About the Program
The Department of Bioengineering offers a Master of Engineering (MEng) in Bioengineering, PhD in Bioengineering, and a Master of Translational Medicine (MTM). The PhD and MTM are operated in partnership with UC San Francisco, and degrees are granted jointly by UCSF and UC Berkeley.
Master of Engineering (MEng)
The Master of Engineering is a one-year master’s degree with a strong emphasis on engineering and entrepreneurship designed for students planning to move directly into industry after completing the program.
Master of Translational Medicine (MTM)
The Master of Translational Medicine is a unique one-year program designed for engineers, scientists, and clinicians who seek to bring innovative treatments and devices into clinical use.
Doctor of Philosophy (PhD)
The PhD in Bioengineering is granted jointly by Berkeley and UCSF, two of the top public universities in the world in engineering and health sciences. Our interdisciplinary program combines the outstanding resources in biomedical and clinical sciences at UCSF with the excellence in engineering, physical, and life sciences at Berkeley.
Administered by the Department of Bioengineering at UC Berkeley and the Department of Bioengineering and Therapeutic Sciences at UCSF, all students in the program are simultaneously enrolled in the graduate divisions of both the San Francisco and Berkeley campuses and are free to take advantage of courses and research opportunities on both campuses. The program awards the PhD in Bioengineering degree from both campuses.
Admissions
Admission to the Master of Engineering
Please see more information on the department website .
Admission to the Master of Translational Medicine
Please see more information about the MTM Program .
Admission to the Doctor of Philosophy
Please see detailed guidelines and instructions on the graduate program website .
Admission to the University
Minimum Requirements for Admission
The following minimum requirements apply to all graduate programs and will be verified by the Graduate Division:
- A bachelor’s degree or recognized equivalent from an accredited institution;
- A grade point average of B or better (3.0);
- If the applicant comes from a country or political entity (e.g., Quebec) where English is not the official language, adequate proficiency in English to do graduate work, as evidenced by a TOEFL score of at least 90 on the iBT test, 570 on the paper-and-pencil test, 230 on the computer-based test, or an IELTS Band score of at least 7 (note that individual programs may set higher levels for any of these); and
- Sufficient undergraduate training to do graduate work in the given field.
Applicants Who Already Hold a Graduate Degree
The Graduate Council views academic degrees not as vocational training certificates but as evidence of broad training in research methods, independent study, and articulation of learning. Therefore, applicants who already have academic graduate degrees should be able to pursue new subject matter at an advanced level without need to enroll in a related or similar graduate program.
Programs may consider students for an additional academic master’s or professional master’s degree only if the additional degree is in a distinctly different field.
Applicants admitted to a doctoral program that requires a master’s degree to be earned at Berkeley as a prerequisite (even though the applicant already has a master’s degree from another institution in the same or a closely allied field of study) will be permitted to undertake the second master’s degree, despite the overlap in field.
The Graduate Division will admit students for a second doctoral degree only if they meet the following guidelines:
- Applicants with doctoral degrees may be admitted for an additional doctoral degree only if that degree program is in a general area of knowledge distinctly different from the field in which they earned their original degree. For example, a physics PhD could be admitted to a doctoral degree program in music or history; however, a student with a doctoral degree in mathematics would not be permitted to add a PhD in statistics.
- Applicants who hold the PhD degree may be admitted to a professional doctorate or professional master’s degree program if there is no duplication of training involved.
Applicants may apply only to one single degree program or one concurrent degree program per admission cycle.
Any applicant who was previously registered at Berkeley as a graduate student, no matter how briefly, must apply for readmission, not admission, even if the new application is to a different program.
Required Documents for Applications
- Transcripts: Applicants may upload unofficial transcripts with your application for the departmental initial review. If the applicant is admitted, then official transcripts of all college-level work will be required. Admitted applicants must request a current transcript from every post-secondary school attended, including community colleges, summer sessions, and extension programs. Official transcripts must be in sealed envelopes as issued by the school(s) attended. If you have attended Berkeley, upload your unofficial transcript with your application for the departmental initial review. If you are admitted, an official transcript with evidence of degree conferral will not be required.
- Letters of recommendation: Applicants may request online letters of recommendation through the online application system. Hard copies of recommendation letters must be sent directly to the program, not the Graduate Division.
- Evidence of English language proficiency: All applicants from countries or political entities in which the official language is not English are required to submit official evidence of English language proficiency. This applies to applicants from Bangladesh, Burma, Nepal, India, Pakistan, Latin America, the Middle East, the People’s Republic of China, Taiwan, Japan, Korea, Southeast Asia, most European countries, and Quebec (Canada). However, applicants who, at the time of application, have already completed at least one year of full-time academic course work with grades of B or better at a US university may submit an official transcript from the US university to fulfill this requirement. The following courses will not fulfill this requirement: 1) courses in English as a Second Language, 2) courses conducted in a language other than English, 3) courses that will be completed after the application is submitted, and 4) courses of a non-academic nature. If applicants have previously been denied admission to Berkeley on the basis of their English language proficiency, they must submit new test scores that meet the current minimum from one of the standardized tests.
Where to Apply
Visit the Berkeley Graduate Division application page .
Doctoral Degree Requirements
Curriculum
In general, the program of study includes a major and a minor field of study. Due to the wide variety of topics included in bioengineering and the variety of student interests, major and minor sub fields will be chosen by the student in consultation with their primary graduate adviser, taking into account the student’s prior training, research interests, and career goals. Students who already hold a master’s degree or other professional degree (MD, DDS, or DVM) may not be required to complete minor coursework.
Sixteen semester units of graduate level coursework must be taken in the major field and 8 units of upper division or graduate coursework in the minor field, excluding seminars and research. The course requirements are designed to develop a strong and useful knowledge base in both biology and engineering. Students must also enroll in two graduate seminar courses and complete two semester or three quarter units in ethics.
Laboratory Rotations
Students should perform three 12-week rotations in different graduate group faculty laboratories during the first year. The objective of the research rotation is to allow students to become familiar with different areas of research, learn new experimental techniques, obtain experience in unique research laboratories, and ultimately to identify a lab in which to conduct dissertation research. The research being performed during a rotation may correspond to the initial stages of a thesis project or may be on a totally different topic.
Teaching
Anticipating future careers which may include teaching, all graduate students participate in undergraduate instruction by serving as a Graduate Student Instructor for at least one semester.
Qualifying Examination
An oral qualifying examination must be taken in the spring of the second year or the fall of the third year. In this examination, students demonstrate their ability to recognize research problems of fundamental importance, to propose appropriate experimental approaches to address these problems, and to display comprehensive knowledge of their disciplinary area and related subjects.
