Biomedical Engineering

• ENG BE 511: Biomedical Instrumentation
  Physiological signals, origin of biopotentials (ECG, EMG, EEG), biomedical transducers and electrodes. Biomedical signal detection, amplifications and filtering. Analog front-ends of biomedical instruments. Electrical safety in medical environment. Laboratory experiments supplement lectures.
• ENG BE 512: Biomedical Instrument Design
  An introduction to techniques for the design of biomedical instrumentation including sensors and their associated electronics. Mathematical models for a wide variety of sensors ranging from resistive sensors to biosensors are reviewed along with the resulting implications for the design of signal-conditioning electronics. A case-study approach is used in which specific sensor systems are evaluated for sensitivity, selectivity, dynamic range, response time, and reproducibility. Includes lab.
• ENG BE 513: Biological and Environmental Acoustics
  Application of acoustics to biological and environmental research. Introduction to physical acoustics with examples from actual terrestrial and marine environments. The use of sound by animals for communication and echolocation. Application of acoustics to conservation biology.
• ENG BE 515: Introduction to Medical Imaging
  Methods of obtaining useful images of the interior of the body using X-rays, ultrasound, and radionuclides. Image formation and display. Projection radiography. Radiation detectors. Conventional and computerized tomography. Nuclear imaging. Automating diagnosis and non-invasive testing. Radiation safety.
• ENG BE 517: Practical Optical Microscopy of Biological Materials
  In this course students will learn the practice and the underlying theory of imaging with a focus on state-of-the-art live cell microscopy. Students will have the opportunity to use laser scanning confocal as well as widefield and near-field imaging to address experimental questions related to ion fluxes in cells, protein dynamics and association, and will use phase and interference techniques to enhance the detection of low contrast biological material. Exploration and discussion of detector technology, signals and signal processing, spectral separation methods and physical mechanisms used to determine protein associations and protein diffusion in cells are integrated throughout the course. Students will be assigned weekly lab reports, a mid-term and a final project consisting of a paper and an oral presentation on a current research topic involving optical microscopy.
• ENG BE 521: Continuum Mechanics
  The main goal of this course is to present a unified, mathematically rigorous approach to two classical branches of mechanics: the mechanics of fluids and the mechanics of solids. Topics will include kinematics, stress analysis, balance laws (mass, momentum, and energy), the entropy inequality, and constitutive equations in the framework of Cartesian vectors and tensors. Emphasis will be placed on mechanical principles that apply to all materials by using the unifying mathematical framework of Cartesian vectors and tensors. Illustrative examples from biology and physiology will be used to describe basic concepts in continuum mechanics. The course will end at the point from which specialized courses devoted to problems in fluid mechanics (e.g. biotransport) and solid mechanics (e.g. cellular biomechanics) could logically proceed. Same as ENG ME 521; students may not receive credit for both.
• ENG BE 523: Mechanics of Biomaterials
  Covers the chemical composition, physical structure, and mechanical behavior of engineering materials and the tissues they sometimes replace. Study of materials classes; materials selection; deformation of an elastic solid; yield and fracture; fundamentals of viscoelastic phenomena such as creep, stress relaxation, stress rupture, mechanical damping, impact; effects of chemical composition and structure on mechanical properties; methods of chemical property evaluation. Fracture and fatigue. Influences of plastics fabrication methods on mechanical properties. Emphasis on recent research techniques and results. Discussion of practical matters in medical device design including regulatory approvals, sterilization, packaging and quality control. Students will complete a semester-long design project. Same as ENG ME 523 and ENG MS 523; students can only receive credit for one of these courses. 4 cr.
• ENG BE 524: Skeletal Tissue Mechanics
  The course is structured around classical topics in mechanics of materials and their application to study of the mechanical behavior of skeletal tissues, whole bones, bone-implant systems, and diarthroidal joints. Topics include: mechanical behavior of tissues, (anisotropy, viscoelasticity, fracture and fatigue) with emphasis on the role of the microstructure of these tissues; structural properties of whole bones and implants (composite and asymmetric bean theories); and mechanical function of joints (contact mechanics, lubrication, and wear). Emphasis is placed on using experimental data to test and to develop theoretical models, as well as on using the knowledge gained to address common health related problems related to aging, disease, and injury. Same as ENGME524 and ENGMS524. Students may not receive credit for both.
• ENG BE 526: Fundamentals of Biomaterials
  Provides the chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on the fundamental principles in biomedical engineering, material science, and chemistry. Covers the structure and properties of hard materials (ceramics and metals) and soft materials (polymers, colloids, and hydrogels). Meets with BE726 lectures. Note that the laboratory portion is not offered in BE 526.
• ENG BE 527: Principles and Applications of Tissue Engineering
  Provides the chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on cell-biomaterial interactions, biomaterial-host response, and inflammation. Covers the rheological properties of polymers and gels as well as fatigue and fracture of materials. Specific applications of tissue engineering. Meets with BE 727 lectures. Note that the laboratory portion is not offered in BE 527.
