BIOL 5137 Ion Channels Journal Club
BIOL 5496 Seminar in Computational Molecular Biology
BME 301B Quantitative Physiology II
BME 314 Physics of the Heart
BME 450 Numerical Methods for Computational Modeling in Biomedicine
BME 459 Intermediate Biomechanics
BME 471 Bioelectric Phenomena
BME 502 Cardiovascular MRI-Physics to Clinical Application
BME 506 Seminar in Imaging Science and Engineering
BME 573 Applied Bioelectricity


L41 BIOL 5137 Ion Channels Journal Club Nichols Return to Top
How do ion channels work at the fundamental molecular level? And what do they do for the tissue they are in? How do alterations in channel biology cause myriad diseases - from diabetes to heart attacks, from cystic fibrosis to epilepsy. Students attend journal club each week for 8 weeks and participate in group discussion of recent paper. Once per semester student will choose a paper and present it to the group.
L41 BIOL 5496 Seminar in Computational Molecular Biology Buhler, Cohen Return to Top
Students present current research papers and the appropriate background material in the field of Computational Biology. **Arts and Sciences students must take this course for credit; Engineering students must take this course Pass/Fail.**
E62 BME 301B Quantitative Physiology II Cui, Efimov, Widder Return to Top
A course (lecture and supervised laboratory sessions) designed to elaborate the physiological background necessary for advanced work in biomedical engineering. A quantitative model-oriented approach to physiological systems is stressed. Topics include electrocardiography; heart contractility; pulse wave propagation in arteries; pulmonary function; renal function; immune system; drug delivery. Prereqs: BME 140, CSE 131 or 200, ESE 230, ESE 317, Biol 3058, or permission of instructor.Corequisites: EP 310 or permission of the instructor.
E62 BME 314 Physics of the Heart Miller Return to Top
A lecture and demonstration course which may be of particular interest to premedical and life-science students. Basic physics of the human cardiovascular system. Elasticity of vessels: properties of elastin and collagen. Energetics of the circulation: arterial and venous blood pressure, total fluid energy, gravitational potential energy, kinetic energy. Streamline flow and turbulence: effects of stenosis. Static and dynamic energy consumption of the heart: cardiac efficiency, the tension-time integral, Laplace's law, Starling's law. Metabolism of cardiac muscle. Electrophysiology: the heartbeat and cardiac arrhythmias. The physics of phonocardiograms, echocardiograms, and other non-invasive techniques for physical assessment of cardiac abnormalities, including ischemia and myocardial infarction. Models of mechanical properties: contractile element, series elastic and parallel elastic elements. Prereq:Prior completion (or concurrent registration in) Phys 118A, or permission of instructor.
E62 BME 450 Numerical Methods for Computational Modeling in Biomedicine Silva Return to Top
Advanced computational methods are required for the creation of biological models, from protein folding to whole-organ function.Students will be introduced to the process of model development from beginning to end, which includes model formulation, how to solve and parameterize equations, and how to evaluate model success.To illustrate the potential of these methods, participants will systematically build a model to simulate a "real-life" biological system that is applicable to their research or interest.A mechanistic appreciation of the methods will be gained by programming the methods in a low-level language (C++) in a Linux environment.While extensive programming knowledge is not required, participants are likely to find that some programming background will be helpful.Prereqs:Introductory programming course similar to E81 131
E62  BME 471 Bioelectric Phenomena Moran Return to Top
This course is a quantitative introduction to the origins of bioelectricity with an emphasis on neural and cardiac electrophysiology.Topics will include electric fields and current flow in volume conductors; cell membrane channels and their role in generating membrane potentials; action potentials and their propagation in myelinated and unmyelinated axons as well as cardiac tissue. Minor topics of discussion will include both skeletal muscle and non-human (e.g. electric fish)sources of bioelectricity. Prerequisite: ESE 330
E62  BME 502 Cardiovascular MRI-Physics to Clinical Application Caruthers Return to Top
This graduate course (seniors welcome) will cover the basic physics involved in creating an image by magnetic resonance technology. The use of this technology, specifically as it applies to the unique challenges of cardiovascular applications, will be examined. This will include topics such as motion compensation techniques, real-time imaging, exogenous contrast enhancement, and quantitative flow measurements, for example. As much as one-third of the class will involve actual case studies and the discussion of clinical use for cardiovascular MRI. Students will demonstrate competence in the subject through a combination of homework, a final examination, and a small semester project. Prereqs: Calculus, introductory human physiology/anatomy/biology course.
E62  BME 506 Seminar in Imaging Science and Engineering O'Sullivan Return to Top
This seminar course consists of a series of tutorial lectures on Imaging Science and Engineering with emphasis on applications of imaging technology. Students are exposed to a variety of imaging applications that vary depending on the semester, but may include multispectral remote sensing, astronomical imaging, microscopic imaging, ultrasound imaging, and tomographic imaging. Guest lecturers come from several parts of the university. This course is required of all students in the Imaging Science and Engineering program; the only requirement is attendance. This course is graded Pass/Fail. Prerequisite: Admission to Imaging Science and Engineering Program.