Dissertation Work
After advancing to candidacy, a student meets each fall semester with his or her thesis committee to discuss the dissertation project, to review results, and to chart directions in their third and subsequent years. In the final years in the program, students complete a dissertation based on original laboratory research. It generally takes five and a half years to complete the doctoral program.
Master's Degree Requirements
Curriculum
Please see the department website for the full MEng curriculum, and the MTM website for MTM curriculum.
Both degrees culminate with a capstone experience requiring significant work on a group design project.
Courses
Bioengineering
BIO ENG 200 The Graduate Group Introductory Seminar 1 Unit
Terms offered: Fall 2017, Spring 2017, Fall 2016
An introduction to research in bioengineering including specific case studies and organization of this rapidly expanding and diverse field.
Rules & Requirements
Prerequisites: Enrollment in PhD Program in Bioengineering or consent of instructor
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of seminar per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
BIO ENG C208 Biological Performance of Materials 4 Units
Terms offered: Fall 2017, Fall 2015
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 will be addressed. Applications of the concepts developed include blood-materials compatibility, biomimetic materials, hard and soft tissue-materials interactions, drug delivery, tissue engineering, and biotechnology.
Objectives & Outcomes
Course Objectives: The course is separated into four parts spanning the principles of synthetic materials and surfaces, principles of biological materials, biological performance of materials and devices, and state-of-the-art materials design. Students are required to attend class and master the material therein. In addition, readings from the clinical, life and materials science literature are assigned. Students are encouraged to seek out additional reference material to complement the readings assigned. A mid-term examination is given on basic principles (parts 1 and 2 of the outline). A comprehensive final examination is given as well.
The purpose of this course is to introduce students to problems associated with the selection and function of biomaterials. Through class lectures and readings in both the physical and life science literature, students will gain broad knowledge of the criteria used to select biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance. Materials used in devices for medicine, dentistry, tissue engineering, drug delivery, and the biotechnology industry will be addressed.
This course also has a significant design component (~35%). Students will form small teams (five or less) and undertake a semester-long design project related to the subject matter of the course. The project includes the preparation of a paper and a 20 minute oral presentation critically analyzing a current material-tissue or material-solution problem. Students will be expected to design improvements to materials and devices to overcome the problems identified in class with existing materials.
Student Learning Outcomes: Work independently and function on a team, and develop solid communication skills (oral, graphic & written) through the class design project.
• Develop an understanding of the social, safety and medical consequences of biomaterial use and regulatory issues associated with the selection of biomaterials in the context of the silicone breast implant controversy and subsequent biomaterials crisis.
• Design experiments and analyze data from the literature in the context of the class design project.
• Understanding of the origin of surface forces and interfacial free energy, and how they contribute to the development of the biomaterial interface and ultimately biomaterial performance.
• Apply math, science & engineering principles to the understanding of soft materials, surface chemistry, DLVO theory, protein adsorption kinetics, viscoelasticity, mass diffusion, and molecular (i.e., drug) delivery kinetics.
• Apply core concepts in materials science to solve engineering problems related to the selection biomaterials, especially in devices where the material-tissue or material-solution interface dominates performance.
Rules & Requirements
Prerequisites: Engineering 45; Chemistry C130/Molecular and Cell Biology C100A or Engineering 115 or equivalent; Bioengineering 102 and 104 recommended
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Healy
Also listed as: MAT SCI C208
BIO ENG C209 Advanced Orthopedic Biomechanics 4 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
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.
Objectives & Outcomes
Course Objectives: The purpose of this course is twofold:
• to learn the fundamental concepts of orthopaedic biomechanics;
• to enhance skills in mechanical engineering and bioengineering by analyzing the mechanical behavior of various complex biomedical problems.
Student Learning Outcomes: Working knowledge of various engineering concepts such as composite beam theory, beam-on-elastic-foundation theory, Hertz contact theory and MATLAB-based optimization design analysis. Understanding of basic concepts in orthopaedic biomechanics and the ability to apply the appropriate engineering concepts to solve realistic biomechanical problems, knowing clearly the assumptions involved.
Rules & Requirements
Prerequisites: ME C85/CE C30 or Bio Eng 102; concurrent enrollment OK. Proficiency in MatLab or equivalent. Prior knowledge of biology or anatomy is not assumed
Credit Restrictions: Students will not receive credit for this course if they have taken ME C176/Bio E C119.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 1 hour of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: O'Connell, Keaveny
Also listed as: MEC ENG C210
BIO ENG 211 Cell and Tissue Mechanotransduction 3 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
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.
Rules & Requirements
Prerequisites: Undergraduate cell biology or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Kumar
BIO ENG C212 Heat and Mass Transport in Biomedical Engineering 3 Units
Terms offered: Spring 2008, Fall 2007, Spring 2006
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.
Rules & Requirements
Prerequisites: 106 and 109 (106 and 109 may be taken concurrently)
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Formerly known as: Mechanical Engineering 212
Also listed as: MEC ENG C212
BIO ENG C213 Fluid Mechanics of Biological Systems 3 Units
Terms offered: Spring 2016, Spring 2014, Fall 2011
Fluid mechanical aspects of various physiological systems, the circulatory, respiratory, and renal systems. Motion in large and small blood vessels. Pulsatile and peristaltic flows. Other biofluidmechanical flows: the ear, eye, etc. Instrumentation for fluid measurements in biological systems and for medical diagnosis and applications. Artificial devices for replacement of organs and/or functions, e.g. blood oxygenators, kidney dialysis machines, artificial hearts/circulatory assist devices.
Rules & Requirements
Prerequisites: 106 or equivalent; 265A or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Berger, Liepmann
Also listed as: MEC ENG C213
BIO ENG C214 Advanced Tissue Mechanics 3 Units
Terms offered: Spring 2017, Spring 2015, Spring 2010
The goal of this course is to provide a foundation for characterizing and understanding the mechanical behavior 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.
Rules & Requirements
Prerequisites: 102A, 176, 185; graduate standing or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Also listed as: MEC ENG C214
BIO ENG C215 Molecular Biomechanics and Mechanobiology of the Cell 4 Units
Terms offered: Spring 2016, Spring 2015, Spring 2014
This course develops and applies scaling laws and the methods of continuum and statistical mechanics to understand micro- and nano-scale mechanobiological phenomena involved in the living cell with particular attention the nucleus and the cytoskelton as well as the interactions of the cell with the extracellular matrix and how these interactions may cause changes in cell architecture and biology, consequently leading to functional adaptation or pathological conditions.
Objectives & Outcomes
Course Objectives: This course, which is open to graduate students in diverse disciplines ranging from engineering to biology to chemistry and physics, is aimed at exposing students to subcellular biomechanical phenomena spanning scales from molecules to the whole cell.
