 |
 Curriculum |
|
|
| BioE 10 | Introduction to Biomedicine for Engineers (4)
This course is intended for lower division students interested in acquiring a foundation in biomedicine with topics ranging from evolutionary biology to human physiology. The emphasis is on the integration of engineering applications to biology and health. The goal is for undergraduate engineering students to gain sufficient biology and human physiology fundamentals so that they are better prepared to study specialized topics e.g., biomechanics, imaging, computational biology, tissue engineering, biomonitoring, drug development, robotics, and other topics covered by upper division and graduate courses in UCB Molecular and Cellular Biology; Integrative Biology; Bioengineering; Electrical Engineering and Computer Science; Mechanical Engineering; and courses at UCSF Division of Bioengineering. Weekly discussion section will be required for students to attend.
The specific lecture topics and exercises will include key aspects genomics and proteomics as well as topics on plant and animal evolution, stem cell biomedicine and tissue regeneration and replacement. Medical physiology topics include relevant engineering aspects of human brain, heart, musculoskeletal and other systems.
An underlying theme of the course include engineering concepts in evolution, tissue growth, plant, animal, and human development, aging, and renewal.
(F/SP) Sanjay Kumar, Irina Conboy
| BioE 22
| Biotechnology (3)
This course is intended to introduce students to a variety of fields that fall under the
biotechnology umbrella. In general, these fields include medical, microbial, agricultural, animal, and forensic biotechnology. Students in this course will learn the types of biotechnology projects currently being worked on, as well as the techniques and assays used within these projects.
Prerequisites: 22L (must be taken concurrently)
Megan Dueck | | BioE 22L | Biotechnology Laboratory (2)
This course is intended to introduce students to a variety of laboratory techniques that are used in current day biotechnology projects. During this course, students will get hands-on molecular and cellular biotechnology experience working with E. coli, Yeast, Human and Mouse Cell Lines, DNA, RNA, and proteins. This is a bioengineering course; the focus of these exercises will be on the critical understanding of biological,
biochemical, or physical mechanisms, and theories of different experiemental methods, techniques, and instrumentation used. Second, students leaving this class should understand how to address a critical biological question and design experiments in a quantitative manner.
Prerequisites: 22 (must be taken concurrently)
Megan Dueck | | BioE 24 | Aspects of Bioengineering (1)
Course may be repeated for credit. One hour of seminar per week. Must be taken on a passed/not passed basis.
This introductory seminar is designed to give freshmen and sophomores a glimpse of a broad selection of bioengineering research that is currently underway at Berkeley and UCSF. The goal is to help students gain a feeling for the breadth of interesting problems in bioengineering and also the variety of ways that engineering principles can be applied to biological and medical problems. A series of one-hour seminars will be presented by researchers, professors, and doctors on their particular research areas.
(F/SP) BioE Faculty | | BioE 25 | Careers in Biotechnology (1)
Course may be repeated for credit. One hour of seminar per week. Must be taken on a passed/not passed basis based on attendance. Can be substituted for BioE 24.
This introductory seminar is designed to give freshmen and sophomores an opportunity to explore specialties related to engineering in the pharmaceutical/biotech field A series of one-hour seminars will be presented by industry professionals, professors and researchers. Topics may include: Biotechnology and Pharmaceutical Manufacturing; Process and Controls Engineering; Drug Inspection Process; Research and Development; Compliance and Validation; Construction Process for a GMP facility; Project Management; and Engineered Solution to Environmental Challenges. This course is of interest to students in all areas of engineering and biology, including: IEOR, Manufacturing, Chemical Engineering and Bioengineering.
(F/SP) Staff | | BioE 39 | Freshman and Sophomore Seminar (2-4)
Course may be repeated for credit. Two to four hours of seminar per week. Sections 1-2 to be graded on a letter-grade basis. Sections 3-4 to be graded on a passed/not passed basis.
Prerequisites: Priority is given to freshmen and sophomores. Freshman and sophomore seminars offer lower division students the opportunity to explore an intellectual topic with a faculty member and a group of peers in a small seminar setting. These seminars are offered in all campus departments; topics vary from department to department and from semester to semester. Enrollment limits are set by the faculty, but the suggested limit is 25. (F,SP) Staff | | BioE 84 | Sophomore Seminar (1,2)
Course may be repeated for credit.
One hour of seminar per week per unit for fifteen weeks. One and a half hours of seminar per week per unit for ten weeks. Two hours of seminar per week per unit for eight weeks.Three hours of seminar per week per unit for five weeks.
Sections 1-2 to be graded on a passed/not passed basis. Sections 3-4 to be graded on a letter-grade basis.
Sophomore seminars are small interactive courses offered by faculty members all across the campus.Sophomore seminars offer opportunity for close, regular intellectual contact between faculty members and students in the crucial second year. Topics vary from semester to semester.
Enrollment limited to 15 sophomores.
Prerequisites: At discretion of instructor.
(F,SP) Staff
| | BioE 98 | Supervised Independent Group Studies (1-4)
Course may be repeated for credit. Group study meetings.
Must be taken on a passed/not passed basis.
Prerequisites: Consent of instructor. Organized group study on various topics under the sponsorship of a member of the Bioengineering faculty. (F,SP) Staff | | BioE 99 | Supervised Independent Study and Research (1-4)
Course may be repeated for credit.
Enrollment is restricted; see the Introduction to Courses and Curricula section of this catalog. Must be taken on a passed/not passed basis.
