Santa Clara University

Graduate School of Engineering

Department of Bioengineering

Professors: Yuling Yan (Chair)
Associate Professor: Zhiwen (Jonathan) Zhang
Assistant Professors: Prashanth Asuri, Emre Araci Ismail, Unyoung (Ashley) Kim, Biao Lu
Adjunct Faculty: Yvan Chanthery, Paul Consigny, Paul Davison, Brian Green, Ying Hao, Gary Li, Sathish Manickam, Maryam Mobed-Miremadi, Menahem Nassi, Gerardo Noriega, Stephanie Norman, Janet Warrington

OVERVIEW

Bioengineering is the fastest-growing area of engineering and holds the promise of improving the lives of all people in very direct and diverse ways. Bioengineering focuses on the application of electrical, chemical, mechanical, and other engineering principles to understand, modify, or control biological systems. As such the curriculum teaches principles and practices at the interface of engineering, medicine and the life sciences. The Department of Bioengineering currently offers a M.S. degree program with a focus on biodevice engineering, biomaterials and tissue engineering, and biomolecular engineering.

A number of faculty offer research projects to bioengineering students that are engaging and involve problem-solving at the interface of engineering, medicine and biology. Dr. Yan’s current research focuses on basic and translational aspects of human voice that include the development of new imaging modalities to study laryngeal dynamics and function, with associated methods in the analysis and modeling of human voice production. She is also participating in a multi-PI project, funded by NIH, on the development of optical switch probes and novel detection and image analyses of this novel class of probe for applications in high contrast imaging within living cells and tissues. Dr. Zhang is currently engaged in research on several NIH-funded projects spanning protein engineering to drug discovery. Dr. Kim investigates the application of integrated microfluidic systems for multiple applications in diagnostics as well as experimental science, and Dr. Asuri’s research interests involve integrating tools and concepts from biomaterials engineering, biotechnology, and cell biology to explore the role of biomaterial properties such porosity, matrix stiffness, etc. on protein structure and function and in regulating cell fate.

DEGREE PROGRAM

The bioengineering graduate program at Santa Clara University is designed to accommodate the needs of students interested in advanced study in the areas of medical devices/bioinstrumentation and molecular and cellular bioengineering. An individual may pursue the degree of Master of Science (M.S.), either as a full-time or part-time student, through a customized balance of coursework, directed research and/or thesis research. Students are also required to supplement their technical work with coursework on other topics that are specified in the graduate engineering core curriculum.

Master of Science in Bioengineering

To be considered for admission to the graduate program in bioengineering, an applicant must meet the following requirements:

  • A bachelor’s degree in bioengineering or related areas from an ABET accredited four-year B.S. degree program, or its equivalent An overall grade point average (GPA) of at least 3.0 (based on a 4.0 maximum scale)
  • Graduate Record Examination (GRE)-general test
  • For students whose native language is not English, Test of English as a Foreign Language (TOEFL) or the International English Language Testing Systems (IELTS) exam scores are required before applications are processed.

Applicants who have taken graduate-level courses at other institutions may qualify to transfer a maximum of nine quarter units of approved credit to their graduate program at Santa Clara University.

Upon acceptance, or conditional acceptance, to the graduate program in bioengineering, a student will be required to select a graduate advisor (full-time faculty member) from within the Department of Bioengineering. The student’s advisor will be responsible for approving the student’s course of study. Any changes to a student’s initial course of study must have the written approval of the student’s advisor.

To qualify for the degree of Master of Science in Bioengineering, students must complete a minimum of 45 quarter units, including required core and elective courses, within the School of Engineering. Required and elective courses for the bioengineering programs are provided below. Students undertaking thesis work are required to engage in research that results, for example, in the development of a new method or approach to solve a bioengineering relevant problem, or a technical tool, a design criteria, or a biomedical application. This work should be documented in a journal publication, conference, or research report, and must also be included in a Master’s thesis. Alternatively, students may elect to take only courses to fulfill the requirement for the M.S. degree.

Course requirements

  • Graduate Core (minimum 6 units including BIOE 210 Bioethics) (See descriptions in Chapter 4, Academic Information)
  • Applied Mathematics (4 units)
    Select from AMTH 200, 201, 202, 210, 211 (or consult with advisor)
  • Bioengineering Core (15 units)
    Students must take 6 units from one of the three primary focus areas, 4 units from other focus areas, 3 units from biostatistics (BIOE 232 L&L) and 2 quarter research seminar units (BIOE 200, 2 x 1 unit)
  • Three primary focus areas are:
    1. Biomolecular Engineering BIOE 280, 282, 286, 300, or 301
    2. Biomaterials and Tissue Engineering BIOE 208, 240, 269, 272, 278
    3. BioDevice Engineering BIOE 207, 208, 209, 245 268, 270, 275, 276
  • Bioengineering Technical Electives (11~20 units)

Select from the approved list of Technical Elective (TE) graduate level courses. Students who pursue the thesis option will obtain nine units from thesis work, and thus 11 TE units are required; for those who pursue the course work only, 20 TE units are required. Directed research may count as a maximum of six TE units. Total: 45 Units

Alternative elective graduate courses may be taken subject to approval from the student’s advisor. Courses used to meet the 45-unit minimum total for the Master of Science in Bioengineering degree cannot include courses that were used to satisfy a previous undergraduate degree program requirement. This includes cross-listed undergraduate courses at Santa Clara University and/or their equivalent courses at other institutions. If some required courses in the SCU graduate bioengineering program have been completed prior to graduate-level matriculation at SCU, additional elective courses will be required to satisfy the minimum unit total requirement as necessary.