E62  BME 573 Applied Bioelectricity Efimov, Moran Return to Top
This course focuses on the design of bioelectric devices for use in clinical patients. Cardiac pacemakers and defibrillators as well as neural stimulators (eg. deep brain, vagal) will be the basis for a case-study approach to designing and developing new bioelectrical medical devices. In addition to the engineering design aspects, issues such as product liability, FDA approval, etc. will be discussed. Prerequisites: BME 471 Bioelectric Phenomena or instructor's permission.
E62  BME 574 Quantitative Bioelectricity and Cardiac Excitation Rudy Return to Top
Action potential generation, action potential propagation, source-field relationships in homogeneous and inhomogeneous media, models of cardiac excitation and arrhythmia, quantitative electrocardiography. Prerequisites: Differential equations, Laplace transform, electromagnetic field theory (undergraduate level).
E62  BME 575 Molecular Basis of Bioelectrical Excitation Cui Return to Top
Ion channels are the molecular basis of membrane excitability in all cell types, including neuronal, heart, and muscle cells. This course presents the structure and the mechanism of function of ion channels at the molecular level. It introduces the basic principles and methods in the ion channel study as well as the structure-function relation of various types of channels. Exemplary channels that have been best studied will be discussed to illustrate the current understanding. Prerequisites: Knowledge of differential equations, electrical circuits, and chemical kinetics.
E62  BME 589 Biological Imaging Technology O'Sullivan Return to Top
This class will develop a fundamental understanding of the physics and mathematical methods that underlie biological imaging and critically examine case studies of seminal biological imaging technology literature. The physics section will examine how electromagnetic and acoustic waves interact with tissues and cells, how waves can be used to image the biological structure and function, image formation methods and diffraction limited imaging. The math section will examine image decomposition using basis functions (e.g. fourier transforms), synthesis of measurement data, image analysis for feature extraction, reduction of multi-dimensional imaging datasets, multivariate regression, and statistical image analysis. Original literature on electron, confocal and two photon microscopy, ultrasound, computed tomography, functional and structural magnetic resonance imaging and other emerging imaging technology will be critiqued.
E62 BME 5901 Integrative Cardiac Electrophysiology Cui, Efimov, Rudy, Silva Return to Top
Quantitative electrophysiology of the heart, integrating from the molecular level (ion channels, regulatory pathways, cell signaling) to the cardiac cell (action potential and calcium transient), multicellular tissue (cell-cell communication) and the whole heart (SA and AV nodes, specialized conduction system, fiber structure and anisotropy, anatomical considerations). Prereq.: Consent of instructor
E62 BME 5907 Advanced Concepts in Image Science Anastasio Return to Top
The course will expose students to a unified treatment of the mathematical and statistical principles of imaging. This will include the deterministic analysis of imaging systems that includes continuous-to-continuous, continuous-to-discrete, and discrete-to-discrete mappings from objects to images. In addition, imaging systems will be analyzed in a statistical framework where stochastic models for objects and images will be introduced. Methodologies for task-based image quality assessment will be reviewed, which will include classification tasks and receiver operator characteristic (ROC) analysis. Basics concepts of inverse problems and tomography will also be covered. Prereq.: Graduate standing or consent of instructor.
E62 BME 5909 Physiology of the Heart Efimov Return to Top
This is a comprehensive cardiac physiology course for biomedical engineers, which includes (1) history, philosophy and methodology of cardiac physiology and cardiac engineering, (2) structure, biochemistry and biophysics of the heart, (3) signal transduction and regulation, (4) normal physiology and pathophysiology, and (5) current approaches to therapy of heart disease. Textbook: Arnold M. Katz, Physiology of the Heart, 5th edition.
E62 BME 5911 Cardiovascular Biophysics Journal Club Kovacs Return to Top
This journal club is intended for beginning graduate students, advanced undergraduates, and MSTP students with a background in the quantitative sciences (engineering, physics, math, chemistry, etc). The subjects covered are inherently multidisciplinary. We will review landmark and recent publications in quantitative cardiovascular physiology, mathematical modeling of physiologic systems and related topics such as chaos theory and nonlinear dynamics of biological systems. Familiarity with calculus, differential equations, and basic engineering/thermodynamic principles is assumed. Knowledge of anatomy/physiology is optional.
E62 BME 5913 Molecular Systems Biology: Computation & Measurements for Understanding Cell Physiology and Disease Naegle Return to Top
This project-based (MATLAB) class will introduce several current techniques for systems-level measurement of molecules and a set of computational techniques for inferring biological meaning from such experiments. Several molecular types and measurement techniques will be covered. How to determine the quality of measurements will lay the groundwork for understanding a new measurement technique. From there, computational topics will include dimensionality reduction techniques, correlations between measurements and outcomes, and network modeling and inference. A working knowledge of molecular biology, differential equations, linear algebra, and statistics is required.
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