Bioengineering

Courses

For course descriptions not found in the 2008-2009 General Catalog, please contact the department for more information.

Note: The department will endeavor to offer the courses as outlined below; however, unforeseen circumstances sometimes mandate a change of scheduled offerings. Students are strongly advised to check with the department’s Student Affairs Office. This is of particular importance in planning schedules to satisfy graduation requirements.

The following schedule is tentative for the academic year 2008-09 only. The quarter in which a course is scheduled may differ in subsequent academic years. Students should consult TritonLink and the Student Affairs Office to obtain current information.

Prerequisites are enforced when students register for courses. Students who have satisfied prerequisites at another institution or by AP credit need to be pre-authorized to register in these courses. If pre-authorization is necessary, students should contact the Student Affairs Office before the scheduled registration period.

Some courses require a course material fee.

Lower-Division

1. Introduction to Bioengineering (1)   An introduction to the central topics of bioengineering in a seminar format. The principles of problem definition, team design, engineering inventiveness, information access, communication, ethics, and social responsibility will be emphasized. P/NP grading only. Prerequisite: none. (W)

87. Freshman Seminar (1)    The Freshman 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. Freshman 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 freshmen. (F,W,S)

97. Internship/Field Studies (1-4)    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 UCSD’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 UCSD undergraduate study, a minimum UCSD GPA of 3.0, and a completed and approved Special Studies form. (F,W,S)

98. Directed Group Study (1-4)    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 UCSD with a UCSD GPA of at least 3.0 and consent of a Bioengineering faculty member; completed and approved Special Studies form.

99. Independent Study for Undergraduates (4)    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 UCSD with a UCSD GPA of at least 3.0 and consent of a Bioengineering faculty member; completed and approved Special Studies form.

Upper-Division

100. Introduction to Bioengineering Design (4)    A general introduction to bioengineering design, including examples of engineering analysis and design applied to representative topics in biomechanics, bioinstrumentation, biomaterials, biotechnology, and related areas. A review of technological needs, design methodology, testing procedures, statistical analysis, governmental regulation, evaluation of costs and benefits, quality of life, and ethical issues. Prerequisites: BENG 1; grade of C– or better in Math. 21C or Math. 20C and Math. 21D or Math. 20D, and Physics 2C; majors only. (S)

101. Foundations of Biomedical Imaging (4)    An introduction to the principles and applications of biomedical imaging, with emphasis on the acquisition, processing, display of imagery, and design of imaging systems. Filtering, convolution, and Fourier methods. Microscopy, radiography, computed tomography, magnetic resonance, ultrasound, and nuclear imaging. Prerequisites: Grade of C- or better in BENG 100; majors only or consent of department. (F)

103B. Bioengineering Mass Transfer (4)    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: grade of C– or better in CENG 101A or BENG 112A; majors only or consent of instructor. (S)

109. Bioengineering Statics and Dynamics (4)    Newton’s Laws. Static resultant forces and moments. Conservation laws of dynamics. Muscle and joint loads. Human body dynamics, locomotion, and clinical applications. Bodies in contact: friction, momentum, and impulse; impact and injury. Work, power, and energy relationships. Bioengineering design problems. Prerequisites: grade of C– or better in Math. 21D or Math. 20D; Physics 2C; majors only or consent of instructor. (W)

110. Continuum Mechanics (4)    An introduction to continuum mechanics of both living and nonliving bodies. The laws of motion and free-body diagrams. Stresses. Deformation. Compatibility conditions. Constitutive equations. Properties of common fluids and solids. Derivation of field equations and boundary conditions. Applications to bioengineering design. Prerequisites: grades of C– or better in Physics 2A, 2B, 2C, and BENG 109; majors only or consent of instructor.. (F)

112A. Biomechanics (4)    Introduction to physiological systems, with emphasis on structure and function of major tissues and organs. Application of mechanics to understand the behavior of these tissues and organs at gross and microscopic levels. Bioelastic solids. Rigid body biomechanics. Biofluids. Bioengineering and medical design. Prerequisites: grade of C– or better in BENG 110; majors only or consent of instructor. (W)