Bioengineering Laboratory Facilities:
The Tissue Engineering Laboratory supports teaching and research activities conducted by Faculty and students in the Bioengineering Program in the broad areas of tissue engineering and stem cellular bioengineering. The research conducted in this lab will help identify optimal biochemical and biomaterial cues that enable the engineering of instructive cell culture systems that direct the fate of human stem cells. Instrumentation includes: micro-plate reader, rotational rheometer, microscopes, PCR, gel electrophoresis and cell culture facilities.

TheMolecular Bioengineering Laboratory is dedicated to teaching and research topics on designing, testing and processing biosynthetic molecules including proteins, peptides, antibodies and antibiotics towards biomedical applications. Instrumentation includes: FPCL, Isothermal Titration Calorimeter and UV spectrometer etc.

The Biosignals Laboratoryprovides a full range of measurement and analysis capability including Electrocardiography (ECG), Electroencephalography (EEG) and Electromyography (EMG) measurement system, vocal signal recording and analysis software.

COURSE DESCRIPTIONS

Undergraduate Courses

BIOE 100. Bioengineering Research Seminar
A series of one-hour seminars will be presented by guest professors and researchers on their particular research topics in bioengineering or related fields. Students are required to attend four to five seminars and submit a one-page report summarizing the presentation for each seminar. May be repeated for credits. Also listed as BIOE 200. Prerequisite: Sophomore standing or higher. P/NP grading. (1 unit)

BIOE 107. Medical Device Product Development
The purpose of this course is to provide background information and knowledge to start or enhance a career in medical device product development. Discusses medical device examples, product development processes, regulation, industry information, and intellectual property. Also listed as EMGT 307. Prerequisite: BIOE 10. (2 units)

BIOE 108. Biomedical Devices: Role of Polymers
This course is designed to highlight the role of polymers play in the design and fabrication of various medical devices ranging from simple intravenous drip systems to complex cardiac defibrillator implants and transcatheter heart valves. Topics include polymer basics, biocompatibility, biodegradation and other tangentially related topics such as regulatory body approvals and intellectual property. Also listed as BIOE 208. (2 units)

BIOE 111 Bioengineering Innovation and Design
Introduces bioengineers to healthcare and medical device technology innovation for advanced and emerging markets. Students in the course will work as teams on problem identification and assessment, iterative value proposition design, as well as concept and business model development. Prerequisite: BIOE 10. (2 units)

BIOE 115. Fundamentals of Cell Culture
This course will introduce the basic concepts and fundamentals of mammalian cell culture techniques and its application in tissue engineering. Also listed as BIOE 205. Co-requisite: BIOE 115L. Prerequisite: BIOL 25/BIOE 22. (1 unit)

BIOE 115L. Laboratory for BIOE 115
Also listed as BIOE 205L. Co-requisite: BIOE 115. (1 unit)

BIOE 120. Experimental Methods in Bioengineering
This course will cover the principles of data representation, analysis, and experimental designs in bioreactors, biomaterials, and medical devices. Topics include error analysis, modeling, normality testing, hypothesis testing, and design of experiments. Special emphases will be placed on the interpretation of data from high-throughput assays used in “omics”/tissue engineering, and formulation designs used for optimal drug delivery. Prerequisite: MATH 14. (4 units)

BIOE 140. Biomaterials Engineering and Characterization
This course will cover the fundamental principles of soft biomaterials characterization in terms of mechanical and rheological properties related to biocompatibility. Areas of focus in the lab include study and fabrication of implantable hydrogels for eukaryotic cell immobilization in scaffolds and microscapsules, cytotoxicity measurements in the engineered micro-environment and nutrient diffusion visualized by fluorescence microscopy. Also listed as BIOE 240. Prerequisite: CHEM 13. (2 units)

BIOE 140L. Laboratory for BIOE 140.
Also listed as BIOE 240L. Co-requisite: BIOE 140. (1 unit)

BIOE 153. Biomaterials Science
An introduction into materials used for medical devices. Focus areas include materials science, biology, biochemistry, practical aspects of biomaterials, industry literature, and applications. Prerequisite: CHEM 13. (4 units)

BIOE 154. Introduction to Biomechanics
Engineering mechanics and applications in the analysis of human body movement, function, and injury. Review of issues related to designing devices for use in, or around, the human body including safety, biocompatibility, ethics, and Food and Drug Administration (FDA) regulations. Prerequisites: BIOE 10, PHYS 33. (4 units)

BIOE 155. Biological Transport Phenomena
The transport of mass, momentum, and energy are critical to the function of living systems and the design of medical devices. 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. Also listed as BIOE 215. Prerequisites: BIOE 10, PHYS 33, AMTH 106. (4 units)

BIOE 157. Introduction to Biofuel Engineering
Introduction to biofuel science and production for engineers. Basic cell physiology and biochemical energetics will be reviewed. Fundamentals of bioreactor technology will be introduced as a foundation for biofuel manufacturing. This will include cell growth models, biochemical and photobioreactor systems, and other processes related to the production of biofuels such as ethanol, methane, and biodiesel. Promising technologies such as algae-based systems, genetically engineered enzymes and microbes, and microbial fuel cells will be discussed. An overview of the economics of production, including feedstock, manufacturing, and capital and operating costs, as well as current biofuel prices, will be given. Also listed as BIOE 257 and ENGR 257. (2 units)

