Introduction and in-depth treatment of theory relevant to fluid flow in microfluidic and nanofluidic systems supplemented by critical assessment of recent applications drawn from the literature. Topics include low Reynolds Number flow, mass transport including diffusion phenomena, and emphasis on electrokinetic systems and bioanalytical applications of said phenomena.
Score: 5.084447 Details | Listing | Web page
This course teaches fundamental principles of optics and examines contemporary methods of optical microscopy for cells and molecules. Students will learn how to design simple optical systems, calculate system performance, and apply imaging techniques including transmission, reflection, phase, and fluorescence microscopy to investigate biological samples. The capabilities of optical microscopy will be compared with complementary techniques including electron microscopy, coherence tomography, and atomic force microscopy. Students will also be responsible for researching their final project outside of class and presenting a specific application of modern microscopy to biological research as part of an end-of-semester project.
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Linear systems and Fourier transforms in two and three dimensions. Basic image processing. Theory and algorithms for image reconstruction from projections. Physics of imaging systems including magnetic resonance, X-ray tomography, positron emission tomography, ultrasound, and biomagnetic imaging. Data analysis including hypothesis testing, parameter estimation by least squares, and compartmental kinetic modelling. Field trips to medical imaging laboratories. Also listed as Electrical Engineering C145B.
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This laboratory course is designed for students interested in obtaining practical hands-on training in optical imaging and instrumentation. Using a combination of lenses, cameras, and data acquisition equipment, students will construct simple light microscopes that introduce basic concepts and limitations important in biomedical optical imaging. Topics include compound microscopes, Kohler illumination, Rayleigh two-point resolution, image contrast including dark-field and fluorescence microscopy, and specialized techniques such as fluorescence recovery after photobleaching (FRAP). Intended for students in both engineering and the sciences, this course will emphasize applied aspects of optical imaging and provide a base of practical skill and reference material that students can leverage in their own research or in industry.
Score: 5.084447 Details | Listing | Web page
These courses cover current topics of research interest in bioengineering. The course content may vary from semester to semester.
Score: 5.084447 Details | Listing | Web page
This semester-long course introduces students to bioengineering project-based learning in small teams, with a strong emphasis on need-based solutions for real medical and research problems through prototype solution selection, design, and testing. The course is designed to provide a "capstone" design experience for bioengineering seniors. The course is structured around didactic lectures, and a textbook, from which assigned readings will be drawn, and supplemented by additional handouts, readings, and lecture material. Where appropriate, the syllabus includes guest lectures from clinicians and practicing engineers from academia and industry. The course includes active learning through organized activities, during which teams will participate in exercises meant to reinforce lecture material through direct application to the team design project.
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Supervised research. This course will satisfy the Senior Bioengineering Design project requirement. Students with junior or senior status may pursue research under the direction of one of the members of the staff. May be taken a second time for credit only. A final report or presentation is required.
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An introduction to research in bioengineering including specific case studies and organization of this rapidly expanding and diverse field.
Score: 5.084447 Details | Listing | Web page
This course explores emerging biophysical descriptions of the cell based on molecular details of the cytoskeleton and its interactions with the cellular microenvironment. Through lectures, discussions, and reading of the research literature, students will learn about current questions facing the field of cell mechanics and its connections with health and disease. Fundamental biology of the cytoskeleton and associated molecular motors will be discussed in the context of cell motility, shape change, and mechanotransduction. Modern techniques for quantifying mechanical properties of the cell and its structural components, including optical trapping, magnetic tweezers, atomic force microscopy, and traction-force microscopy will be presented, and recent models of cell mechanics and their predictions will be discussed and debated.
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This course will focus on biophysical and bioengineering aspects of mechanotransduction, the process through which living cells sense and respond to their mechanical environment. Students will learn how mechanical inputs to cells influence both subcellular biochemistry and whole-cell behavior. They will also study newly-engineered technologies for force manipulation and measurement in living cells, and synthetic strategies to control the mechanics and chemistry of the extracellular matrix. Finally, students will learn about the role of mechanotransduction in selected human organ systems and how these mechanisms may go awry in the setting of the disease. Instruction will feature lectures, discussions, analysis of relevant research papers, assembly of a literature review and a research proposal, and an oral presentation.
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Fundamental processes of heat and mass transport in biological systems; organic molecules, cells, biological organs, whole animals. Derivation of mathematical models and discussion of experimental procedures. Applications to biomedical engineering. Also listed as Mechanical Engineering C212.
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Fluid mechanical aspects of various physiological systems, the circulatory, respiratory, and renal systems. Motion in large and small blood vessels. Pulsatile and peristaltic flows. Other biofluidmechanical flows: the ear, eye, etc. Instrumentation for fluid measurements in biological systems and for medical diagnosis and applications. Artificial devices for replacement of organs and/or functions, e.g. blood oxygenators, kidney dialysis machines, artificial hearts/circulatory assist devices. Also listed as Mechanical Engineering C213.
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The goal of this course is to provide a foundation for characterizing and understanding the mechanical behavior of load-bearing tissues. A variety of mechanics topics will be introduced, including anisotropic elasticity and failure, cellular solid theory, biphasic theory, and quasi-linear viscoelasticity (QLV) theory. Building from this theoretical basis, we will explore the constitutive behavior of a wide variety of biological tissues. After taking this course, students should have sufficient background to independently study the mechanical behavior of most biological tissues. Formal discussion section will include a seminar series with external speakers. Also listed as Mechanical Engineering C214.
