printer friendly pageBIOE 279: Computational Biology: Structure and Organization of Biomolecules and Cells (BIOMEDIN 279, BIOPHYS 279, CME 279, CS 279)
Computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules and cells. These computational methods play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course topics include protein structure prediction, protein design, drug screening, molecular simulation, cellular-level simulation, image analysis for microscopy, and methods for solving structures from crystallography and electron microscopy data. Prerequisites: elementary programming background (
CS 106A or equivalent) and an introductory course in biology or biochemistry.
Terms: Aut
| Units: 3
Instructors:
Dror, R. (PI)
;
Bresette, L. (TA)
;
Li, D. (TA)
;
McAvity, J. (TA)
;
Sayana, R. (TA)
;
Suriana, P. (TA)
;
Xu, J. (TA)
BIOE 281: Biomechanics of Movement (ME 281)
Experimental techniques to study human and animal movement including motion capture systems, EMG, force plates, medical imaging, and animation. The mechanical properties of muscle and tendon, and quantitative analysis of musculoskeletal geometry. Projects and demonstrations emphasize applications of mechanics in sports, orthopedics, and rehabilitation.
Terms: Win
| Units: 3
Instructors:
Delp, S. (PI)
;
Gunnarsson, L. (TA)
;
Heigold, H. (TA)
...
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Instructors:
Delp, S. (PI)
;
Gunnarsson, L. (TA)
;
Heigold, H. (TA)
;
Joyce, M. (TA)
;
Pai S, A. (TA)
BIOE 282: Introduction to Biomechanics and Mechanobiology (ME 283)
Introduction to the mechanical analysis of tissues (biomechanics), and how mechanical cues play a role in regulating tissue development, adaptation, regeneration, and aging (mechanobiology). Topics include tissue viscoelasticity, cardiovascular biomechanics, blood rheology, interstitial flow, bone mechanics, muscle contraction and mechanics, and mechanobiology of the musculoskeletal system. Undergraduates should have taken ME70 and
ME80, or equivalent courses.
Terms: Win
| Units: 3
BIOE 283: Mechanotransduction in Cells and Tissues (BIOPHYS 244, ME 244)
Mechanical cues play a critical role in development, normal functioning of cells and tissues, and various diseases. This course will cover what is known about cellular mechanotransduction, or the processes by which living cells sense and respond to physical cues such as physiological forces or mechanical properties of the tissue microenvironment. Experimental techniques and current areas of active investigation will be highlighted. This class is for graduate students only.
Terms: Win
| Units: 3
Instructors:
Chaudhuri, O. (PI)
;
Slyman, R. (TA)
BIOE 285: Computational Modeling in the Cardiovascular System (CME 285, ME 285)
This course introduces computational modeling methods for cardiovascular blood flow and physiology. Topics in this course include analytical and computational methods for solutions of flow in deformable vessels, one-dimensional equations of blood flow, cardiovascular anatomy, lumped parameter models, vascular trees, scaling laws, biomechanics of the circulatory system, and 3D patient specific modeling with finite elements; course will provide an overview of the diagnosis and treatment of adult and congenital cardiovascular diseases and review recent research in the literature in a journal club format. Students will use SimVascular software to do clinically-oriented projects in patient specific blood flow simulations. Pre-requisites:
CME102, ME133 and
CME192.
Last offered: Winter 2023
BIOE 291: Principles and Practice of Optogenetics for Optical Control of Biological Tissues
Principles and practice of optical control of biological processes (optogenetics), emphasizing bioengineering approaches. Theoretical, historical, and current practice of the field. Requisite molecular-genetic, optoelectronic, behavioral, clinical, and ethical concepts, and mentored analysis and presentation of relevant papers. Final projects of research proposals and a laboratory component in BioX to provide hands-on training. Contact instructor before registering.
Terms: Aut
| Units: 3
BIOE 293: Bioengineering Department Colloquium
This course runs in parallel with the bioengineering departmental seminars featuring external speakers. While the seminars are open to the public, the attendance of enrolled students is required. Following each seminar, enrolled students have the opportunity to engage in an open dialogue with the speaker to discuss topics including the speaker's paths into science and their methodologies for selecting scientific problems.
Terms: Spr
| Units: 1
| Repeatable
for credit
Instructors:
Wang, B. (PI)
;
Espinoza Campomanes, L. (TA)
BIOE 296: Promoting Effective and Equitable Teaching in Bioengineering
This weekly seminar will explore best practices through guided discussions and workshops on effective and equitable pedagogy. Emphasis is on building practical skills for defining and accomplishing course objectives. Participants will be able to implement these actionable inclusive teaching strategies to foster a community of belonging and equity within the classroom. Activities also build personal and professional skills useful for diverse future careers.
Terms: Spr
| Units: 1
| Repeatable
2 times
(up to 2 units total)
BIOE 299B: Practical Training
Educational opportunities in high technology research and development labs in industry. Students engage in internship work and integrate that work into their academic program. Following internship work, students complete a research report outlining work activity, problems investigated, key results, and follow-up projects they expect to perform. Meets the requirements for curricular practical training for students on F-1 visas. Student is responsible for arranging own internship/employment and faculty sponsorship. Register under faculty sponsor's section number. All paperwork must be completed by student and faculty sponsor, as the student services office does not sponsor CPT. Students are allowed only two quarters of CPT per degree program. Course may be repeated twice.
Terms: Spr, Sum
| Units: 1
| Repeatable
2 times
(up to 2 units total)
BIOE 300A: Molecular and Cellular Bioengineering
Learn some of the fundamental principles and cutting edge research topics in molecular and cellular bioengineering, while improving your scientific communication and quantitative skills. The course is structured around weekly discussions of selected articles, and includes oral presentations, written critiques, and problem sets. Example topics: DNA sequencing, transcriptional regulation, genetic engineering, protein engineering, cell signaling, and synthetic biological circuits. In addition, you will practice computing probabilities, solving differential equations, and coding stochastic simulations (some require Python).
Terms: Win
| Units: 3
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