BIOE 161. Bioinstrumentation
Transducers and biosensors from traditional to nanotechnology; bioelectronics and measurement system design; interface between biological system and instrumentation; data analysis; clinical safety. Laboratory component will include traditional clinical measurements and design and test of a measurement system with appropriate transducers. Also listed as BIOE 211 and ELEN 161. Prerequisites: BIOE 10, BIOE 21 (or BIOL 21), ELEN 50. (4 units)

BIOE 161L. Laboratory for BIOE 161
Co-requisite: Also listed as BIOE 211L and ELEN 161L BIOE 161. (1 unit)

BIOE 162. BioSignals and Processing
Origin and characteristics of bioelectric, bio-optical, and bioacoustic signals generated from biological systems. Behavior and response of biological systems to stimulation. Acquisition and interpretation of signals. Signal processing methods include FFT spectral analysis and time-frequency analysis. Laboratory component will include modeling of signal generation and analysis of signals such as electrocardiogram (ECG), electromyogram (EMG), and vocal sound pressure waveforms. Also listed as BIOE 212 and ELEN 162. Prerequisites: BIOE 10, AMTH 106, ELEN 50. (4 units)

BIOE 162L. Laboratory for BIOE 162
Also listed as BIOE 212L and ELEN 162L. Co-requisite: BIOE 162. (1 unit)

BIOE 163. Bio-Device Engineering
This course will instruct students with the fundamental principles of bio-device design, fabrication and biocompatibility, and let students experiment with the state-of-the-art bio-devices. Students will gain the hands-on experience with these bio-instruments which are also used in the field. Emphasis is given to the cutting-edge applications in biomedical diagnostics and pharmaceutical drug discovery and development, particularly detection and monitoring interaction, and activity of biomolecules, such as enzymes, receptors, antibody, nucleic acids, and bioanalytes. Also listed as BIOE 213. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31. (4 units)

BIOE 163L. Laboratory for BIOE 163
Also listed as BIOE 213L Co-requisite: BIOE 163. (1 unit)

BIOE 167. Medical Imaging Systems
Overview of medical imaging systems including sensors and electrical interfaces for date acquisition, mathematical models of the relationship of structural and physiological information to senor measurements, resolution and accuracy limits based on the acquisition system parameters, impact of the imaging system on the volume being imaged, data measured, and conversion process from electronic signals to image synthesis. Analysis of the specification and interaction of the functional units of imaging systems and the expected performance. Focus on MRI, CT, ultrasound, PET, and impedance imaging. Also listed as ELEN 167. Prerequisites: BIOE 162/ELEN 162, ELEN 110 or MECH 142. (4 units)

BIOE 168. Biophotonics and Bioimaging
This course focuses on the interactions of light with biological matter and included topics on the absorption of light by biomolecules, cells and tissues, and emission of light from these molecules via fluorescence and phosphorescence. The course will cover the application of biophotonics in cell biology, biotechnology, and biomedical imaging. Also listed as BIOE 268. Prerequisites: BIOE 10 and PHYS 33. (4 units)

BIOE 171. Physiology and Anatomy for Engineers
Examines the structure and function of the human body and the mechanisms for maintaining homeostasis. The course will provide a molecular-level understanding of human anatomy and physiology in select organ systems. The course will include lectures, class discussions, case studies, computer simulations, field trips, lab exercises, and team projects. Prerequisite: BIOE 21 or BIOL 21. (4 units)

BIOE 171L. Laboratory for BIOE 171
Co-requisite: BIOE 171. (1 unit)

BIOE 172. Tissue Engineering I
Introduces the basic principles underlying the design and engineering of functional biological substitutes to restore tissue function. Cell sourcing, manipulation of cell fate, biomaterial properties and cell-material interactions, and specific biochemical and biophysical cues presented by the extracellular matrix will be discussed, as well as the current status and future possibilities in the development of biological substitutes for various tissue types. Prerequisite: BIOE 22 or BIOL 25. (4 units)

BIOE 172L. Laboratory for BIOE 172
Co-requisite: BIOE 172. (1 unit)

BIOE 173. Tissue Engineering II
Overview of the progress achieved in developing tissue engineering therapies for a variety of human diseases and disorders, as well as a summary of current tools and strategies to design tissues and organs and emerging technologies. Lectures will be complemented by a series of student-led discussion sessions and a student team project. Also listed as BIOE 273. (4 units)

BIOE 174. Microfabrication and Microfluidics for Bioengineering Applications
Focuses on those aspects of micro/nanofabrication that are best suited to BioMEMS and microfluidics to better understand and manipulate biological molecules and cells. The course aims to introduce students to the state-of-art applications in biological and biomedical research through lectures and discussion of current literature. A team design project that stresses interdisciplinary communication and problem solving is one of the course requirements. Also listed as BIOE 214. Prerequisite: BIOE 10, BIOE 21 or BIOL 21. (4 units)

BIOE 175. Biomolecular and Cellular Engineering I
This course will focus on solving problems encountered in the design and manufacturing of biopharmaceutical products, including antibiotics, antibodies, protein drugs and molecular biosensors, with particular emphasis on the principle and application of protein engineering and reprogramming cellular metabolic networks. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31, or equivalent knowledge and instructor approval. Also listed as BIOE 225. BIOE 153 is recommended. (4 units)

BIOE 175L. Laboratory for BIOE 175
Also listed as BIOE 225L Co-requisite: BIOE 175. (1 unit)

