Chapter 9: Department of Bioengineering

Professor: Yuling Yan
Associate Professors: Prashanth Asuri, Unyoung (Ashley) Kim, Biao (Bill) Lu, Zhiwen (Jonathan) Zhang (Department Chair)
Assistant Professor: Ismail Emre Araci
Lecturers: Maryam Mobed-Miremadi, Eun Ju (Emily) Park
Adjunct Faculty: Zeynep Araci, Eric Chan, Parsa Hosseini, Sathish Manickam, Gerardo Noriega, Verna Rodriguez, Navid Shaghaghi, Erhan Yenilmez

Overview

Bioengineering is the fastest-growing area of engineering and holds the promise of improving the lives of all people in straightforward 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 an 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 research interests center on bioimaging, image and signal analysis, and AI-assisted medical diagnosis. Notable achievements of her lab include the development of new imaging modalities to study laryngeal dynamics and function, with associated analytical methods for the classification of laryngeal pathologies.

Dr. Zhang is currently engaged in research on several NIH-funded projects spanning protein engineering to drug discovery.

Dr. Araci’s research goals are directed toward the development and application of novel microfluidic and optofluidic technologies for biology and medicine. His work is focused on two major areas: i) implantable and miniaturized devices for telemedicine and ii) single molecule protein counting.

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.

Dr. Kim investigates the application of integrated microfluidic systems for multiple uses in diagnostics as well as experimental science.

Dr. Lu’s research focuses on medical translations of protein engineering that includes protein therapeutics and drug delivery as well as molecular sensor and imaging technology.

Dr. Mobed-Miremadi’s research interests are in the areas of mesoscience, specifically the interface of cellular engineering/chemical engineering, bio-device development based on membrane-based therapies and bio-fabrication.

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 it’s 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 (ILETS) exam scores are required before application is 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 46 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 solving a bioengineering related problem, or a technical tool, 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

• Enrichment Experience (minimum eight units including BIOE 210 Bioethics) (See descriptions in Chapter 4, Academic Information)

• Applied Mathematics (4 units) Select from AMTH 200 & 201 (or 202), 210 & 211 (or 212), or AMTH 245 & 246

• Bioengineering Core (15 or 21* units)

Students must take six units from one of the five primary focus areas (additional six units are required for Computational Bioengineering or Translational Bioengineering), four units from other focus areas, three units from biostatistics (BIOE 232 L&L) and two quarter research seminar units (BIOE 200, 2 x 1 unit).

• Five primary focus areas are:

Biomolecular Engineering/Biotechnology BIOE 257, 282, 283, 286, 288, 300, 301
Biomaterials and Tissue Engineering BIOE 208, 240, 245, 269, 273, 378
Microfluidics/Biosensors and Imaging BIOE 203, 260, 267, 268, 276, 277, 308
Computational Bioengineering BIOE 251, 252, 261, 263, 281, 310, 312 Advanced Applied Mathematics* AMTH 240, 364, 370, 371, 377
Translational Bioengineering BIOE 206, 263, 279, 285, 302, 307, 320, 380 Graduate Capstone Project* BIOE 294, 295, 296 *additional six units required for primary focus in Computational Bioengineering or Translational Bioengineering

• Bioengineering Technical Electives (13* or 19 units)

All graduate-level BIOE courses (except BIOE 210) may count as Technical Elective (TE) units. Select graduate courses from ELEN, MECH, or COEN may be credited as Technical Electives upon approval by faculty advisor. A maximum of 4 units total from ENGR and EMGT graduate courses may be credited as Technical Electives. A maximum of 3 units total of Directed Research (BIOE 297) may be credited for Technical Electives if also doing the Master’s Thesis option (BIOE 397, maximum 9 units total), otherwise a maximum of 6 units total of BIOE 297 is allowed. Submission of a Master’s Thesis is required for BIOE 397.

For students in the five-year BS/MS program, a maximum of 20 units may be transferred. Courses used to meet the 46-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.