Student Learning Outcomes: The students will develop tools and skills to (1) understand and analyze subcelluar biomechanics and transport phenomena, and (2) ultimately apply these skills to novel biological and biomedical applications.
Rules & Requirements
Prerequisites: MATH 54; PHYSICS 7A; BioE 102 or ME C85 or instructor’s consent
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Mofrad
Also listed as: MEC ENG C216
BIO ENG C216 Macromolecular Science in Biotechnology and Medicine 4 Units
Terms offered: Spring 2017, Spring 2015, Spring 2014
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.
Rules & Requirements
Prerequisites: Bioengineering 115 or equivalent; open to seniors with consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Healy
Also listed as: MAT SCI C216
BIO ENG C217 Biomimetic Engineering -- Engineering from Biology 3 Units
Terms offered: Spring 2014, Fall 2010, Fall 2009
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.
Rules & Requirements
Prerequisites: Graduate standing in engineering or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Dharan
Also listed as: INTEGBI C217/MEC ENG C217
BIO ENG C218 Stem Cells and Directed Organogenesis 3 Units
Terms offered: Spring 2015, Spring 2014, Spring 2013
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.
Rules & Requirements
Prerequisites: Consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 6 hours of laboratory and 1 hour of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Conboy
Also listed as: MCELLBI C237
BIO ENG C219 Protein Engineering 3 Units
Terms offered: Fall 2015, Fall 2014, Spring 2011
An in-depth study of the current methods used to design and engineer proteins. Emphasis on how strategies can be applied in the laboratory. Relevant case studies presented to illustrate method variations and applications. Intended for graduate students.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Tullman-Ercek
Also listed as: CHM ENG C270
BIO ENG 220L Cells and Biomaterials Laboratory 4 Units
Terms offered: Prior to 2007
The objective of this course is to teach graduate students the essential laboratory techniques in the design and characterization and analysis of cells and biomaterials. The course will cover basics on synthetic biomaterials and native matrix, cellular responses to biomaterials, three-dimensional culture, and tissue engineering. The course includes a lecture and a laboratory section each week. There will be a midterm exam, final exam, and a tissue engineering group project.
Rules & Requirements
Prerequisites: Cell and tissue engineering; upper division cell biology course or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture and 6 hours of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Li
BIO ENG 221 Advanced BioMEMS and Bionanotechnology 4 Units
Terms offered: Fall 2017, Spring 2017, Fall 2016
Biophysical and chemical principles of biomedical devices, bionanotechnology, bionanophotonics, and biomedical microelectromechanical systems (BioMEMS). Topics include basics of nano-& microfabrication, soft-lithography, DNA arrays, protein arrays, electrokinetics, electrochemical transducers, microfluidic devices, biosensor, point of care diagnostics, lab-on-a-chip, drug delivery microsystems, clinical lab-on-a-chip, advanced biomolecular probes, biomolecular spectroscopy, and etc.
Rules & Requirements
Prerequisites: Chemistry 3A, PHYSICS 7A and 7B, Electrical Engineering 143 or equivalent
Repeat rules: Students will receive no credit for 221 after taking 121. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Summer:
6 weeks - 7.5 hours of lecture per week
8 weeks - 5.5 hours of lecture per week
10 weeks - 4.5 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: L. Lee
BIO ENG 221L BioMEMS and BioNanotechnology Laboratory 4 Units
Terms offered: Fall 2016, Spring 2015, Spring 2014
Students will become familiar with BioMEMS and Lab-on-a-Chip research. Students will design and fabricate their own novel micro- or nano-scale device to address a specific problem in biotechnology using the latest micro- and nano-technological tools and fabrication techniques. This will involve an intensive primary literature review, experimental design, and quantitative data analysis. Results will be presented during class presentations and at a final poster symposium.
Objectives & Outcomes
Course Objectives: Students will become familiar with research associated with BioMEMS and Lab-on-a-Chip technologies. Students will gain experience in using creative design to solve a technological problem. Students will learn basic microfabrication techniques. Working in engineering teams, students will learn how to properly characterize a novel device
by choosing and collecting informative metrics. Students will design and carry out carefully controlled experiments that will result in the analysis of quantitative data.
Student Learning Outcomes: Students will learn how to critically read BioMEMS and Lab-on-a-Chip primary literature. Students will learn how to use AutoCAD software to design microscale device features. Students will gain hands-on experience in basic photolithography and soft lithography. Students will get experience with a variety of fluid loading interfaces and
microscopy techniques. Students will learn how to design properly controlled uantitative experiments. Students will gain experience in presenting data to their peers in the form of powerpoint presentations and also at a poster symposium.
Rules & Requirements
Prerequisites: BioE 103 or equivalent, BioE 104
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: D. Liepmann
BIO ENG C222 Advanced Structural Aspects of Biomaterials 4 Units
Terms offered: Spring 2016, Fall 2013, Spring 2012
This course covers the structure and mechanical functions of load bearing tissues and their replacements. Biocompatibility of biomaterials and host response to structural implants are examined. Quantitative treatment of biomechanical issues and constitutive relationships of materials are covered in order to design implants for structural function. Material selection for load bearing applications including reconstructive surgery, orthopedics, dentistry, and cardiology are addressed.
Rules & Requirements
Credit Restrictions: Students should not receive credit if they've taken ME ME C117 or Bio Eng C117.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Also listed as: MEC ENG C215
BIO ENG C223 Polymer Engineering 3 Units
Terms offered: Fall 2017, Fall 2015, Fall 2014
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.
Rules & Requirements
Prerequisites: Civil Engineering 130, Engineering 45
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Also listed as: MEC ENG C223
BIO ENG 224 Basic Principles of Drug Delivery 3 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
This course focuses on providing students with the foundations needed to understand contemporary literature in drug delivery. Concepts in organic chemistry, biochemistry, and physical chemistry needed to understand current problems in drug delivery are emphasized.
Objectives & Outcomes
Course Objectives: The goal of this course is to give students the ability to understand problems in drug delivery. Emphasis is placed on the design and synthesis of new molecules for drug delivery.
Student Learning Outcomes: At the completion of this course students should be able to design new molecules to solve drug delivery problems.
Rules & Requirements
Prerequisites: BioE 103 or equivalent
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Murthy
BIO ENG 225 Biomolecular Structure Determination 3 Units
Terms offered: Fall 2017
The detailed, atomic-level structure of biomolecules is at the basis of our understanding of many biochemical processes. The knowledge of these 3D structures has provided fundamental insights in the organization and inner workings of the living cell and has directly impacted the daily lives of many through the development of novel therapeutic agents. This graduate level course is designed to provide students with an in-depth understanding of
crystallography for macromolecular structure determination. The underlying theory, computational approaches, and practical considerations for each step in the process will be discussed.