BIOE 176. Biomolecular and Cellular Engineering II
This course will focus on the principle of designing, manufacturing synthetic materials and their biomedical and pharmaceutical applications. Emphasis of this class will be given to chemically synthetic materials, such as polymers, inorganic and organic compounds. Also listed as BIOE 226. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31, or equivalent knowledge and instructor approval. BIOE 175 and BIOE 171 is recommended. (4 units)

BIOE 177L. Advanced Molecular Bioengineering Laboratory
This course is the lab session of BIOE 176. Lab sections are designed for students to experience the concepts of bioprocess engineering and biochemical engineering. Prerequisite BIOE 176. (1 unit)

BIOE 178. Clinical Biomaterials
The objective of this course is to convey the state-of-the-art of biomaterials currently used in medical devices. The course is taught as a series of semi-independent modules on each class of biomaterial, each with examples of medical applications. Students will explore the research, commercial and regulatory literature. In teams of two to four, students will prepare and orally present a design study for a solution to a medical problem requiring one or more biomaterials, covering alternatives and selection criteria, manufacture and use of the proposed medical device, and economic, regulatory, legal and ethical aspects. Students should be familiar with or prepared to learn medical, anatomical and physiological terminology. Written assignments are an annotated bibliography on the topic of the design study and an individually written section of the team’s report. Material from lectures and student presentations will be covered on a mid-term quiz and a final examination. Also listed as BIOE 278 and MECH 256. Prerequisites: BIOE 153 or
instructor approval.
(2 units)

BIOE 179. Physiology and Disease Biology
The course will provide a molecular-level understanding of human physiology and disease biology, an overview of cardiovascular disease, diagnostic methods, and treatment strategies. Engineering principles to evaluate the performance of cardiovascular devices and the efficacy of treatment strategies will also be discussed. The course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 275. Prerequisites: BIOE 21 and BIOE 22 or BIO 21 and BIO 24 and BIO 25. (2 units)

BIOE 180. Clinical Trials: Design, Analysis and Ethical Issues
This course will cover the principles behind the logistics of design and analysis of clinical trials from the statistical and ethical perspectives. Topics include methods used for quantification of treatment effect(s) and associated bias interpretation, cross-over designs used in randomized clinical trials and clinical equipoise. Also listed as BIOE 380. Prerequisites: BIOE 10, AMTH 108 or BIOE 120 or instructor approval. (4 units)

BIOE 185. Physiology and Disease Biology II**
The course will provide a molecular-level understanding of physiology and disease biology, an overview of gastrointestinal diseases, and an introduction to medical devices used in the diagnosis and treatment as well as challenges in this field. The course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 285. (2 units)

BIOE 186. Current and Emerging Techniques in Molecular Bioengineering
The course is designed to introduce basic and practical biotechniques to students with minimum training and background in biomolecular engineering. The basic principles and concepts of modern biotechniques will be illustrated and highlighted by studying real cases in lectures. Also listed as BIOE 286. Prerequisite: BIOE 22 or BIOL 24. (2 units)

BIOE 188. Co-op Education
This course is designed to prepare students for the working environment, and enable them to relate their experience in the industry to their academic program. They will then engage in practical work experience related to their academic field of study and career objectives. All students must enroll in BIOE 188 before enrolling in BIOE 189. Students can take BIOE 188 during the first quarter of work experience, or before an internship begins. International students who wish to start (or continue) their CPT after they have taken BIOE 188 must be enrolled in BIOE 189. Prerequisites: junior status and cum GPA ≥ 2.75. (2 units)

BIOE 189. Work Experience and Co-op Technical Report
Credit is given for a technical report on a specific activity, such as a design or research activity, after completing a co-op work assignment. Letter grades will be based on the content and quality of the report. May be taken more than once. Prerequisites: junior status, cum GPA ≥ 2.75, and approval of
department co-op advisor.
(2 units)

BIOE 192. Junior Design
Establishes a foundation for the Senior Design sequence. Students will be given broad overview of the possible project offerings and will be directed to meet potential project advisors to learn more about their research and previous senior design projects. As a part of this course, students will also be introduced to the necessary ‘soft skills,; (e.g. literature review, documentation, market research, experimental design, etc.) as they develop feasible senior design concepts. P/NP grading. Prerequisite: Junior standing. (1 unit)

BIOE 194. Design Project I
Specification of an engineering project, selected with the mutual agreement of the student and the project advisor. Complete initial design with sufficient detail to estimate the effectiveness of the project. Initial draft of the project report. Prerequisite: Senior standing. (2 units)

BIOE 195. Design Project II
Continued design and construction of the project, system, or device. Second draft of project report. Prerequisite: BIOE 194. (2 units)

BIOE 196. Design Project III
Continued design and construction of the project, system, or device. Final report. Prerequisite: BIOE 195. (2 units)

BIOE 198. Internship
Directed internship in local bioengineering and biotech companies or research in off-campus programs under the guidance of research scientists or faculty advisors. Required to submit a professional research report. Open to upper-division students. (Variable units)

BIOE 199. Supervised Independent Research
By arrangement. Prerequisite: Advisor approval. (1–4 units)

Graduate Courses

IOE 200. Graduate Research Seminar
Seminar lectures on the progress and current challenges in fields related to bioengineering. P/NP grading. Also listed as BIOE 100. (1 unit)