Ph.D. in Electrical Engineering/Bioengineering

The departments of Electrical and Computer Engineering and Bioengineering are collaborating to offer a Ph.D. in interdisciplinary topics related to Bioengineering. Faculty from both departments will co-advise the Ph.D. students, and the degree will be awarded by the Department of Electrical Engineering.

Bioengineering Laboratory Facilities

The Anatomy & Physiology Laboratory provides a full range of activities to study human anatomy and organ function. Through computational modeling, organ dissection, and design projects, students will develop essential skills in conceiving and implementing engineering solutions to medical problems.

The Bioimaging/Image and Signal Analysis Laboratory carries out fundamental and translational research on voice. Current research in the laboratory includes the development of imaging modalities to study laryngeal dynamics and function, and novel approaches for image/biosignal-based analysis and assessment of voice pathologies. The lab also supports the development of new detection and analytical methods using optical probes for applications in high-contrast fluorescence imaging in cells and tissues.

The Biological Micro/Nanosystems Laboratory supports research and teaching activities in the broad areas of microfluidics/biosensing. Utilizing microfluidic technologies, spectroscopy, and microfabrication techniques, we develop innovative microfluidic platforms for applications in basic biology, diagnostics, and cellular engineering.

The Biomaterials Engineering Laboratory focuses on the use of hydrogels to develop in vitro platforms that explore the role of in vivo-like microenvironmental cues on controlling protein structure and function and regulating cell fate. The lab also supports the design and characterization of biomaterial nanocomposites for applications in tissue engineering.

The Biomolecular Engineering Laboratory conducts “bioengineering towards therapy.” The idea is to engineer novel materials (particularly proteins and peptides) and devices and apply them to study basic biological and medical questions that ultimately lead to drug discovery and disease diagnosis.

The Biophotonics & Bioimaging Laboratory supports research and teaching on portable imaging systems for wearable/implantable biosensors as well as on optical coherence tomography (OCT) probes for stereotactic neurosurgery. The time-lapse fluorescence microscopy setup is used for measuring enzyme activity and single cell protein expression at the single molecular level.

The Biosignals Laboratory provides a full range of measurement and analysis capabilities including electrocardiography (ECG), electroencephalography (EEG), and electromyography (EMG) measurement system, vocal signal recording, and analysis software.

The Micro-devices & Microfluidics Laboratory focuses on the fabrication and testing of microfluidic devices for biomedical research and teaching. The soft-lithography room is equipped with necessary instruments (e.g., mixer, spinner, plasma cleaner) to build micro-devices using a wide variety of materials and processes. Multiple microfluidic test setups (i.e., computer-controlled solenoid valves and microscopes) allow several tests to be run simultaneously.

The Tissue Engineering Laboratory supports research and teaching activities related to mammalian cell and tissue culture. Activities include but are not limited to 2D and 3D mammalian cell culture, investigation of the role of biophysical cues on cancer cell migration and response to drugs, and genetic manipulation of mammalian cells.

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 credit up to three times. P/NP grading. Also listed as BIOE 200.
(1 unit)

BIOE 106. Design Control for Medical Devices

This course will cover the principles behind design control. All of the essential elements required in the regulated medical device environment will be covered from design planning, inputs and outputs to verification, validation, risk management and design transfer. A problem-based learning approach will be utilized so that students will develop proficiency to apply the principles. Knowledge will be acquired through lectures, class activities, industry guest lectures and field trips. Also listed as BIOE 206.
(2 units)

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 BIOE 307 and EMGT 307.
(2 units)

BIOE 108. Biomedical Devices: Role of Polymers

This course is designed to highlight the role that 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. Prerequisites: BIOE 10.
(2 units)

BIOE 109. Translational Development for Emerging Biomedical Devices

This course exposes the student to ongoing case-based interventional cardiology diagnostic and therapeutic biomedical device and clinical translational problems, where real-world bioengineering innovative solutions are being envisioned, and at times successfully being applied by startup teams of bioengineers and medical professionals. Bioengineering device design concepts and clinical translational development considerations are analyzed and case-based team project reports are assigned for final grading. Prerequisites: BIOE 10 and BIOE 21, BIOE 108 or BIOE 153 preferred.
(4 units)

