Biomedical Engineering

• ENG BE 570: Introduction to Computational Vision
  . Introductory course in biological visual neuroscience and computational vision. Provides a survey of the psychophysical, neuroanatomical and neurophysiological substrates of visual mechanisms underlying perception of visual motion, depth, objects, and space and of decision making mechanisms. Discussion of theoretical, explanatory, paradigms for these visual mechanisms. Topics addressed include psychophysics, methods from single cell recording physiology and low field potentials (LFP),multimodal imaging and computational modeling of various visual tasks and their modulation by attention. We will briefly address learning mechanisms and their relationship to brain plasticity. A term project is required for graduate credit. 4 cr.
• ENG BE 700: Advanced Topics in Biomedical Engineering
  Advanced study of a specific research topic in biomedical engineering. Intended primarily for advanced graduate students.
• ENG BE 703: Numerical Methods and Modeling in Biomedical Engineering
  This graduate course is an introduction to the computational tools most commonly applied in biological and physiological research, with emphasis on the art of using models, programming and simulation to reach useful conclusions and insights. The first half of the course is an introduction to the Unix operating system, the elements of programming, and basic methods of numerical analysis. Specific topics include exact and iterative methods for the solution of large systems, differentiation and interpolation numerical integration, Monte Carlo methods and statistical bootstrap methods, Fourier transform and spectral methods, and also finite element and finite difference methods for the solution of ordinary and partial differential equations. Each weekly lecture is accompanied by a computer lab in which the students will gain experience in the use of the techniques under study. The last half of the course uses a case study approach comprised of several two-week modules designed to immerse students in a variety of specific bioengineeering applications covering the range from genes and molecules to cells organs and systems. Each module will begin with lectures on the derivation and implementation of a particular model or computational algorithm and be accompanied by a related computational mini-project.
• ENG BE 705: Single Molecule Approaches for Biophysics and Bioengineering - Fundamentals and Applications
  The emergence of single-molecule (SM) methods in biology and bioengineering in the past decade have revolutionized the way scientists approach the molecular biology of the cell. The ability to directly probe biomolecular process in real-time, in their native cellular environment, revealed the mechanism of fundamental processes in biology with unprecedented detail and accuracy. As SM methods are refined they are increasingly recruited by bioengineers to invent the future platforms for molecular diagnostics and analytical detection. This course covers experimental methods for investigating the molecular machinery of a living cell in vitro and in live cells, and novel tools for sensing biomolecules and their application in biotechnology. Fundamental principles underlying fluorescence of single molecules, force measurements of biomolecules, ion channel kinetics, and stochastic sensing, will be covered in the context of relevant biological and biotechnological examples. There will be an emphasis on fundamental physical concepts underlying these systems, coming from statistical mechanics of soft matter. 4 cr. 1st sem.
• ENG BE 706: Quantitative Physiology for Engineers
  Course in human physiology for biomedical engineering students. Fundamentals of cellular and systems physiology, including the nervous, muscular, cardiovascular, respiratory, renal, gastrointestinal, endocrine, and immune systems. Quantitative and engineering approaches will be applied to understanding physiological concepts.
• ENG BE 707: Quantitative Studies of Excitable Cells
  Focuses on the properties of the membranes of nerve and muscle cells. Classical models of resting potentials, action potentials, synaptic transmission, and sensory receptors are treated. The structure and function of single ionic channels are characterized in detail from patch-clamp recordings, neuropharmacological studies, and molecular studies. Mechanisms of muscle contraction and other forms of cellular motility are also covered.
• ENG BE 710: Neural Plasticity and Perceptual Learning
  This course explores the capacity of cortical sensory and motor maps in the adult brain to change as a result of alterations in the effectiveness of the input, direct damage, or practice. The lectures will describe and discuss (1) the physiology and anatomy underlying adult dynamics; (2) psychophysical methods and experimental paradigms that have been used to study cortical plasticity in the early stages of the sensory and motor pathways; (3) evidence for perceptual learning; and (4) biologically plausible computational models of learning. We will discuss applications of functional neuroimaging to study perceptual learning and restorative plasticity in the human brain.
• ENG BE 721: Continuum Mechanics
  Foundations of the classical theories of continuum mechanics: elasticity and fluid mechanics. A rigorous mathematical approach to kinematics, stress analysis, balance laws (mass, momentum, and energy), entropy inequality, and constitutive equations using vectors and tensors.
• ENG BE 722: Advanced Continuum Biomechanics and Biofluid Dynamics
  This is the second course in a two-semester sequence, which emphasizes the application of continuum mechanics to problems in physiology, biology, and medicine. Material will be presented through topical examples, which will employ the governing equations and field theory of continuum mechanics and illustrate how to apply these principles to formulate and solve problems in biomechanics and biofluid dynamics. Examples will be presented in the context of four three-week long modules. Utilizing various problem solving techniques (e.g., the finite element method, Monte Carlo simulation, perturbation methods, etc.), each module will take a multidisciplinary approach that will illustrate the necessity to incorporate concepts and tools from a variety of fields (e.g., chemistry, physical chemistry, thermodynamics, acoustics, electrostatics, molecular dynamics, etc.), and which might include non-continuum approaches (e.g., statistical physics, structural mechanics, etc.). Some modules will include wet/computer lab components.
• ENG BE 726: 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 and hydrogels). Note that the laboratory portion is not offered in BE 726. Same as ME 726/MS 726. Students may not receive credit for both.