BIOE 205. Fundamentals of Cell Culture
This course will introduce the basic concepts and fundamentals of mammalian cell culture techniques and its application in tissue engineering. Also listed as BIOE 115. Co-requisite: BIOE 205L. Prerequisite: BIOL 25/BIOE 22. (1 unit)

BIOE 205L. Laboratory for BIOE 205
Also listed as BIOE 115L. Co-requisite: BIOE 205. (1 unit)

BIOE 207. Medical Device Invention - From Ideas to Business Plan
This course will introduce students to various tools and processes that will improve their ability to identify and prioritize clinical needs, select the best medical device concepts that address those needs, and create a plan to implement inventions. Also listed as ENGR 207. (2 units)

BIOE 208. Biomedical Devices: Role of Polymers**
This course is designed to highlight the role of polymers play in the design and fabrication of various medical devices ranging from simple intravenous drip systems to complex cardiac defibrillator implants and transcatheter heart valves. Topics include polymer basics, biocompatibility, biodegradation and other tangentially related topics such as regulatory body approvals and intellectual property. Also listed as BIOE 108. (2 units)

BIOE 209. Development of Medical Devices in Interventional Cardiology
This course will be an in-depth, case-based review of medical devices that are currently used in clinical practice, meeting the heart patient’s medical needs. Directed reading will be assigned and the in-class discussions will focus on bioengineering design considerations including: measurements of physiology vs anatomy, intracoronary blood flow vs pressure, invasive vs non-invasive imaging; as well as, the significant economic challenges facing innovative start-ups developing medical devices within our changing health care delivery system. (2 units)

BIOE 210. Ethical Issues in Bioengineering
This course serves to introduce bioengineering students to ethical issues related to their work. This includes introductions to ethical theories, ethical decision-making, accessibility and social justice concerns, issues in personalized medicine, environmental concerns, and so on. This course will also cover ethical and technical issues related to biomedical devices. (2 units)

BIOE 211. Bioinstrumentation
Transducers and biosensors from traditional to nanotechnology; bioelectronics and measurement system design; interface between biological system and instrumentation; data analysis; clinical safety. Laboratory component will include traditional clinical measurements and design and test of a measurement system with appropriate transducers. Also listed as BIOE 161 and ELEN 161. Prerequisites: BIOE 10, BIOE 21 (or BIOL 21), ELEN 50. (4 units)
BIOE 211L. Laboratory for BIOE 211 Also listed as BIOE 161L and ELEN 161L. Co-requisite: BIOE 211.
(1 unit)

BIOE 212. Signals and Systems for Bioengineers
Origin and characteristics of bioelectric, bio-optical, and bioacoustic signals generated from biological systems. Behavior and response of biological systems to stimulation. Acquisition and interpretation of signals. Signal processing methods include FFT spectral analysis and time-frequency analysis. Laboratory component will include modeling of signal generation and analysis of signals such as electrocardiogram (ECG), electromyogram (EMG), and vocal sound pressure waveforms. Also listed as BIOE 162 and ELEN 162. Prerequisites: BIOE 10, AMTH 106, ELEN 50. (4 units)

BIOE 212L. Laboratory for BIOE 212
Also listed as BIOE 162L and ELEN 162L. Co-requisite: BIOE 212. (1 unit)

BIOE 213. Bio-Device Engineering
This course will instruct students with the fundamental principles of bio-device design, fabrication and biocompatibility, and let students experiment with the state-of-the-art bio-devices. Students will gain the hands-on experience with these bio-instruments which are also used in the field. Emphasis is given to the cutting-edge applications in biomedical diagnostics and pharmaceutical drug discovery and development, particularly detection and monitoring interaction, and activity of biomolecules, such as enzymes, receptors, antibody, nucleic acids, and bioanalytes. Also listed as BIOE 163. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31. (4 units)

BIOE 213L. Laboratory for BIOE 213
Also listed as BIOE 163L. Co-requisite: BIOE 213. (1 unit)

BIOE 214. Microfabrication and Microfluidics for Bioengineering Applications
Focuses on those aspects of micro/nanofabrication that are best suited to BioMEMS and microfluidics to better understand and manipulate biological molecules and cells. The course aims to introduce students to the state-of-art applications in biological and biomedical research through lectures and discussion of current literature. A team design project that stresses interdisciplinary communication and problem solving is one of the course requirements. Also listed as BIOE 174. Prerequisite: BIOE 10, BIOE 21 or BIOL 21. (4 units)

BIOE 215. Biological Transport Phenomena
The transport of mass, momentum, and energy are critical to the function of living systems and the design of medical devices. 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. Also listed as BIOE 155. Prerequisites: BIOE 10, PHYS 33, AMTH 106. (4 units)

BIOE 225. Biomolecular and Cellular Engineering I
This course will focus on solving problems encountered in the design and manufacturing of biopharmaceutical products, including antibiotics, antibodies, protein drugs and molecular biosensors, with particular emphasis on the principle and application of protein engineering and reprogramming cellular metabolic networks. Also listed as BIOE 175. BIOE 153 is recommended. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31, or equivalent knowledge and instructor approval. (4 units)

BIOE 225L. Laboratory for BIOE 225
Also listed as BIOE 175L. Co-requisite: BIOE 225. (1 unit)

BIOE 226. Biomolecular and Cellular Engineering II
This course will focus on the principle of designing, manufacturing synthetic materials and their biomedical and pharmaceutical applications. Emphasis of this class will be given to chemically synthetic materials, such as polymers, inorganic and organic compounds. Also listed as BIOE 176. Prerequisites: BIOL 25 or BIOE 22 and CHEM 31, or equivalent knowledge and instructor approval. BIOE 175 and BIOE 171 is recommended. (4 units)

