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BIOE 44: Fundamentals for Engineering Biology Lab

Introduction to next-generation techniques in genetic, molecular, biochemical, and cellular engineering. Lab modules build upon current research including: gene and genome engineering via decoupled design and construction of genetic material; component engineering focusing on molecular design and quantitative analysis of experiments; device and system engineering using abstracted genetically encoded objects; and product development based on useful applications of biological technologies. Concurrent or previous enrollment in BIO 82 or BIO 83.
Terms: Aut, Spr | Units: 4 | UG Reqs: WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 102: 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 19, 20, 21; CHEM 31A, B (or 31X); strongly recommended: PHYSICS 41, CME 100 or MATH 51, and CME 106; or instructor approval.
Terms: not given this year, last offered Winter 2019 | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 103: Systems Physiology and Design

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: CME 102; PHYSICS 41; BIO 82, BIO 84.
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 103B: Systems Physiology and Design

*ONLINE Offering of BIOE 103. This pilot class, BIOE103B, is an entirely online offering with the same content, learning goals, and prerequisites as BIOE 103. 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: CME 102; PHYSICS 41; BIO 82, BIO 84. strongly recommended PHYSICS 43. Enrollment with Instructor approval
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

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. n nLearning goals: 1) Design, fabricate, integrate, and characterize practical electronic and mechanical hardware systems that meet clear requirements in the context of Bioengineering (i.e., build something that works). 2) Use prototyping tools, techniques, and instruments, including: CAD, 3D printing, laser cutting, microcontrollers, and oscilloscopes. 3) Create quantitative system specifications and test measurement plans to demonstrate that a design meets user requirements. 4) Communicate design elements, choices, specifications, and performance through design reviews and written reports. 5) Collaborate as a team member on a complex system design project (e.g., a fermenter). n nLimited enrollment, with priority for Bioengineering undergraduates. Prerequisites: Physics 43, or equivalent. Experience with Matlab and/or Python is recommended.
Terms: Win | Units: 4 | UG Reqs: WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 158: Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life (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. Recommended: ENGR 50 and Chem 31A or equivalent.
Terms: Win | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter or Credit/No Credit

BIOHOPK 14: Bio-logging and Bio-telemetry

Bio-logging is a rapidly growing discipline that includes diverse fields such as consumer electronics, medicine, and marine biology. The use of animal-attached digital tags is a powerful approach to study the movement and ecology of individuals over a wide range of temporal and spatial scales. This course is an introduction to bio-logging methods and analysis. Using whales as a model system, students will learn how use multi-sensor tags to study behavioral biomechanics.
Terms: not given this year, last offered Spring 2018 | Units: 3 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOHOPK 47: Introduction to Research in Ecology and Ecological Physiology

This course is a field-based inquiry into rocky intertidal shores that introducesnstudents to ecology and environmental physiology and the research methods used to study them. Students will learn how to detect patterns quantitatively in nature through appropriate sampling methods & statistical analysis. Following exploration of appropriate background material in class and through exploration of the scientific literature, students will learn how to formulate testable hypotheses regarding the underlying causes of the patterns they discern. A variety of different aspects of ecology and physiology will be investigated cooperatively by the students during the quarter, culminating in development of an individual final paper in the form of a research proposal based on data collected during the course. The course will provide a broad conceptual introduction to the underlying biological principles that influence adaptation to the planet¿s dynamic habitats, as well as inquiry-based experience in how to explore and understand complex systems in nature. nThis course fulfills the same laboratory requirement as BIO 47. Satisfies WIM in Biology.
Terms: Spr | Units: 5 | UG Reqs: GER: DB-NatSci, WAY-SMA | Grading: Letter or Credit/No Credit

BIOHOPK 150H: Ecological Mechanics (BIOHOPK 250H)

(Graduate students register for 250H.) The principles of life's physical interactions. We will explore basic physics. fluid mechanics, thermal dynamics, and materials science to see how the principles of these fields can be used to investigate ecology at levels from the individual to the community. Topics include: diffusion, boundary layers, fluid-dynamic forces, locomotion, heat-budget models, fracture mechanics, adhesion, beam theory, the statistics of extremes, and the theory of self-organization. Open to students from all backgrounds. Some familiarity with basic physics and calculus advantageous but not necessary.
Terms: not given this year, last offered Spring 2019 | Units: 3 | UG Reqs: WAY-SMA | Grading: Letter or Credit/No Credit

BIOHOPK 154H: Animal Diversity: An Introduction to Evolution of Animal Form and Function from Larvae to Adults (BIOHOPK 254H)

Survey of invertebrate diversity, emphasizing form and function of both adult and larval life history stages. Focuses on how morphology, life histories, and development contribute to current views of the evolutionary diversification of multicellular animals. Labs are a hands-on exploration of animal diversity using local marine species as examples, as well as techniques of obtaining, handling, and maintaining larvae from early development through settlement. Lectures, labs, plus field trips. Satisfies Central Menu Area 3 for Bio majors. Prerequisite: Biology core or consent of instructors.
Terms: not given this year, last offered Winter 2015 | Units: 7 | UG Reqs: WAY-SMA | Grading: Letter or Credit/No Credit
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