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The field of cell mechanics has recently undergone rapid development with particular attention to the dynamics of the cytoskeleton as well as its interactions with the extracellular matrix and how this interaction may cause changes in cell architecture, consequently leading to functional adaptation or pathological conditions. A wide range of models exist for cytoskeletal mechanics, ranging from continuum models for cell deformation to actin filament-based models for cell mobility. Numerous experimental techniques have also been established to quantify the cytoskeletal mechanics via perturbing the cell by exerting some sort of deformation and examining the static and dynamic response of the cell. These experimental observations along with theoretical approaches to the cell have given rise to several theories for describing the mechanics of living cells, modeling the cytoskeleton as a simple mechanical elastic, viscoelastic, or poroviscoelastic continuum, porous gel or soft glassy material, tensegrity network incorporating discrete structural elements that bear compression.
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Overview of the problems associated with the selection and function of polymers used in biotechnology and medicine. Principles of polymer science, polymer synthesis, and structure-property-performance relationships of polymers. Particular emphasis is placed on the performance of polymers in biological environments. Interactions between macromolecular and biological systems for therapy and diagnosis. Specific applications will include drug delivery, gene therapy, tissue engineering, and surface engineering. Also listed as Materials Science and Engineering C216.
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Study of nature's solutions to specific problems with the aim of determining appropriate engineering analogs. Morphology, scaling, and design in organisms applied to engineering structures. Mechanical principles in nature and their application to engineering devices. Mechanical behavior of biological materials as governed by underlying microstructure, with the potential for synthesis into engineered materials. Trade-offs between redundancy and efficiency. Students will work in teams on projects where they will take examples of designs, concepts, and models from biology and determine their potential in specific engineering applications. Also listed as Integrative Biology C217 and Mechanical Engineering C217.
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This course will provide an overview of basic and applied embryonic stem cell (ESC) biology. Topics will include early embryonic development, ESC laboratory methods, biomaterials for directed differentiation and other stem cell manipulations, and clinical uses of stem cells. Also listed as Molecular and Cell Biology C237.
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Biophysical and chemical principles of biomedical microelectromechanical systems (bioMEMS) for the measurement of biological phenomena and clinical applications. Micro- and nano-scale devices for the manipulation of cells and biomolecules. Topics include solid-state transducers, optical transducers, electrochemical transducers, biomedical microelectronics, microfluidics, and hybrid integration of microfabrication technology.
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A survey of the structure and mechanical properties of advanced engineering polymers. Topics include rubber elasticity, viscoelasticity, mechanical properties, yielding, deformation, and fracture mechanisms of various classes of polymers. The course will discuss degradation schemes of polymers and long-term performance issues. The class will include polymer applications in bioengineering and medicine. Also listed as Mechanical Engineering C223.
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Topics include computational approaches and techniques to gene structure and finding, sequence alignment using dynamic programming, protein folding and structure prediction, protein-drug interactions, genetic and biochemical pathways and networks, and microarray analysis. Various case studies in these areas are reviewed and web-based computational biology tools will be used by students. Computational biology research connections to biotechnology will be explored. Bioengineering content: fulfills biological and statistical requirement. Bioengineering Breadth, Core B (Informatics and Genomics) and Core D (Computational Biology).
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This course is aimed at graduate and advanced undergraduate students from the (bio) engineering and chemo-physical sciences interested in a research-oriented introduction to current topics in systems biology. Focusing mainly on two well studied microbiological model systems--the chemotaxis network and Lambda bacteriophage infection--the class systematically introduces key concepts and techniques for biological network deduction, modelling, analysis, evolution and synthetic network design. Students analyze the impact of approaches from the quantitative sciences--such as deterministic modelling, stochastic processes, statistics, non-linear dynamics, control theory, information theory, graph theory, etc.--on understanding biological processes, including (stochastic) gene regulation, signalling, network evolution, and synthetic network design. The course aims identify unsolved problems and discusses possible novel approaches while encouraging students to develop ideas to explore new directions in their own research.
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This course reviews the statistical and algorithmic foundations of bioinformatics viewed through the lens of paleogenetics, the science of "Jurassic Park", i.e., the reconstruction of ancient genes and genomes by reverse Bayesian inference under various stochastic models of molecular evolution. Such methods, first proposed in the 1960s by Linus Pauling (and others), are now in reach of practical experimentation due to the falling cost of DNA synthesis technology. Applications of these methods are granting insight into the origin of life and of the human species, and may be powerful tools of synthetic biology. Lectures will review the theoretical content; homework and laboratory exercises will involve writing and applying programs for computational reconstruction of ancient protein and DNA sequences and other measurably evolving entities, both biological (e.g., gene families) and otherwise (e.g., natural language).
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An introduction to biophysical simulation methods and algorithms, including molecular dynamics, Monte Carlo, mathematical optimization, and "non-algorithmic" computation such as neural networks. Various case studies in applying these areas in the areas of protein folding, protein structure prediction, drug docking, and enzymatics will be covered. Core Specialization: Core B (Informatics and Genomics); Core D (Computational Biology); Bioengineering Content: Biological.
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This course will introduce students to the fundamentals of molecular biology, and to the bioinformatics tools and databases used for the prediction of protein function and structure. It is designed to impart both a theoretical understanding of popular computational methods, as well as some experience with protein sequence analysis methods applied to real data. This class includes no programming, and no programming background required. Also listed as Plant and Microbial Biology C244.
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This course is intended to introduce students to a variety of bioinformatics techniques that are used to predict protein function and structure. It is designed to be taken concurrently with C244 (which provides the theoretical foundations for the methods used in the laboratory class), although students can petition to take this laboratory course separately. No programming is performed in this class, and no prior programming experience is required. Also listed as Plant and Microbial Biology C244L.
Score: 5.084447 Details | Listing | Web page
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