Biomedical Engineering

• ENG BE 509: Quantitative Physiology of the Auditory System
  Undergraduate Prerequisites: CAS BI 315 ; ENG BE 401 ; ENG BE 200; or permission of instructor.
  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. 4 cr
• ENG BE 511: Biomedical Instrumentation
  Undergraduate Prerequisites: ENG EC 412 and ENG BE 402.
  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 513: Biological and Environmental Acoustics
  Undergraduate Prerequisites: ENG BE 401-; or permission of instructor or graduate standing.
  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
  Undergraduate Prerequisites: ENG EC 401 or ENG BE 401 or ENG EK 510; and elementary knowledge of atomic physics.
  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. 4 cr
• 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. 4 cr
• ENG BE 519: Speech Signal Processing
  Undergraduate Prerequisites: ENG BE 401 or equivalent (e.g. ENG EC 401); ENG BE 200 or equivalent (ENG EC 381).
  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 first, and then concentrates on a range of signal processing methods for representing and processing the speech signal. 4 cr
• ENG BE 521: Continuum Mechanics
  Undergraduate Prerequisites: ENGEK424 or ENGME309 and either ENGME304, ENGME421, ENGME422, ENGBE420, ENGBE436, or consent of instructor.
  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. 4 cr
• ENG BE 524: Skeletal Tissue Mechanics
  Undergraduate Prerequisites: ENG EK 301 ; ENG ME 302 ; ENG ME 305; or ENG BE 420 or ENG ME 308 and CAS MA 242 or equivalent.
  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. 4 cr
• ENG BE 526: Fundamentals of Biomaterials
  Undergraduate Prerequisites: ENG EK 301 ; ENG EK 424 ; CAS CH 101 ; CAS CH 102 ; ENG BE 209.
  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. 4 cr
• ENG BE 527: Principles and Applications of Tissue Engineering
  Undergraduate Prerequisites: ENG EK 301 ; ENG EK 424 ; CAS CH 101 ; CAS CH 102 ; ENG BE 209 ; ENG BE 526.
  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. 4 cr
• ENG BE 533: Biorheology
  Undergraduate Prerequisites: ENG BE 420 ; ENG EK 424 ; ENG BE 521.
  An introductory course emphasizing those rheological properties (such as elasticity, viscoelasticity, poroelasticity, plasticity, and viscoplasticity) that often characterize solid biological tissues and cells. 4 cr
• ENG BE 535: Cell Mechanics
  Undergraduate Prerequisites: ENG BE 209 ; ENG EK 424 ; ENG ME 305; or ENG BE436
  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. 4 cr.
• 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. 4 cr.
• ENG BE 560: Biomolecular Architecture
  Undergraduate Prerequisites: CAS PY 212 and CAS CH 131; or CASCH102
  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. 4 cr
• ENG BE 562: Computational Biology: Genomes, Networks, Evolution
  Undergraduate Prerequisites: Fundamentals of programming and algorithm design (EK 127 or equivalent), basic molecular biology (BE 209 or equivalent), statistics and probability (BE 200 or equivalent), or consent of instructor.
  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
  Undergraduate Prerequisites: CAS CH 102 and ENG BE 401.
  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 566: DNA Structure and Function
  Undergraduate Prerequisites: CAS CH 102 and CAS PY 212.
  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. 4 cr
• ENG BE 567: Nonlinear Systems in Biomedical Engineering
  Undergraduate Prerequisites: Graduate standing or consent of instructor. Ordinary differential equations required; linear algebra recommended.
  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.
• ENG BE 568: Systems Biology of Human Disease
  This course will train students to apply or develop computational network, modeling, and machine learning concepts to probe into the systems biology of disease. The aim of this course is to cover general concepts in biological computing that provide the foundation of thinking computationally about anomalous behavior in biological systems that cause diseases. The course also aims to teach students to work in teams and develop the skills to plan and coordinate a scientific project. The course will cover computational frameworks, such as biological networks (including metabolic, regulatory, and signal transduction networks), micro array analysis, proteomic analysis, next generation sequencing, imaging, machine learning, probabilistic inference, genetics, pathway analysis, network and graph theory, and other technologies to medical diseases initially focusing on clincal problems such as cancer, diabetes, inflammation, and aging. The course is aimed at seniors and graduate students in biomedical engineering or bioinformatics; however, students from other disciplines ranging from medicine to physics or computer science can attend the class with some prerequisites. 4 cr.
• ENG BE 569: Next Generation Sequencing
  Undergraduate Prerequisites: ENG BE 200, ENG BE 401 or permission of instructor.
  The advent of high throughput sequencing is virtually changing biology and medicine. The technology enables us to catalog the entire functional parts list of living organisms from bacteria to human, develop and validate regulatory networks for controlling gene expression in systems biology models and develop novel biomarkers for personalized medicine that guide pharmacological treatments. In this course we will review the foundations of the field, starting from the biophysical foundations of current or emerging single molecule DNA sequencing techniques, through an introduction to the analytical tools to model and analyze NGS Data, and finally discussing clinical applications such as predicting drug response focusing on cancer. The course will involve bi-weekly homework assignments that include theoretical analysis and modeling, working with multiple analysis tools for NGS data including assembly, re-sequencing, alignments, RNA-seq, ChIP-seq, DNA methylation, mutation analysis and detection, copy number variation detection, and their applications to cancer. 4 cr