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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 211: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 311, BIOPHYS 311, DBIO 211)

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 42, or equivalent.
Terms: Win | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Riedel-Kruse, I. (PI)

BIOE 260: Tissue Engineering (ORTHO 260)

Principles of tissue engineering and design strategies for practical applications for tissue repair. Topics include tissue morphogenesis, stem cells, biomaterials, controlled drug and gene delivery, and paper discussions. Students will learn skills for lab research through interactive lectures, paper discussions and research proposal development. Students work in small teams to work on develop research proposal for authentic tissue engineering problems. Lab sessions will teach techniques for culturing cells in 3D, as well as fabricating and characterizing hydrogels as 3D cell niche.
Terms: Spr | Units: 4 | Grading: Letter (ABCD/NP)

BIOE 300B: Engineering Concepts Applied to Physiology

This course focuses on engineering approaches to quantifying, modeling and controlling the physiology and pathophysiology of complex systems, from the level of individual cells to tissue, organ and multi-organ systems.
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 311: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 211, BIOPHYS 311, DBIO 211)

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 42, or equivalent.
Terms: Win | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Riedel-Kruse, I. (PI)

BIOE 361: Biomaterials in Regenerative Medicine (MATSCI 381)

Materials design and engineering for regenerative medicine. How materials interact with cells through their micro- and nanostructure, mechanical properties, degradation characteristics, surface chemistry, and biochemistry. Examples include novel materials for drug and gene delivery, materials for stem cell proliferation and differentiation, and tissue engineering scaffolds. Prerequisites: undergraduate chemistry, and cell/molecular biology or biochemistry.
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Heilshorn, S. (PI)

BIOE 393: Bioengineering Departmental Research Colloquium

Bioengineering department labs at Stanford present recent research projects and results. Guest lecturers. Topics include applications of engineering to biology, medicine, biotechnology, and medical technology, including biodesign and devices, molecular and cellular engineering, regenerative medicine and tissue engineering, biomedical imaging, and biomedical computation. Aut, Win, Spr (Lin, Riedel-Kruse, Barron)
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit

BIOPHYS 311: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 211, BIOE 311, DBIO 211)

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 42, or equivalent.
Terms: Win | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Riedel-Kruse, I. (PI)

CEE 177L: Smart Cities & Communities (CEE 277L)

A city is comprised of people and a complex system of systems. Data provides the connective tissue between those systems. Smart cities use information technology (IT) to harness that data for operational efficiency, efficacy of government services, and sustainability. Key enablers covered include: IoT, open data, analytics, cloud and cognitive computing, and systems of engagement. System case studies will include: water, energy, transportation, buildings, food production, urban design, and social services. The evolving relationship between a city and its citizens as well as the risks / challenges of smart cities will also be explored.
Terms: Sum | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Lechner, R. (PI)

CEE 277L: Smart Cities & Communities (CEE 177L)

A city is comprised of people and a complex system of systems. Data provides the connective tissue between those systems. Smart cities use information technology (IT) to harness that data for operational efficiency, efficacy of government services, and sustainability. Key enablers covered include: IoT, open data, analytics, cloud and cognitive computing, and systems of engagement. System case studies will include: water, energy, transportation, buildings, food production, urban design, and social services. The evolving relationship between a city and its citizens as well as the risks / challenges of smart cities will also be explored.
Terms: Sum | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Lechner, R. (PI)

CHEMENG 420: Growth and Form

Advanced topics course examining the role of physical forces in shaping living cells, tissues, and organs, making use of D'Arcy Thompson's classic text On Growth and Form. The course begins with a review of relevant physical principles drawn from statistical physics, polymer theory, rheology and materials science. We then examine current knowledge of cellular mechanotransduction pathways, the roles of physical forces in guiding embryonic development, and the contribution of aberrant cellular response to mechanical cues in heart disease and cancer. The course concludes by examining current frontiers in stem cell biology and tissue engineering.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Dunn, A. (PI); Miller, C. (TA)

DBIO 211: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 211, BIOE 311, BIOPHYS 311)

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 42, or equivalent.
Terms: Win | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Riedel-Kruse, I. (PI)