112B. Biomechanics (4)    Biomechanics of living tissues with emphasis on continuum analysis of problems in biofluid and cell mechanics. Engineering design and problem solving in the biomechanics of mammalian tissues, especially those of the cardiovascular system. Prerequisites: grade of C– or better in BENG 112A; majors only or consent of instructor. (S)

119A. Design Development in Biomechanics (3)    Development of design project in biomechanics. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

119B. Design Implementation in Biomechanics (3)    Implementation of design project in biomechanics. Prerequisites: grade of C– or above in BENG 119A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

122A. Biosystems and Control (4)    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 term project using MATLAB and an oral presentation are required. Prerequisites: grade of C– or better in MAE 140; majors only or consent of department. (W)

123. Systems Biology and Bioengineering (4)    Systems biology and bioengineering consists of (1) enumeration of biological components participating in a biological process, (2) reconstruction of interactions to form a network, (3) mathematical representation for analysis, interpretation, and prediction, (4) model validation and use in prospective design. Prerequisites: grade of C– or better in BIBC 100; majors only or consent of instructor. (W)

125. Modeling and Computation in Bioengineering (4)    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: grade of C– or better in BENG 122A or BENG 123; majors only or consent of instructor. (S)

126A. Design Development in Bioinformatics Bioengineering (3)    Development of design project in bioinformatics bioengineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

126B. Design Implementation in Bioinformatics Bioengineering (3)    Implementation of design project in bioinformatics bioengineering. Prerequisites: grade of C– or above in BENG 126A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

127A. Design Development in Molecular Systems Bioengineering (3)    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)

127B. Design Implementation in Molecular Systems Bioengineering (3)    Implementation of design project in molecular systems bioengineering. Prerequisites: grade of C– or above in BENG 127A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

128A. Design Development in Genetic Circuits Bioengineering (3)    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)

128B. Design Implementation in Genetic Circuits Bioengineering (3)    Implementation of design project in genetic circuits bioengineering. Prerequisites: grade of C– or above in BENG 128A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

129A. Design Development in Cell Systems Bioengineering (3)    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)

129B. Design Implementation in Cell Systems Bioengineering (3)    Implementation of design project in cell systems bioengineering. Prerequisites: grade of C– or above in BENG 129A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

130. Molecular Physical Chemistry (4)    An introduction to physical principles that govern biological matter and processes. Thermodynamic principles and their molecular origin, structural basis of life and physical and conceptual models to illustrate life phenomena. (Credit allowed for one of the following: Chem. 126, Chem. 127, Chem. 131, or BENG 130.) Prerequisites: grade of C– or better in Chem 6B, Math. 20A, 20B, Physics 2A, 2B, 2C. (Physics 2C may be taken concurrently.); majors only or consent of instructor. (W)

139A. Design Development in Molecular Bioengineering (3)    Development of design project in molecular bioengineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

139B. Design Implementation in Molecular Bioengineering (3)    Implementation of design project in molecular bioengineering. Prerequisites: grade of C– or above in BENG 139A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

140A. Bioengineering Physiology (4)    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: grade of C– or better in Chem. 6A, 6B, Physics 2A, 2B, 2C, BILD 1; majors only or consent of instructor. (W)

140B. Bioengineering Physiology (4)    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.) Prerequisite: grade of C– or better in BENG 140A; majors only or consent of instructor. (S)

147A. Design Development in Neural Engineering (3)    Development of design project in neural engineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

147B. Design Implementation in Neural Engineering (3)    Implementation of design project in neural engineering. Prerequisites: grade of C– or above in BENG 147A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

148A. Design Development in Cardiac Bioengineering (3)    Development of design project in cardiac bioengineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

148B. Design Implementation in Cardiac Bioengineering (3)    Implementation of design project in cardiac bioengineering. Prerequisites: grade of C– or above in BENG 148A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

149A. Design Development in Vascular Bioengineering (3)    Development of design project in vascular bioengineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

149B. Design Implementation in Vascular Bioengineering (3)    Implementation of design project in vascular bioengineering. Prerequisites: grade of C– or above in BENG 149A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

160. Chemical and Molecular Bioengineering Techniques (4)    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. Prerequisites: grade of C– or better in BIBC 102, BICD 100, BENG 100, MAE 170; majors only or consent of instructor. (S)