BIOE 232. Biostatistics**
This course will cover the statistical principles used in Bioengineering encompassing distribution-based analyses and Bayesian methods applied to biomedical device and disease testing; methods for categorical data, comparing groups (analysis of variance) and analyzing associations (linear and logistic regression). Special emphases will be placed on computational approaches used in model optimization, test-method validation, sensitivity analysis (ROC curve) and survival analysis. Also listed as AMTH 232. Prerequisite: AMTH 108 or BIOE 120 or equivalent. (2 units)

BIOE 232L. Laboratory for BIOE 232.**
Also listed as AMTH 232L. Co-requisite: BIOE 232. (1 unit)

BIOE 240. Biomaterials Engineering and Characterization**
This course will cover the fundamental principles of soft biomaterials characterization in terms of mechanical and rheological properties related to biocompatibility. Areas of focus in the lab include study and fabrication of implantable hydrogels for eukaryotic cell immobilization in scaffolds and microscapsules, cytotoxicity measurements in the engineered micro-environment and nutrient diffusion visualized by fluorescence microscopy. Also listed as BIOE 140. Prerequisite: CHEM 13. (2 units).

BIOE 240L. Laboratory for BIOE 240**
Also listed as BIOE 140L. Co-requisite: BIOE 240. (1 unit)

BIOE 241. Advanced Biomaterials Engineering**
This course will cover a review of mechanical characterization methods and processing of bio-inert and bio-resorbable materials. Ares of focus in lab include simulated prototyping into a device using CAD-based software followed by 3D printing; and; micro-mechanical testing conducted on tissue phantoms and scaffolds. (2 units)

BIOE 241L. Laboratory for BIOE 241.**
Co-requisite BIOE 214. (1 unit)

BIOE 245. Introductory Biotribology for Orthopedic Implants
This course will provide an introduction to surface mechanics and tribology as applied to biological systems and medical devices, with specific focus on orthopedic tissues and implants. Students will learn about the mechanisms of friction, lubrication, and wear in tissues and considerations for the design of implants to minimize adverse interactions in vivo while maximizing lifespan. Topics will include dry, lubricated, and mixed mode contact and the physiological conditions resulting in each case. Class discussions will primarily center around assigned readings of published literature guided by lecture topics. Prerequisites: BIOE 240 or BIOE 153, 154, BIOE 21 or BioE 24. (2 units)

BIOE 249. Topics in Bioengineering**
*
An introduction to the central topics of bioengineering including physiological modeling and cellular biomechanics (e.g., modeling of the human voice production and speech biomechanics), biomedical imaging, visualizaion technology and applications, biosignals and analysis methods, bioinstrumentation and bio-nanotechnology. Also listed as ENGR 249. (2 units)

BIOE 250. Introduction to Bioinformatics and Sequence Analysis**
Overview of bioinformatics. Brief introduction to molecular biology including DNA, RNA, and protein. Pairwise sequence alignment. Multiple sequence alignment. Hidden Markov models and protein sequence motifs. Phylogenetic analysis. Fragment assembly. Microarray data analysis. Protein structure analysis. Genome rearrangement. DNA computing. Also listed as ENGR 250. Prerequisites: AMTH 377, MATH 163 or equivalent and programming experience. (4 units)

BIOE 251. Molecular Biology for Engineers**
Comprehensive introduction to molecular biology for the non-biologist. Study of macromolecules that are critical to understanding and manipulating living systems. Proteins. Nucleic acids, DNA, and RNA. Genes and genetic code. Transcriptions, translations, and protein synthesis. Information storage and replication in DNA. Mechanics and regulation of gene expression. Splicing. Chromosomes. The human genome project. Scientific, social, and ethical issues. Also listed as ENGR 251. (2 units)

BIOE 253. Molecular Biology for Engineers II**
The science underlying biotechnology: how DNA, genes, and cells work, and how they can be studied and manipulated in fields as diverse as biomedical research, bioengineering, pharmaceutical and vaccine development, forensics, and agriculture. Laboratory experiments will focus on isolating, studying, and using DNA in a variety of contexts. The course includes a laboratory component. Also listed as ENGR 253. Prerequisite or co-requisite: BIOE 251 or equivalent. (2 units)

BIOE 256. Introduction to NanoBioengineering**
This course is designed to present a broad overview of diverse topics in nanobioengineering, with emphasis on areas that directly impact applications in biotechnology and medicine. Specific examples that highlight interactions between nanomaterials and various biomolecules will be discussed, as well as the current status and future possibilities in the development of functional nanohybrids that can sense, assemble, clean, and heal. Also listed as ENGR 256. (2 units)

BIOE 257. Introduction to Biofuel Engineering**
This course will cover the basic principles used to classify and evaluate biofuels in terms of thermodynamic and economic efficiencies as well environmental impact for resource recovery. Special emphases will be placed on emerging applications namely Microbial Fuel Cell Technology and Photo-bioreactors. Also listed as ENGR 257 and BIOE 157. (2 units)

BIOE 258. Synthetic Biology & Metabolic Engineering**
This course covers current topics and trend in the emerging field of synthetic biology. These topics include applying the retro-synthetic analysis approach in classic organic chemistry, identifying and engineering metabolic pathways and mechanisms for bioproduction of antibiotics, biofuel compounds, novel bio-building blocks and non-natural proteins. Genetic regulation of biosynthetic pathways, e.g. genetic circuit will also be discussed. (2 units)

