182, and CHEM 182.) This course provides an introduction to the features of biological data, how those data are organized efficiently in databases, and how existing data resources can be utilized to solve a variety of biological problems. Object-oriented databases, data modeling, and data description. Survey of current biological database with respect to above; implementation of database focused on a biological topic. Prerequisites: CSE 100; bioinformatics majors only. (S)

Prerequisite of 1 other course

Principles and technologies for using genomic information for biomedical applications. Technologies will be introduced progressively, from DNA to RNA to protein to whole cell systems. The integration of biology, chemistry, engineering, and computation will be stressed. Topics include technology for the genome, DNA chips, RNA technologies, proteomic technologies, aphysiomic and phenomic technologies, and analysis of cell function. Prerequisites: BIMM 100 or CHEM 114C, or consent of department. (F)

Prerequisite of 1 other course

(Cross-listed as BIMM 184, CSE 184, and CHEM 184.) This advanced course covers the application of machine learning and modeling techniques to biological systems. Topics include gene structure, recognition of DNA and protein sequence patterns, classification, and protein structure prediction. Pattern discovery, hidden Markov models/support vector machines/neural network/profiles, protein structure prediction, functional characterization of proteins, functional genomics/proteomics, metabolic pathways/gene networks. Prerequisites: BENG 181 or BIMM 181 or CSE 181; BENG 182 or BIMM 182 or CSE 182 or CHEM 182; bioinformatics majors only. (S)

Fundamentals of materials science as applied to bioengineering design. Natural and synthetic polymeric materials. Materials characterization and design. Wound repair, blood clotting, foreign body response, transplantation biology, biocompatibility of materials, tissue engineering. Artificial organs and medical devices. Government regulations. Patenting. Economic impact. Ethical issues. A term project and oral presentation are required. Prerequisites: BENG 112B or BENG 123, or consent of department. (S)

Biophysical phenomena, transducers, and electronics as related to the design of biomedical instrumentation. Potentiometric and amperometric signals and amplifiers. Biopotentials, membrane potentials, chemical sensors. Electrical safety. Mechanical transducers for displacement, force, and pressure. Temperature sensors. Flow sensors. Light-based instrumentation. Prerequisites: ECE 35 or MAE 140; ECE 45 or MAE 170; or consent of department. (W)

Prerequisite of 1 other course

General engineering design topics including project planning and design objectives, background research, engineering needs assessment, technical design specifications, engineering standards, and design requirements and constraints. Introduction to biomedical and biotechnology design projects. Career and professional advising. Majors must enroll in the course for a letter grade in order to count the sequence toward the major. No exceptions will be approved. Prerequisites: BENG 112A or BENG 152 or BENG 168; bioengineering, bioengineering: biotechnology, or bioengineering: biosystems majors only or consent of department. (S)

Prerequisite of 1 other course

Development of an original bioengineering design for solution of a problem in biology or medicine. Analysis of economic issues, manufacturing and quality assurance, ethics, safety, design constraints, government regulations, and patent requirements. Oral presentation and formal engineering reports. Career and professional advising. Majors must enroll in the course for a letter grade in order to count the sequence toward the major. No exceptions will be approved. Prerequisites: BENG 187A; concurrent enrollment in one of BENG 119A, BENG 126A, BENG 127A, BENG 128A, BENG 129A, BENG 139A, BENG 147A, BENG 148A, BENG 149A, BENG 169A, or BENG 179A; bioengineering, bioengineering: biotechnology, or bioengineering: biosystems majors only or consent of instructor. (F)

Prerequisite of 1 other course

Approaches to implementation of senior design project, including final report. Teams will report on construction of prototypes, conduct of testing, collection of data, and assessment of reliability and failure. Majors must enroll in the course for a letter grade in order to count the sequence toward the major. No exceptions will be approved. Prerequisites: BENG 187B; concurrent enrollment in one of the following lab sections: BENG 119B, BENG 126B, BENG 127B, BENG 128B, BENG 129B, BENG 139B, BENG 147B, BENG 148B, BENG 149B, BENG 169B, or BENG 179B; bioengineering, bioengineering: biotechnology, or bioengineering: biosystems majors only or consent of instructor. (W)

