The transport of mass, momentum, and energy are critical to the function of living systems and the design of medical devices. Biological transport phenomena are present at a wide range of length scales: molecular, cellular, organ (whole and by functional unit), and organism. This course develops and applies scaling laws and the methods of continuum mechanics to biological transport phenomena over a range of length and time scales. The course is intended for undergraduate students who have taken a course in differential equations and an introductory course in physics. Students should be familiar with basic biology; an understanding of physiology is useful, but not assumed.
Score: 5.084447 Details | Listing | Web page
This course introduces the basic principles of thermodynamics and their application to a variety of biological processes and systems. Some coverage of conventional engineering applications is also included. Also listed as Mechanical Engineering C105B.
Score: 5.084447 Details | Listing | Web page
This course introduces students to the physiology of human organ systems, with an emphasis on quantitative problem solving, engineering-style modeling, and applications to clinical medicine. The course will begin with a review of basic principles of cellular physiology, including membrane transport and electrophysiology, and then take a system-by-system approach to the physiology of various organ systems, including the cardiovascular, pulmonary, renal, and endocrine systems. Throughout, the course will feature extensive discussions of clinical conditions associated with dysfunction in specific physiological processes as well as the role of medical devices and prostheses. This course is geared towards upper-division bioengineering students who wish to solidify their foundation in physiology, especially in preparation for a career in clinical medicine or the biomedical device industry.
Score: 5.084447 Details | Listing | Web page
This course is intended for upper level engineering undergraduate students interested in the development of novel functional proteins and peptide motifs and characterization of their physical and biological properties using various instrumentation tools in quantitative manners.
Score: 5.084447 Details | Listing | Web page
This course develops and applies scaling laws and the methods of continuum and statistical mechanics to biomechanical phenomena over a range of length scales, from molecular to cellular levels. It is intended for senior undergraduate students who have been exposed to differential equations, mechanics, and certain aspects of modern biology.
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This course will teach the main concepts and current views on key attributes of embryonic stem cells (ESC), will introduce theory of their function in embryonic development, methods of ESC derivation, propagation, and characterization, and will discuss currently developing stem cell technologies.
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The structural and functional characteristics of tissues are altered by cells in response to culture conditions, loading, injury, and various other factors. A contemporary understanding of the form, function, and longevity of tissues includes knowledge of tissue microstructure, composition of matrix, and cell function. Students will be introduced to molecular biology techniques as applied to cells and tissues including immunofluorescence, image analysis, protein quantification, gene expression, and cell culture.
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The goal of tissue engineering is to fabricate substitutes to restore tissue structure and functions. Understanding cell function in response to environmental cues will help us to establish design criteria and develop engineering tools for tissue fabrication. This course will introduce the basic concepts and approaches in the field, and train students to design and engineer biological substitutes. Lectures will be based on the textbook, the reference books and recent literature. Discussion sections will include the discussion of current literature and issues related to course content, homework, exams, and projects. Homework includes quantitative analysis, essay questions, and literature research. There will be a midterm exam, final exam, and a design project (presentation and paper). The final project will be a group project (three to four students) or independent project (required for graduate students). The topic will be chosen by each group and approved by instructor/GSIs.
Score: 5.084447 Details | Listing | Web page
This course covers the structure and mechanical functions of load bearing tissues and their replacements. Natural and synthetic load-bearing biomaterials for clinical applications are reviewed. Biocompatibility of biomaterials and host response to structural implants are examined. Quantitative treatment of biomechanical issues and constitutive relationships of tissues are covered in order to design biomaterial replacements for structural function. Material selection for load bearing applications including reconstructive surgery, orthopedics, dentistry, and cardiology are addressed. Mechanical design for longevity including topics of fatigue, wear, and fracture are reviewed. Case studies that examine failures of devices are presented. This course includes a teaching/design laboratory component that involves design analysis of medical devices and outreach teaching to the public community. Several problem-based projects are utilized throughout the semester for design analysis. In addition to technical content, this course involves rigorous technical writing assignments, oral communication skill development and teamwork. Also listed as Mechanical Engineering C117.
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This course is intended to give students the opportunity to expand their knowledge of topics related to biomedical materials selection and design. Structure-property relationships of biomedical materials and their interaction with biological systems will be addressed. Applications of the concepts developed include blood-materials compatibility, biomimetic materials, hard and soft tissue-materials interactions, drug delivery, tissue engineering, and biotechnology. Also listed as Materials Science and Engineering C118.
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Students will learn the application of engineering concepts including statics, dynamics, optimization theory, composite beam theory, beam-on-elastic foundation theory, Hertz contact theory and materials behavior. Topics will include forces and moments acting on human joints; composition and mechanical behavior of orthopedic biomaterials; design/analysis of artificial joint, spine, and fracture fixation prostheses; musculoskeletal tissues including bone, cartilage, tendon, ligament, and muscle; osteoporosis and fracture-risk predication of bones; and bone adaptation. Students will be challenged in a MATLAB-based project to integrate the course material in an attempt to gain insight into contemporary design/analysis/problems. Also listed as Mechanical Engineering C176.
