Bioengineering
Courses
For course descriptions not found in the 2005-2006 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 2005-2006
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.
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)
90. Undergraduate Seminar (1) Selected
topics of interest to the faculty will be used to introduce students
to bioengineering science and design concepts. (Not open to upper-division
bioengineering students.) (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; majors only. (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 is comprised 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 : 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. Prerequisite:
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. Prerequisite:
grade of C or better in 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. (W)
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.
Prerequisite: admission to the major or consent of department;
senior standing and (BENG 103B OR BENG 112B). (F)
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:
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/CHEM182. 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. Prerequisite: 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.
Prerequisite: 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. Prerequisite: grade of C or better in BENG 112B
or senior standing in Bioengineering: Biotechnology major; majors
only or consent of department. (F)
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 BENG 187A, 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)
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 adviser 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 is needed. 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 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)
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: consent of instructor;
upper-division standing, completion of ninety units of UCSD undergraduate
study, a minimum UCSD GPA of 2.5, and a completed and approved “Special
Studies” form, “Application for UCSD Special Studies
Course Enrollment.” (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: consent of instructor;
upper-division standing, completion of ninety units of UCSD undergraduate
study, a minimum UCSD GPA of 2.5, and a completed and approved “Special
Studies” form, “Application for UCSD Special Studies
Course Enrollment.” (F,W,S,Su)
Graduate
202/CSE 257A. Bioinformatics II: Sequence and Structure AnalysisMethods
and Applications (4) 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. Bioinformatics III: Genomes Analysis (4) Annotating
genomes, characterizing functional genes, profiling, reconstructing
pathways. Prerequisites: Pharm. 201, BENG 202/CSE 257A 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 (2 or 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. 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)
220. Project Design and Development (4) The
design of a research/development project for an industrial setting.
Project objectives and organization, funding sources, review of
previous developments in the area, proposal writing and review,
project management, intellectual property, regulatory issues. The
term project will involve preparing a small business proposal for
development of a medical device. Prerequisite: open to students
with graduate standing in bioengineering. (W)
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 (8)
potentially disruptive technologies. The format is highly interactive
and learning is enhanced by means of exercises, team presentations,
and case studies. Prerequisites: for bioengineering MEng degree
students 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. 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. Molecular Biology of the Cardiovascular System (4) This
course will give an overview of heart and vascular development and
disease 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)
241B. Methods in Tissue Engineering Science (4) Isolation
of cells, cell and tissue culture systems. Fluorescence and confocal
microscopy. Intracellular imaging. Mechanical testing of tissues.
Micromechanical measurement and analysis of cell deformability and
cell interaction. Methods in microcirculation and angiogenesis.
Prerequisite: BENG 241A or consent of instructor. (F)
241C. Applications of Tissue Engineering Science (4) A
lecture/seminar series featuring speakers from academia and industry
emphasizing principles of tissue engineering science as applied
to clinical medicine and industrial production. Topics include skin
replacement, guide tubes for nerve regeneration, blood substitutes,
pancreatic islet replacement, and drug delivery devices, among others.
Ethics of tissue replacement. Prerequisite: BENG 241B or consent
of instructor. (W)
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. 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. 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 103B 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)
275. Computational Biomechanics (4) Finite
element methods for anatomical modeling and boundary value problems
in the biomechanics of tissues and biomedical devices. Nonlinear
biodynamics, heat flow, cardiac impulse propagation, anatomic modeling,
and biomechanics. Prerequisite: consent of instructor. (F)
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)
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 adviser. (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) (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)
Bioengineering Courses
|