Oral presentations of design projects, including design, development, and implementation strategies and results of prototype testing. Majors must enroll in the course for a letter grade in order to count the sequence toward the major. No exceptions will be approved. Prerequisites: BENG 187C; bioengineering, bioengineering: biotechnology, or bioengineering: biosystems majors only or consent of instructor. (S)

Quantitative description of physiological systems, e.g., electrical and mechanical properties of muscle (skeletal and cardiac). Modeling and simulation of properties. Kidney, transport, and models. Neural circuits and models. Prerequisites: BENG 133, 134, 135, 140A and 140B, or consent of department. (S) Not offered until spring 2017.

(Conjoined with BENG 291.) Instills skills for personal and organizational development during lifelong learning. Student prepares portfolio of personal attributes and experiences, prepares for career interviews plus oral report of interviewing organizational CEO. Graduate students will prepare a NIH small business research grant. Prerequisites: consent of instructor. (F)

Introduction on the integration of bioengineering and clinical medicine through lectures and rotations with clinical faculty. Students will work with clinical mentors and course faculty to identify areas where engineering can improve diagnostics, clinical practice, and/or treatment. May be coscheduled with BENG 294C. Prerequisites: BENG 140A or BIPN 100; BENG 140B or BIPN 102; consent of instructor required. A GPA of 3.5 is requested as a requirement per the agreement with the School of Medicine to ensure that students who are participating in the program have a strong academic background to be in the clinic as an undergraduate. (S)

Teaching and tutorial assistance in a bioengineering course under supervision of instructor. Not more than four units may be used to satisfy graduation requirements. (P/NP grades only.) Prerequisites: 3.0 GPA in the major and department approval. (F,W,S)

Under the joint supervision of a faculty adviser and industry mentor, the student will work at or be mentored at a bioengineering industrial company to gain practical bioengineering experience, summarized in a technical report. May be taken for credit up to three times. With department approval, four units of credit may substitute for a technical elective. (P/NP grades only.) Prerequisites: consent of department and completion of all lower-division course requirements, including general-science requirement; laboratory experience. (F,W,S,Su)

An enrichment program, available to a limited number of undergraduate students, which provides work experience with industry, government offices, hospitals, and their practices. Subject to the availability of positions, students will work in a local industry or hospital (on a salaried or unsalaried basis) under the supervision of a faculty member and industrial, government, or hospital employee. Coordination of the Engineering Internship is conducted through UC San Diego’s Academic Internship Program. Time and effort to be arranged. Units may not be applied toward major graduation requirements unless prior approval of a faculty adviser is obtained, and internship is an unsalaried position. Prerequisites: completion of ninety units with a 2.5 GPA and consent of a bioengineering faculty coordinator. (F,W,S,Su)

Directed group study, on a topic or in a field not included in the regular department curriculum, by arrangement with a bioengineering faculty member. (P/NP grades only.) Prerequisites: upper-division standing, completion of ninety units of UC San Diego undergraduate study, a minimum UC San Diego GPA of 2.5, consent of instructor, and a completed and approved Special Studies form. (F,W,S)

Independent reading or research by arrangement with a bioengineering faculty member. May be taken for credit three times. (P/NP grades only.) Prerequisites: upper-division standing, completion of ninety units of UC San Diego undergraduate study, a minimum UC San Diego GPA of 2.5, consent of instructor, and a completed and approved Special Studies form. (F,W,S,Su)

Prerequisite of 2 other courses

(Formerly BENG 202/CSE 257A.) Introduction to methods for sequence analysis. Application to genome and proteome sequences. Protein structure, sequence-structure analysis. Prerequisites: Pharm 201 or consent of instructor. (W)

Annotating genomes, characterizing functional genes, profiling, reconstructing pathways. Prerequisites: Pharm 201, BENG 202/CSE 282, or consent of instructor. (S)

