Bioengineering

University of California, Berkeley

This is an archived copy of the 2014-15 guide. To access the most recent version of the guide, please visit http://guide.berkeley.edu/.

Overview

Bioengineering applies engineering principles and practices to living things in order to solve some of the most challenging problems that face the world today. In Bioengineering, also known as Biomedical Engineering, work is concentrated on high-impact applications instrumentation, molecular and cellular engineering, and computational biosciences that will bring about major advances in medicine and the life sciences.

Founded in 1998, the Department is supported by exceptional faculty, strong ties to other departments on campus, and close collaborations with other institutions such as UC San Francisco and Lawrence Berkeley National Laboratory. The Department continues to expand with new faculty, staff, facilities, and research programs.

Undergraduate Programs

Bioengineering : BS (major) or Minor
Bionegineering/Materials Science and Engineering : BS (Joint Major)

Graduate Programs

Bioengineering : MEng, PhD (Joint PhD, in cooperation with UCSF)

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Courses

Bioengineering

BIO ENG 10 Introduction to Biomedicine for Engineers 4 Units

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 UC Berkeley departments of Molecular and Cell Biology, Integrative Biology, Bioengineering, Electrical Engineering and Computer Science, Mechanical Engineering, and courses in the UC San Francisco Division of Bioengineering. The specific lecture topics and exercises will include the key aspects of 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.

BIO ENG 24 Aspects of Bioengineering 1 Unit

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. Students will become familiar with bioengineering applications in the various concentration areas and see how engineering principles can be applied to biological and medical problems.

BIO ENG 25 Careers in Biotechnology 1 Unit

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 control engineering; drug inspection process; research and development; compliance and validation; construction process for a GMP facility; project management; and engineered solutions to environmental challenges. This course is of interest to students in all areas of engineering and biology, including industrial engineering and manufacturing, chemical engineering, and bioengineering.

BIO ENG 84 Sophomore Seminar 1 or 2 Units

Sophomore seminars are small interactive courses offered by faculty members in departments all across the campus. Sophomore seminars offer opportunity for close, regular intellectual contact between faculty members and students in the crucial second year. The topics vary from department to department and semester to semester. Enrollment limited to 15 sophomores.

BIO ENG 98 Supervised Independent Group Studies 1 - 4 Units

Organized group study on various topics under the sponsorship of a member of the Bioengineering faculty.

BIO ENG 99 Supervised Independent Study and Research 1 - 4 Units

Supervised independent study for lower division students.

BIO ENG 100 Ethics in Science and Engineering 3 Units

The goal of this semester course is to present the issues of professional conduct in the practice of engineering, research, publication, public and private disclosures, and in managing professional and financial conflicts. The method is through historical didactic presentations, case studies, presentations of methods for problem solving in ethical matters, and classroom debates on contemporary ethical issues. The faculty will be drawn from national experts and faculty from religious studies, journalism, and law from the UC Berkeley campus.

BIO ENG 101 Instrumentation in Biology and Medicine 4 Units

This course teaches the fundamental principles underlying modern sensing and control instrumentation used in biology and medicine. The course takes an integrative analytic and hands-on approach to measurement theory and practice by presenting and analyzing example instruments currently used for biology and medical research, including EEG, ECG, pulsed oximeters, Complete Blood Count (CBC), etc.

BIO ENG 102 Biomechanics: Analysis and Design 4 Units

This course introduces, develops and applies the methods of continuum mechanics to biomechanical phenomena abundant in biology and medicine. It is intended for upper level undergraduate students who have been exposed to vectors, differential equations, and undergraduate course(s) in physics and certain aspects of modern biology.

BIO ENG 104 Biological Transport Phenomena 4 Units

The transport of mass, momentum, and energy are critical to the function of living systems and the design of medical devices. Biological transport phenomena are present at a wide range of length scales: molecular, cellular, organ (whole and by functional unit), and organism. This course develops and applies scaling laws and the methods of continuum mechanics to biological transport phenomena over a range of length and time scales. The course is intended for undergraduate students who have taken a course in differential equations and an introductory course in physics. Students should be familiar with basic biology; an understanding of physiology is useful, but not assumed.

BIO ENG 110 Biomedical Physiology for Engineers 4 Units

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.

BIO ENG 111 Functional Biomaterials Development and Characterization 4 Units

This course is intended for upper level engineering undergraduate students interested in the development of novel functional proteins and peptide motifs and characterization of their physical and biological properties using various instrumentation tools in quantitative manners.

BIO ENG 112 Molecular Cell Biomechanics 4 Units

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.