161A. Bioreactor Engineering (4)    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: grade of C– or better in Chem 114B or BIBC 102 (may be taken concurrently), BENG 122A or BENG 123, and BIB 103 or BENG 160; majors only or consent of instructor. (F)

161B. Biochemical Engineering (4)     Commercial production of biochemical commodity products. Application of genetic control systems and mutant populations. Recombinant DNA and eucaryotic 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: grade of C– or better in BENG 161A; majors only or consent of instructor. (W)

161C. Metabolic Engineering (4)     Engineering systems analysis of metabolic and regulatory processes. Use of high-throughput data for network reconstruction. Formulation of the stoichiometric matrix and its uses to determine steady state flux distributions. Kinetics of individual enzymatic reactions. Computer simulations of metabolic networks, systemic sensitivity coefficients, bifurcations to study dynamic network functions. Temporal decomposition of metabolic processes into multiple time scales and the physiologic roles of metabolic events in each scale. Prerequisites: grade of C– or better in BENG 160B or BENG 161B; majors only or consent of instructor. (S)

162. Biotechnology Laboratory (4)    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. Prerequisites: grade of C– or above in MAE 170; BIBC 102; BIBC 103 or BENG 160; BENG 161A (may be taken concurrently); BENG 166A (may be taken concurrently); majors only or consent of instructor. (F)

166A. Cell and Tissue Engineering (4)    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: grade of C– or better in BENG 103B or BENG 112B; senior standing; majors only or consent of department. (F)

167. Cell and Tissue Engineering Laboratory (4)    An introduction to contemporary methods and applications. Students will formulate and test hypotheses related to the design and production of functional tissue substitutes. Topics to be explored include tissue characterization, biomaterial scaffolds, cell migration, adhesion, and growth. Prerequisite: BENG 166A; majors only or consent of instructor. (S)

168. Biomolecular Engineering (4)    Basic molecular biology; recombinant DNA technologies; design and manufacture of recombinant proteins and genetically engineered cells; architecture and mechanism of molecular nano-machineries that perform gene regulation, energy conversion, enzymatic catalysis, and active transport. Prerequisites: grade of C– or better in BILD 1 and BENG 100; majors only or consent of instructor. (S)

169A. Design Development in Tissue Engineering (3)    Development of design project in tissue bioengineering. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

169B. Design Implementation in Tissue Engineering (3)    Implementation of design project in tissue bioengineering. Prerequisites: grade of C– or above in BENG 169A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

172. Bioengineering Laboratory (4)    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. Prerequisites: grade of C– or better in MAE 170; and junior or senior standing in the major or consent of instructor. (S)

173. Bioengineering Project Laboratory (4)    Applications of bioengineering concepts to the solution of practical and research problems. Planning, design, and testing of prototype devices. Term project and oral presentation are required. Prerequisites: majors only; consent of instructor; BENG 112B, BENG 172. (S)

179A. Design Development in Bioinstrumentation (3)    Development of design project in bioinstrumentation. Prerequisites: concurrent enrollment in BENG 187B; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (F)

179B. Design Implementation in Bioinstrumentation (3)    Implementation of design project in bioinstrumentation. Prerequisites: grade of C– or above in BENG 179A; concurrent enrollment in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (W)

181/BIMM 181/CSE 181. Molecular Sequence Analysis (4)    (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 or Math. 176, CSE 101 or Math. 188, BIMM 100 or Chem. 114C; Bioinformatics majors only. (S)

182/BIMM 182/CSE 182/CHEM 182. Biological Databases (4)    (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 description. Survey of current biological database with respect to above, implementation of database focused on a biological topic. Prerequisites: CSE 100 or Math. 176; Bioinformatics majors only. (F)

183. Applied Genomic Technologies (4)    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, Physiomic and Phenomic Technologies, Analysis of Cell Function. Prerequisites: grade of C– or better in BIMM 100 or Chem 114C; BICD 110; Bioinformatics majors only. (F)

184/BIMM 184/CSE 184/CHEM 184. Computational Molecular Biology (4)    (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. (W)

186A. Principles of Biomaterials Design (4)    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: grade of C– or better in BENG 112B or senior standing in Bioengineering: Biotechnology major; majors only or consent of department. (S)

