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BIO 186: Archaeobotany (ARCHLGY 126, ARCHLGY 226, BIO 286)

Archaeobotany, also known as paleoethnobotany, is the study of the interrelationships of plants and humans through the archaeological record. Knowledge and understanding of Archaeobotany sufficient to interpret, evaluate, and understand archaeobotanical data. Dominant approaches in the study of archaeobotanical remains: plant macro-remains, pollen, phytoliths, and starch grains in the identification of diet and environmental reconstruction.
Terms: Win | Units: 5 | UG Reqs: WAY-SMA
Instructors: Grauer, K. (PI)

BIO 190: Geomicrobiology (EARTHSYS 158, EARTHSYS 258, ESS 158, ESS 258)

How microorganisms shape the geochemistry of the Earth's crust including oceans, lakes, estuaries, subsurface environments, sediments, soils, mineral deposits, and rocks. Topics include mineral formation and dissolution; biogeochemical cycling of elements (carbon, nitrogen, sulfur, and metals); geochemical and mineralogical controls on microbial activity, diversity, and evolution; life in extreme environments; and the application of new techniques to geomicrobial systems. Recommended: introductory chemistry and microbiology such as CEE 274A.
| UG Reqs: WAY-SMA

BIOE 42: Physical Biology

BIOE 42 is designed to introduce students to general engineering principles that have emerged from theory and experiments in biology. Topics covered will cover the scales from molecules to cells to organisms, including fundamental principles of entropy, diffusion, and continuum mechanics. These topics will link to several biological questions, including DNA organization, ligand binding, cytoskeletal mechanics, and the electromagnetic origin of nerve impulses. In all cases, students will learn to develop toy models that can explain quantitative measurements of the function of biological systems. Prerequisites: MATH 19, 20, 21 CHEM 31A, B (or 31X), PHYSICS 41; strongly recommended: CS 106A, CME 100 or MATH 51, and CME 106; or instructor approval.
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA

BIOE 44: Fundamentals for Engineering Biology Lab

An introduction to techniques in genetic, molecular, biochemical, cellular and tissue engineering. Lectures cover advances in the field of synthetic biology with emphasis on genetic engineering, plasmid design, gene synthesis, genetic circuits, and safety and bioethics. Lab modules will teach students how to conduct basic lab techniques, add/remove DNA from living matter, and engineer prokaryotic and eukaryotic cells. Team projects will support practice in component engineering with a focus on molecular design and quantitative analysis of experiments, device and system engineering using abstracted genetically encoded objects, and product development. Concurrent or previous enrollment in BIO 82 or BIO 83. Preference to declared BioE students. Students who have not declared BioE should email Alex Engel to get on a waitlist for a permission code to enroll. Class meets in Shriram 112, lab meets in Shriram 114. Scientific Method and Analysis (SMA).
Terms: Aut, Win | Units: 4 | UG Reqs: WAY-SMA

BIOE 72N: Pathophysiology and Design for Cardiovascular Disease

Future physicians, social and biological scientists, and engineers will be the core of teams that solve major problems threatening human health. Bridging these diverse areas will require thinkers who can understand human biology and also think broadly about approaching such challenges. Focusing on heart disease, students in this seminar will learn about the multi-factorial problems leading to the leading cause of death in the U.S., along with how to apply design thinking to innovate in the context of healthcare.
Terms: Spr | Units: 3 | UG Reqs: WAY-SMA

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.
Last offered: Winter 2019 | UG Reqs: WAY-AQR, WAY-SMA

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 OR 83; BIO 84. CS 106A or programming experience highly recommended.
Terms: Spr | Units: 4 | UG Reqs: WAY-SMA, WAY-AQR

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. The class is open to BioE-declared students who are not on campus in the spring. Students attend class by watching videos and completing assignments remotely. 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 OR 83; BIO 84. CS 106A or programming experience highly recommended.
Last offered: Spring 2023 | UG Reqs: WAY-AQR, WAY-SMA

BIOE 123: Bioengineering Systems 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 bioengineering-relevant system (e.g., centrifuge) 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 system that meets the teams' self-determined metrics. Learning 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: more »
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 bioengineering-relevant system (e.g., centrifuge) 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 system that meets the teams' self-determined metrics. Learning 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 centrifuge). Limited 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

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.
Last offered: Winter 2020 | UG Reqs: WAY-AQR, WAY-SMA
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