## BIOE 103B: Systems Physiology and Design

*ONLINE Offering of
BIOE103. This pilot class,
BIOE103B, is an entirely online offering with the same content, learning goals, and prerequisites as
BIOE103. Students attend class by watching videos and completing assignments remotely. Students may attend recitation and office hours in person, but cannot attend the BIOE103 in-person lecture due to room capacity restraints.* Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics. Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs. Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites:
MATH 41, 42;
CME 102; PHY 41;
BIO 41, 42; strongly recommended PHY 43; or instructor approval.

Terms: Spr
| Units: 4
| UG Reqs: WAY-AQR, WAY-SMA

Instructors:
Deisseroth, K. (PI)
;
Rogers, K. (PI)
;
Taylor, C. (PI)
...
more instructors for BIOE 103B »

Instructors:
Deisseroth, K. (PI)
;
Rogers, K. (PI)
;
Taylor, C. (PI)
;
Filsinger Interrante, M. (TA)
;
Hammoor, B. (TA)
;
Raffiee, M. (TA)

## BIOE 115: Computational Modeling of Microbial Communities (MI 245)

Provides biologists with basic computational tools and knowledge to confront large datasets in a quantitative manner. Students learn basic programming skills focused on Matlab, but also are introduced to Perl and Python. Topics include: image analysis, bioinformatics algorithms, reaction diffusion modeling, Monte Carlo algorithms, and population dynamics. Students apply computational skills to a miniature research project studying the human gut microbiota.

Last offered: Spring 2014

## BIOE 123: Biomedical System Prototyping Lab

The Bioengineering System Prototyping Laboratory is a fast-paced, team-based system engineering experience, in which teams of 2-3 students design and build a fermenter that meets a set of common requirements along with a set of unique team-determined requirements. Students learn-by-doing hands-on skills in electronics and mechanical design and fabrication. Teams also develop process skills and an engineering mindset by aligning specifications with requirements, developing output metrics and measuring performance, and creating project proposals and plans. The course culminates in demonstration of a fully functioning fermenter that meets the teams' self-determined metrics.nnLearning goals:n1. Hands-on skills and experience with design, fabrication, integration, and characterization of practical electronic and mechanical hardware systems relevant to Bioengineeringn2. Practice using modern rapid prototyping and device equipment and techniques, including CAD, 3D printing, laser cutting, microcontrollers, design thinkingn3. Experience working as a team to build an end-to-end functional biomedical system (e.g., a fermenter)nnPrerequisites:
BIOE 41 and Matlab recommended.

Terms: Win
| Units: 4
| UG Reqs: WAY-SMA

Instructors:
Boahen, K. (PI)
;
Riedel-Kruse, I. (PI)
;
Venook, R. (PI)
...
more instructors for BIOE 123 »

Instructors:
Boahen, K. (PI)
;
Riedel-Kruse, I. (PI)
;
Venook, R. (PI)
;
Li, E. (TA)
;
Liu, Y. (TA)
;
Longwell, S. (TA)
;
Sganga, J. (TA)

## BIOE 131: Ethics in Bioengineering (ETHICSOC 131X)

Bioengineering focuses on the development and application of new technologies in the biology and medicine. These technologies often have powerful effects on living systems at the microscopic and macroscopic level. They can provide great benefit to society, but they also can be used in dangerous or damaging ways. These effects may be positive or negative, and so it is critical that bioengineers understand the basic principles of ethics when thinking about how the technologies they develop can and should be applied. On a personal level, every bioengineer should understand the basic principles of ethical behavior in the professional setting. This course will involve substantial writing, and will use case-study methodology to introduce both societal and personal ethical principles, with a focus on practical applications.

Terms: Spr
| Units: 3
| UG Reqs: GER:EC-EthicReas, WAY-ER

Instructors:
Altman, R. (PI)
;
Magnus, D. (PI)

## BIOE 140: Physical Biology of Macromolecules

Principles of statistical physics, thermodynamics, and kinetics with applications to molecular biology. Topics include entropy, temperature, chemical forces, enzyme kinetics, free energy and its uses, self assembly, cooperative transitions in macromolecules, molecular machines, feedback, and accurate replication. Prerequisites:
MATH 41, 42;
CHEM 31A, B (or 31X); strongly recommended:
PHYSICS 41,
CME 100 or
MATH 51, and
CME 106; or instructor approval.

| UG Reqs: WAY-AQR, WAY-SMA

## BIOE 141A: Senior Capstone Design I

Lecture/Lab. First course of two-quarter capstone sequence. Team based project introduces students to the process of designing new biological technologies to address societal needs. Topics include methods for validating societal needs, brainstorming, concept selection, and the engineering design process. First quarter deliverable is a design for the top concept. Second quarter involves implementation and testing. Guest lectures and practical demonstrations are incorporated. Prerequisites:
BIOE 123 and
BIOE 44. This course is open only to seniors in the undergraduate Bioengineering program.

