Santa Clara University

bioengineering

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 108. 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. (2 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, 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 microcapsules, cytotoxicity measurements in the engineered micro-environment and nutrient diffusion visualized by fluorescence microscopy. Prerequisite: CHEM 13. (2 units)
 
BIOE 140L. Laboratory for BIOE 140
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. 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
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. (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 Systems
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. (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. Prerequisites: BIOE 22 and CHEM 31 (or BIOL 25), BIOE 162 or with instructor's consent. (2 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. Prerequisites: 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 recommended. (4 units)
 
BIOE 177L. Advanced Molecular Bioengineering Lab
Prerequisite: BIOE 176. (1 unit)
 
BIOE 179. 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 275. (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. Prerequisites: BIOE 10, AMTH 108 or BIOE 120 (or with consent of the instructor). (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. Prerequisite: BIOE 22 or BIOL 24. (2 units)
 
BIOE 192. Junior Design
Establishes a foundation for the Senior Design sequence. Students will be given a 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. Prerequisite: Junior standing. P/NP grading. (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. 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 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 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 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 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. Prerequisite: AMTH 108, BIOE 120, or equivalent. (2 units)
 
BIOE 232L. Laboratory for BIOE 232
Co-requisite: BIOE 232. (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. Areas 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 241 (1 unit)
 
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 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. Prerequisite: 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 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 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 157/ENGR 257. (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 transport and heat transfer used in the analysis of living systems applied to the design and mathematical modeling of bio-device/ body interface.Topics include vapor-liquid equilibrium thermodynamics and extraction, bio-membrane transport and design, bio-heat transfer and thermal therapy applications, pharmacokinetics and PK/PD modeling, and, transport in extra-corporeal devices. Prerequisites: BIOE 21 or BIOL 21, and BIOE 155 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 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 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. (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 175 or equivalent. (2 units)
 
BIOE 282. BioProcess Engineering I
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. Prerequisites: BIOE 21 or BIOL 21, BIOE 10, AMATH 106 or equivalent.(2 units)
 
BIOE 283. BioProcess Engineering II
This course will cover the 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. (2 units)
 
BIOE 286. 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 186. (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 1 and phase 0 trial design will be covered. Prerequisites: BIOE 175 and BIOE 176 or equivalent. (2 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.