186B. Principles of Bioinstrumentation Design (4)     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: grade of C– or better in MAE 140 and MAE 170; majors only or consent of instructor. (W)

186C. Bioengineering Design (4)     Development of a bioengineering design described in a formal engineering report. Engineering analysis and application of methodology from applied sciences, biology, physiology, and biochemistry. Analysis of economic, environmental, manufacture, ethical, health and safety, social issues, and application of governmental regulations. Prerequisites: grade of C– or better in BENG 103B, BENG 106B, BENG 112B, BENG 186B, and MAE 130A; majors only or consent of instructor. (W)

187A. Bioengineering Design Project: Planning (1)    Attendance at a weekly planning session on design projects. Prerequisites: grade of C– or better in MAE 170; BENG 101 or BICD 100; BENG 112A or CENG 101A; BENG 140A or BIBC 102; BENG 186B or BENG 123; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (S)

187B. Bioengineering Design Project: Development (1)    Development of original bioengineering design to solution of problem in biology or medicine. Analysis of economic issues, manufacturing and quality assurance, ethics, safety, government regulations, and patent requirements. Oral presentation and formal engineering reports. Prerequisites: grade of C– or better in MAE 170, and BENG 112B or BENG 123; 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 or Bioengineering: Biotechnology majors only or consent of instructor. (F)

187C. Bioengineering Design Project: Implementation (1)    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. Prerequisites: grade of C– or better in BENG 187B; concurrent enrollment in one o 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 or Bioengineering: Biotechnology majors only or consent of instructor. (W)

187D. Bioengineering Design Project: Presentation (1)    Oral presentations of design projects, including design, development, and implementation strategies and results of prototype testing. Prerequisites: grade of C– or better in BENG 187C; Bioengineering or Bioengineering: Biotechnology majors only or consent of instructor. (S)

186B. Principles of Bioinstrumentation Design (4)    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: grade of C– or better in MAE 140 and MAE 170; majors only or consent of department. (W)

191. Senior Seminar I: Professional Issues in Bioengineering (2)    Role of bioengineers in industry. Professional identity. Structure of bioengineering industries and product development process. Job market analysis. Current employment opportunities. Recruiting process and interview. Analysis of the employer. Marketing vs. engineering. Management by objective. Role of higher degrees. Prerequisite: consent of instructor. (W)

192. Senior Seminar in Bioengineering (1)    The Senior Seminar Program is designed to allow senior undergraduates to meet with faculty members in a small group setting to explore an intellectual topic in bioengineering (at the upper-division level). Senior seminars may be offered in all campus departments. Topics will vary from quarter to quarter. Senior seminars may be taken for credit up to four times with a change in topic and permission of the department. Enrollment is limited to twenty students, with preference given to seniors.

195. Teaching (2-4)    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: B average in the major and departmental approval. (F,W,S)

196. Bioengineering Industrial Internship (1-4)    Under the joint supervision of a faculty advisor and industry mentor, the student will work at a bioengineering industrial site to gain practical bioengineering experience. No more than twelve units may be used to satisfy graduation unit requirements. (P/NP grades only.) Prerequisites: consent of department and completion of all lower-division course requirements, including general-science requirements; some laboratory experience; completion of ninety units with a 2.5 GPA; and consent of a bioengineering faculty coordinator. (F,W,S,Su)

197. Engineering Internship (1-4)    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 UCSD’s Academic Internship Program. Time and effort to be arranged. Units may not be applied towards major graduation requirements unless prior approval of a faculty advisor 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)

198. Directed Group Study (1-4)    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 UCSD undergraduate study, a minimum UCSD GPA of 2.5, consent of instructor, and a completed and approved Special Studies form.(F,W,S)

199. Independent Study for Undergraduates (4)    Independent reading or research by arrangement with a bioengineering faculty member. (P/NP grades only.)Prerequisites: upper-division standing, completion of ninety units of UCSD undergraduate study, a minimum UCSD GPA of 2.5, consent of instructor, and a completed and approved Special Studies form.(F,W,S,Su)