Objectives & Outcomes
Course Objectives: (1) Introduce students to the atomic structure of macromolecules,
2) review methods for structure determination, (3) describe the basic theory of diffraction, and (4) provide students with a detailed knowledge of macromolecular crystallography. At the end of the course students will have a solid theoretical and practical understanding of how macromolecular structures are determined to atomic resolution using crystallographic methods. The application of the method to problems in biomolecular engineering will be reviewed.
Student Learning Outcomes: The students will be able to (1) interpret diffraction data to determine reciprocal and real space parameters, (2) plan diffraction experiments, (3) use computational methods to solve the crystallographic phase problem (an inverse problem), (4) interpret complex 3-dimensional maps to build atomic models, (5) determine which optimization methods are appropriate for obtaining a refined, validated model, and (6) apply the knowledge to the engineering of biomolecules.
Rules & Requirements
Prerequisites: Consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Paul Adams
BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units
Terms offered: Prior to 2007
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.,Terms offered: Spring 2007
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.
Rules & Requirements
Prerequisites: Consent of instructor
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Arkin, Keasling
Also listed as: CHM ENG C295L
BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units
Terms offered: Prior to 2007
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.,Terms offered: Spring 2007
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.
Rules & Requirements
Prerequisites: Consent of instructor
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Arkin, Keasling
Also listed as: CHM ENG C295L
BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units
Terms offered: Prior to 2007
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.,Terms offered: Spring 2007
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.
Rules & Requirements
Prerequisites: Consent of instructor
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Arkin, Keasling
Also listed as: CHM ENG C295L
BIO ENG C230 Implications and Applications of Synthetic Biology 3 Units
Terms offered: Prior to 2007
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.,Terms offered: Spring 2007
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.
Rules & Requirements
Prerequisites: Consent of instructor
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Arkin, Keasling
Also listed as: CHM ENG C295L
BIO ENG 231 Introduction to Computational Molecular and Cellular Biology 4 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
Topics include computational approaches and techniques to gene structure and genome annotation, sequence alignment using dynamic programming, protein domain analysis, RNA folding and structure prediction, RNA sequence design for synthetic biology, genetic and biochemical pathways and networks, UNIX and scripting languages, basic probability and information theory. Various "case studies" in these areas are reviewed and web-based computational biology tools will be used by students and programming projects will be given.
Rules & Requirements
Credit Restrictions: Students will receive no credit for 231 after taking 131.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1.5 hours of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Holmes
BIO ENG 232 Genetic Devices 4 Units
Terms offered: Fall 2014, Fall 2013, Fall 2012
This graduate-level course is a comprehensive survey of genetic devices. These DNA-based constructs are comprised of multiple "parts" that together encode a higher-level biological behavior and perform useful human-defined functions. Such constructs are the engineering target for most projects in synthetic biology. Included within this class of constructs are genetic circuits, sensors, biosynthetic pathways, and microbiological functions.
Objectives & Outcomes
Course Objectives: (1) To introduce the basic biology and engineering principles for constructing genetic devices including biochemical devices, microbiological devices, genetic circuits, eukaryotic devices, and developmental devices, (2) To familiarize students with current literature examples of genetic devices and develop literature searching skills; (3) To develop the students' ability to apply computational tools to the design of genetic devices.
Student Learning Outcomes: Students will be able to (1) use mathematical models to describe the dynamics of genetic devices, (2) comprehend and evaluate publications related to any type of genetic device, (3) perform a thorough literature search, (4) evaluate the technical plausibility of a proposed genetic device, (5) analyze a design challenge and propose a plausible solution to it in the form of a genetic device, and (6) assess any ethical or safety issues associated with a proposed genetic device.
Rules & Requirements
Prerequisites: Engineering 7 or Computer Science 61A, Mathematics 54, Chemistry 3A, and BioE103 or equivalent
Credit Restrictions: Students will receive no credit for 232 after taking 132.
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Anderson
BIO ENG 235 Frontiers in Microbial Systems Biology 4 Units
Terms offered: Spring 2017, Fall 2010, Fall 2009
This course 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 identify unsolved problems and discusses possible novel approaches while encouraging students to develop ideas to explore new directions in their own research.
Rules & Requirements
Prerequisites: Designed for graduates with background in differential equations and probability. Course work in molecular cell biology or biochemistry helpful
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Arkin, Bischofs-Pfeifer, Wolf
BIO ENG 241 Probabilistic Modeling in Computational Biology 4 Units
Terms offered: Spring 2017, Spring 2016, Spring 2014
This course covers applications of probabilistic modeling to topics in bioinformatics, with an emphasis on literature study and novel tool development. Areas covered vary from year to year but typically include finite-state Markov models as models of point substitution processes; graphical models and dynamic programming; basic coalescent theory; grammar theory; birth-death processes and the Thorne-Kishino-Felsenstein model of indels; general PDE methods and applications to continuous-state models; the Chinese restaurant process in population genetics and ecology; data compression algorithms; general techniques including conjugate priors, MCMC, and variational methods.
Objectives & Outcomes
Course Objectives: To introduce the most commonly used statistical models and associated inference techniques for the analysis and organization of biological sequences, with a focus on models based on evolutionary theory.
Student Learning Outcomes: Students will be familiar with the bioinformatics literature and underyling theory for discrete Markov processes, Bayesian networks, stochastic grammars, birth-death processes, Chinese restaurant processes, data compression algorithms, and related methods such as dynamic programming and MCMC.
Rules & Requirements
Prerequisites: Recommended preparation: <BR/>MATH 53: multivariable calculus (or equivalent) <BR/>MATH 54: linear algebra (or equivalent), <BR/>MATH 126: partial differential equations (or equivalent)<BR/>or consent of instructor
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 3 hours of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Holmes
BIO ENG 243 Computational Methods in Biology 4 Units
Terms offered: Fall 2012, Fall 2011, Fall 2010
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.
Rules & Requirements
Prerequisites: Mathematics 53 and 54; programming experience preferred but not required
Credit Restrictions: Students will receive no credit for 243 after taking 143.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 2 hours of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Head-Gordon
BIO ENG 244 Introduction to Protein Informatics 4 Units
Terms offered: Spring 2017, Fall 2008, Fall 2007
This course will introduce students to the bioinformatics algorithms used by biologists to identify homologs, construct multiple sequence alignments, predict protein structure, estimate phylogenetic trees, identify orthologs, predict protein-protein interaction, and build hidden Markov models. The focus is on the algorithms used, and on the sources of various types of errors in these methods. This class includes no programming, and no programming background is required.