Course given at the discretion of the faculty on current topics of interest in bioengineering. (F,W,S)

Course given at the discretion of the faculty on topics of current interest in engineering science. This course is intended to be a lecture and lab companion topics course. Prerequisites: consent of instructor. (S)

Components of biological systems, their biochemical properties and function. The technology used for obtaining component lists. Relationship within and integration of component lists. Structured vocabularies and component ontologies. Algorithms for comparative approaches in deciphering and mining component lists. Prerequisites: BENG 230A or BIMM 100, or consent of instructor. (F)

Prerequisite of 1 other course

Analysis of biological data can be performed at four levels: 1) statistical analysis, 2) integration of knowledge, 3) integration of networks, and 4) integration of biophysical laws. This course teaches the first two levels. The first level consists of specialized topics in statistical analysis of large-scale data sets and machine learning. The second level consists of leveraging prior knowledge for the analysis of diverse, multi-omic datasets and network reconstruction. Prerequisites: graduate standing. (W)

Analysis of biological data can be performed at four levels: 1) statistical analysis, 2) integration of knowledge, 3) integration of networks, and 4) integration of biophysical laws. This course teaches the last two levels. The third level consists of integrating data in the context of genome-scale models to simulate and predict cellular phenotypes. The fourth level consists of analyzing data in the context of kinetic and thermodynamic laws that govern cellular function. Prerequisites: BENG 212 and graduate standing. (S)

Prerequisite of 2 other courses

Introduction of the foundations of engineering by teaching the mathematical methods that describe the engineering principles. Analytical and numerical approaches to solving the equations. Prerequisites: graduate standing in bioengineering or consent of instructor. (F)

Thermodynamics, statistical mechanics, and interfacial phenomena that emphasize the chemical natures of living systems. Topics include intermolecular and surface forces, calculation of energetic processes, computation of electrical forces and fields, and principles of physics in multiscale engineering and design. Prerequisites: graduate standing in bioengineering or consent of instructor. (W)

Introduces real-world tools and skills that product development engineers are expected to master in a medical device company. Students will be introduced to all stages of medical device development in an FDA-regulated environment with an emphasis in design controls and building a design history file. Students will also be exposed to other relevant topics such as project management, legal consideration, medical reimbursement, regulatory submissions, commercialization, and product improvements. Prerequisites: graduate standing in bioengineering only or consent of department.

This course broadly covers the business of biotech with emphasis on innovation and communication skills. Topics include (1) disruptive technologies, (2) FDA regulation, (3) licensing and spinouts, (4) financing, (5) business models, and (6) business development and acquisitions. The format is intensive and interactive. Prerequisites: graduate standing in bioengineering or consent of department.

Prerequisite of 1 other course

Modern development of biomechanics at an advanced mathematical level. Description of internal stresses and deformation in living tissues and fluids, thermodynamics. Mechanics of soft connective tissue, extracellular matrix, cells, membranes, and cytoskeleton. Mechanotransduction, migration, adhesion. Blood flow in microvessels. Biomechanical analysis of tissue injury. Recommended preparation: a previous background in biomechanics is strongly recommended prior to taking this course. Prerequisites: graduate standing or consent of instructor. (S)

Prerequisite of 1 other course

This course describes the movement of heat and chemical mass in biological systems. Diffusion, convection and biochemical reactions in a variety of biological and engineering examples are analyzed and modeled. Students that have taken BENG 222 cannot take BENG 227 for credit. Prerequisites: BENG 221, graduate standing, or consent of instructor. (S)

Prerequisite of 2 other courses

A graduate course in biochemistry especially tailored to the requirements and background of bioengineering graduate students. It will cover the important macro- and small molecules in cells that are the major constituents, or that function as signaling molecules or molecular machineries. The structures, pathways, interactions, methodologies, and molecular designs using recombinant DNA technology will be covered. Prerequisites: restricted to bioengineering graduate students with major code BE75. (F)