Graduate

202/CSE 282. Bioinformatics II: Sequence and Structure Analysis—Methods and Applications (4)    (Formerly BENG 202/CSE 257A.) Introduction to methods for sequence analysis. Applications to genome and proteome sequences. Protein structure, sequence-structure analysis. Prerequisite: Pharm. 201 or consent of instructor. (W)

203/CSE 283. Bioinformatics III:Functional Genomics(4)    Annotating genomes, characterizing functional genes, profiling, reconstructing pathways. Prerequisites: Pharm. 201, BENG 202/CSE 282 or consent of instructor. (S)

207. Topics in Bioengineering (4)    Course given at the discretion of the faculty on current topics of interest in bioengineering. (F,W,S)

208. Topics in Bioengineering with Lab (4)    A course to be 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. Prerequisite: consent of instructor. (S)

209/MAE 209. Continuum Mechanics Applied to Medicine/Biology (4)     Introduction to the basic definitions of Continuum Mechanics and their mathematical formulation at the graduate level with applications to problems in medicine and biology. This course is intended for students with little or no background in mechanics; it is an introduction to the Biomechanics courses BENG 250 A-B in the Department of Bioengineering and to Solid and Fluid Mechanics courses MAE 210A and MAE 231A in the Department of Mechanical and Aerospace Engineering. This course should NOT be taken concurrently with MAE 210A or MAE 231A. Prerequisite: consent of instructor. (F)

211. Systems Biology and Bioengineering I: Biological Components (4)     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. Prerequisite: BENG 230A or BIMM 100 or consent of instructor.(F)

212. Systems Biology and Bioengineering II: Network Reconstruction (4)     This course will cover the process of reconstructing complex biological reaction networks. Reconstruction of metabolic networks, regulatory networks and signaling networks. Bottom-up and top-down approaches. The use of collections of historical data. The principles underlying high-throughput experimental technologies and examples given on how this data is used for network reconstruction, consistency checking, and validation. Prerequisite: BENG 211 or consent of instructor. (W)

213. Systems Biology and Bioengineering III: Building and Simulating Large-scale In Silico Models (4)     Mathematical models of reconstructed reaction networks and simulation of their emergent properties. Classical kinetic theory, stochastic simulation methods and constraints-based models. Methods that are scalable and integrate multiple cellular processes will be emphasized. Existing genome-scale models will be described and computations performed. Emphasis will be on studying the genotype-phenotype relationship in an in silico model driven fashion. Comparisons with phenotypic data will be emphasized. Prerequisite: BENG 212 or consent of instructor. (S)

225. BioBusiness: Starting, Growing, and Harvesting a Biotech Company (4)    Biotech is a special breed of business, especially in the start-up and early phases. Whether you are considering joining a biotech start-up or want to be successful in a life science organization, it pays to understand this unique business model. In this course, you will study and analyze (1) start-up proposals (2) the genesis of the biotech industry (3) biotech categories and growth strategies (4) the process of spinning out viable product concepts from academia (5) financing techniques (6) business development (7) acquisition/IPO valuation methods and (8) potentially disruptive technologies. The format is highly interactive and learning is enhanced by means of exercises, team presentations, and case studies. Prerequisite: bioengineering MEng degree student or consent of instructor. (F,W)

230A. Biochemistry (4)    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: BIPN 100 and 102 or consent of instructor. (F)

230B. Cell and Molecular Biology (4)    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: BIPN 100 and 102, and BENG 230A, or consent of instructor. (W)

230C/BIOM 271. Cardiovascular Physiology (4)    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: BIPN 100 ,102 , and BENG 230B, or consent of instructor. (S)

230D. Respiratory and Renal Physiology (4)    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)

238/MED 238. Molecular Biology of the Cardiovascular System (4)    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. (S)

241A. Foundations of Tissue Engineering Science (4)    Molecular and cell biological basis of tissue engineering science. Paracrine control of tissue growth and differentiation. Biomechanics and the molecular basis of cell-cell and cell-matrix interactions. Cell motility, mechanics of tissue growth and assembly, tissue repair. Mass transfer in tissues. Microcirculation of blood and lymph. Prerequisite: BENG 230A or consent of instructor. (S)