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 analyses, modeling, normality testing, hypothesis testing. Special emphasis will be placed on the interpretation of data from high-throughput assays used in “omics”/tissue engineering. Prerequisite: MATH 14.
(4 units)

BIOE 130. Immune System for Engineers

This course will discuss two significant aspects of human immune systems in bioengineering: 1) Complex hurdles associated with the body’s immune systems for biomaterials, biodevice, and implants; and 2) profound opportunities with engineered therapeutics. Also listed as BIOE 230.
(4 units)

BIOE 153. Biomaterials Science

Basic principles of material properties, biomaterials categories, biomaterials engineering concepts and selected applications and practical aspects are taught in this class. This course is a foundation for an entry level medical device engineer or bioengineering advanced degree. Prerequisite: CHEM 12.
(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 and biocompatibility. 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 157. 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 as environmental impact for resource recovery. Special emphases will be placed on emerging applications, namely, microbial fuel cell technology and photo-bioreactors. Also listed as BIOE 257/ENGR 257. Prerequisites: BIOE 21 (or BIOL 1B), CHEM 13, PHYS 33. (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. Prerequisites: BIOE 10, BIOE 21 (or BIOL 1B), ELEN 50. Co-requisite: BIOE 161L.
(4 units)

BIOE 161L. Bioinstrumentation Laboratory

Laboratory for BIOE 161. Co-requisite: BIOE 161.
(1 unit)

BIOE 162. 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. Prerequisites: BIOE 10, BIOE 45, ELEN 50, AMTH 106. Co-requisite: BIOE 162L.
(4 units)

BIOE 162L. Signals and Systems for Bioengineers Laboratory

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: BIOE 22 (or BIOL 1C) and CHEM 31. Co-requisite: BIOE 163L.
(4 units)

BIOE 163L. Bio-Device Engineering Laboratory

Laboratory for BIOE 163. Co-requisite: BIOE 163.
(1 unit)

BIOE 167. Introduction to Medical Imaging

This course will cover basics of technical aspects and clinical applications of medical imaging. Practicing radiologists will introduce the students to the history of radiology and medical imaging, as well as specific modalities such as X-ray, CT, MR, ultrasound, nuclear medicine, and interventional radiology. A brief discussion of applications of information technology to radiology is also included. Also listed as BIOE 267.
(2 units)

BIOE 168. 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 the 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 22 (or BIOL 1C) and CHEM 31, PHYS 33. Co-requisite: BIOE 168L.
(2 units)

BIOE 168L. Biophotonics and Bioimaging Laboratory

The lab will provide hands-on experience for essential imaging and microscopy techniques as well as advanced techniques such as fiber-optics and optical coherence tomography. Some of the experiments that will be conducted are: measuring the focal length of lenses and imaging using a single lens and a lens system, determining the magnification of optical systems (e.g., of a microscope), interference in Young’s double slit and Michelson configuration, diffraction, polarization, and polarization rotation. Also listed as BIOE 268L. Co-requisite: BIOE 168.
(1 unit)

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 1B). Co-requisite: BIOE 171L.
(4 units)

BIOE 171L. Physiology and Anatomy for Engineers Laboratory

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

BIOE 172. Introduction to Tissue Engineering

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 1C).
(4 units)

BIOE 173. Advanced Topics in Tissue Engineering

Overview of the progress achieved in developing tools, technologies, and strategies for tissue engineering-based therapies for a variety of human diseases and disorders. Lectures will be complemented by a series of student-led discussion sessions and student team projects. Also listed as BIOE 273. Prerequisite: BIOE 172 or instructor approval.
(2 units)

BIOE 174. Microfabrication and Microfluidics for Bioengineering Applications

Microfluidics uses principles from a broad range of disciplines including fluid mechanics, material science and optics for miniaturization, and automation of biochemical applications. This course will introduce the basic physical and engineering concepts which have practical importance in microfluidics and will allow better understanding of molecule and cell manipulation in the micro-domain. The course aims to introduce students to the state-of-art applications of various microfluidic techniques (e.g. mLSI, droplet and paper-based), in biological and biomedical research through lectures and discussion of current literature. Prerequisites: BIOE 10, BIOE 21 (or BIOL 1B). Co-requisite: BIOE 174L.
(4 units)