Objectives & Outcomes
Course Objectives: This course is designed to provide a theoretical framework for protein sequence and structure analysis using bioinformatics software tools. Students completing this course will be prepared for subsequent in-depth studies in bioinformatics, for algorithm development, and for the use of bioinformatics methods for biological discovery. It is aimed at two populations: students in the life sciences who need to become expert users of bioinformatics tools, and students in engineering and mathematics/computer science who wish to become the developers of the next generation of bioinformatics methods. As virtually all the problems in this field are very complex, there are many opportunities for research and development of new methods.
Student Learning Outcomes: Students completing this course are likely to find several potential areas of research of interest, which they may want to work on as independent study projects during undergraduate work, or take on as Master’s or Ph.D. thesis topics for advanced work.
Rules & Requirements
Prerequisites: Prior coursework in algorithms (e.g., CS 170) is highly recommended. The class does not include programming, and no prior programming experience is required, although students need to be comfortable reading and writing pseudocode (precise text descriptions of algorithms
Credit Restrictions: BioE 144 or previous BioE/PMB C144
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Sjolander
Formerly known as: Bioengineering C244/Plant and Microbial Biology C244
BIO ENG 244L Protein Informatics Laboratory 3 Units
Terms offered: Not yet offered
This course is intended to provide hands-on experience with a variety of bioinformatics tools, web servers and databases that are used to predict protein function and structure. This course will cover numerous bioinformatics tasks including: homolog detection using BLAST and PSI-BLAST, hidden Markov model construction and use, multiple sequence alignment, phylogenetic tree construction, ortholog identification, protein structure prediction, active site prediction, cellular localization, protein-protein interaction and phylogenomic analysis. Some minimal programming/scripting skills (e.g., Perl or Python) are required to complete some of the labs.
Rules & Requirements
Prerequisites: One upper-division course in molecular biology or biochemistry (e.g., MCB 100A/CHEM C130 or equivalent). Python programming (e.g., CS 61A) and experience using command-line tools in a Unix environment
Credit Restrictions: BioE 144L or BioE C144L/PMB C144L
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of laboratory and 2 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Sjolander
Formerly known as: Bioengineering C244L/Plant and Microbial Biology C244L
BIO ENG 247 Principles of Synthetic Biology 4 Units
Terms offered: Fall 2016, Fall 2015, Fall 2014
The field of synthetic biology is quickly emerging as potentially one of the most important and profound ways by which we can understand and manipulate our physical world for desired purposes. In this course, the field and its natural scientific and engineering basis are introduced. Relevant topics in cellular and molecular biology and biophysics, dynamical and engineering systems, and design and operation of natural and synthetic circuits are covered in a concise manner that then allows the student to begin to design new biology-based systems.
Objectives & Outcomes
Course Objectives: (1) To introduce the basics of Synthetic Biology, including quantitative cellular network characterization and modeling, (2) to introduce the principles of discovery and genetic factoring of useful cellular activities into reusable functions for design, (3) to inculcate the principles of biomolecular system design and diagnosis of designed systems, and (4) to illustrate cutting-edge applications in Synthetic Biology and to enhance skull sin analyzing and designing synthetic biological applications.
Student Learning Outcomes: The goals of this course are to enable students to: (1) design simple cellular circuitry to meet engineering specification using both rational/model-based and library-based approaches, (2) design experiments to characterize and diagnose operation of natural and synthetic biomolecular network functions, and (3) understand scientific, safety and ethical issues of synthetic biology.
Rules & Requirements
Prerequisites: MATH 53/54, BioE 103 or equivalent, or consent of instructor
Credit Restrictions: Students will receive no credit for 247 after taking 147.
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Arkin
Terms offered: Fall 2017, Fall 2016, Fall 2015
This course will cover metabolic engineering and the various synthetic biology approaches for optimizing pathway performance. Use of metabolic engineering to produce biofuels and general "green technology" will be emphasized since these aims are currently pushing these fields. The course is meant to be a practical guide for metabolic engineering and the related advances in synthetic biology as well the related industrial research and opportunities.
Rules & Requirements
Prerequisites: Chemistry 3A and Molecular and Cell Biology C100A/Chemistry C130A or equivalent
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Dueber
BIO ENG C250 Nanomaterials in Medicine 3 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
The course is designed for graduate students interested in the emerging field of nanomedicine. The course will involve lectures, literature reviews and proposal writing. Students will be required to formulate a nanomedicine research project and write an NIH-style proposal during the course. The culmination of this project will involve a mock review panel in which students will serve as peer reviewers to read and evaluate the proposals.
Objectives & Outcomes
Course Objectives: To review the current literature regarding the use of nanomaterials in medical applications; (2) To describe approaches to nanomaterial synthesis and surface modification; (3) To understand the interaction of nanomaterials with proteins, cells and biological systems; (4) To familiarize students with proposal writing and scientific peer review.
Student Learning Outcomes: Students should be able to (1) identify the important properties of metal, polymer and ceramic nanomaterials used in healthcare; (2) understand the role of size, shape and surface chemistry of nanomaterials in influencing biological fate and performance; (3) understand common methods employed for surface modification of nanomaterials; (4) comprehend the range of cell-nanomaterial interactions and methods for assaying these interactions; (5) read and critically review the scientific literature relating to nanomedicine; (6) formulate and design an experimental nanomedicine research project; (7) understand the principles of the peer review system.
Rules & Requirements
Prerequisites: Graduate Standing
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Messersmith
Also listed as: MAT SCI C250
BIO ENG 251 Micro/Nanofluidics for Bioengineering and Lab-On-A-Chip 4 Units
Terms offered: Spring 2015, Spring 2014, Spring 2013
Introduction and in-depth treatment of theory relevant to fluid flow in microfluidic and nanofluidic systems supplemented by critical assessment of recent applications drawn from the literature. Topics include low Reynolds Number flow, mass transport including diffusion phenomena, and emphasis on electrokinetic systems and bioanalytical applications of said phenomena.
Objectives & Outcomes
Course Objectives: The course is an introduction to the physicochemical dynamics associated with fluid flow in nanoscale and microscale devices for graduate students and advance undergraduate students. The course has been created in response to the active field of microfluidics and nanofluidics, as well as the associated interest from industry, government, and academic research groups. The course provides an theoretical treatment of micro/nanofluidic phenomena that complements the well-established laboratory and research content offered in the Department.
We will study mass and momentum transport phenomena of microscale and nanoscale flow devices. Throughout the course, we will place an emphasis on bioanalytical microfluidic system applications where electrophoresis, electroosmosis, molecular diffusion, and/or Brownian motion effects dominate. Successful completion of the course will prepare students to design micro/nanofluidic engineering solutions, as well as critically assess academic and industrial developments in these areas.