Prerequisite of 1 other course

A general survey of structure-function relationships at the molecular and cellular levels. Emphasis on basic genetic mechanisms; control of gene expression; membrane structure, transport and traffic; cell signaling; cell adhesion; mechanics of cell division; and cytoskeleton. Prerequisites: BENG 230A; restricted to bioengineering graduate students with major code BE75. (W)

Prerequisite of 1 other course

Physical concepts of behavior of heart, large blood vessels, vascular beds in major organs and the microcirculation. Physical and physiological principles of blood flow, blood pressure, cardiac work, electrophysiology of the heart. Special vascular beds, including their biological and hemodynamic importance. Integration through nervous and humoral controls. Prerequisites: BENG 230B or consent of instructor.

Mechanics of breathing. Gas diffusion. Pulmonary blood flow. Stress distribution. Gas transport by blood. Kinetics of oxygen and carbon dioxide exchange. VA/Q relations. Control of ventilation. Glomerular and proximal tubule functions. Water metabolism. Control of sodium and potassium in the kidney. Prerequisites: BIPN 100, 102, and BENG 230C, or consent of instructor. (F,W,S)

An overview of the musculoskeletal system from a bioengineering perspective. Health, injury, disease of bone, cartilage, tendon, ligament, meniscus, synovium, intervertebral disc, skeletal muscle, peripheral nerve. Mechanisms and models underlying current and future therapies. Prerequisites: graduate standing or consent of instructor. (S)

Mechanical properties of structures involved in movement (muscles, tendons, bones). Models of neuromuscular adaptation to chronic electrical stimulation, voluntary exercise, surgical overload, spinal cord injury, denervation, limb immobilization, exercise-induced injury and muscle regeneration. Stem cells in muscle function and plasticity. Prerequisites: graduate standing or consent of instructor.

Introduction to molecular and cellular neurobiology and their integration with systems neurophysiology. Homeostasis will be an organizing theme. The material will be presented both qualitatively and quantitatively, emphasizing the mathematical, physical, and chemical foundations and dynamics that underlie neurophysiological functions. Prerequisites: graduate standing or consent of instructor. (S)

This course will introduce quantitative fluorescence microscopy techniques for imaging, manipulating, and quantifying the spatiotemporal characteristics of molecular events in live cells. A laboratory component will be integrated with students organized into small teams for projects. Recommended preparation: basic optics at the level of ECE 181, introductory molecular and cellular biology at the level of BIMM 100 and BICD 110, respectively. Prerequisites: graduate standing or consent of instructor. (S)

An overview of heart, vascular development and associated diseases from a molecular biological perspective. Current approaches for generating mouse models of cardiovascular disease and recently developed technologies for physiological assessment in small animal models will be presented. (W)

Prerequisite of 2 other courses

Overview and foundations of tissue engineering and regenerative medicine. Tissue structure, function, and dynamics in health and disease. Cells, microenvironment, extracellular matrix, and biomaterials as components of engineered tissues and organs. Functional goals, design, testing, and evaluation of therapies. Prerequisites: graduate standing. (F)

The role of the cellular microenvironment in directing cell behavior and function in health and disease. Cell adherence and deformation and cell-mediated matrix remodeling. Bioengineering of the microenvironment in tissue engineering and regenerative medicine. Prerequisites: BENG 241A, graduate standing, or consent of instructor.

Development, morphogenesis, growth, and remodeling of tissues and organs in health and disease. Integrative metabolism and biomechanics of cells and extracellular matrix at tissue, organ, and organism scales. Bioengineering restoration of tissues and organs. Industry applications and regulations. Prerequisites: BENG 241A, graduate standing, or consent of instructor.

Quantitative basic understanding of different branches of polymer science varying from polymer chemistry, characterization, thermodynamics, rheological properties, smart materials, self-assembly in biopolymers (natural) and synthetic polymers, and applications of polymers ranging from medicine to structure. Prerequisites: graduate standing in bioengineering, nanoengineering, or materials science, or consent of instructor.