174L. Microfabrication and Microfluidics for Bioengineering Applications Laboratory

Multilayer soft-lithography will be taught and integrated microfluidic chips will be built. Basic pressure driven microfluidic chip tests will be performed. A team design project that stresses interdisciplinary communication and problem-solving is required in this course. Co-requisite: BIOE 174.
(1 unit)

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: BIOE 22 (or BIOL 1C) and CHEM 31, or equivalent knowledge and by instructor’s permission. BIOE 153 is recommended. Co-requisite: BIOE 175L.
(4 units)

BIOE 175L. Biomolecular and Cellular Engineering I Laboratory

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, and inorganic and organic compounds. Also listed as BIOE 226. Prerequisites: BIOE 22 (or BIOL 1C) and CHEM 31, or equivalent knowledge and by instructor’s permission. BIOE 171 and 175 are recommended.
(4 units)

BIOE 177A. Machine Learning and Applications in Biomedical Engineering

This course covers fundamental methods that form the core of modern machine learning (ML)/deep learning (DL). Supervised and unsupervised learning techniques, and neural networks will be introduced. Selected biomedical applications will be presented. A second course of this series (BIOE 177B) will introduce programming in Python and include building ML projects with TensorFlow. Prerequisite: MATH 14.
(2 units)

BIOE 177B. Machine Learning and Algorithm Implementation

This course will introduce programming in Python and focus on building machine learning projects with TensorFlow, Keras, and NumPy. Prerequisite: BIOE 177A.
(2 units)

BIOE 179. Introduction to Neural Engineering

This course provides a foundation in the neural principles underlying existing and upcoming neurotechnologies. The goal is to understand the design criteria necessary for engineering interventions in neural structure and function with application to neurological diseases, disorders, and injuries. Topics include brain imaging and stimulation, neural implants, nanotechnologies, stem cell and tissue engineering. This course includes lectures, literature critiques, and design projects. Also listed as BIOE 275. Prerequisites: BIOE 21 (or BIOL 1B). BIOE 171 recommended.
(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 statistical and ethical perspectives. Topics include methods used for quantification of treatment effect(s) and associated bias interpretation, crossover designs used in randomized clinical trials, and clinical equipoise. Also listed as BIOE 380. Prerequisites: BIOE 10, BIOE 120 (or AMTH 108), or with consent of the instructor.
(4 units)

BIOE 185. Physiology and Disease Biology

This 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 diagnosis and treatment, as well as challenges in this field. This course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 285. Prerequisite: BIOE 21 (or BIOL 1B). BIOE 171 recommended.
(2 units)

BIOE 186. Introduction to Biotechnology

This 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 1C.
(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 departmental co-op advisor.
(2 units)

BIOE 190. Biotechnology III - Drug Development Process

This course is designed to discuss an overview of the modern pharmaceutical development process, from drug discovery and development, manufacturing, and the regulatory approval process. Specific topics will include current concepts of drug discovery, advanced drug screening methods, preclinical studies and requirements, and the four major phases of clinical development. There will be an emphasis on product development and manufacturing processes for biologics, such as monoclonal antibody-based drugs. Also listed as BIOE 290.
(2 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. Prerequisite: Advisor approval.
(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. Also listed as BIOE 100.
(1 unit)

BIOE 203. Bio-Electromagnetics

Fundamentals of electromagnetics applied to bioengineering. Dielectric characteristics of biological materials. Tissue characterization. Wave propagation in layered medium. RF/Microwave interaction mechanisms in biological materials. Electromagnetic field absorption and SAR. Safety and standards. Microwave hyperthermia. Design of on-body and implant antennas. Also listed as ELEN 203. Prerequisite: ELEN 201 or BIOE 168/268.
(2 units)