Prerequisites: Freshman or sophomore standing and consent of instructor. Supervised independent study for lower division students. (F,SP) Staff | | BioE 100 | Ethics in Science and Engineering (3)
Three hours of lecture per week.
The goal of this course is to present the issues of professional conduct in the practice of engineering, in the conduct of research, in publication, in private and public disclosures, and in managing professional and financial conflicts. The method is through historical didactic presentations, case studies, presentations of technical methods for problem solving in ethical matters, and classroom debates on contemporary ethical issues. Faculty from religious studies, journalism, and law from the UC Berkeley campus will give guest lectures.
(SP) Budinger | BioE 101
| Instrumentation in Biology and Medicine. (4) Three hours of lecture and three hours of discussion/computer laboratory per week. Prerequisites: Electrical Engineering 100, Mathematics 53, 54, Physics 7A-7B, or consent of instructor. This course teaches the fundamental principles underlying modern instrumentation used in biology and medicine. Organized around three classes of instruments--bioelectronics, optical microscopy, and medical imaging--the course takes an integrative approach to measurement theory and practice by presenting and analyzing example instruments currently used for biological and medical research. For each instrument, students will learn the fundamentals of operation, methods of control, mechanisms of contrast, devices for detection, and methods for signal processing and error estimation. Current biological questions and medical problems investigated with each type of instrument will be discussed. (F,SP) Conolly, D. Fletcher
| | BioE 102 | Biomechanics (4)
Three hours of lecture and three hours of computer laboratory per week.
Prerequisites: Math 53, 54; Physics 7A; programming experience; biology or anatomy is not assumed.
Introduction to the main concepts related to the mechanics and material behavior of biological systems. Emphasis is placed on development of a fundamental mathematical understanding of the key engineering principles and their application to biological systems. Examples of engineering concepts covered include statics and dynamics of solids and fluids; material behavior including elasticity, viscoelasticity, fatigue, and failure; beam theory, scaling, biological heterogeneity, and uncertainty. Applications, examples, and assignments will elucidate normal and pathological human physiology, as well as diagnosis and treatment of major clinical problems. A series of mini-projects, some of which will be computational assignments, will integrate the course material in an attempt to gain insight into more complex problems. Working in small teams, students will also make a poster or oral presentation to the class on a topic of their choice. (F,SP) Mofrad | BioE 104
| Biological Transport Phenomena. (4) Three hours of lecture and one hour of discussion per week. Prerequisites: Mathematics 54 and Physics 7A; 102 is recommended. The transport of mass, momentum, and energy in living systems. Application of scaling laws and methods of continuum mechanics to biological transport phenomena. Sample application areas include biomolecular transport in biological tissues, living organs, and biomedical microdevices. Preliminary understanding of biology and physiology is useful, but not assumed. (SP) Mofrad
| | BioE C105B | Thermodynamics and Biothermodynamics (3)
Students will receive no credit for C105B after taking Mechanical Engineering 105.
Three hours of lecture and one hour of discussion per week.
This course introduces the basic principles of thermodynamics and their application to a variety of biological processes and systems. Some coverage of conventional engineering applications is also included. Also listed as Mechanical Engineering C105B.
Prerequisites: Chemistry 1A, Mathematics 53, Physics 7A, Engineering 77N, or equivalents.
(F,SP) Carey | BioE 110
| Biomedical Physiology for Engineers (4)
This course introduces students to the physiology of human organ systems, with an emphasis on quantitative problem solving, engineering-style modeling, and applications to clinical medicine. The course will begin with a review of basic principles of cellular physiology, including membrane transport and electrophysiology, and then take a system-by-system approach to the physiology of various organ systems, including the cardiovascular, pulmonary, renal, and endocrine systems. Throughout, the course will feature extensive discussions of clinical conditions associated with dysfunction in specific physiological processes as well as the role of medical devices and prostheses. This course is geared towards upper-division bioengineering students who wish to solidify their foundation in physiology, especially in preparation for a career in clinical medicine or the biomedical device industry.
Prerequisites: 10, Biology 1A; Math 54 (may be taken concurrently).
(SP) Kumar
| | BioE 112 | Molecular Cell Biomechanics (4)
This course develops and applies scaling laws and the methods of continuum and statistical mechanics to biomechanical phenomena over a range of length scales, from molecular to cellular levels. It is intended for senior undergraduate students who have been exposed to differential equations, mechanics, and certain aspects of modern biology.
Prerequisites: Mathematics 54, Physics 7A, 102, or consent of instructors.
(F,SP) Mofrad | BioE 115
| Cell Biology Laboratory for Engineers (4)
Two hours of lecture and six hours of laboratory per week.
The structural and functional characteristics of musculoskeletal tissues (e.g., bone, tendon, cartilage) are altered by cells in response to loading, injury, nutrition, and
other factors. A contemporary understanding of the structural form, function and longevity includes knowledge of tissue ultra structure, composition of matrix, and cell
function. Students will be introduced to cellular and molecular biology and biochemistry techniques as applied to musculoskeletal tissues including histology, image analysis, protein quantification, gene analysis and expression, and cell culture. By applying these techniques to structural tissues in the laboratory, students can learn the reliability and limitations of these tools.
Prerequisites: Molecular and Cell Biology 110 or 130
(F) Li, Johnson
| | BioE 116 | Cell and Tissue Engineering (4)
Three hours of lecture and one hour of discussion per week.