Student Learning Outcomes: 1. To introduce students to the governing principles of fluid flow in microfluidic and nanofluidic regimes, with emphasis on phenomena relevant to bioanalytical devices.
2. To provide students with an understanding of scaling laws that define the performance of microfluidic and nanofluidic systems.
3. To provide students with a detailed investigation of applications that do and do not benefit from miniaturization.
4. To give students adequate didactic background for critical assessment of literature reports and conference presentations regarding advances in the topical areas of microfluidics and nanofluidics.
Rules & Requirements
Prerequisites: BioE 11 or Chem 3B, BioE 104 or ME 106 or consent of instructor
Credit Restrictions: Students will receive no credit for 251 after taking 151.
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Herr
BIO ENG 252 Clinical Need-Based Therapy Solutions 2 Units
Terms offered: Fall 2017, Fall 2016
Students will be introduced to clinical areas with unmet needs, be introduced to the current standard of care or state of the art solutions for those needs, and learn to methodically conceptualize potential alternatives. The course will emphasize interaction between students and subject matter experts in these clinical areas and in the related fields of medtech and biotech innovation. Open innovative ideas from students are encouraged during the course.
Objectives & Outcomes
Course Objectives: (1) To expose students to clinical areas with major unmet need; (2) Expose students to current state of the art in therapy solutions for the above clinical need; (3) Stimulate innovation concept targeting high-impact clinical needs
Student Learning Outcomes: Students will be able to (1) Immerse in an enabling innovation environment stemming from the solution ideas by the students and mentor faculties; (2) Obtain potential avenues to enable capstone projects, UCSF collaborations, SBIR, etc.
Hours & Format
Fall and/or spring: 15 weeks - 2 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Hossiany
BIO ENG C261 Medical Imaging Signals and Systems 4 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
Biomedical imaging is a clinically important application of engineering, applied mathematics, physics, and medicine. In this course, we apply linear systems theory and basic physics to analyze X-ray imaging, computerized tomography, nuclear medicine, and MRI. We cover the basic physics and instrumentation that characterizes medical image as an ideal perfect-resolution image blurred by an impulse response. This material could prepare the student for a career in designing new medical imaging systems that reliably detect small tumors or infarcts.
Objectives & Outcomes
Course Objectives: • understand how 2D impulse response or 2D spatial frequency transfer function (or Modulation Transfer Function) allow one to quantify the spatial resolution of an imaging system.
• understand 2D sampling requirements to avoid aliasing
• understand 2D filtered backprojection reconstruction from projections based on the projection-slice theorem of Fourier Transforms
• understand the concept of image reconstruction as solving a mathematical inverse problem.
• understand the limitations of poorly conditioned inverse problems and noise amplification
• understand how diffraction can limit resolution---but not for the imaging systems in this class
• understand the hardware components of an X-ray imaging scanner
•
• understand the physics and hardware limits to spatial resolution of an X-ray imaging system
• understand tradeoffs between depth, contrast, and dose for X-ray sources
• understand resolution limits for CT scanners
• understand how to reconstruct a 2D CT image from projection data using the filtered backprojection algorithm
• understand the hardware and physics of Nuclear Medicine scanners
• understand how PET and SPECT images are created using filtered backprojection
• understand resolution limits of nuclear medicine scanners
• understand MRI hardware components, resolution limits and image reconstruction via a 2D FFT
• understand how to construct a medical imaging scanner that will achieve a desired spatial resolution specification.
Student Learning Outcomes: • students will be tested for their understanding of the key concepts above
• undergraduate students will apply to graduate programs and be admitted
• students will apply this knowledge to their research at Berkeley, UCSF, the national labs or elsewhere
• students will be hired by companies that create, sell, operate or consult in biomedical imaging
Rules & Requirements
Prerequisites: El Eng 20N and Engineering 7 or equivalent. Knowledge of Matlab or linear algebra assumed
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Conolly
Also listed as: EL ENG C261
BIO ENG 263 Principles of Molecular and Cellular Biophotonics 4 Units
Terms offered: Fall 2017, Fall 2016, Fall 2015
Topics in the emerging field of biophotonics with an emphasis on fluorescence spectroscopy, biosensors, and devices for optical imaging and detection of biomolecules. The course will cover the photophysics and photochemistry of organic molecules, the design and characterization of biosensors, and their applications within diverse environments, ranging from the detection of single molecules in vitro and in cells to studies of detection, diagnosis, and monitoring of specific health conditions and disease.
Rules & Requirements
Prerequisites: 102 or consent of instructor, and Chemistry 3A and PHYSICS 7B
Credit Restrictions: Students will receive no credit for 263 after taking 163.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture and 1 hour of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Marriott
BIO ENG 263L Molecular and Cellular Biophotonics Laboratory 4 Units
Terms offered: Spring 2017, Spring 2015, Fall 2013
This course provides undergraduate and graduate bioengineering students with an opportunity to acquire essential experimental skills in fluorescence spectroscopy and the design, evaluation, and optimization of optical biosensors for quantitative measurements of proteins and their targets. Groups of students will be responsible for the research, design, and development of a biosensor or diagnostic device for the detection, diagnosis, and monitoring of a specific biomarker(s).
Rules & Requirements
Prerequisites: 263; experience in a research lab and consent of instructor
Credit Restrictions: Students will receive no credit for 263L after taking 163L.
Hours & Format
Fall and/or spring: 15 weeks - 6 hours of laboratory and 2 hours of discussion per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructor: Marriott
BIO ENG C265 Principles of Magnetic Resonance Imaging 4 Units
Terms offered: Spring 2017, Spring 2016, Spring 2015
Fundamentals of MRI including signal-to-noise ratio, resolution, and contrast as dictated by physics, pulse sequences, and instrumentation. Image reconstruction via 2D FFT methods. Fast imaging reconstruction via convolution-back projection and gridding methods and FFTs. Hardware for modern MRI scanners including main field, gradient fields, RF coils, and shim supplies. Software for MRI including imaging methods such as 2D FT, RARE, SSFP, spiral and echo planar imaging methods.