BIOE 206. Design Control for Medical Devices

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.
(2 units)

BIOE 208. Biomedical Devices: Role of Polymers

This course is designed to highlight the role 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 which includes introductions to ethical theories, ethical decision-making, accessibility, and social justice concerns, questions in personalized medicine, environmental concerns, and so on. This course will also cover ethical and technical issues related to biomedical devices.
(2 units)

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: BIOE 22 (or BIOL 1C) and CHEM 31, or equivalent knowledge and instructor approval. BIOE 175 and 171 is recommended.
(4 units)

BIOE 230. Immune System for Engineers

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 including 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. Biostatistics Laboratory

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. Prerequisite: CHEM 13.
(2 units)

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 a 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 BIOL 1B).
(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, visualization technology and applications, biosignals and analysis methods, bioinstrumentation and bio-nanotechnology. Also listed as ENGR 249.
(2 units)

BIOE 251. Introduction to Bioinformatics

This course provides an introduction to tools and databases essential for bioengineering including DNA, RNA, and protein. Topics include but are not limited to pairwise sequence alignment, multiple sequence alignment, hidden Markov models and protein sequence motifs, phylogenetic analysis, and fragment assembly. Protein structure and domain analysis, as well as genome rearrangement and DNA computing, are also covered. Students will become proficient in searching multiple databases (Genome, GenBank, Protein, and Conserved Domain), retrieving and analyzing sequences, and working with metadata. Students will design a new gene/protein or write an original program to complete an independent search project. Prerequisite: BIOE 22 or BIOL 1C. Programming experience and BIOL 175 recommended.
(2 units)

BIOE 252. Computational Neuroscience I

This course provides a foundation in cellular and molecular neuroscience and applied computational techniques for the purpose of modeling neuronal and whole brain structural and functional network organization. The central ideas, methods, and practice of modern computational neuroscience will be discussed in the context of relevant applications in biomedical interventions.
(2 units)

BIOE 252L. Computational Neuroscience Lab

Laboratory for BIOE 252. Co-requisite: BIOE 252.
(1 unit)

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. Prerequisites: BIOE 21 (or BIOL 1B), CHEM 13, PHYS 33.
(2 units)

BIOE 258. Synthetic Biology & Metabolic Engineering

This course covers current topics and trends 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 circuits will also be discussed.
(2 units)

BIOE 259. Engineering In Drug Delivery

Engineering is a major contributor to the advancement of drug delivery systems, which improves treatment and enhances patients’ quality of life. In this course, we will explore engineering principles, applications, and techniques in drug delivery systems. The purpose of this course is to identify the roles of engineers in the pharmaceutical industry and how to propose a solution to an emerging topic in this subject.
(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. Prerequisite: BIOE 155 or equivalent. BIOE 232 recommended.
(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 21.
(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 systems. Key applications will be discussed comparatively to understand the advantages/disadvantages of each system better. In addition, informatics tools that facilitate the application design, implementation, data analysis will be covered. Prerequisites BIOE 22 or BIOL 1C or equivalent.
(2 units)

BIOE 266. Advanced Nano-Bioengineering

In Introduction to Nano-bioengineering (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 267. Introduction to Medical Imaging

BIOE 268. Biophotonics and Bioimaging

This course starts with an introduction of optics and basic optical components (e.g. lenses, mirrors, diffraction grating, etc.), then focuses on light propagation and propagation modeling to examine interactions of light with biological matter (e.g. absorption, scattering). Other topics that will be covered in this course are: laser concepts, optical coherence tomography, microscopy, confocal microscopy, polarization in tissue, absorption, diffuse reflection, light scattering, Raman spectroscopy, and fluorescence lifetime imaging. Graduate students will prepare a presentation/report on one of the state-of-the-art biophotonics technologies. Also listed as BIOE 168. Prerequisite: PHYS 33.
(4 units)