BIOE 260. Selected Topics in Bio-Transport Phenomena**
This course will cover the principles of mass and oxygen transport and across extra-corporeal devices and bio-membrane design principles, dialyzers, blood-oxygenators, hollow-fiber based bio-artificial organs and PK/PD. Prerequisites: BIOE 155 or equivalent, BIOE 232 preferred. (2 units)

BIOE 261. Omics: Global High-throughput Technologies in Life Sciences Discovery Research**
This course provides a practical application focused survey of global high-throughput technologies in life sciences discovery research. The impact of all facets of study design and execution on obtaining valuable molecular insights from genomics, metagenomics, transcriptomics, metabolomics, and proteomics methods will be explored. Strategies for integration and interpretation of data-rich read-outs will be applied to case studies focused on research and development of companion diagnostics. Prerequisite: BIOE 251. (2 units)

BIOE 263. Applications of Genome Engineering and Informatics in Mammalian System
Advances in genome engineering technologies offer versatile solutions to systematic interrogation and alteration of mammalian genome function. Among them, zinc finger transcription factor nuclease (ZNF), transcription activator-like effector nuclease (TALEN) and CRSPR-associated RNA-guided Cas9 endonuclease (CRISPR/Cas9) have become major drivers for innovative applications from basic biology to biotechnology. This course covers principles and real cases of genome engineering using either ZFN/TALEN or CRSPR/Cas9-based system. Key applications will be discussed in a comparative fashion to better understand the advantages/disadvantages of each system. In addition, informatics’ tools that facilitate the application design, implementation, data analysis will be covered. Prerequisites: BIOE 22 or BIOL 25 or equivalent. (2 units)

BIOE 266. Advanced Nano-Bioengineering**
In Introduction to Nanobioengineering (BIOE 256), students were introduced to how nanomaterials offer the unique possibility of interacting with biological entities (cells, proteins, DNA, etc) at their most fundamental level. This course will provide a detailed overview of nanobioengineering approaches that support research in life sciences and medicine. Topics will include nanotopographical control of in vivo and in vitro cell fate, miniaturization and parallelization of biological assays, and early diagnosis of human disease. Prerequisite: BIOE 256. (2 units)

BIOE 268. Biophotonics and Bioimaging**
This course focuses on the interactions of light with biological matter and includes topics on the absorption of light by biomolecules, cells and tissues and emission of light from these molecules via fluorescence and phosphorescence. The course will cover the application of biophotonics in cell biology, biotechnology and biomedical imaging. Also listed as BIOE 168. (2 units)

BIOE 269. Stem Cell Bioengineering**
A majority of recent research in bioengineering has focused on engineering stem cells for applications in tissue engineering and regenerative medicine. The aim of this graduate level course is to illuminate the breadth of this interdisciplinary research area, with an emphasis on engineering approaches currently being used to understand and manipulate stem cells. The course topics will include basic principles of stem cell biology, methods to engineer the stem cell microenvironment, and the potential of stem cells in modern medicine. (2 units)

BIOE 270. Mechanobiology**
This course will focus on the mechanical regulation of biological systems. Students will gain an understanding of how mechanical forces are converted into biochemical activity. The mechanisms by which cells respond to mechanical stimuli and current techniques to determine these processes will be discussed. Class discussions will primarily center around assigned readings of published literature guided by lecture topics. Prerequisite: BIOE 154. (2 units)

BIOE 272. Fundamentals in Tissue Engineering**
This course introduces the basic principles underlying the design and engineering of functional biological substitutes to restore tissue function. Cell sourcing, manipulation of cell fate, biomaterial properties and cell-material interactions, and specific biochemical and biophysical cues presented by the extracellular matrix will be discussed. (2 units)

BIOE 273. Tissue Engineering II
Overview of the progress achieved in developing tissue engineering therapies for a variety of human diseases and disorders, as well as a summary of current tools and strategies to design tissues and organs and emerging technologies. Lectures will be complemented by a series of student-led discussion sessions and a student team project. Also listed as BIOE 173. (2 units)

BIOE 275. Physiology and Disease Biology I**
The course will provide a molecular-level understanding of human physiology and disease biology, an overview of cardiovascular disease, diagnostic methods, and treatment strategies. Engineering principles to evaluate the performance of cardiovascular devices and the efficacy of treatment strategies will also be discussed. The course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 179.(2 units)

BIOE 276. Microfluidics and Lab-on-a-Chip**
The interface between engineering and miniaturization is among the most intriguing and active areas of inquiry in modern technology. This course aims to illuminate and explore microfluidics and LOC (lab-on-a-chip) as an interdisciplinary research area, with an emphasis on emerging microfluidics disciplines, LOC device design, and micro/nanofabrication. Prerequisite: BIOE 155 or instructor approval. (2 units)

BIOE 278. Clinical Biomaterials**
The objective of this course is to convey the state-of-the-art of biomaterials currently used in medical devices. The course is taught as a series of semi-independent modules on each class of biomaterial, each with examples of medical applications. Students will explore the research, commercial and regulatory literature. In teams of two to four, students will prepare and orally present a design study for a solution to a medical problem requiring one or more biomaterials, covering alternatives and selection criteria, manufacture and use of the proposed medical device, and economic, regulatory, legal and ethical aspects. Students should be familiar with or prepared to learn medical, anatomical and physiological terminology. Written assignments are an annotated bibliography on the topic of the design study and an individually written section of the team’s report. Material from lectures and student presentations will be covered on a mid-term quiz and a final examination. Also listed as BIOE 178 and MECH 256. Prerequisites: BIOE 153 or
instructor approval.
(2 units)