Terms: Aut
| Units: 4

Instructors:
Camarillo, D. (PI)
;
Fan, R. (PI)
;
Rogers, K. (PI)
...
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Instructors:
Camarillo, D. (PI)
;
Fan, R. (PI)
;
Rogers, K. (PI)
;
Venook, R. (PI)
;
Wall, J. (PI)
;
Deshmukh, S. (TA)
;
Robinson, E. (TA)
;
Welker, C. (TA)
;
Xu, N. (TA)

## BIOE 141B: Senior Capstone Design II

Lecture/Lab. Second course of two-quarter capstone sequence. Team based project introduces students to the process of designing new biological technologies to address societal needs. Emphasis is on implementing and testing the design from the first quarter with the at least one round of prototype iteration. Guest lectures and practical demonstrations are incorporated. Prerequisites: BIOE123 and
BIOE44. This course is open only to seniors in the undergraduate Bioengineering program.nIMPORTANT NOTE: class meets in Shriram 112.

Terms: Win
| Units: 4

Instructors:
Camarillo, D. (PI)
;
Rogers, K. (PI)
;
Venook, R. (PI)
...
more instructors for BIOE 141B »

Instructors:
Camarillo, D. (PI)
;
Rogers, K. (PI)
;
Venook, R. (PI)
;
Yang, F. (PI)
;
Dadgar-Kiani, E. (TA)
;
Kintzing, J. (TA)
;
Rao, A. (TA)
;
Steele, A. (TA)

## BIOE 158: Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life (CHEMENG 160, MATSCI 158)

The relationships between molecular structure, morphology, and the unique physical, chemical, and mechanical behavior of polymers and other types of ¿soft matter¿ are discussed. Topics include methods for preparing synthetic polymers and examination of how enthalpy and entropy determine conformation, solubility, mechanical behavior, microphase separation, crystallinity, glass transitions, elasticity, and linear viscoelasticity. Case studies covering polymers in biomedical devices and microelectronics will be covered. Prerequisites: ENG 50 or equivalent.

Terms: Win
| Units: 4

## BIOE 191: Bioengineering Problems and Experimental Investigation

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff)

Terms: Aut, Win, Spr, Sum
| Units: 1-5
| Repeatable for credit

Instructors:
Altman, R. (PI)
;
Andriacchi, T. (PI)
;
Appel, E. (PI)
...
more instructors for BIOE 191 »

Instructors:
Altman, R. (PI)
;
Andriacchi, T. (PI)
;
Appel, E. (PI)
;
Bammer, R. (PI)
;
Barron, A. (PI)
;
Batzoglou, S. (PI)
;
Bintu, L. (PI)
;
Boahen, K. (PI)
;
Bryant, Z. (PI)
;
Butte, A. (PI)
;
Camarillo, D. (PI)
;
Carter, D. (PI)
;
Cochran, J. (PI)
;
Covert, M. (PI)
;
Deisseroth, K. (PI)
;
Delp, S. (PI)
;
Endy, D. (PI)
;
Fahrig, R. (PI)
;
Feinstein, J. (PI)
;
Fisher, D. (PI)
;
Fordyce, P. (PI)
;
Gambhir, S. (PI)
;
Gold, G. (PI)
;
Goodman, S. (PI)
;
Graves, E. (PI)
;
Hargreaves, B. (PI)
;
Heilshorn, S. (PI)
;
Huang, K. (PI)
;
Huang, P. (PI)
;
Kovacs, G. (PI)
;
Krummel, T. (PI)
;
Kuhl, E. (PI)
;
Lee, J. (PI)
;
Levenston, M. (PI)
;
Levin, C. (PI)
;
Lin, M. (PI)
;
Liphardt, J. (PI)
;
Longaker, M. (PI)
;
Magnus, D. (PI)
;
Moore, T. (PI)
;
Nuyujukian, P. (PI)
;
Pauly, K. (PI)
;
Pelc, N. (PI)
;
Plevritis, S. (PI)
;
Prakash, M. (PI)
;
Qi, S. (PI)
;
Quake, S. (PI)
;
Riedel-Kruse, I. (PI)
;
Rogers, K. (PI)
;
Sanger, T. (PI)
;
Sapolsky, R. (PI)
;
Schnitzer, M. (PI)
;
Scott, M. (PI)
;
Shenoy, K. (PI)
;
Smolke, C. (PI)
;
Spielman, D. (PI)
;
Swartz, J. (PI)
;
Taylor, C. (PI)
;
Venook, R. (PI)
;
Wang, B. (PI)
;
Wang, P. (PI)
;
Wu, J. (PI)
;
Yang, F. (PI)
;
Yang, Y. (PI)
;
Yock, P. (PI)
;
Zenios, S. (PI)