EE 303: Autonomous Implantable Systems

Integrating electronics with sensing, stimulation, and locomotion capabilities into the body will allow us to restore or enhance physiological functions. In order to be able to insert these electronics into the body, energy source is a major obstacle. This course focuses on the analysis and design of wirelessly powered catheter-deliverable electronics. Emphases will be on the interaction between human and electromagnetic fields in order to transfer power to the embedded electronics via electromagnetic fields, power harvesting circuitry, electrical-tissue interface, and sensing and actuating frontend designs. Prerequisites: EE 252 or equivalent.
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Poon, A. (PI)

EE 331: Biophotonics: Light in Medicine and Biology

Current topics and trends in the use of light in medicine and for advanced microscopy. Course begins with a review of relevant optical principles (basic physics required). Key topics include: light-tissue interactions; sensing and spectroscopy; contrast-enhanced imaging; super-resolution and label-free microscopy; medical applications of light for diagnostics, in-vivo imaging, and therapy; nanophotonics and array technologies. Open to non-majors; programming experience (Matlab and/or C) required.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Bowden, A. (PI)

MATSCI 81N: Bioengineering Materials to Heal the Body

Preference to freshmen. Real-world examples of materials developed for tissue engineering and regenerative medicine therapies. How scientists and engineers design new materials for surgeons to use in replacing body parts such as damaged heart or spinal cord tissue. How cells interact with implanted materials. Students identify a clinically important disease or injury that requires a better material, proposed research approaches to the problem, and debate possible engineering solutions.
Terms: Aut | Units: 3 | UG Reqs: GER:DB-EngrAppSci | Grading: Letter or Credit/No Credit
Instructors: ; Heilshorn, S. (PI)

MATSCI 381: Biomaterials in Regenerative Medicine (BIOE 361)

Materials design and engineering for regenerative medicine. How materials interact with cells through their micro- and nanostructure, mechanical properties, degradation characteristics, surface chemistry, and biochemistry. Examples include novel materials for drug and gene delivery, materials for stem cell proliferation and differentiation, and tissue engineering scaffolds. Prerequisites: undergraduate chemistry, and cell/molecular biology or biochemistry.
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Heilshorn, S. (PI)

ME 234: Introduction to Neuromechanics

Understanding the role of mechanics in brain development, physiology, and pathology. Mechanics of brain cells: neurons, mechanobiology, mechanotransduction. Mechanics of brain tissue: experimental testing, constitutive modeling, computational modeling. Mechanics of brain development: gyrification, cortical folding, axon elongation, lissencephaly, polymicrogyria. Mechanics of traumatic brain injury: high impact loading, neural injury. Mechanics of brain tumors, brain cancer, tumor growth, altered cytoskeletal mechanics. Mechanics of neurological disorders: autism, dementia, schizophrenia. Mechanics of brain surgery.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit

ME 235: Understanding Superfans and their Heroes

Harness the power of the hero coefficient through a radical team-based, hands-on, multidisciplinary class. Students will learn and utilize the principles of Empathy-Define-Ideate-Prototype-Test components of the d.thinking process. Why do superfans love their heroes? You'll get to prototype and explore how superfans connect with their heroes, understanding this connective tissue works will give your own ideas a boost. We'll be studying heroes the likes of Dale Earnhardt, Michael Jordan and Stephen Colbert. Expect to leave this class ready to spread the word about heroes and superfans and make everyone at your company or on your team feel like one. You will hear from special guests and take a field trip to a racetrack. Sponsored by the Revs Program. Limited enrollment. FAQ and apply here: http://revs.stanford.edu/course/693
Terms: not given this year | Units: 2-3 | Grading: Letter or Credit/No Credit

ME 244: Mechanotransduction in Cells and Tissues (BIOE 283, BIOPHYS 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.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Chaudhuri, O. (PI)

ME 287: Mechanics of Biological Tissues

Introduction to the mechanical behaviors of biological tissues in health and disease. Overview of experimental approaches to evaluating tissue properties and mathematical constitutive models. Elastic behaviors of hard tissues, nonlinear elastic and viscoelastic models for soft tissues.
Terms: Win | Units: 4 | Grading: Letter (ABCD/NP)

ME 337: Mechanics of Growth

Introduction to continuum theory and computational simulation of living matter. Kinematics of finite growth. Balance equations in open system thermodynamics. Constitutive equations for living systems. Custom-designed finite element solution strategies. Analytical solutions for simple model problems. Numerical solutions for clinically relevant problems such as: bone remodeling; wound healing; tumor growth; atherosclerosis; heart failure; tissue expansion; and high performance training.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Kuhl, E. (PI)