BIOE 280. Special Topics in Bio-therapeutic Engineering **
This class will cover current topics on the engineering of biomimetic drugs, particularly protein drugs, and the development of vaccine, therapeutic antibodoy and biomarkers. Prerequisite: BIOE 270 or equivalent. (2 units)

BIOE 282. BioProcess Engineering**
This course will cover the principles of designing, production and purification of biologicals using living cells in a large scale and industrial scale, including bio-reactor design. Prerequisite: BIOE 21, BIOL 21, BIOE 10, AMTH 106 or equivalent. (2 units)

BIOE 283. BioProcess Engineering II**
This course will cover principles of bio-separation processes. Driving forces behind upstream and downstream separation processes from post-culture cell collection to end stage purification will be analyzed. Special emphasis will be placed on scale-up and economics of implementation of additional purification processes vs cost illustrated by the use of Simulink software. Prerequisite: BIOE 282 or equivalent. (2 units)

BIOE 285. Physiology and Disease Biology II**
The course will provide a molecular-level understanding of physiology and disease biology, an overview of gastrointestinal diseases, and an introduction to medical devices used in the diagnosis and treatment as well as challenges in this field. The course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 185. (2 units)

BIOE 286. Biotechnology**
The course is designed to introduce basic and practical biotechniques to the students with minimum training and background in biomolecular engineering. The basic principles and concepts of modern biotechniques will be illustrated and highlighted by studying the real cases in lectures. Also listed as BIOE 186. Prerequisite: BIOE 22 or BIOL 24. (2 units)

BIOE 297. Directed Research
By arrangement. (1–6 units)

BIOE 298. Internship
Directed internship in partner bioengineering/biotech companies or research in off-campus programs under the guidance of research scientists or faculty advisors. Required to submit a professional research report. P/NP grading. (Variable units)

BIOE 300. Antibody Bioengineering**
This course will cover major areas of antibody engineering including recent progress in the development of antibody-based products and future direction of antibody engineering and therapeutics. The product concept and targets for antibody-based products are outlined and basic antibody structure, and the underlying genetic organization which allows easy antibody gene manipulation, and the isolation of novel antibody binding sites will be described. Anti-body library design and affinity maturation techniques and deep-sequencing of antibody responses, together with biomarkers, imaging and companion diagnostics for antibody drug and diagnostic applications of antibodies, as well as clinical design strategies for antibody drugs, including phase one and phase zero trial design will be covered. Prerequisites: BIOE 176 or equivalent. (2 units)

BIOE 301. Protein Engineering and Therapeutics**
Protein-based therapeutics has played an increasingly important role in medicine. Future protein drugs are likely to be more extensively engineered to improve their efficacy in patients. Such technologies might ultimately be used to treat cancer, neurodegenerative diseases, diabetes, and cardiovascular or immune disorders. This course will provide an overview of protein therapeutics and its enabling technology, protein engineering. Topics will cover the following areas of interest: therapeutic bioengineering, genome and druggable genes, classification of pharmacological proteins, advantages and challenges of protein-based therapeutics, principles of recombinant protein design, approaches of protein production, and potential modifications. Specific applications will include drug delivery, gene therapy, vaccination, tissue engineering, and surface engineering. Students will work on teams where they will take examples of concepts, designs, or models of protein therapeutics from literature and determine their potential in specific engineering applications. Prerequisite: BIOE 176 or equivalent. (2 units)

BIOE 378. Advanced Biomaterials
The objective of this course is to examine the range of new biomaterials potentially applicable to medical and biotechnology devices. The content will focus on chemistry and fabrication of polymeric biomaterials, surface properties, nano-scale analytical tools, effects of the biological environment and interaction with cells and tissues. In teams of 2 to 4, students will prepare and orally present a design study for a solution to a medical problem requiring one or more biomaterials, using tissue engineering and regenerative approaches. Students should be familiar with or prepared to learn medical, anatomical and physiological terminology. Written assignments are an annotated bibliography drawn from research literature on the topic of the design study and an individually-written section of the team’s report. Material from lectures and student presentations will be covered in short quizzes and a final examination. (2 units)

BIOE 380. Clinical Trials: Design, Analysis, and Ethical Issues
This course will cover the principles behind the logistics of design and analysis of clinical trials from the statistical and ethical perspectives. Topics include methods used for quantification of treatment effect(s) and associated bias interpretation, cross-over designs used in randomized clinical trials and clinical equipoise. Also listed as BIOE 180. Prerequisites: BIOE 10, AMTH 108 or BIOE 120 or with consent of the instructor. (4 units)

BIOE 397. Master’s thesis research
By arrangement. (1–9 units)

BIOE 642. Medical Imaging **
Image formation from noninvasive measurements in computerized tomography, magnetic resonance imaging, and other modalities used clinically and in research. Analysis of accuracy and resolution of image formation based on measurement geometry and statistics. Offered in alternate years. Also listed as ELEN 642. Prerequisites: AMTH 211 and either ELEN 234 or AMTH 358. (2 units)

** These BIOE courses are eligible for the technical stem in Engineering Management.

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