Score: 5.084447 Details | Listing | Web page
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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Hands-on project experience in applying microfabrication techniques to problems in biotechnology using the latest micro- and nano-technological tools. Experimental design and analysis of micro- and nano-scale device interfaces. Students will give poster sessions and oral presentations on their results.
Score: 5.084447 Details | Listing | Web page
An introduction to the kinematics, dynamics, and control of robot manipulators, robotic vision, and sensing. The course covers forward and inverse kinematics of serial chain manipulators, the manipulator Jacobian, force relations, dynamics, and control. It presents elementary principles on proximity, tactile, and force sensing, vision sensors, camera calibration, stereo construction, and motion detection. The course concludes with current applications of robotics in active perception, medical robotics, and other areas. Also listed as Electrical Engineering C125.
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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.
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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 to 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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Introduction to laboratory and field study of the biomechanics of animals and plants using fundamental biomechanical techniques and equipment. Course has a series of rotations involving students in experiments demonstrating how solid and fluid mechanics can be used to discover the way in which diverse organisms move and interact with their physical environment. The laboratories emphasize sampling methodology, experimental design, and statistical interpretation of results. Latter third of course devoted to independent research projects. Written reports and class presentation of project results are required. Also listed as Electrical Engineering C145O, Mechanical Engineering C177L, and Integrative Biology C135L.
Score: 5.084447 Details | Listing | Web page
This laboratory course is designed as an introduction to research in synthetic biology, a ground-up approach to genetic engineering with applications in bioenergy, heathcare, materials science, and chemical production. In this course, we will design and execute a real research project. Each student will be responsible for designing and constructing components for the group project and then performing experiments to analyze the system. In addition to laboratory work, we will have lectures on methods and design concepts in synthetic biology including an introduction to Biobricks, gene synthesis, computer modeling, directed evolution, practical molecular biology, and biochemistry.
Score: 5.084447 Details | Listing | Web page
Study of bioinformatics problems such as DNA pattern finding, gene expression data analysis, molecular evolution models, and biomolecular sequence database searching. Introduction of the necessary probability and statistics: events, (conditional) probability, random variables, estimation, testing, and linear regression. Also listed as Statistics C141.
Score: 5.084447 Details | Listing | Web page
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); BioE Content: Biological.
Score: 5.084447 Details | Listing | Web page
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 is required. Also listed as Plant and Microbial Biology C144.
Score: 5.084447 Details | Listing | Web page
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 C144 (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 C144L.
Score: 5.084447 Details | Listing | Web page
Laboratory exercises exploring a variety of electronic transducers for measuring physical quantities such as temperature, force, displacement, sound, light, ionic potential; the use of circuits for low-level differential amplification and analog signal processing; and the use of microcomputers for digital sampling and display. Lectures cover principles explored in the laboratory exercises; construction, response and signal to noise of electronic transducers and actuators; and design of circuits for sensing and controlling physical quantities. Also listed as Electrical Engineering C145L.
Score: 5.084447 Details | Listing | Web page
Laboratory exercises constructing basic interfacing circuits and writing 20-100 line C programs for data acquisition, storage, analysis, display, and control. Use of the IBM PC with microprogrammable digital counter/timer, parallel I/O port. Circuit components include anti-aliasing filters, the S/H amplifier, A/D and D/A converters. Exercises include effects of aliasing in periodic sampling, fast Fourier transforms of basic waveforms, the use of the Hanning filter for leakage reduction, Fourier analysis of the human voice, digital filters, and control using Fourier deconvolution. Lectures cover principles explored in the lab exercises and design of microcomputer-based systems for data acquisitions, analysis and control. Also listed as Electrical Engineering C145M.
Score: 5.084447 Details | Listing | Web page
This course is intended for the bioengineering or engineering undergraduate students interested in acquiring a background in recent development of bio-nanomaterials and bio-nanotechnology. The emphasis of the class is to understand the properties of biological basis building blocks, their assembly principles in nature, and their application to build functional materials and devices. The goal is for the bioengineering students to gain sufficient chemical and physical aspects of biological materials through the case study of spider webs, silks, sea shells, diatoms, bones, and teeth, as well as recently developed self-assembled nanostructures inspired by nature. The course covers the structures and properties of amino acids, DNAs, sugars, lipids, and their natural and artifical assembly structures. It also covers nanoscale inorganic materials used to develop nano medicines, bio-imaging, bio-sensors, bioelectronics, and machinery.
Score: 5.084447 Details | Listing | Web page
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