Basic physics and chemistry of interaction of photons with matter; photonic radiation pressure; advanced optoelectronic detection systems, devices, methods, time-resolved fluorescent, chemiluminescent methods, fluorescent energy transfer techniques, quantum dots, near-field optical techniques, mechanisms of light sensitive biological systems including chloroplasts for photosynthetic energy conversion and basis of vision processes. Prerequisites: graduate standing. (F)

Topics include photolithographic techniques for high-density DNA microarray production, incorporation of CMOS control into electronic DNA microarrays, direct electronic detection technology, biofuel cells, highly integrated devices (lab-on-a-chip, in vivo biosensors, etc.). Form heterogeneous materials and components. Prerequisites: graduate standing. (W)

Bionanotechnology is defined as science and engineering that involve working with biomolecules on the nanoscale. DNA and protein-based nanostructures or even entire microorganisms are subject of study and development of nanomachines. Another avenue is the nanoscale biomimicry in which synthetic systems are engineered to mimic what nature has already achieved. Bionanotechnology finds utility in medicine, materials, the environment. Students may receive credit for one of the following: NANO 247C, BENG 247C, or ECE 247C. Prerequisites: graduate standing. (S)

Introduction to genetic circuits in natural systems, engineering principles in biology, characterization of biological components, numerical methods for systems analysis and design, fabrication of genetic systems in theory and practice, transformation and characterization, and examples of engineered systems. Prerequisites: graduate bioengineering majors only or consent of instructor. (S)

Introduction to the nonlinear dynamics of neurons and neural systems using bifurcation theory and chaotic motions, at different levels of abstraction, e.g., biophysical and “reduced” models for analysis of regularly spiking and bursting cells. Laboratory exercises will accompany the lectures. Prerequisites: graduate standing or consent of instructor. (F)

Structural and functional aspects of transport and blood-tissue exchange in key organs during circulatory shock, bacterial toxemia, hypertension. Physical and ultrastructural techniques used to analyze small-vessel dynamics. Prerequisites: consent of instructor. (S)

Introduces mathematical tools to simulate biological processes at multiple scales. Numerical methods for ordinary and partial differential equations (deterministic and stochastic), and methods for parallel computing and visualization. Hands-on use of computers emphasized; students will apply numerical methods in individual projects. Prerequisites: consent of instructor. (W)

Students will learn to conduct tissue engineering and developmental biology experiments, microfabricate cell culture systems, engineer biopolymer materials, and develop and analyze quantitative models of transport, cell fate, and growth mechanics. The understanding and manipulation of multicellular processes that comprise development and growth involves specialized areas of biomechanics, developmental biology, biomaterials, and the tools of molecular biology, as well as the integration of theory and experiment. To fabricate functional tissues, it is important to establish underlying molecular and physical mechanisms and then control and integrate these. Prerequisites: consent of instructor. (W)

This lab course provides hands-on experience with MR physics, data acquisition, image formation, and data analysis, using a human MRI scanner. It will cover basic principles of MRI and key applications, including scanner hardware, spin echoes, gradient echoes, echo-planar imaging, MR angiography, fMRI, and perfusion imaging. This will be accomplished through one hour of formal instruction and four hours of scanner time per week. Each week will cover one topic, and grading will be based on lab reports. The last two weeks are reserved for a final project, which can be student initiated. Prerequisites: BENG 280A or basic knowledge of linear systems and MRI, or consent of instructor. (W)

Prerequisite of 2 other courses

Fundamentals of Fourier transform and linear systems theory including convolution, sampling, noise, filtering, image reconstruction and visualization with an emphasis on applications to biomedical imaging. Examples from optical imaging, CT, MR, ultrasound, nuclear, PET, and radiography. Prerequisites: graduate standing. (F)

Prerequisite of 1 other course

Application of biomedical imaging to the measurement of structure, function, and dynamics of organ systems from the microscopic to the organ level. Emphasis on detailed evaluation and comparison of specific imaging modalities. Prerequisites: consent of instructor. (W,S)

This course will focus on the imaging modalities used to diagnose and guide treatment of cardiovascular disease such as echocardiography, single photon computed tomography (SPECT), X-ray angiography, computed tomography (CT), and magnetic resonance imaging (MRI). Prerequisites: graduate standing. (S)