ME 387: Soft Tissue Mechanics

Structure/function relationships and mechanical properties of soft tissues, including nonlinear elasticity, viscoelasticity, and poroelasticity.
Terms: Sum | Units: 3 | Grading: Letter (ABCD/NP)

ME 388: Transport Modeling for Biological Systems

Introduction to electric fields, fluid flows, transport phenomena and their application to biological systems. Maxwell's equations, electrostatics, electro-chemical-mechanical driving forces in physiological systems. Ionic diffusion in electrolytes and membrane transport. Fluid and solid continua theory for porous, hydrated biological tissues. Applications include ionic and molecular transport in tissues and cells, electrophoresis, electromechanical and physicochemical interactions in cells and the extracellular matrix of connective tissue.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

ORTHO 260: Tissue Engineering (BIOE 260)

Principles of tissue engineering and design strategies for practical applications for tissue repair. Topics include tissue morphogenesis, stem cells, biomaterials, controlled drug and gene delivery, and paper discussions. Students will learn skills for lab research through interactive lectures, paper discussions and research proposal development. Students work in small teams to work on develop research proposal for authentic tissue engineering problems. Lab sessions will teach techniques for culturing cells in 3D, as well as fabricating and characterizing hydrogels as 3D cell niche.
Terms: Spr | Units: 4 | Grading: Letter (ABCD/NP)

ORTHO 270: Orthopaedic Tissue Engineering

Biological principles underlying the use of engineering strategies and biocompatible materials for tissue repair and regeneration. Structure, physiology, and mechanics of articular cartilage, bone, and dense soft connective tissues. Current ideas, approaches, and applications being implemented as therapeutic regimens for arthritis, spinal deformities, and limb salvage. Multidisciplinary constraints on the design and creation of tissue constructs. Students enrolling for 2 units prepare a presentation and final project. Prerequisite: familiarity with basic cell and molecular mechanisms underlying tissue differentiation.
Terms: Win | Units: 1-2 | Grading: Medical Option (Med-Ltr-CR/NC)

RAD 70N: Surgery, Without All the Blood

What if you could do brain surgery completely noninvasively? This is possible now. There are many ways to focus energy into the body, and these can be used for surgery. We will explore methods for minimally invasive treatments of various conditions such as cancer, atrial fibrillation, and movement disorders. We will start with radiation therapy and its application to cancer. We will discuss the application of thermal energy to heat and ablate tissue. We'll discuss delivery systems including ultrasound, laser, and radiofrequency ablation systems, as well as monitoring imaging methods MRI, CT and ultrasound. Lastly, we will discuss neuromodulation and neurostimulation with deep brain simulators, transcranial magnetic stimulation, direct current stimulation, and ultrasound. We will touch on the biology of these treatments and their clinical application, but the emphasis is on the physics and engineering. High school Physics required.
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Pauly, K. (PI)

SIS 135Q: Stanford Introductory Seminar: Tissue Engineering: Ethics, Genes and Cells

Units: 3 | Grading: Letter (ABCD/NP)

SURG 68Q: Current Concepts in Transplantation

Preference to sophomores. Biological aspects of cell and organ transplantation, including issues that arise in the popular media. Diseases for which transplantation is a treatment, the state of the art in human transplantation, transplantation of animal tissue into humans (xenotransplantation), development of new tissue and organs in the laboratory (tissue engineering and cloning), and development of drugs and biological strategies to promote long-term survival of the tissue or organ (tolerance). How to write a scientific abstract, critique scientific literature, and research and present topics in contemporary transplantation.
Terms: Spr | Units: 3 | UG Reqs: Writing 2 | Grading: Letter or Credit/No Credit

SURG 70Q: Surgical Anatomy of the Hand: From Rodin to Reconstruction

The surgical anatomy of the hand is extremely complex in terms of structure and function. Exploration of the anatomy of the hand in different contexts: its representation in art forms, the historical development of the study of hand anatomy, current operative techniques for reconstruction, advances in tissue engineering, and the future of hand transplantation.
Terms: Win | Units: 2 | Grading: Letter or Credit/No Credit
Instructors: ; Chang, J. (PI)
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