Introduction to tissue engineering, analysis of cellular process, and cell engineering. Topics include bioreactor and mass transport, transplantation, artifical tissues, cell-matrix interaction, cell migration and cell mechanics, cell proliferation, stem cells, and cell manipulation.
Prerequisites: MCB102 and Engineering 45, or consent of instructor (Letter, P/NP, S/U)
Li | | BioE C117 | Structural Aspects of Biomaterials. (4) Three hours of lecture and two hours of laboratory per week. Prerequisites: Biology 1A, Engineering 45, Bio Engineering 102, and Civil Engineering 130. This course covers the structure and mechanical functions of load bearing tissues and their replacements. Natural and synthetic load-bearing biomaterials for clinical applications are reviewed. Biocompatibility of biomaterials and host response to structural implants are examined. Quantitative treatment of biomechanical issues and constitutive relationships of tissues are covered in order to design biomaterial replacements for structural function. Material selection for load bearing applications including reconstructive surgery, orthopedics, dentistry, and cardiology are addressed. Mechanical design for longevity including topics of fatigue, wear, and fracture are reviewed. Case studies that examine failures of devices are presented. This course includes a teaching/design laboratory component that involves design analysis of medical devices and outreach teaching to the public community. Several problem-based projects are utilized throughout the semester for design analysis. In addition to technical content, this course involves rigorous technical writing assignments, oral communication skill development and teamwork. Also listed as Mechanical Engineering C117. (SP) Pruitt | | BioE C118 | Biological Performance of Materials (4)
Three hours of lecture and one hour of discussion per week.
This course is intended to give students the opportunity to expand their knowledge of topics related to biomedical
materials selection and design. Structure-property relationships of biomedical materials and their interaction with biological systems willbe addressed. Applications of the concepts developed include blood-materials compatibility biomimetic materials, hard and soft tissue-materials interactions, drug delivery, tissue engineering, and biotechnology. Also listed as Materials Science and Engineering C118.
Prerequisites: Molecular and Cell Biology 102, 130 (recommended), and Engineering 115 or equivalent
(F, SP) Healy | | BioE C119 | Orthopedic Biomechanics (4)
Three hours of lecture and one hour of discussion/computer workshop per week.
Students will learn the application of engineering concepts including statics, dynamics, optimization theory, composite beam theory, beam-on-elastic foundation theory, Hertz contact theory and materials behavior. Topics will include forces and moments acting on human joints; composition and mechanical behavior of orthopedic biomaterials; design/analysis of artificial joint, spine, and fracture fixation prostheses; musculoskeletal tissues including bone, cartilage, tendon, ligament, and muscle; osteoporosis and fracture-risk predication of bones; and bone adaptation. Students will be challenged in a MATLAB-based project to integrate the course material in an attempt to gain insight into contemporary design/analysis/problems.
Prerequisites: Civil Engineering 130.
Formerly C176.
(F, SP) Keaveny | | BioE 121 | Introduction to Micro and Nanobiotechnology: BioMEMS (3)
Three hours of lecture per week.
Biophysical and chemical principles of biomedical microelectromechanical systems (bioMEMS) for the measurement of biological phenomena and clinical applications. micro-and nano-scale devices for the manipulation of cells and biomolecules. Topics include solid-state transducers, optical transducers, electrochemical transducers, biomedical microelectronics, microfluidics, and hybrid integration of microfabrication technology.
Prerequisites: Chemistry 3B and Physics 7B or consent of instructor
(F,SP) Lee, L & M. Dueck
| | BioE 121L | BioMems and BioNanotechnology Laboratory (4)
Six hours of laboratory and two hours of lecture per week.
Prerequisites: 121, Chemistry 130A, Electrical Engineering 143, Mechanical Engineering 106, or Chemical Engineering 150A.
Hands-on project experience in applying microfabrication techniques to problems in biotechnology using the latest micro- and nano-technological tools. Experimental design and analysis of micro- and nano-scale device interfaces. Students will give poster sessions and oral presentations on their results. (F) M. Dueck | | BioE C125 | Introduction to Robotics (4)
Three hours of lecture and one hour of discussion per week.
An introduction to the kinematics, dynamics, and control of robot manipulators, robotic vision, sensing, and the programming of robots. The course will cover forward, inverse kinematics of serial chain manipulators . The manipulator Jacobian, force relations, dynamics, and control-position, and force control. Trajectory generation, collision avoidance, automatic planning of fine and gross motion strategies; robot programming languages. Proximity, tactile, and force sensing. Network modeling, stability, and fidelity in teleoperation. Biological analogies and medical applications of robotics. Also listed as Electrical Engineering C 125.
Prerequisites: Electrical Engineering 120 or equivalent, and consent of instructor
(F,SP) C. Tomlin
| | BioE 131 | Introduction to Computational Molecular and Cell Biology (4)
Three hours of lecture and three hours of laboratory per week.
Topics include computational approaches and techniques to gene structure and finding, sequence alignment using dynamic programming, protein folding and structure prediction, protein drug interactions, genetic and biochemical pathways and networks, and microarray analysis. Various case studies in these areas are reviewed and web-based computational biology tools will be used by students. Computational biology research connections to biotechnology will be explored.
Prerequisites: Biology 1A, Mathematics 53 and 54 or Engineering 77, Computer Science 61A-61B; or consent of instructor
(F,SP) Holmes | | BioE C141 | Statistics for Bioinformatics (4)
Three hours of lecture and two hours laboratory per week.