Objectives & Outcomes
Course Objectives: Graduate level understanding of physics, hardware, and systems engineering description of image formation, and image reconstruction in MRI. Experience in Imaging with different MR Imaging systems. This course should enable students to begin graduate level research at Berkeley (Neuroscience labs, EECS and Bioengineering), LBNL or at UCSF (Radiology and Bioengineering) at an advanced level and make research-level contribution
Rules & Requirements
Prerequisites: Either Electrical Engineering 120 or Bioengineering C165/Electrical Engineering C145B or consent of instructor
Credit Restrictions: Students will receive no credit for Bioengineering C265/El Engineering C225E after taking El Engineering 265.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture, 1 hour of discussion, and 3 hours of laboratory per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Lustig, Conolly
Also listed as: EL ENG C225E
BIO ENG 280 Ethical and Social Issues in Translational Medicine 1 Unit
Terms offered: Fall 2017, Spring 2017, Fall 2016
This class is designed to introduce MTM students to their professional responsibilities
as engineers and translational scientists. By the end of it, students will have
experience communicating their ideas appropriately and effectively to their peers,
their superiors, and those whom they manage or mentor. We will also discuss
methods for having a successful graduate school experience - choosing and working
on a project and preparing to meet post-graduate goals. Finally, some of the ethical
challenges likely to be met by a working bioengineer will be explored.
While this syllabus is meant to be an accurate description of the course and its content,
it may be modified at the instructor’s discretion.
Objectives & Outcomes
Course Objectives: Objectives
● Communications skills and best practices
● Research ethics in translational medicine
● Professional development for MTM graduate students
Student Learning Outcomes: MTM students will become aware of ethical issues commonly confronted in
translational medicine and learn how to evaluate and act accordingly. They will also
leave capable of independently considering new ethical issues that arise during their
careers.
Rules & Requirements
Prerequisites: Open only to students in the Masters of Translational Medicine Graduate program
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Johnson, Terry
BIO ENG C280 Introduction to Nano-Science and Engineering 3 Units
Terms offered: Spring 2015, Spring 2013, Spring 2012
A three-module introduction to the fundamental topics of Nano-Science and Engineering (NSE) theory and research within chemistry, physics, biology, and engineering. This course includes quantum and solid-state physics; chemical synthesis, growth fabrication, and characterization techniques; structures and properties of semiconductors, polymer, and biomedical materials on nanoscales; and devices based on nanostructures. Students must take this course to satisfy the NSE Designated Emphasis core requirement.
Rules & Requirements
Prerequisites: Major in physical science such as chemistry, physics, etc., or engineering; consent of advisor or instructor
Repeat rules: Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Gronsky, S.W. Lee, Wu
Also listed as: MAT SCI C261/NSE C201/PHYSICS C201
BIO ENG C281 The Berkeley Lectures on Energy: Energy from Biomass 3 Units
Terms offered: Fall 2015, Fall 2014, Fall 2013
After an introduction to the different aspects of our global energy consumption, the course will focus on the role of biomass. The course will illustrate how the global scale of energy guides the biomass research. Emphasis will be places on the integration of the biological aspects (crop selection, harvesting, storage, and distribution, and chemical composition of biomass) with the chemical aspects to convert biomass to energy. The course aims to engage students in state-of-art research.
Rules & Requirements
Prerequisites: BIOLOGY 1A; Chemistry 1B or 4B, Mathematics 1B
Repeat rules: Repeatable when topic changes with consent of instructor.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Bell, Blanch, Clark, Smit, C. Somerville
Also listed as: CHEM C238/CHM ENG C295A/PLANTBI C224
BIO ENG 290 Advanced Topics in Bioengineering 1 - 4 Units
Terms offered: Fall 2017, Spring 2017, Fall 2016
This course covers current topics of research interest in bioengineering. The course content may vary from semester to semester.
Rules & Requirements
Prerequisites: Consent of instructor
Credit Restrictions: One hour of lecture per week per unit.
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 1-4 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
BIO ENG C290D Advanced Technical Communication: Proposals, Patents, and Presentations 3 Units
Terms offered: Spring 2016, Spring 2012, Spring 2011
This course will help the advanced Ph.D. student further develop critically important technical communication traits via a series of lectures, interactive workshops, and student projects that will address the structure and creation of effective research papers, technical reports, patents, proposals, business plans, and oral presentations. One key concept will be the emphasis on focus and clarity--achieved through critical thinking regarding objectives and context. Examples will be drawn primarily from health care and bioengineering multidisciplinary applications.
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
Instructors: Keaveny, Pruitt
Also listed as: MEC ENG C290X
BIO ENG 295 Bringing Biomedical Devices to Market 3 Units
Terms offered: Spring 2017
Engineering design is the process by which an idea is generated, developed, constructed, tested, and managed. Typical bioengineering courses often focus on idea conception and construction. True engineering design integrates not only these two essential elements, but also the process of evaluating, planning, and testing a product. This course highlights the context and value of product development: the formalized process bridging the gap between device proof-of-concept and an FDA approved biomedical product in the marketplace. Instructor led lectures and student led case studies and exercises will form the core of the coursework.
Objectives & Outcomes
Course Objectives: To provide students with a fundamental understanding of the biomedical device R&D pathway including: design proof-of-concept, design input/output, design verification and validation, and regulatory approval.
• To give graduates the tools to be leaders in the medtech/biotech industry with a clear understanding of the design development process.
• To give students the opportunity to apply and implement the strategies learned in concurrent leadership and capstone coursework
Student Learning Outcomes: Students will gain an understanding of:
• Biomedical Device Design & Development
• Design Risk Analysis
• Design Documentation
• Verification & Validation Testing
• FDA Design Control
• Quality Systems (cGMP)
• Regulatory Clearance/Approval Strategy
• Device Commercialization Pathways
Rules & Requirements
Prerequisites: Engineering 271 or equivalent recommended
Hours & Format
Fall and/or spring: 15 weeks - 3 hours of lecture per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: H. Lam, S. Patel
BIO ENG 296 MTM Capstone Project 3 Units
Terms offered: Spring 2016, Fall 2015, Spring 2015
Members of the MTM Program Committee will help design several capstone projects in collaboration with clinical, academic, and/or industry partners, aiming to incorporate emerging technologies, industry requirements, and the potential for significant economic or social impact with regard to medicine and health care. All projects will be designed and vetted by the MTM Program Committee and in consultation with the MTM Advisory Board. For each selected project, an Academic Senate member from the Department of Bioengineering or BTS will serve as research adviser.
Objectives & Outcomes
Course Objectives: The objective of the one year professional MTM program is to develop engineering leaders who can synthesize the technical, environmental, economic, and social issues involved in the design and operation of complex engineering devices, systems, and organizations. Students will develop and demonstrate this skill at synthesis through the capstone project.
Student Learning Outcomes: Projects will provide practical instruction and experience in solving real problems in translational medicine, and it is anticipated that some will lead to innovations with commercial potential. This experience, undertaken by each student as a member of a team and marked by extensive interaction with faculty, peers, and industry partners, enables the student to integrate the leadership and technical dimensions of the professional MTM curriculum.
Rules & Requirements
Prerequisites: Graduate status in the MTM program
Repeat rules: Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 9-9 hours of independent study per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Letter grade.