Weekly seminars by faculty, visitors, postdoctoral research fellows, and graduate students concerning research topics in bioengineering and related subjects. May be repeated for credit. Course does not apply toward MS graduation requirements. (S/U grades only.) (F,W,S)

Weekly seminars by bioengineering faculty presenting their research. May be repeated for credit. Course does not apply toward MS or PhD graduation requirements. (S/U grades only.) (F)

A laboratory course combining hands-on mass spectrometry and bioinformatics tools to explore the relationship between structure and function in macromolecules. Tools for peptide sequencing, analysis of post-translational modification, and fragmentation analysis by mass spectrometry are examples of experiments students will run. Prerequisites: consent of instructor.

A hallmark of bioinformatics is the computational analysis of complex data. The combination of statistics and algorithms produces statistical learning methods that automate the analysis of complex data. Such machine learning methods are widely used in systems biology and bioinformatics. This course provides an introduction to statistical learning and assumes familiarity with key statistical methods. Students may not receive credit for BENG 285 and ECE 204 and BNFO 285. Prerequisites: ECE 271A or ECE 271B or MATH 283; or consent of instructor.

(Conjoined with BENG 191.) Instills skills for personal and organizational development during lifelong learning. Student prepares portfolio of personal attributes and experiences, prepares for career interviews plus oral report of interviewing organizational CEO. Graduate students will prepare a NIH small business research grant. Prerequisites: consent of instructor. (F)

Lectures, readings, and discussions about the responsible conduct and reporting of research, working with others in science, and social responsibilities; the course is designed as an option for meeting federal regulations for such training. Students should review the following web page prior to enrollment: https://ethics.ucsd.edu/courses/ethics/index.html. (S/U grades only.) Prerequisites: doctoral students only or consent of department. (F,W,S)

Prerequisite of 1 other course

Case-based introduction to patient-focused reasoning. Covers principles of quantitative physiology, medical devices (diagnostic and therapeutic), and complexities of real-world care settings. Emphasis on cardiopulmonary diseases. Prerequisites: bioengineering MS medicine majors only or consent of department.

Prerequisite of 1 other course

Evaluation of medical schools in terms of historical background, specialties, graduating MDs metrics, and employment; and their societal, environmental, economic, political, and research impact. Coordination with medical school interviews with assigned off-campus time allocation. Report on results attained. Prerequisites: BENG 294A; bioengineering MS medicine majors only or consent of department.

Capstone experiential learning course where students are to integrate bioengineering training and clinical medicine through lectures and rotations with clinical faculty. Students will identify problems with diagnostics, clinical practice, and/or treatment, and use engineering principles to design solutions. May be coscheduled with BENG 193. Prerequisites: BENG 294B; bioengineering MS medicine majors only or consent of department.

Independent work by graduate students focused on design, applied research, and professional experience. Prerequisites: consent of instructor and department approval. (F,W,S)

Prerequisites: consent of instructor. (F,W,S)

Directed group study on a topic or in a field not included in regular department curriculum, by special arrangement with a faculty member. (S/U grades only.) Prerequisites: consent of instructor. (F,W,S)

Laboratory research rotation for first-year BENG PhD students. Students will write a final paper. (S/U grades only.) Prerequisites: PhD student in bioengineering. (F,W,S)

Independent work by graduate students engaged in research and writing theses. (S/U grades only.) Prerequisites: consent of instructor. (F,W,S)

Teaching experience in one of the six bioengineering lab courses designated as a part of the BENG PhD Specialization in Multi-Scale Biology. Student is under the direction of the faculty member in charge of the course. (S/U grades only.) Prerequisites: consent of instructor and department approval. (F,W,S)

Teaching experience in an appropriate bioengineering undergraduate course under direction of the faculty member in charge of the course. Lecturing one to two hours per week in either a problem-solving section or regular lecture. (S/U grades only.) Prerequisites: consent of instructor and department approval. (F,W,S)