BIOE 268L. Biophotonics and Bioimaging Laboratory

The lab will provide hands-on experience for basic imaging and microscopy techniques as well as advanced techniques such as fiber-optics and optical coherence tomography. Some of the experiments that will be conducted are: measuring the focal length of lenses and imaging using a single lens and a lens system, determining the magnification of optical systems (e.g. of a microscope), interference in Young’s double slit and in Michelson configuration, diffraction, polarization and polarization rotation. Also listed as BIOE 168L.
(1 unit)

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 graduate level course aims 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 273. Advanced Topics in Tissue Engineering

Overview of the progress achieved in developing tools, technologies, and strategies for tissue engineering-based therapies for a variety of human diseases and disorders. Lectures will be complemented by a series of student-led discussion sessions and student team projects. Also listed as BIOE 173. Prerequisite: BIOE 172 or instructor approval.
(2 units)

BIOE 275. Introduction to Neural Engineering

This course provides a foundation in the neural principles underlying existing and upcoming neurotechnologies. The goal is to understand the design criteria necessary for engineering interventions in neural structure and function with application to neurological diseases, disorders, and injuries. Topics include brain imaging and stimulation, neural implants, nanotechnologies, stem cell and tissue engineering. This course includes lectures, literature critiques, and design projects. Also listed as BIOE 179. Prerequisites: BIOE 21 (or BIOL 21). BIOE 171 recommended.
(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 277. Biosensors

This course focuses on underlying engineering principles used to detect DNA, small molecules, proteins, and cells in the context of applications in diagnostics, fundamental research, and environmental monitoring. Sensor approaches include electrochemistry, fluorescence, optics, and impedance with case studies and analysis of commercial biosensors.
(2 units)

BIOE 279. Stem Cell & Regenerative Medicine

Few events in science have captured the same level of sustained interest and imagination of the non-scientific community as Stem Cells and Regenerative Medicine. The fundamental concept of Regenerative Medicine is appealing to scientists, physicians, and laypeople alike: to heal tissue or organ defects that the current medical practice deems difficult or impossible to cure. Regenerative medicine is a new branch of medicine that attempts to change the course of chronic disease; in many instances regenerating failing organ systems lost due to age, disease, damage, or congenital defects. The area is rapidly becoming one of the most promising treatment options for patients suffering from tissue failure. This course covers principles and real cases of stem cell and regenerative medicine. Its major applications will be discussed comparatively to understand the advantages/disadvantages of each system better. Overall, this course provides a more in-depth exploration of the next generation biotechnology - a wide variety of cells, biomaterials, interfaces and applications for tissue engineering. Prerequisite: BIOE 269.
(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 antibody and biomarkers. Prerequisite: BIOE 270 or equivalent.
(2 units)

BIOE 281. Deep Learning in Medical Image Analysis and Disease Classification

This course covers the fundamentals of deep learning and methods for medical image analysis with focus on Convolutional Neural Network (CNN) and its applications in image-based disease classifications. The analysis of high-dimensional datasets with still images and volumetric data will be discussed.
(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 (or BIOL 1B), 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

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. Prerequisite: BIOE 21 (or BIOL 1B). BIOE 171 recommended.
(2 units)

BIOE 286. Biotechnology

The course is designed to introduce fundamental 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 real cases in lectures. Also listed as BIOE 186. Prerequisite: BIOE 22 or BIOL 1C.
(2 units)

BIOE 287. Pharmaceutical Drug Development and Chemical Analysis

This course will introduce the fundamental principles of drug discovery and development, also discussing essential drug targets in drug discovery. While addressing analytical-chemical characteristics of selected drug substances, basic concepts for the common analytical methods that are used in the quantitative and qualitative chemical analysis of pharmaceutical drugs will be addressed. International Pharmacopoeias, Regulations and Guidelines will also be reviewed.
(2 units)

BIOE 288. Biotechnology II

The course is designed to discuss practical applications of recombinant DNA technologies, data science, and other modern technologies in the biotechnology industry beyond pharmaceutical development. Specific topics include microbial, industrial, agricultural, environmental biotechnologies, and forensic science. The technical principles and concepts will be highlighted by reviewing real-world cases in lectures. The course will also discuss critical issues such as ethics, regulations, market, and business. Also listed as BIOE 187.
(2 units)