Study of bioinformatics problems such as DNA pattern finding, gene expression data analysis, molecular evolution models, and biomolecular sequence database searching. Introduction of the necessary probability and statistics: events, (conditional) probability, random variables, estimation, testing, and linear regression. Also listed as Statistics C141.
Prerequisites: Compsci 9C, Compsci 9E, Math 05, Math 054.
(F,SP) Huang
| | BioE 142 | Programming & Algorithm Design for Computational Biology & Genomics Applications (4)
Three hours of lecture and one hour of discussion per week.
This course will introduce students to structured software development and select principles of computer science with applications in computational biology and allied disciplines. The principle language used for instruction will be Java with a course module on Perl. Examples and tutorials will draw from problems in computational biology. The course will require one significant programming project, preferably biologically oriented.
Prerequisites: Math 54 and Molecular and Cell Biology 102; Engineering 77N, or Computer Science 61A, or Computer Science 61B; or consent of instructor.
(F) Arkin | | BioE 143 | Computational Methods in Biology (4)
Three hours of lecture per week. Description: Topics include thermodynamics, statistical mechanics, classical mechanics, and quantum mechanics that connect most directly to modern simulation methodology. Various case studies in the areas of classical dynamical simulations, ab initio dynamics, and Monte Carlo techniques will be covered. The areas of mathematical optimization and "non-algorithmic" computation such as neural networks and Hidden Markov Models will also be considered.
Prerequisites: Math 53, Math 54, Chemistry 130A, and Bioengineering 142; or consent of instructor. A course in thermodynamics, such as Mechanical Engineering 105B, is recommended.
(F,SP) Head-Gordon | | BioE 144 | Introduction to Protein Informatics (4)
This course will introduce students to the fundamentals of molecular biology, and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods, as well as practical hands-on experience with protein sequence analysis methods applied to real data.
Prerequisites: MCB 100 or MCB 102
(F) Sjolander | | BioE C145L | Introductory Electronic Transducer Laboratory (3)
Two hours lecture and three hours of laboratory per week.
Laboratory exercises exploring a variety of electronic transducers for measuring physical quantities such as temperature, force, displacement, sound, light, ionic potential; the use of circuits for low-level differential amplification and analog signal processing; and the use of microcomputers for digital sampling and display. Lectures cover principles explored in the laboratory exercises; construction, response and signal to noise of electronic transducers and actuators; and design of circuits for sensing and controlling physical quantities.
(F) Derenzo | | BioE C145M | Introductory Microcomputer Interfacing Laboratory (3)
Two hours lecture and three hours of laboratory per week.
Laboratory exercises constructing basic interfacing circuits and writing 20-100 line C programs for data acquisition, storage, analysis, display, and control. Use of the IBM PC with microprogrammable digital counter/timer, parallel I/O port, and analog I/O port. Circuit components include anti-aliasing filters, the S/H amplifier, A/D and D/A converters. Exercises include effects of aliasing in periodic sampling, fast Fourier transforms of basic waveforms, the use of the Hanning filter for leakage reduction, Fourier analysis of the human voice, digital filters, and control using Fourier deconvolution. Lectures cover principles explored in the laboratory exercises and design of microcomputer-based systems for data acquisition, analysis, and control.
(SP) Derenzo | | BioE C146 | Topics in Computational Biology and Genomics. (4) Three hours of lecture and one hour of discussion per week. Prerequisites: Bioengineering 142, Computer Science 61A, or equivalent ability to write programs in Java, Perl, C, or C++; Molecular and Cell Biology 100, 102, or equivalent; or consent of instructor. Instruction and discussion of topics in genomics and computational biology. Working from evolutionary concepts, the course will cover principles and application of molecular sequence comparison, genome sequencing and functional annotation, and phylogenetic analysis. Also listed as Molecular and Cell Biology C146 and Plant and Microbial Biology C146. (SP) Brenner, Eisen
| | BioE 155 | Introduction to Bioastronautics (4)
Three hours of lecture and one hour of discussion per week.
This course aims to bring undergraduate students into the world of space science related research including bioastronautics and high altitude human physiology. Students will gain a strong knowledge base of specific topics in bioastronautics, an introduction to research methods, and learn how to structure a research team. Additionally, students will develop leadership, management, teamwork, and communication skills. The topics to be covered include: history of manned space flight, the space environment, mars and lunar environments, space flight and life support systems, space suit technology, human physiological responses to space flight, countermeasures to space deconditioning, and space medicine
Prerequisites: None Budinger
| | BioE 164 | Optics & Microscopy (3)
Course Description: This course teaches fundamental principles of optics and examines contemporary methods of optical microscopy for cells and molecules. Students will learn how to design simple optical systems, calculate system performance, and apply imaging techniques including transmission, reflection, phase, and flurescence microscopy to investigate biological samples. The capabilities of optical microscopy will be compared with complimentary techniques including electron microscopy, coherence tomography, and atomic force microscopy.
Bioengineering Content: design, biological
Core Specialization: A, C, F A (Biomechanics and Tissue Engineering), C (Micromachines and Robotics) and F (Biomedical Imaging and Signal Processing)
Prerequisites: Physics 7A-B-C or 8A-B or equivalent introductory physics course
Fletcher | | BioE C165 | Image Processing and Reconstruction Tomography (4)
Three hours of lecture and one hour of discussion per week.
