printer friendly pageBIOE 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-SMA, WAY-AQR
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
Instructors:
Boahen, K. (PI)
;
Riedel-Kruse, I. (PI)
;
Venook, R. (PI)
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Instructors:
Boahen, K. (PI)
;
Riedel-Kruse, I. (PI)
;
Venook, R. (PI)
;
Dadgar-Kiani, E. (TA)
;
Longwell, S. (TA)
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 19, 20, 21;
CHEM 31A, B (or 31X); strongly recommended:
PHYSICS 41,
CME 100 or
MATH 51, and
CME 106; or instructor approval.
Terms: Win
| Units: 4
| UG Reqs: WAY-AQR, WAY-SMA
Instructors:
Prakash, M. (PI)
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: Spr
| Units: 3
| UG Reqs: WAY-SMA, WAY-AQR
Instructors:
Goldbogen, J. (PI)
;
Gough, W. (TA)
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: WAY-SMA, GER: DB-NatSci
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.
Last offered: Spring 2016
| UG Reqs: WAY-SMA
BIOHOPK 161H: Invertebrate Zoology (BIOHOPK 261H)
(Graduate students register for 261H.) Survey of invertebrate diversity emphasizing form and function in a phylogenetic framework. Morphological diversity, life histories, physiology, and ecology of the major invertebrate groups, concentrating on local marine forms as examples. Current views on the phylogenetic relationships and evolution of the invertebrates. Lectures, lab, plus field trips. Satisfies Central Menu Area 3 for Bio majors.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
Instructors:
Watanabe, J. (PI)
BIOHOPK 163H: Oceanic Biology (BIOHOPK 263H)
(Graduate students register for 263H.) How the physics and chemistry of the oceanic environment affect marine plants and animals. Topics: seawater and ocean circulation, separation of light and nutrients in the two-layered ocean, oceanic food webs and trophic interactions, oceanic environments, biogeography, and global change. Lectures, discussion, and field trips. Satisfies Central Menu Area 4 for Bio majors. Recommended:
PHYSICS 21 or 51,
CHEM 31, or consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
Instructors:
Denny, M. (PI)
;
Somero, G. (PI)
BIOHOPK 172H: Marine Ecology: From Organisms to Ecosystems (BIOHOPK 272H)
(Graduate students register for 272H.) This course incorporates the approaches of experimental ecology, biomechanics (ecomechanics), and physiology to develop an integrated perspective on the factors that govern the structures of marine ecosystems and how environment change, including anthropogenic influences, affects ecosystems' species composition and health. Focus is on rocky intertidal, kelp forest, estuarine, and midwater ecosystems of Monterey Bay. Experimental projects done in the field offer experience in a variety of ecological techniques and in analysis of ecological data. Students will engage in presentation and debates of current topics in marine ecology and conservation. Satisfies Central Menu Area 4 for Bio majors. Prerequisite: consent of instructor. Fulfills WIM in Biology.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
Instructors:
Micheli, F. (PI)
BIOHOPK 182H: Stanford at Sea (BIOHOPK 323H, EARTHSYS 323, ESS 323)
(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.
Last offered: Spring 2017
| UG Reqs: GER: DB-NatSci, WAY-SMA
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