Courses

The listing of a course description here does not guarantee a course’s being offered in a particular semester. Please refer to the published schedule of classes on the Student Link for confirmation a class is actually being taught and for specific course meeting dates and times.

• ENG BE 505: Molecular Bioengineering I
  Provides engineering perspectives on the building blocks of living cells and materials for biotechnology. Focuses on origins and synthesis in life and the laboratory, including biological pathways for sythesis of DNA, RNA and proteins; transduction, transmission, storage and retrieval of biological informatin by macromoleclues; polyerase chain reaction, restriction enzymes, DNA sequencing; energetics of protein folding and trafficking; mechanisms of enzymatic catalysts and receptor-ligand binding; cooperative proteins, multi- protein complexes and control of metabolic pathways; generation, storage, transmission and release of biomolecular energy; and methods for study and manipulation of molecules which will include isolation, purification, detection, chemical characterization, imaging and visualization of structure.
• ENG BE 506: Physical Chemistry of Cell Structure and Machinery
  Building on the engineering perspective of molecular-cell biology presented in ENG BE 505, the objective of this course is to provide a basic understanding of the physical chemistry of molecular structures important in living cells and in technological applications. Topics include: noncovalent interactions of biomolecules in water, thermodynamics of solutions and phase mixtures; nonequilibrium kinetics; polymer physics and elasticity; lipid self-assembly and interfacial thermodynamics; biomembranes; adhesion and molecular bonding; chemical grafting and surface analysis.
• ENG BE 508: Quantitative Studies of the Respiratory and Cardiovascular Systems
  The quantitative physiological aspects of the respiratory and cardiovascular systems are studied. Classical models of these systems are considered including lumped element models, branching tree structures, and distributed parameter models to predict wave propagation in compliant walled tubes filled with compressible or incompressible fluids. Extensive computer models are developed to simulate the behavior of these systems in the frequency and time domains. Includes lab.
• ENG BE 509: Perception and Quantitative Physiology of the Auditory System
  Introduction to the mammalian auditory system from a systems prospective. The class follows how sound propagates into the ear, how mechanical energy is transformed into a neural code, how that code is transformed through the mammalian auditory pathway from the cochlea to the cortex, and how auditory sensation and perception are related to this chain of neural processing. Anatomy and physiology will cover the structure and function of the middle ear, cochlea, brainstem, midbrain, thalamus, and cortex. Perceptual topics include basic sensitivity, spatial hearing, pitch perception, auditory scene analysis, attention, and speech perception. Implications for hearing impairment and prosthetic hearing devices will be covered. Associated discussion sessions cover recent research findings from general-interest, high-impact publications.
• 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: 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 519: Speech Processing by Humans and Machines
  Speech (naturally spoken) is the main mode of communication between humans. Speech technology aims at providing the means for speech-controlled man- machine interaction. The goal of this course is to provide the basic concepts and theories of speech production, speech perception, and speech signal processing. The course is organized in a manner that builds a strong foundation of basics, followed by a range of signal processing methods for representing and processing the speech signal. A familiarity with signals and systems, including continuous- time and discrete-time frequency analysis, sampling and filtering theory. A basic familiarity with probability, including Bayes theory. A familiarity with MATLAB.
• 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.
• 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 530: Structure and Function of the Extracellular Matrix
  This is an introductory course dealing with the detailed structure of the basic units of the extracellular matrix including collagen, elastin, microfibrils and proteoglycans as well as the functional properties of these molecules. The focus is mostly on how the structure of these components determine the functional properties such as elasticity at different scales from molecule to fibrils to organ level behavior. The biological role of these components and their interaction with cells is also covered. Interaction of enzymes and the matrix in the presence of mechanical forces is discussed. Mathematical modeling is applied at various length scales of the extracellular matrix that provides quantitative understanding of the structure and function relationship. Special topics include how diseases affect extracellular matrix in the lung, cartilage and vasculature. The relevance of the properties of native extracellular matrix for tissue engineering is also discussed.
• ENG BE 533: Biorheology
  This is an introductory course whose main goal is to acquaint students with basic concepts of elasticity, viscoelasticity, plasticity, viscoplasticity, poroelasticity, non-Newtonian flow and related phenomena that often characterize mechanical behavior of biological materials. In studying these phenomena, different approaches have been utilized, including methods of continuum mechanics, phenomenological approaches, mathematical modeling and microstructural approaches that relate structural features with the overall behavior. Illustrative examples of application of these methods to studies of various biological materials at the system, organ, tissue, cellular and molecular levels will be presented. The course provides good foundations for further studies in the areas of rheology, mechanics of solids, cellular and tissue mechanics and mechanobiology.
• ENG BE 535: Cell Mechanics
  Provides an introduction to 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 549: Structure and Function of the Extracellular Matrix
  This is an introductory course dealing with the detailed structure of the basic units of the extracellular matrix including collagen, elastin, microfibrils and proteoglycans as well as the functional properties of these molecules. The focus is mostly on how the structure of these components determine the functional properties such as elasticity at different scales from molecule to fibrils to organ level behavior. The biological role of these components and their interaction with cells is also covered. Interaction of enzymes and the matrix in the presence of mechanical forces is discussed. Mathematical modeling is applied at various length scales of the extracellular matrix that provides quantitative understanding of the structure and function relationship. Special topics include how diseases affect extracellular matrix in the lung, cartilage and vasculature. The relevance of the properties of native extracellular matrix for tissue engineering is also discussed. Meets with MS 549 and ME 549.
• ENG BE 555: Introduction to Biomedical Optics
  This course surveys the applications of optical science and engineering to a variety of biomedical problems, with emphasis on optical and photonics technologies that enable real, minimally-invasive clinical and laboratory applications. The course teaches only those aspects of the biology itself that are necessary to understand the purpose of the applications. The first weeks introduce the optical properties of tissue, and following lectures cover a range of topics in three general areas: 1) Optical spectroscopy applied to diagnosis of cancer and other tissue diseases; 2) Photon migration and diffuse optical imagine of subsurface structures in tissue; and 3) laser-tissue interactions and other applications of light for therapeutic purposes. Some classes will invoke traditional lectures, and others will be "inverted," devoted to discussing and understanding application problems, with students having read textbook sections or online material prior to class.

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