Linear systems and Fourier transforms in two and three dimensions. Basic image processing. Theory and algorithms for image reconstruction from projections. Physics of imaging systems including magnetic resonance, X-ray tomography, positron emission tomography, ultrasound, and biomagnetic imaging. Data analysis including hypothesis testing, parameter estimation by least squares, and compartmental kinetic modeling. Field trips to medical imaging laboratories. Also listed as Electrical Engineering C 145B.
Prerequisites: Electrical Engineering 120; basic programming ability in C or FORTRAN.
(SP) Conolly | BioE 168L
| Practical Light Microscopy (3)
This laboratory course is designed for students interested in obtaining practical hands-on training in optical imaging and instrumentation. Using a combination of lenses, cameras, and data acquisition equipment, students will construct simple light microscopes that introduce basic concepts and limitations important in biomedical optical imaging. Topics include compound microscopes, Kohler illumination, Rayleigh two-point resolution, image contrast including dark-field and fluorescence microscopy, and specialized techniques such as fluorescence recovery after photobleaching (FRAP). Intended for students in both engineering and the sciences, this course will emphasize applied aspects of optical imaging and provide a base of practical skill and reference material that students can leverage in their own research or in industry.
(F,SP) Fletcher
| BioE 190
| Advanced Topics in Bioengineering. Course may be repeated for credit. One to four hours of lecture per week. Sections 1-3 to be graded on a letter-grade basis. Sections 4-6 to be graded on a passed/not passed basis. Prerequisites: Consent of instructor. These courses cover current topics of research interest in bioengineering. The course content may vary from semester to semester. (F,SP) Staff
| BioE 190A
| Physical Methods of Quantitative Biology for Engineers (3)
This course is intended for the upper level engineering undergraduate students interested in acquiring knowledge about the quantitative measurement skills in biochemistry and biology using various instrumentations. The course covers the physical chemistry of the amino acids, DNAs, sugars, lipids, and proteins which are related to the measurements covered in the classes. The course also covers the principle of various instrumentations including UV-visible, IR and Raman spectroscopy, NMR, X-ray crystallography, light scattering, mass spectroscopy, circular dichroism, electron microscopy, isothermal calorimeter, electrophoresis, using biological examples to measure their thermodynamic parameters. Through this course, engineering student will be more familiar with biological phenomena and their quantitative measurement using instrumentation.
Prerequisites: Bioanalytical chemistry or quantitative biology class
(Fall 07) SW Lee
| BioE 190F
| Introduction to Medical Imaging: from Xrays to Magnetic Resonance (3)
The goal is to introduce undergraduate and graduate students to medical imaging and in particular to magnetic resonance imaging and spectroscopy. As an introductory course taught at a level of undergraduates without previous engineering or college physics, it will give not only breadth of the character of all of the current medical imaging methods but a depth in understanding of the mechanisms and some applications of magnetic resonance imaging and spectroscopy Fourteen lectures, in class exercises and field trips are planned. Field trip depending on the size of the class. LBNL will have a 1.5 T magnet and UCSF will have one or more magnets that the students can see in operation. If we go to LBNL, PET, SPECT and CT will be demonstrated. Alternatively or in addition the subject of contrast imaging will be introduced preferably during the field trip demonstration using magnevist.
Prerequisites: none
(Fall 07) Budinger
| | BioE 191 | Junior and Senior Seminar (1-3)
Course may be repeated for credit.
One to three hours of seminar per week. Must be taken on a passed/not passed basis.
Prerequisites: Priority given to juniors and seniors. Junior and senior seminars are small interactive courses offered by faculty members in Bioengineering. These seminars offer opportunity for close, regular intellectual contact between faculty members and students. The topics vary from semester to semester. (F,SP) Staff | BioE H194
| Honors Undergraduate Research (1-4)
Course may be repeated for credit. Variable format. Students who have completed a satisfactory number of advanced courses may pursue original research under the direction of one of the members of the staff. A maximum of 3 units of H194 may be used to fulfill technical elective requirements in the bioengineering program Final report required.
Prerequisite: Upper division technical GPA 3.3 or higher and consent of instructor and advisor
(F,SP) Staff | BioE 196*
| Undergraduate Design Research (1-4)
*Fulfills the Senior Engineering Design Project or BioE Research requirement in new curriculum. This is for Juniors and Seniors only. Students need to obtain a course approval form from 467 Evans, have faculty researcher sign form and return to 467 Evans for course control number.*
Course may be repeated for credit once. Individual research. Prerequisites: Junior or senior status, consent of instructor and faculty adviser. Supervised research. This course will satisfy the Senior Bioengineering Design project requirement. Students with junior or senior status may pursue research under the direction of one of the
members of the staff. May be taken a second time for credit only. A
final report or presentation is required.
(F,SP) Staff | BioE 198
| Directed Group Study for Advanced Undergraduates (1-4)
May be repeated for credit. Must be taken on a passed/not passed basis.
Group study of a selected topic or topics in Bioengineering, usually relating to new developments. Credit for 198 or 199 courses combined may not exceed 4 units in any single term. See College of Engineering for other restrictions. Offering a Decal Spring 2007.
