Santa Clara University

Master of Science in Bioengineering

Associate Professors: Yuling Yan (Chair), Zhiwen (Jonathan) Zhang
Assistant Professors: Prashanth Asuri, Unyoung (Ashley) Kim
Adjunct Faculty: Paul Consigny, Paul Davison, Rajeev Kelkar, Gerardo Noriega, Vidyodhaya Sundaram, Dan Zaraga

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 MS degree program with a focus on medical devices and biomolecular engineering.

A number of faculty can 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. Asuri’s research interests focus on tissue engineering and regenerative medicine and involves integrating tools and concepts from material science, cellular bioengineering, and stem cell biology to engineer instructive cellular microenvironments that determine stem cell fate. Dr. Kim investigates the application of integrated microfluidic systems for multiple applications in diagnostics as well as experimental science.

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 BS degree program, or its equivalent
• An overall grade point average (GPA) of at least 3.0 (based on a 4.0 maximum scale) for students with a B.S. in Bioengineering; an overall grade point average (GPA) of at least 3.2 (based on a 4.0 maximum) for all other engineering majors
• 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.
• Three letters of recommendation

Applicants who have taken graduate-level courses at other institutions may qualify to transfer a maximum of 9 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 MS degree.

Course requirements are as follows:

Alternative elective 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:

	Course	Topic	Units
Major Requirements	AMTH courses	Suggested topics: Advanced Calculus, Probability, Statistics and Numerical Methods (in consultation with advisors on the course choices)	6
Technical electives	BIOE 270 + BIOE 270L BIOE 272 BIOE 275	Molecular and Cellular Bioengineering & Lab Fundamentals in Tissue Engineering Physiology and Disease Biology	5 2 2
SCU Graduate core	Three to seven (or more) electives from graduate level courses in protein and tissue engineering, device invention, imaging, microfluidics, or synthetic biology; A maximum 9 units from undergraduate upper-division courses; 1-6 units from Directed research 9 units from thesis		24
	Three courses from Emerging Topics in Engineering, Engineering and Business/Entrepreneurship, and Bioethics (BIOE 210)		6
		Total: 45 Units

The Tissue Engineering Laboratory supports teaching and research activities conducted by Faulty and students in the Bioengineering Program in the broad areas of tissue engineering and stem cell 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.

The Molecular 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 Laboratory provides 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. 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 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. Prerequisites: BIOE 10, PHYS 33, AMTH 106. (4 units)

BIOE 156. Introduction to Biomaterials
Introduction to each class of biomaterial. Exploration of research, commercial, and regulatory literature. Written and oral reports by students on a selected application requiring one or more biomaterials. Also listed as MECH 256. Offered every other year. (2 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 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 ELEN 161. Prerequisites: BIOE 10, BIOE 21 (or BIOL 21), ELEN 50. (4 units)

BIOE 161L. Laboratory for BIOE 161
Co-requisite: 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 ELEN 162. Prerequisites: BIOE 10, AMTH 106, ELEN 50. (4 units)

BIOE 162L. Laboratory for BIOE 162
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. Prerequisites: BIOL 25 or BIOE 22 & CHEM 31 (4 units)

BIOE 163L. Laboratory for BIOE 163
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 or 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. Prerequisite: 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
This course will provide a detailed overview of the progress achieved in developing tissue engineering therapies for a wide variety of human diseases and disorders. It will organized into two sections; the first section will provide a basic overview of in vivo tissue growth and development, tools and materials needed to design tissues and organs, stem cell biology and other emerging technologies. This basic section will be complemented by a series of recent examples in applying tissue engineering to various organ systems. Prerequisite: BIOE 172. (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 274/ENGR 254. 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 & CHEM 31, or equivalent knowledge and by instructor’s permission. BIOE 153 is recommended. (4-units)

BIOE 175L. Laboratory for BIOE 175
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. Prerequisites: BIOL 25 or BIOE 22 & CHEM 31, or equivalent knowledge and by instructor’s permission. BIOE 175 and BIOE 171 is recommended. (4 units)

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. Faculty advisor required. (1–4 units)

Graduate Courses

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

BIOE 206. Bioengineering Applications in Resource Poor Countries
This course will introduce students to bioengineering opportunities and the challenges in emerging markets in the world. We will focus specially on global health and medical devices which save lives. Topics will include: creative problem solving techniques, social constraints, engineering design process, development and commercialization of medical technologies in the global setting, focusing primarily on Africa, India and other emerging regions. Students are required to write and deliver a final paper. (2 units)

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 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 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 or 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 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 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. Molecular & Cellular Bioengineering**
This course covers molecular and cellular bases of life from an engineering perspective. Analysis and engineering of biomolecular structure and dynamics, enzyme function, molecular interactions, metabolic pathways, signal transduction, and cellular mechanics will be discussed. (4 units)

BIOE 270L. Laboratory for BIOE 270**
Co-requisite: BIOE 270. (1 unit)

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 274. 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 BIOE174/ENGR 254. (4 units)

BIOE 275. 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. (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 270 or equivalent. (2 units)

BIOE 297. Directed Research**
By arrangement. (1–6 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.