• ENG BE 533: Biorheology
  An introductory course emphasizing those rheological properties (such as elasticity, viscoelasticity, poroelasticity, plasticity, and viscoplasticity) that often characterize solid biological tissues and cells.
• ENG BE 535: Cell Mechanics
  The physical and chemical basis for the mechanical properties and activities of living cells considered from an engineering perspective. The instructional approach emphasizes in-depth study of a limited number of cases and relies heavily on selected readings from the literature. Topics studied include cell adhesion and elasticity of red cells as well as phenomena in which active motility is involved (e.g., the first cleavage division of the sea urchin egg, the contraction of skeletal muscle, the crawling motility of fibroblastic cells, and the beating of flagella). Lectures and assignments emphasize the role of quantitative theory and mathematical models in elucidating the molecular basis of physiological observations in these diverse areas.
• ENG BE 537: Biomedical/Biochemical Microsystems
  Focuses on fundamental micro and nanofabrication approaches to engineer the cellular and subcellular environment. The course covers applications of these technologies in the biomedical and biochemical fields, ranging from micro-analytical systems to implantable drug delivery microsystems.
• ENG BE 560: Biomolecular Architecture
  Provides an introduction to the molecular building blocks and the structure of three major components of the living cells: the nucleic acids, the phospho-lipids membrane, and the proteins. The nucleic acids, DNA and RNA, linear information storing structure as well as their three-dimensional structure are covered in relationship to their function. This includes an introduction to information and coding theory. The analysis tools used in pattern identification representation and functional association are introduced and used to discuss the patterns characteristic of DNA and protein structure and biochemical function. The problems and current approaches to predicting protein structure including those using homology, energy minimization, and modeling are introduced. The future implications of our expanding biomolecular knowledge and of rational drug design are also discussed.
• ENG BE 561: DNA and Protein Sequence Analysis
  Fundamental concepts from molecular biology and molecular genetics are presented. Biological inferences are made from DNA and protein sequence data using mathematical and computer science techniques. Pairwise sequence comparative analyses and homolog identification are studied in detail. The dynamic programming algorithm is extended to deal with more general cases and is applied to RNA structure prediction. Additional topics include: multiple sequence alignment, and conserved sequence pattern recognition methods, phylogenetic tree reconstruction to study molecular evolution, methods of identifying coding regions in genomic data, algorithms to solve the fragment assembly problem of DNA sequencing, techniques for physical mapping, mathematical models and computations alogrithms for genetic regulation. An introduction to protein 3-dimensional structure predictions is also given.
• ENG BE 562: Computational Biology: Genomes, Networks, Evolution
  The algorithmic and machine learning foundations of computational biology, combining theory with practice are covered. Principles of algorithm design and core methods in computational biology, and an introduction of important problems in computational biology. Hands on experience analyzing large-scale biological data sets. 4 cr.
• ENG BE 564: Biophysics of Large Molecules
  . The course considers the fundamental concepts of physical and mathematical description of polyatomic molecules and macromolecules on the basis of quantum and statistical mechanics. Special emphasis is given to molecular spectroscopy, the interaction of polyatomic molecules with electromagnetic radiation (visual light, ultraviolet and infrared radiation). Physics of macromolecules (or polymers) is treated in detail. Numerous biomedical applications of the fundamental concepts are considered including photosyntheses, molecular mechanism of vision, DNA damage under UV irradiation, structure of major biological molecules (proteins and nucleic acids). 4 cr.
• ENG BE 565: Molecular Biotechnology
  Covers the basic properties of biological macromolecules and assemblies including proteins, nucleic acids, and membranes. Among the topics covered are the forces that govern biological structures, how proteins act as catalysts, how membranes act to store energy, and how nucleic acids and proteins are synthesized in cells. Methods for manipulating the living cells to change their properties and to produce specific proteins of nucleic acids are detailed.
• ENG BE 566: DNA Structure and Function
  Physical structure and properties of DNA. The physical principles of the major experimental methods to study DNA are explained, among them: X-ray analysis, NMR, optical methods (absorption, circular dichroism, fluorescence), centrifugation, gel electrophoresis, chemical and enzymatic probing. Different theoretical models of DNA are presented, among them the melting (helix-coil) model, the polyelectrolyte model, the elastic-rod model, and the topological model. Theoretical approaches to treat the models, (e.g., the Monte Carlo method) are covered. Special emphasis is placed on DNA topology and DNA unusual structures and their biological significance. Major structural features of RNA are considered in parallel with DNA. The main principles of DNA-protein interaction are presented. the role of DNA and RNA structure in most fundamental biological proceses, replication, transcription, recombination, reparation, and translation is considered.
• ENG BE 567: Nonlinear Systems in Biomedical Engineering
  Introduction to nonlinear dynamical systems in biomedical engineering. Qualitative, analytical and computational techniques. Stability, bifurcations, oscillations, multistability, hysteresis, multiple time-scales, chaos. Introduction to experimental data analysis and control techniques. Applications discussed include population dynamics, biochemical systems, genetic circuits, neural oscillators, etc. 4 cr.

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