Prerequisites: Upper division standing and good academic standing (2.0 GPA and above)
(F,SP,Summer) Staff | | BioE 98/198 | Stem Cells: Science and Society (2)
Many believe the cures to most diseases lie in stem cell research, while others fear its repercussions will irreversibly and negatively alter our social conscience for life. This class takes you on a journey inside the stem cell revolution, where scientists, policy-makers, and philosophers will challenge you to think about the social, political, and even spiritual implications of this uncharted scientific frontier and formulate your own position on stem cell research. As a result of this course, you will have a basic understanding of the science behind stem cell research, its applications and potential, and its social implications. We hope you will have enough knowledge on this subject to be able to, after your completion of this course, understand and participate in stem cell activities on campus and be informed about the political stances surrounding this developing field. The format of this course includes weekly, hour-long presentations on a variety of stem-cell-related topics by guest lecturers and facilitators. Also, hour-long class discussions will be held weekly to review the lectures, creatively instruct you about the basics of stem cell research, and converse about current developments in
this field. Pertinent weekly readings will be assigned.
(Fall 07) Conboy
| BioE 199
| Supervised Independent Study (1-4)
Course may be repeated for credit. Must be taken on a passed/not passed basis. Supervised independent study.
(F,SP) Staff | | BioE 200 | The Graduate Group Introductory Seminar (1)
Course may be repeated for credit.
One hour of seminar per week. Must be taken on a satisfactory/unsatisfactory basis.
Prerequisites: Enrollment in PhD Program in Bioengineering or consent of instructor. An introduction to research in bioengineering including specific case studies and organization of this rapidly expanding and diverse field. (F) Staff | BioE 210
| Cell Mechanics and the Cytoskeleton. (3) Three hours of lecture per week. Prerequisites: Undergraduate physics and cell biology or consent of instructor. This course explores emerging biophysical descriptions of the cell based on molecular details of the cytoskeleton and its interactions with the cellular microenvironment. Through lectures, discussions, and reading of the research literature, students will learn about current questions facing the field of cell mechanics and its connections with health and disease. Fundamental biology of the cytoskeleton and associated molecular motors will be discussed in the context of cell motility, shape change, and mechanotransduction. Modern techniques for quantifying mechanical properties of the cell and its structural components, including optical trapping, magnetic tweezers, atomic force microscopy, and traction-force microscopy will be presented, and recent models of cell mechanics and their predictions will be discussed and debated. (F,SP) Fletcher
| BioE 211
| Cell and Tissue Mechanotransduction. (3) Three hours of lecture per week. Prerequisites: Undergraduate cell biology or consent of instructor. This course will focus on biophysical and bioengineering aspects of mechanotransduction, the process through which living cells sense and respond to their mechanical environment. Students will learn how mechanical inputs to cells influence both subcellular biochemistry and whole-cell behavior. They will also study newly-engineered technologies for force manipulation and measurement in living cells, and synthetic strategies to control the mechanics and chemistry of the extracellular matrix. Finally, students will learn about the role of mechanotransduction in selected human organ systems and how these mechanisms may go awry in the setting of the disease. Instruction will feature lectures, discussions, analysis of relevant research papers, assembly of a literature review and a research proposal, and an oral presentation. (F,SP) Kumar | | BioE C212 | Heat and Mass Transport in Biomedical Engineering (3)
Three hours of lecture per week.
Fundamental processes of heat and mass transport in biological systems; organic molecules, cells, biological organs, whole animals. Derivation of mathematical models and discussion of experimental procedures. Applications to biomedical engineering.
Prerequisites: Mechanical Engineering 106 & 109
(F,SP) Berger | | BioE 213 | Fluid Mechanics of Biological Systems (3)
Formerly Mechanical Engineering 213
Three hours of lecture per week.
Investigation of fluid mechanical aspects of various physiological systems including circulatory, pulmonary, and renal systems. Motion in the large and small blood vessels. Pulsatile and peristaltic flow. Analysis of prosthetic devices. Fluid flow related in biological systems in bioprocessing application. Instrumentation for fluid flow measurements in biological systems.
Prerequisite: Mechanical Engineering 106
(F, SP) Berger | BioE 215
| Models of Cell Mechanics: Dynamics of the Cytoskeleton and Nucleus. (3) Three hours of lecture per week. Prerequisites: Open to bioengineering graduate students or consent of instructor. The field of cell mechanics has recently undergone rapid development with particular attention to the dynamics of the cytoskeleton as well as its interactions with the extracellular matrix and how this interaction may cause changes in cell architecture, consequently leading to functional adaptation or pathological conditions. A wide range of models exist for cytoskeletal mechanics, ranging from continuum models for cell deformation to actin filament-based models for cell mobility. Numerous experimental techniques have also been established to quantify the cytoskeletal mechanics via perturbing the cell by exerting some sort of deformation and examining the static and dynamic response of the cell. These experimental observations along with theoretical approaches to the cell have given rise to several theories for describing the mechanics of living cells, modeling the cytoskeleton as a simple mechanical elastic, viscoelastic, or poroviscoelastic continuum, porous gel or soft glassy material, tensegrity network incorporating discrete structural elements that bear compression. (F,SP) Mofrad
| | BioE C214 | Advanced Tissue Mechanics (3)
Three hours of lecture and one hour of discussion per week.
The goal of this course is to provide a foundation for characterizing and understanding the mechanical behaviors of load-bearing tissues. A variety of mechanics topics will be introduced, including anisotropic elasticity and failure, cellular solid theory, biphasic theory, and quasi-linear viscoelasticity (QLV) theory. Building from this theoretical basis, we will explore the constitutive behavior of a wide variety of biological tissues. After taking this course, students should have sufficient background to independently study the mechanical behavior of most biological tissues. Formal discussion section will include a seminar series with external speakers.