BIO ENG C112 Molecular Biomechanics and Mechanobiology of the Cell 4 Units

This course applies methods of statistical continuum mechanics to subcellar biomechanical phenomena ranging from nanoscale (molecular) to microscale (whole cell and cell population) biological processes at the interface of mechanics, biology, and chemistry.

BIO ENG 113 Stem Cells and Technologies 4 Units

This course will teach the main concepts and current views on key attributes of embryonic stem cells (ESC), will introduce theory of their function in embryonic development, methods of ESC derivation, propagation, and characterization, and will discuss currently developing stem cell technologies.

BIO ENG 115 Cell Biology for Engineers 4 Units

This course aims to provide a practical understanding of the nature of cell and tissue biology research. Students will be introduced to cell biology techniques as applied to cells and tissues including immunofluorescence, image analysis, protein quantification, protein expression, gene expression, and cell culture. The course culminates with a group project which synthesizes literature review, experimental design, implementation, troubleshooting, and analysis of results.

BIO ENG 116 Cell and Tissue Engineering 4 Units

The goal of tissue engineering is to fabricate substitutes to restore tissue structure and functions. Understanding cell function in response to environmental cues will help us to establish design criteria and develop engineering tools for tissue fabrication. This course will introduce the basic concepts and approaches in the field, and train students to design and engineer biological substitutes. Lectures will be based on the textbook, the reference books and recent literature. Discussion sections will include the discussion of current literature and issues related to course content, homework, exams, and projects. Homework includes quantitative analysis, essay questions, and literature research. There will be a midterm exam, final exam, and a design project (presentation and paper). The final project will be a group project (three to four students) or independent project (required for graduate students). The topic will be chosen by each group and approved by instructor/GSIs.

BIO ENG C117 Structural Aspects of Biomaterials 4 Units

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.

BIO ENG C118 Biological Performance of Materials 4 Units

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.

BIO ENG C119 Orthopedic Biomechanics 4 Units

Statics, dynamics, optimization theory, composite beam theory, beam-on-elastic foundation theory, Hertz contact theory, and materials behavior. 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. MATLAB-based project to integrate the course material.

BIO ENG 121 BioMEMS and Medical Devices 4 Units

Biophysical and chemical principles of biomedical devices, bionanotechnology, bionanophotonics, and biomedical microelectromechanical systems (BioMEMS). Topics include basics of nano- and 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, etc.

BIO ENG 121L BioMems and BioNanotechnology Laboratory 4 Units

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.

BIO ENG 124 Basic Principles of Drug Delivery 3 Units

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.

BIO ENG 125B Robotic Manipulation and Interaction 4 Units

This course is a sequel to Electrical Engineering C106A/Bioengineering C125, which covers kinematics, dynamics and control of a single robot. This course will cover dynamics and control of groups of robotic manipulators coordinating with each other and interacting with the environment. Concepts will include an introduction to grasping and the constrained manipulation, contacts and force control for interaction with the environment. We will also cover active perception guided manipulation, as well as the manipulation of non-rigid objects. Throughout, we will emphasize design and human-robot interactions, and applications to applications in manufacturing, service robotics, tele-surgery, and locomotion.

BIO ENG C125 Introduction to Robotics 4 Units

An introduction to the kinematics, dynamics, and control of robot manipulators, robotic vision, and sensing. The course covers forward and inverse kinematics of serial chain manipulators, the manipulator Jacobian, force relations, dynamics, and control. It presents elementary principles on proximity, tactile, and force sensing, vision sensors, camera calibration, stereo construction, and motion detection. The course concludes with current applications of robotics in active perception, medical robotics, and other areas.

BIO ENG 131 Introduction to Computational Molecular and Cell Biology 4 Units

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; web-based computational biology tools will be used by students and programming projects will be given. Computational biology research connections to biotechnology will be explored.

BIO ENG 132 Genetic Devices 4 Units

This senior-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.

BIO ENG 135 Frontiers in Microbial Systems Biology 4 Units

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 to identify unsolved problems and discusses possible novel approaches while encouraging students to develop ideas to explore new directions in their own research.

BIO ENG C136L Laboratory in the Mechanics of Organisms 3 Units

Introduction to laboratory and field study of the biomechanics of animals and plants using fundamental biomechanical techniques and equipment. Course has a series of rotations involving students in experiments demonstrating how solid and fluid mechanics can be used to discover the way in which diverse organisms move and interact with their physical environment. The laboratories emphasize sampling methodology, experimental design, and statistical interpretation of results. Latter third of course devoted to independent research projects. Written reports and class presentation of project results are required.