• ENG BE 727: 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, soft tissue mechanics and specific research topics. Students will write a NIH-style grant proposal on a specific research topic. Note that the laboratory portion is not offered in BE 727. Same as ME 727/MS 727. Students may not receive credit for both.
• ENG BE 736: Biomedical Transport Phenomena
  Students are introduced to the analysis and characterization of physiological systems and biomedical devices in which chemical reaction and the transport of mass and momentum play predominant roles. Fundamental scientific issues and analytical techniques are introduced and applied to case studies of specific engineering problems. Some knowledge of a high-level computer programming language is essential. A two-hour computer lab is required. Meets with ENGME736 and ENGMS736. Students may not receive credit for both.
• ENG BE 740: Parameter Estimation and Systems Identification
  Application of models with physical parameters to experimental data. Linear and non-linear systems estimation, system identifiability, time and frequency domain estimation, model sensitivity and experiment multivariate statistical analysis, and optimal design. Application predominantly to biomedical systems (e.g., cardiovascular, respiratory, and pharmokinetics). Other applications included. Same as ENG EC 740; students may not receive credit for both.
• ENG BE 747: Advanced Signals and Systems Analysis for Biomedical Engineering
  Introduction to advanced techniques for signals and systems analysis with applications to problems in biomedical engineering research. Time-domain and frequency-domain analysis of multiple input, multiple output systems using the fundamental matrix approach. Hilbert transform relations; applications to head-related transfer functions. Second-order characterization of stochastic processes: power density spectra, cross-spectra, auto-and cross-correlation functions. Gaussian and Poisson processes. Models of neural firing patterns. Effects of linear systems on spectra and correlation functions. Applications to models of the peripheral auditory system. Optimum processing applications. Applications to psychophysical modeling. Introduction to wavelets and wavelet transforms. Wavelet filter banks and wavelet signal processing.
• ENG BE 760: Structural Bioinformatics
  Principles and significance of protein structure. Protein domains and folds. Functional classification of proteins. Functional and structural annotation. Molecular modeling and simulation methods. Structure validation and refinement. Assignment of structure to genome sequences by homology modeling and fold recognition. The role of structure in functional annotation. Protein families and folds in genomes. Annotation from protein interactions. Interactions between proteins and small molecules. Structure-based drug design. Quantitative Structure-Affinity Relationships (QSAR) and the estimation of affinities. Chemoinformatics, molecular diversity, and combinatorial library design, DNA structure, protein-DNA interactions, and recognition sites. Binding of sall molecules to DNA, RNA structure prediction.
• ENG BE 764: Biophysics of Large Molecules
  Correlation between various physical properties of large molecules and their structure is considered in detail. Physical and mathematical description of polyatomic molecules and macromolecules is elaborated. Methods to study large molecules are described. A special emphasis is given to interaction of large molecules with electromagnetic radiation (visual light, ultraviolet and infrared radiation, X-rays, radiowaves). Physics of macromolecules or Polymers) is treated in detail. Numerous biomedical photosynthesis, DNA damage under irradiation, structure of major biological molecules (proteins and nucleic acids).
• ENG BE 765: Biomedical Optics and Biophotonics
    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 applications. The course teaches only those aspects of biology itself that are necessary to understand the purpose of the application. 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 optical imaging of subsurface structures in tissue; and 3) Laser-tissue interactions and other applications of light for therapeutic purposes. In addition to formal lectures, recent publications from the literature will be selected as illustrative of various topical areas, and for each publication one student will be assigned to prepare an informal presentation (with overhead slides or PowerPoint) reviewing for the class the underlying principles of that paper and outlining the research results. Same as ENG EC 765; students may not receive credit for both.
• ENG BE 767: Protein and Genomic Systems Engineering
  This course will provide a critical review of current research topics in proteomics and systems biology. Emphasis will be placed on protein engineering (gross structural modifications, pathway perturbations, and biomedical applications including therapeutics and diagnostics) and genome engineering (knockout strains, conditional knockouts, and bioproductions optimization). Topics covered will include: mass spectrometry, protein microarrays, protein complex and interaction discovery, uses of antibodies as reagents and therapeutics, and pathway and network analyses.
• ENG BE 768: Biological Database Analysis
  Describes relational data models and database management systems. Teaches the theories and techniques of constructing relational databases with emphasis on those aspects needed for various biological data, including sequences, structures, genetic linkages and maps, and signal pathways. Introduces relational database query language SQL. Summarizes currently existing biological databases and the Web-based programming tools for their access. Object-oriented modeling is introduced primarily as a design aid for dealing with the particular complexities of biological information in standard RDB design. Emphasis will be on those problems associated with dealing with data whose nomenclature and interrelationships are undergoing rapid change.
• ENG BE 773: Advanced Optical Microscopy and Biological Imaging
  This course will present a rigorous and detailed overview of the theory of optical microscopy starting from basic notions in light propagation and covering advanced concepts in imaging theory such as Fourier optics and partial coherence. Topics will include basic geometric optics, photometry, diffraction, optical transfer functions, phase contrast microscopy, 3D imaging theory, basic scattering and fluorescence theory, imaging in turbid media, confocal microscopy, optical coherence tomography (OCT), holographic microscopy, fluorescence correlation spectroscopy (FCS), fluorescence resonant energy transfer (FRET), and nonlinear-optics based techniques such as two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) microscopy. Biological applications such as calcium and membrane-potential imaging will be discussed. A background in optics is preferable. A background in signals and analysis is indispensable. In particular, the student should be comfortable with Fourier transforms, complex analysis, and transfer functions. Meets with ENGEC773. Students may not receive credit for both.

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