Also listed as Mechanial Engineering C214.
Prerequisites: C176, 185, graduate standing or consent of instrutor. Knowledge of MATLAB or equivalent.
(SP) Staff | | BioE C216 | Macromolecular Science in Biotechnology and Medicine (3)
Three hours of lecture per week.
Overview of the problems associated with the selection and function of polymers used in biotechnology and medicine. Principles of polymer science, polymer synthesis, and structure-property-performance relationships of polymers. Particular emphasis is placed on the performance of polymers in biological environments. Interactions between macromolecular and biological systems for therapy and diagnosis. Specific applications will include drug delivery, gene therapy, tissue engineering, and surface engineering.
Also listed as MSE C216.
Prerequisites: Bio Eng 115
(S) Healy | BioE C217
| Biomimetic Engineering -- Engineering from Biology. (3) Prerequisites: Graduate standing in engineering or consent of instructor. Study of nature's solutions to specific problems with the aim of determining appropriate engineering analogs. Morphology, scaling, and design in organisms applied to engineering structures. Mechanical principles in nature and their application to engineering devices. Mechanical behavior of biological materials as governed by underlying microstructure, with the potential for synthesis into engineered materials. Trade-offs between redundancy and efficiency. Students will work in teams on projects where they will take examples of designs, concepts, and models from biology and determine their potential in specific engineering applications. Also listed as Integrative Biology C217 and Mechanical Engineering C217. (F,SP) Dharan
| BioE C218
| Stem Cells and Directed Organogenesis. (3) Three hours of lecture/laboratory per week. Grading: Letter; Satisfactory/Unsatisfactory for CIRM humanities and law fellows. Prerequisites: Consent of instructor. This course will provide an overview of basic and applied embryonic stem cell (ESC) biology. Topics will include early embryonic development, ESC laboratory methods, biomaterials for directed differentiation and other stem cell manipulations, and clinical uses of stem cells. Also listed as Molecular and Cell Biology C237. (SP) Conboy | BioE 221
| Introduction to Micro and Nanobiotechnology: BioMEMS. (3) Three hours of lecture per week. Prerequisites: Chemistry 3B and Physics 7B or consent of instructor. Biophysical and chemical principles of biomedical microelectromechanical systems (bioMEMS) for the measurement of biological phenomena and clinical applications. Micro- and nano-scale devices for the manipulation of cells and biomolecules. Topics include solid-state transducers, optical transducers, electrochemical transducers, biomedical microelectronics, microfluidics L. Lee
| | BioE C223 | Polymer Engineering (3)
Three hours of lecture and one hour of discussion per week.
A survey of the structure and mechanical properties of advanced engineering polymers. Topics include rubber elasticity, viscoelasticity, mechanical properties, yielding, deformation, and fracture mechanisms of various classes of polymers. The course will discuss degradation schemes of polymers and long-term performance issues. The class will include polymer applications in bioengineering and medicine.
Prerequisites: Civil Engineering 130, Engineering 45
(F) Staff | BioE C230
| Implications and Applications of Synthetic Biology. (3) Two hours of lecture and one hour of discussion per week. Prerequisites: Consent of instructor. Explore strategies for maximizing the economic and societal benefits of synthetic biology and minimizing the risks; create "seedlings" for future research projects in synthetic biology at UC Berkeley; increase multidisciplinary collaborations at UC Berkeley on synthetic biology; and introduce students to a wide perspective of SB projects and innovators as well as policy, legal, and ethical experts. Also listed as Chemical Engineering C295L. (SP) Arkin, Keasling
| | BioE 231 | Introduction to Computational Molecular and Cellular Biology (4)
Three hours of lecture and one hour of discussion per week.
Topics include computational approaches and techniques to gene structure and finding, sequence alignment using dynamic programming, protein folding and structure prediction, protein-drug interactions, genetic and biochemical pathways and networks, and microarray analysis. Various case studies in these areas are reviewed and web-based computational biology tools will be used by students. Computational biology research connections to biotechnology will be explored. Bioengineering content: fulfills biological and statistical requirement. Bioengineering Breadth, Core B (Informatics and Genomics) and Core D (Computational Biology).
Prerequisites: Biology 1A, Computer Science 61A or 61B, Engineering 77, Mathematics 53 and 54; consent of instructor
(F,SP) Holmes | BioE 240
| Topics in Computational Biology and Evolution. (3) Three hours of lecture per week. Prerequisites: Graduate standing or consent of instructor. This class is aimed at graduate students from both the life sciences and engineering/mathematics. In addition to learning about bioinformatics methods in computational biology and evolution, we will focus on research and (oral and written) presentation skills and on the development of critical and analytical skills. Readings for the class will be selected from the best papers in the field over the past 20 years, with a focus on review papers and papers presenting important methods. (F,SP) Sjolander
| BioE 241
| Probabilistic Modeling in Computational Biology. (3) Three hours of lecture per week. Prerequisites: Mathematics 53 and 54 or equivalent; Molecular and Cell Biology C100A/102 or equivalent, programming class or consent of instructor. The course is designed to be a self-contained, advanced introduction to the techniques used in designing and implementing probabilistic models for bioinformatics, genomics, and other applications in computational biology and sequence analysis. A high mathematical facility is assumed: this is a course for graduate students (and advanced undergraduates) who are interested in designing their own, novel probabilistic models and approaches, rather than for the casual user of bioinformatics software. (F,SP) Holmes
| | BioE 243 | Computational Methods in Biology (4)
Students will receive no credit for 243 after taking 143.