Instructors: Li, Song
BIO ENG 298 Group Studies, Seminars, or Group Research 1 - 8 Units
Terms offered: Fall 2017, Spring 2017, Fall 2016
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.
Rules & Requirements
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 1-8 hours of directed group study per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
BIO ENG 299 Individual Study or Research 1 - 12 Units
Terms offered: Fall 2017, Spring 2017, Fall 2016
Investigations of advanced problems in bioengineering.
Rules & Requirements
Prerequisites: Graduate standing
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 0 hours of independent study per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
BIO ENG N299 Individual Study or Research 1 - 6 Units
Terms offered: Summer 2017 8 Week Session, Summer 2016 8 Week Session, Summer 2015 8 Week Session
Investigations of advanced problems in bioengineering.
Rules & Requirements
Prerequisites: Graduate standing
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Summer:
6 weeks - 2.5-15 hours of independent study per week
8 weeks - 2-11.5 hours of independent study per week
Additional Details
Subject/Course Level: Bioengineering/Graduate
Grading: Offered for satisfactory/unsatisfactory grade only.
BIO ENG 301 Teaching Techniques for Bioengineering 1 Unit
Terms offered: Fall 2017, Fall 2016, Fall 2015
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.
Rules & Requirements
Prerequisites: Graduate standing
Repeat rules: Course may be repeated for credit. Course may be repeated for credit when topic changes.
Hours & Format
Fall and/or spring: 15 weeks - 1 hour of seminar per week
Additional Details
Subject/Course Level: Bioengineering/Professional course for teachers or prospective teachers
Grading: Offered for satisfactory/unsatisfactory grade only.
Instructor: Johnson
Faculty and Instructors
Faculty
John Anderson, Assistant Professor.
Martin S. Banks, Professor. Stereopsis, virtual reality, optometry, multisensory interactions, self-motion perception, vision, depth perception, displays, picture perception, visual ergonomics.
Research Profile
Steven Brenner, Professor. Molecular biology, computational biology, evolutionary biology, bioengineering, structural genomics, computational genomics, cellular activity, cellular functions, personal genomics.
Research Profile
John Canny, Professor. Computer science, activity-based computing, livenotes, mechatronic devices, flexonics.
Research Profile
Jose M. Carmena, Associate Professor. Brain-machine interfaces, neural ensemble computation, neuroprosthetics, sensorimotor learning and control.
Research Profile
Michelle Chang, Associate Professor.
Irina M. Conboy, Associate Professor. Stem cell niche engineering, tissue repair, stem cell aging and rejuvenation.
Research Profile
Yang Dan, Professor. Neuronal circuits, mammalian visual system, electrophysiological, psychophysical and computational techniques, visual cortical circuits, visual neurons.
Research Profile
John Eugene Dueber, Assistant Professor. Synthetic biology, Metabolic Engineering.
Research Profile
Robert J. Full, Professor. Energetics, comparative biomechanics, arthropod, adhesion, comparative physiology, locomotion, neuromechanics, biomimicry, biological inspiration, reptile, gecko, amphibian, robots, artificial muscles.
Research Profile
Jack L. Gallant, Professor. Vision science, form vision, attention, fMRI, computational neuroscience, natural scene perception, brain encoding, brain decoding.
Research Profile
Xiaohua Gong, Professor. Optometry, vision science, eye development and diseases, lens development.
Research Profile
Amy Herr, Associate Professor. Microfluidics, bioanalytical separations, diagnostics, electrokinetic transport, engineering design.
Research Profile
Tony M. Keaveny, Professor. Biomechanics of bone, orthopaedic biomechanics, design of artificial joints, osteoporosis, finite element modeling, clinical biomechanics.
Research Profile
Stanley A. Klein, Professor. Optometry, vision science, spatial vision modeling, psychophysical methods and vision test design, corneal topography and contact lens design, source localization of evoked potentials, fMRI, amblyopia.
Research Profile
Luke Lee, Professor. Biophotonics, biophysics, bionanoscience, molecular imaging, single cell analysis, bio-nano interfaces, integrated microfluidic devices (iMD) for diagnostics and preventive personalized medicine.
Research Profile
Seung-Wuk Lee, Associate Professor. Nanotechnology, bio-inspired nanomaterials, synthetic viruses, regenerative tissue engineering materials, drug delivery vehicles.
Research Profile
Song Li, Professor. Bioengineering, vascular tissue engineering, stem cell engineering, mechano-chemical signal transduction, biomimetic matrix, molecules, bioinformatic applications in tissue engineering, molecular dynamics.
Research Profile
Michel Maharbiz, Associate Professor. Neural interfaces, bioMEMS, microsystems, MEMS, microsystems for the life sciences.
Research Profile
Gerard Marriott, Professor.
Richard Mathies, Professor. Genomics, biophysical, bioanalytical, physical chemistry; laser spectroscopy, resonance Raman, excited-state reaction dynamics photoactive proteins, rhodopsins, microfabricated chemical biochemical analysis devices, forensics, infectious disease detection.
Research Profile
Mohammad Mofrad, Professor. Nuclear pore complex and nucleocytoplasmic transport, mechanobiology of disease, cellular mechanotransduction, integrin-mediated focal adhesions.
Research Profile
Niren Murthy, Professor.
Alexander Pines, Professor. Theory and experiment in magnetic resonance spectroscopy and imaging, quantum coherence and decoherence, novel concepts and methods including molecular and biomolecular sensors and microfluidics, laser hyperpolarization and detection, laser and zero-field NMR, in areas from material science to biomedicine.
Research Profile
Austin John Roorda, Professor. Adaptive optics, eye, vision, ophthalmoscopy, scanning laser ophthalmoscope, ophthalmology.
Research Profile
Kimmen Sjolander, Professor. Computational biology, algorithms, phylogenetic tree reconstruction, protein structure prediction, multiple sequence alignment, evolution, bioinformatics, hidden Markov models, metagenomics, statistical modeling, phylogenomics, emerging and neglected diseases, machine-learning, genome annotation, metagenome annotation, systems biology, functional site prediction, ortholog identification.
Research Profile
Lydia Sohn, Associate Professor. Micro-nano engineering.
Research Profile
Danielle Tullman-Ercek, Assistant Professor. Bioenergy, synthetic biology, protein engineering, bionanotechnology.
Research Profile
Emeritus Faculty
Thomas F. Budinger, Professor Emeritus. Image processing, biomedical electronics, quantitative aging, cardiovascular physiology, bioastronautics, image reconstruction, nuclear magnetic resonance, positron emission, tomography, reconstruction tomography, inverse problem mathematics.
Research Profile
Contact Information
Department of Bioengineering
306 Stanley Hall
MC 1762
Phone: 510-642-5833