BIO ENG 140L Synthetic Biology Laboratory 4 Units

This laboratory course is designed as an introduction to research in synthetic biology, a ground-up approach to genetic engineering with applications in bioenergy, heathcare, materials science, and chemical production. In this course, we will design and execute a real research project. Each student will be responsible for designing and constructing components for the group project and then performing experiments to analyze the system. In addition to laboratory work, we will have lectures on methods and design concepts in synthetic biology including an introduction to Biobricks, gene synthesis, computer modeling, directed evolution, practical molecular biology, and biochemistry.

BIO ENG 143 Computational Methods in Biology 4 Units

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); BioE Content: Biological.

BIO ENG C144 Introduction to Protein Informatics 4 Units

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 some experience with protein sequence analysis methods applied to real data. This class includes no programming, and no programming background is required.

BIO ENG C144L Protein Informatics Laboratory 3 Units

This course is intended to introduce students to a variety of bioinformatics techniques that are used to predict protein function and structure. It is designed to be taken concurrently with C144 (which provides the theoretical foundations for the methods used in the laboratory class), although students can petition to take this laboratory course separately. No programming is performed in this class, and no prior programming experience is required.

BIO ENG C145L Introductory Electronic Transducers Laboratory 3 Units

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.

BIO ENG C145M Introductory Microcomputer Interfacing Laboratory 3 Units

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. 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 lab exercises and design of microcomputer-based systems for data acquisitions, analysis and control.

BIO ENG 147 Principles of Synthetic Biology 4 Units

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.

BIO ENG 148 Bioenergy and Sustainable Chemical Synthesis: Metabolic Engineering and Synthetic Biology Approaches 3 Units

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.

BIO ENG 150 Introduction of Bionanoscience and Bionanotechnology 4 Units

This course is intended for the bioengineering or engineering undergraduate students interested in acquiring a background in recent development of bio-nanomaterials and bio-nanotechnology. The emphasis of the class is to understand the properties of biological basis building blocks, their assembly principles in nature, and their application to build functional materials and devices. The goal is for the bioengineering students to gain sufficient chemical and physical aspects of biological materials through the case study of spider webs, silks, sea shells, diatoms, bones, and teeth, as well as recently developed self-assembled nanostructures inspired by nature. The course covers the structures and properties of amino acids, DNAs, sugars, lipids, and their natural and artifical assembly structures. It also covers nanoscale inorganic materials used to develop nano medicines, bio-imaging, bio-sensors, bioelectronics, and machinery.

BIO ENG 151 Micro/Nanofluidics for Bioengineering and Lab-On-A-Chip 4 Units

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.

BIO ENG 163 Principles of Molecular and Cellular Biophotonics 4 Units

This course provides undergraduate and graduate bioengineering students with an opportunity to increase their knowledge of topics in the emerging field of biophotonics with an emphasis on fluorescence spectroscopy, biosensors and devices for optical imaging and detection of biomolecules. This course will cover the photophysics and photochemistry of organic molecules, the design and characterization of biosensors and their applications within diverse environments.

BIO ENG 163L Molecular and Cellular Biophotonics Laboratory 4 Units

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).

BIO ENG 164 Optics and Microscopy 4 Units

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 fluorescence microscopy to investigate biological samples. The capabilities of optical microscopy will be compared with complementary techniques including electron microscopy, coherence tomography, and atomic force microscopy. Students will also be responsible for researching their final project outside of class and presenting a specific application of modern microscopy to biological research as part of an end-of-semester project.

BIO ENG C165 Medical Imaging Signals and Systems 4 Units

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.

BIO ENG 168L Practical Light Microscopy 3 Units

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.

BIO ENG C181 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

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 placed 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-the-art research.

BIO ENG 190 Special Topics in Bioengineering 1 - 4 Units

This course covers current topics of research interest in bioengineering. The course content may vary from semester to semester.

BIO ENG 192 Senior Design Projects 4 Units

This semester-long course introduces students to bioengineering project-based learning in small teams, with a strong emphasis on need-based solutions for real medical and research problems through prototype solution selection, design, and testing. The course is designed to provide a "capstone" design experience for bioengineering seniors. The course is structured around didactic lectures, and a textbook, from which assigned readings will be drawn, and supplemented by additional handouts, readings, and lecture material. Where appropriate, the syllabus includes guest lectures from clinicians and practicing engineers from academia and industry. The course includes active learning through organized activities, during which teams will participate in exercises meant to reinforce lecture material through direct application to the team design project.