247A/ECE 247A. Advanced BioPhotonics (4)    Basic physics and chemistry for the interaction of photons with matter, including both biological and synthetic materials; use of photonic radiation pressure for manipulation of objects and materials; advanced optoelectronic detection systems, devices and methods, including time resolved fluorescent and chemiluminescent methods, fluorescent energy transfer (FRET) techniques, quantum dots, and near-field optical techniques; underlying mechanisms of the light sensitive biological systems, including chloroplasts for photosynthetic energy conversion and the basis of vision processes. Prerequisite: graduate standing. (F)

247B/ECE 247B. BioElectronics (4)     Topics to be covered will include photolithographic techniques for high-density DNA microarray production, incorporation of CMOS control into electronic DNA microarrays, direct electronic detection technology used in microarrays and biosensor devices, and focus on problems related to making highly integrated devices (lab-on-a-chip, in vivo biosensors, etc.) form heterogeneous materials and components. Prerequisite: graduate standing. (W)

247C/ECE 247C. Bionanotechnology (4)     Topics include: nanosensors and nanodevices for both clinical diagnostics and biowarfare (bioterror) agent adetection; nanostructures for drug delivery; nanoarrays and nanodevices; use of nanoanalytical devices and systems; methods and techniques for modification or functionalization of nanoparticles and nanostructures with biological molecules; nanostructural aspects of fuel cells and biofuel cells; potential use of DNA and other biomolecules for computing and ultra-high-density data storage. Prerequisite: graduate standing. (S)

250A. Biomechanics (4)    An introduction to biomechanics and transport phenomena in biological systems at the graduate level. Biorheology, biosolid mechanics, muscle mechanics, mass transfer, momentum transfer, energy transfer. Prerequisites: CENG 101C and BENG 112B, or consent of instructor. (W)

250B. Advanced Biomechanics (4)    Modern development of biomechanics at an advanced mathematical level. Selected topics in the dynamics of heart, pulsatile, blood flow, microcirculation, and muscle mechanics. Prerequisite: BENG 253 or consent of instructor. (S)

253. Biomedical Transport Phenomena (4)    Nonequilibrium thermodynamic analysis of transport phenomena. The osmotic effect. Diffusion and exchange in biological systems. Prerequisite: consent of instructor. (W)

267. Microcirculation in Health and Disease (4)    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. Prerequisite: consent of instructor. (S)

276/CHEM 276/MATH 276. Numerical Analysis in Multi-Scale Biology (4)    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. Prerequisite: consent of instructor. (F,W,S)

280A. Principles of Biomedical Imaging (4)     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. Prerequisite: consent of instructor. (F)

280B. Comparative Biomedical Imaging (4)     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. Prerequisite: consent of instructor. (W,S)

281. Seminar in Bioengineering (1)    Weekly seminars by faculty, visitors, postdoctoral research fellows, and graduate students concerning research topics in bioengineering and related subjects. May be repeated for credit. This course does not apply toward the M.S. graduation requirements. (S/U grades only.) (F,W,S)

283/Chem. 283/BIOM 283. Supramolecular Structure Determination Laboratory (4)    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. Prerequisite: consent of instructor.

290. Bioengineering Special Graduate Seminar (1-2)    Seminars by faculty, visitors, post-doctoral research fellows, and/or graduate students in selected topic(s) in bioengineering and/or related subjects. This course does not apply toward M.S. graduation requirements.

295. Bioengineering Design Project and Industrial Training (4)    Independent work by graduate students focused on design, applied research, and professional experience. Prerequisite: consent of department and bioengineering faculty advisor. (F,W,S)

296. Independent Study (4)    Prerequisite: consent of instructor.

298. Directed Group Study (1-4)    Directed group study on a topic or in a field not included in regular department curriculum, by special arrangement with a faculty member. Prerequisite: consent of instructor. (S/U grade only.)

299. Graduate Research (1-12)   Independent work by graduate students engaged in research and writing theses. Prerequisite: consent of instructor. (S/U grades only.)

501. Teaching Experience (2)    Teaching experience in an appropriate bioengineering undergraduate course under direction of the faculty member in charge of the course. Lecturing one hour per week in either a problem-solving section or regular lecture. (S/U grade only.) Prerequisites: consent of instructor and departmental approval. (F,W,S)