BIOE 290. Biotechnology III - Drug Development Process

BIOE 294. Graduate Capstone Project I

Specification of a translational bioengineering project, selected with the mutual agreement of the student and the project advisor, completion of initial design and feasibility analysis, and submission of a preliminary study report.
(2 units)

BIOE 295. Graduate Capstone Project II

Continued design and development of the project (system or prototype), and submission of a draft project report. Prerequisite: BIOE 294.
(2 units)

BIOE 296. Graduate Capstone Project III

Continued design and development of the project (system or prototype), and submission of the final project report. Prerequisite: BIOE 295.
(2 units)

BIOE 297. Directed Research

By arrangement.
(1–6 units)

BIOE 300. Antibody Bioengineering

This course will cover significant 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. Antibody 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. Prerequisite: 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 302. Gene and Cell Therapy

This course covers principles and applications of gene and cell therapy. Key concepts and technologies such as gene and gene expression, gene variation and genetic defect, therapeutic vector design and construction, as well as ex vivo and in vivo gene delivery will be discussed. The course will culminate in a design project focused on implementing gene or cell-based solutions for a specific disease. After taking this course, participants will: 1) Know the concepts and principles of gene therapy; 2) Understand multiple aspects of gene therapy, including disease gene identification, therapeutic gene design and expression vector construction, as well as gene delivery strategy and efficacy evaluation; 3) Gain skills to use analytical software to aid design; 4) Gain skills to use sequence manipulation software in expression vector design; 5) Gain skills to use genome database and other related databases; and 6) Present and critically analyze original research concerning gene and cell therapy.
(2 units)

BIOE 307. Medical Device Product Development

The course purpose is to discuss and practice product development using medical devices as the model. The course includes identification of product need, invention, development and implementation or commercialization. Also listed as BIOE 107 and EMGT 307.
(2 units)

BIOE 308. Wearable Sensors and Actuators for Biomedical Applications

Wearable sensor and robotics technologies have the potential to extend the range of the healthcare system from hospitals to the community, improving diagnostics and monitoring, and maximizing the independence and participation of individuals. In this course, we will cover operation principles, challenges, and promises of wearables for physiological and biochemical sensing, as well as for motion sensing, in depth.
(2 units)

BIOE 310. Machine Learning in Biomedical Engineering

This course presents an overview of Machine Learning, the study of computing systems that improve their performance with learning abilities. The basic ideas and intuition behind modern methods, concepts, techniques, and algorithms are presented. The course has a special emphasis on deep learning as the most representative machine learning method. The applications of machine learning in biomedical engineering are presented and discussed during the course.
(2 units)

BIOE 312. Deep Learning

This course is an introduction to deep learning, a cutting-edge artificial intelligence concerned with the structure, development, and application of modern neural networks. A range of topics from basic neural networks, convolutional architectures, unsupervised learning, recurrent network structures, non-convex optimization, and the mathematical, statistical and computational challenges of building stable representations and analysis for high-dimensional data, such as images and text are discussed. Programming and building projects in TensorFlow, Keras, and NumPy will be discussed.
(4 units)

BIOE 320. Immunotherapy

The goal of this course is to provide conceptual, preclinical and clinical background necessary to understand the strengths and limits of the main types of cancer immunotherapy and to assess efficacy of the treatment using immunoassays. Emphasis will be given to antibody-drug conjugates, checkpoint blockade, CAR-T cell therapy, cancer vaccines, cytokines, and interferon, through lectures and journal club presentations.
(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 357. Root Cause Analysis (RCA) Effective Problem Solving

Solving problems is one of the main functions of engineering and one of the main concerns of engineering managers. This course will focus on a step by step problem solving approach, used by the best engineering practitioners in the world, designed to improve the efficiency and effectiveness of the problem-solving process. Topics will include proper methods of problem description, identification, correction, and containment. Also listed as EMGT 357.
(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, BIOE 120 or AMTH 108, or instructor approval. (4 units)

BIOE 397. Master’s Thesis Research

By arrangement.
(1–9 units)