BIO ENG H194 Honors Undergraduate Research 3 or 4 Units

Supervised research. Students who have completed 3 or more upper division courses may pursue original 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. A maximum of 4 units of this course may be used to fulfill the research or technical elective requirement or in the Bioengineering program.

BIO ENG 196 Undergraduate Design Research 4 Units

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.

BIO ENG 198 Directed Group Study for Advanced Undergraduates 1 - 4 Units

Group study of a selected topic or topics in bioengineering, usually relating to new developments.

BIO ENG 199 Supervised Independent Study 1 - 4 Units

Supervised independent study.

BIO ENG 200 The Graduate Group Introductory Seminar 1 Unit

An introduction to research in bioengineering including specific case studies and organization of this rapidly expanding and diverse field.

BIO ENG C208 Biological Performance of Materials 4 Units

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.

BIO ENG C209 Advanced Orthopedic Biomechanics 4 Units

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.

BIO ENG 211 Cell and Tissue Mechanotransduction 3 Units

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.

BIO ENG C212 Heat and Mass Transport in Biomedical Engineering 3 Units

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.

BIO ENG C213 Fluid Mechanics of Biological Systems 3 Units

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.

BIO ENG C214 Advanced Tissue Mechanics 3 Units

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.

BIO ENG C215 Molecular Biomechanics and Mechanobiology of the Cell 4 Units

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.

BIO ENG C216 Macromolecular Science in Biotechnology and Medicine 4 Units

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.

BIO ENG C217 Biomimetic Engineering -- Engineering from Biology 3 Units

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.

BIO ENG C218 Stem Cells and Directed Organogenesis 3 Units

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.

BIO ENG C219 Protein Engineering 3 Units

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.

BIO ENG 220L Cells and Biomaterials Laboratory 4 Units

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.

BIO ENG 221 Advanced BioMEMS and Bionanotechnology 4 Units

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.

BIO ENG 221L BioMEMS and BioNanotechnology Laboratory 4 Units

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.

BIO ENG C222 Advanced Structural Aspects of Biomaterials 4 Units

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.

BIO ENG C223 Polymer Engineering 3 Units

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.

BIO ENG 224 Basic Principles of Drug Delivery 3 Units

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.

BIO ENG 231 Introduction to Computational Molecular and Cellular Biology 4 Units

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.

BIO ENG 232 Genetic Devices 4 Units

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.

BIO ENG 235 Frontiers in Microbial Systems Biology 4 Units

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.

BIO ENG 241 Probabilistic Modeling in Computational Biology 4 Units

This course reviews the statistical and algorithmic foundations of bioinformatics viewed through the lens of paleogenetics, the science of "Jurassic Park", i.e., the reconstruction of ancient genes and genomes by reverse Bayesian inference under various stochastic models of molecular evolution. Such methods, first proposed in the 1960s by Linus Pauling (and others), are now in reach of practical experimentation due to the falling cost of DNA synthesis technology. Applications of these methods are granting insight into the origin of life and of the human species, and may be powerful tools of synthetic biology. Lectures will review the theoretical content; homework and laboratory exercises will involve writing and applying programs for computational reconstruction of ancient protein and DNA sequences and other measurably evolving entities, both biological (e.g., gene families) and otherwise (e.g., natural language).

BIO ENG 243 Computational Methods in Biology 4 Units

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.

BIO ENG C244 Introduction to Protein Informatics 4 Units

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 some experience with protein sequence analysis methods applied to real data. This class includes no programming, and no programming background required.

BIO ENG C244L Protein Informatics Laboratory 3 Units

This course is intended to introduce students to a variety of bioinformatics techniques that are used to predict protein function and structure. It is designed to be taken concurrently with C244 (which provides the theoretical foundations for the methods used in the laboratory class), although students can petition to take this laboratory course separately. No programming is performed in this class, and no prior programming experience is required.

BIO ENG 247 Principles of Synthetic Biology 4 Units

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.

BIO ENG 248 Bioenergy and Sustainable Chemical Synthesis: Metabolic Engineering and Synthetic Biology Approaches 3 Units

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.

BIO ENG C250 Nanomaterials in Medicine 3 Units

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.

BIO ENG 251 Micro/Nanofluidics for Bioengineering and Lab-On-A-Chip 4 Units

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.

BIO ENG C261 Medical Imaging Signals and Systems 4 Units

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.

BIO ENG 263 Principles of Molecular and Cellular Biophotonics 4 Units

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.

BIO ENG 263L Molecular and Cellular Biophotonics Laboratory 4 Units

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).

