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 MyBU Student Portal for confirmation a class is actually being taught and for specific course meeting dates and times.

• ENG BE 505: Molecular Bioengineering I
  Undergraduate Prerequisites: ENG EK424 or equivalent.
  Provides engineering perspectives on the building blocks of living cells and the use of these components for biotechnological applications. Topics covered include biological pathways for synthesis of DNA, RNA and proteins; transduction, transmission, storage and retrieval of biological information by macromolecules; polymerase chain reaction, restriction enzymes, DNA sequencing and DNA assembly; design principles of synthetic biological circuits; cooperative proteins, multi-protein complexes and control of metabolic pathways; and generation, storage, transmission and release of biomolecular energy. Same as ENG BE 605. Students may not receive credit for both.
• ENG BE 508: Quantitative Studies of the Respiratory and Cardiovascular Systems
  Undergraduate Prerequisites: ENG BE 403; Seniors with consent of instructor.
  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 511: Biomedical Instrumentation
  Undergraduate Prerequisites: ENGBE403 and either BE492 or BE493
  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 515: Introduction to Medical Imaging
  Undergraduate Prerequisites: CAS PY 212 and ENG BE 403.
  Methods for generating images of the interior of a body using X-rays, ultrasound, radiowaves, or radioactivity. 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
  Undergraduate Prerequisites: CAS PY 212.
  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
  Undergraduate Prerequisites: ENG BE 401 or equivalent (e.g. ENG EC 401); ENG EK 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, 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. Same as ENG EC 519. Students may not receive credit for both.
• ENG BE 521: Continuum Mechanics
  Undergraduate Prerequisites: ENG ME 303 or ENG BE 436; and ENGME304 or ENGEK424; and ENGME305 or ENGBE420
  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 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 ENG ME 524 and ENG MS 524. Students may not receive credit for both.
• 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). Same as ENG BE 726, ENG ME 726, ENG MS 726. Student may not receive credit for both. Meets with ENG BE 726 lectures. Note that the laboratory portion is not offered in BE 526.
• 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 physical chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on fundamental physical principles underlying tissue engineering. Requires prior knowledge of biomaterials and basic cell and molecular biology. Team projects and team critical review of primary literature. Same as ENG BE 727, ENG ME 727, ENG MS 727. Students may not receive credit for both. Meets with ENG BE 727 lectures. Note that the laboratory portion is not offered in BE 527.
• ENG BE 533: Biorheology
  Undergraduate Prerequisites: ENG EK 424; One of the following courses: ENG BE 420, ENG BE 436 or ENG BE/ME 521.
  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 549: Structure and Function of the Extracellular Matrix
  Undergraduate Prerequisites: ENG BE 420.
  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. Same as ENG ME 549 and ENG MS 549. Student may not receive credit for both,
• ENG BE 552: Computational Synthetic Biology for Engineers
  This course presents the field of computational synthetic biology through the lens of four distinct activities: Specification, Design, Assembly, and Test. Engineering students of all backgrounds are provided an introduction to synthetic biology and then exposed to core challenges and approaches in each of the four areas. Same as ENG EC 552. Students may not receive credit for both.
• ENG BE 555: Introduction to Biomedical Optics
  Undergraduate Prerequisites: ENG BE 403 or ENG EC 401; Requires senior status.
  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 pathologies; 2) Photon migration and diffuse optical imaging of subsurface structures in tissue; and 3) new tissue imaging methods, laser-tissue interactions and other applications of light for biomedical research. The format of this course is "semi-flipped." There are assigned readings from the required textbook, prior to each class. Half of class time will invoke informal lecture and discussion, to amplify and clarify the readings; and half of the class time will be in the style of a "flipped" class, devoted to working, in small groups, on problems and discussing and understanding the connection to the readings. Dual listed as ENG EC 555. Students may not receive credit for both.
• ENG BE 556: Optical Spectroscopic Imaging
  Undergraduate Prerequisites: PY 212 or equivalent knowledge of lights and waves, EK 122/125 or equivalent Matlab. Suggested: EC 562 or equivalent; EC 555 or equivalent
  This introductory graduate-level course aims to teach students how electromagnetic waves and various forms of molecular spectroscopy can be used to study a complex biological system by pushing the physical limits on engineering system design.The course will cover fundamental concepts of optical spectroscopy and microscopy, followed by specific topics covering fluorescence-based , absorption-based, and scattering-based spectroscopic imaging. In addition, this course will provide in-depth discussions of linear and nonlinear spectroscopic imaging in the aspects of theory, instrumentation, image data analysis and enabling applications. Students will learn how to give a concise and informative presentation of a recent literature to the class. Students will be able to challenge their creativity in designing advanced imaging instrument of data analysis methods as part of their course assignments. The students will learn how to write and present a convincing proposal for the required final project to be designed by interdisciplinary teams formed among the students. Same as ENG EC 556. Students may not receive credit for both.
• 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.
• ENG BE 562: Computational Biology: Machine Learning Fundamentals
  Undergraduate Prerequisites: ENG EK122/125, ENG EK381 AND ENGBE209
  In this course we cover the algorithmic and machine learning foundations of computational biology, combining theory with practice. We study the principles of algorithm design and foundational methods in machine learning. We provide an introduction to important problems in computational biology, and we provide hands on experience analyzing large-scale biological data sets.
• 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.
• 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 clinical 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.
• ENG BE 570: Introduction to Computational Vision
  Undergraduate Prerequisites: ENG EK 125 and ENG EK 381; Either ENGBE403 or ENGEC401.
  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.