Three hours of lecture per week.
Prerequisites: Mathematics 53 and 54. Must be able to program in scientific computing language (C, C++, Fortran), Matlab, or Java. An introduction to biophysical simulation methods and algorithms, including molecular dynamics, Monte Carlo, mathematical optimization, and "non-algorithmic" computation such as neural networks. Various case studies in applying these areas in the areas of protein folding, protein structure prediction, drug docking, and enzymatics will be covered. Core Specialization: Core B (Informatics and Genomics); Core D (Computational Biology); Bioengineering Content: Biological. (F,SP) Head-Gordon | BioE 244
| Introduction to Protein Informatics. (4) Students will receive no credit for 244 after taking 144. Three hours of lecture and three hours of computer laboratory per week. Prerequisites: Molecular and Cell Biology 100 or 102. This course will introduce students to the fundamentals of molecular biology and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods and practical hands-on experience with protein sequence analysis methods applied to real data. (F,SP) Sjolander
| BioE C246
| Topics in Computational Biology and Genomics. (4) Three hours of lecture, one and one-half hours of paper review, and discussion per week. Prerequisites: 142, Computer Science 61A, or equivalent ability to write programs in Java, Perl, C, or C++; Molecular and Cell Biology 100, 102, or equivalent; or consent of instructor. Instruction and discussion of topics in genomics and computational biology. Working from evolutionary concepts, the course will cover principles and application of molecular sequence comparison, genome sequencing and functional annotation, and phylogenetic analysis. Also listed as Plant and Microbial Biology C246 and Molecular and Cell Biology C246. (SP) Brenner, Eisen
| | BioE C279 | Occupational Biomechanics (4)
Three hours of lecture/fieldwork per week.
Overview of ergonomics and occupational biomechanics. Course covers pathophysiology and risk factors of upper extremity and back loading at work, measurement of force and posture, models for risk assessment, anthropometry applied to task and workstation design, tool design, and structure of successful ergonomics programs. Students will conduct a detailed job analysis and design a workplace intervention. Also listed as Public Health C269C.
(SP) Rempel | | BioE 290 | Advanced Topics in Bioengineering (1-3)
Course may be repeated for credit.
One hour of lecture per week per unit. One to three hours of lecture per week.
Prerequisites: Consent of instructor. This course covers current topics of research interest in bioengineering. The course content may vary from semester to semester. (F,SP) | BioE C290C
| Topics in Fluid Mechanics. (1,2) Course may be repeated for credit. One hour of seminar per week. Must be taken on a satisfactory/unsatisfactory basis. Prerequisites: Consent of instructor. Lectures on special topics which will be announced at the beginning of each semester that the course is offered. Topics may include transport and mixing, geophysical fluid dynamics, bio-fluid dynamics, oceanography, free surface flows, non Newtonian fluid mechanics, among other possibilities. Also listed as Environ Sci, Policy, and Management C291, Physics C290I, Mathematics C290C, Chemical Engineering C295M, Nuclear Engineering C290F, Civil and Environmental Engineering C290K, and Mechanical Engineering C298A. (F,SP) Staff
| BioE 290D
| Frontiers in Microbial Systems Biology (3)
Frontiers in (Microbial) Systems Biology is aimed at graduate and advanced undergraduate students from the (bio)engineering and chemo-physical sciences interested in a research-oriented introduction to current topics in systems biology. Focusing mainly on two well studied microbiological model systems - the chemotaxis network and Lambda bacteriophage infection - the class systematically introduces key
concepts and techniques for biological network deduction, modelling, analysis, evolution and synthetic network design. Students analyze the impact of approaches from the quantitative sciences - such as deterministic modelling, stochastic processes, statistics, non-linear dynamics, control theory, information theory, graph theory, etc.- on understanding biological processes, including (stochastic) gene regulation, signalling, network evolution and synthetic network design. The course aims to identify unsolved problems and discusses possible novel approaches while encouraging students to develop ideas to explore new directions in their own research.
Prerequisites: The course is designed for students with a background that includes differential equations and probability. Course work in molecular biology and biochemistry would be helpful, but is not required.
(Fall 07) Arkin
|
BioE 298
| Group Studies, Seminars, or Group Research (1-8)
Course may be repeated for credit. Variable format. Must be taken on a (satisfactory/unsatisfactory) basis. Advanced studies in various subjects through special seminars on topics to be selected each year. Informal group studies of special problems, group participation in comprehensive design problems, or group research on complete problems for analysis and experimentation.
(F,SP) Staff | BioE 299
| Individual Study or Research (1-12)
Course may be repeated for credit. Must be taken on a (satisfactory/unsatisfactory) basis. Prerequisites: Graduate standing. Investigations of advanced problems in bioengineering.
(F,SP) Staff | | BioE 301 | Teaching Techniques for Bioengineers (1)
One hour seminar per week. Must be taken on a passed/not passed basis.
Weekly seminars and discussions of effective teaching techniques. Use of educational objectives, alternative forms of instruction, and special techniques for teaching key concepts and techniques in Bioengineering. Course is intended to orient new graduate student instructors to teaching in the Bioengineering department at Berkeley.
(F) Staff |
|
|
|
|
|
|