BIO ENG C265 Principles of Magnetic Resonance Imaging 4 Units

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.

BIO ENG 280 Ethical and Social Issues in Translational Medicine 1 Unit

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.

BIO ENG C280 Introduction to Nano-Science and Engineering 3 Units

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.

BIO ENG C281 The Berkeley Lectures on Energy: Energy from Biomass 3 Units

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.

BIO ENG 290 Advanced Topics in Bioengineering 1 - 4 Units

This course covers current topics of research interest in bioengineering. The course content may vary from semester to semester.

BIO ENG C290D Advanced Technical Communication: Proposals, Patents, and Presentations 3 Units

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.

BIO ENG 296 MTM Capstone Project 3 Units

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.

BIO ENG 298 Group Studies, Seminars, or Group Research 1 - 8 Units

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.

BIO ENG 299 Individual Study or Research 1 - 12 Units

Investigations of advanced problems in bioengineering.

BIO ENG N299 Individual Study or Research 1 - 6 Units

Investigations of advanced problems in bioengineering.

BIO ENG 301 Teaching Techniques for Bioengineering 1 Unit

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.

Faculty

Professors

Adam Paul Arkin, PhD, Professor. Systems and Synthetic Biology, Environmental Microbiology of Bacteria and Viruses, bioenergy, Biomedicine, Bioremediation.
Research Profile

Steven Michael Conolly, PhD, Professor. Instrumentation, medical imaging reconstruction, contrast, MRI.
Research Profile

Daniel Alden Fletcher, PhD, Professor. Bioengineering, optical and force microscopy, microfabrication, biophysics, mechanical properties of cells.
Research Profile

Kevin E. Healy, PhD, Professor. Bioengineering, biomaterials engineering, tissue engineering, bioinspired materials, tissue and organ regeneration, stem cell engineering, microphysiological systems, organs on a chip, drug screening and discovery, multivalent bioconjugate therapeutics.
Research Profile

Luke P Lee, PhD, Professor. Biophotonics, biophysics, bionanoscience, molecular imaging, single cell analysis, bio-nano interfaces, integrated microfluidic devices (iMD) for diagnostics and preventive personalized medicine.
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

Dorian Liepmann, Professor. Bioengineering, mechanical engineering, bioMEMS, microfluid dynamics, experimental biofluid dynamics, hemodynamics, valvular heart disease, cardiac flows, arterial flows.
Research Profile

Gerard Marriott, Professor.

Phillip B Messersmith, Professor.

Mohammad R. K. Mofrad, PhD, Professor. Nuclear pore complex and nucleocytoplasmic transport, mechanobiology of disease, cellular mechanotransduction, integrin-mediated focal adhesions.
Research Profile

Niren Murthy, Professor.

David Rempel, Professor.

Kimmen Sjolander, PhD, 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

Associate Professors

Irina M Conboy, Associate Professor. Bioengineering, stem cell, tissue repair, tissue regeneration.
Research Profile

Amy E. Herr, Associate Professor. Microfluidics, nanofluidics, bioanalytical separations, disease diagnostics.
Research Profile

Ian Holmes, Associate Professor. Computational biology.
Research Profile

Sanjay Kumar, MD PhD, Associate Professor. Biomaterials, molecular and cellular bioengineering, stem cells, cancer biology, translational medicine.
Research Profile

Seung-Wuk Lee, PhD, Associate Professor. Nanotechnology, bio-inspired nanomaterials, synthetic viruses, regenerative tissue engineering materials, drug delivery vehicles.
Research Profile

Assistant Professors

John Christopher Anderson, PhD, Assistant Professor.

John Eugene Dueber, PhD, Assistant Professor.

Adjunct Faculty

Paul D. Adams, PhD, Adjunct Faculty. Biofuels, computational methods, Macromolecular Crystallography, Structural Biology, abra.
Research Profile

Howard L. Fields, Adjunct Faculty.

Lecturers

Terry D Johnson, Ms, Lecturer.

Hayley Lam, PhD, Lecturer.

Contact Information

Department of Bioengineering

306 Stanley Hall

Phone: 510-642-5833

Fax: 510-642-5835

Visit Department Website

Department Chair

Kevin Healy, PhD

Phone: 510-643-3559

khealy@berkeley.edu

Undergraduate Affairs Officer

Cindy Manly-Fields

306C Stanley Hall

Phone: 510-642-5860

cmanly@berkeley.edu

Graduate Student Affairs Officer

Kristin Olson

306 Stanley Hall

Phone: 510-642-9931

kaolson@berkeley.edu

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