Biomedical Engineering

• ENG BE 504: Polymers and Soft Materials
  Undergraduate Prerequisites: Graduate standing or instructor consent after ENG EK 424 or CAS PY 410 - An introduction to soft matter for students with background in materials science, chemistry and physics. This graduate-level course covers general aspects of structure, interactions, and functions of polymers and soft materials (including colloidal suspensions). Specifically, students will learn key fundamentals behind the unique viscoelastic behavior of polymers and colloids, which an emphasis on understanding conceptual, structure/function, and mathematical roots. Topics include chain behavior and self-avoiding walks, Flory- Huggins theory, and development of DLVO theory for zetapotential measurements. On a practical level, students will leave the class with an understanding of why rubber bands are stretchy, why people can run on cornstarch in water, why mixing polymers is challenging, and why Kevlar is bendable yet bulletproof! This is a fast-paced graduate course that requires thermodynamics as a prereq and assumes a familiarity with basic organic chemistry, differentials equations, and basic linear algebra. Meets with ENG ME and MS 504; students may not receive credit for both.
• ENG BE 505: Molecular Bioengineering 1
  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, 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 511: Biomedical Instrumentation
  Undergraduate Prerequisites: ENGBE403 and 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: (CASPY212 & ENGBE403) - 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 518: Modern Optical Microscopy for Biomedical Imaging
  Undergraduate Prerequisites: (ENG BE 403) Optical microscopy has become a ubiquitous tool in a variety of disciplines. The goal of this course is to provide you a comprehensive overview of modern optical microscopy techniques, with applications in biological imaging. The first half of the course will cover foundations, including basic principles of Fourier optics, image formation, intensity versus phase contrast, and fluorescence imaging. The second half of the course will examine state-of-the-art microscope techniques designed to address different challenges, including imaging in thick media, high-speed imaging, volumetric imaging, super-resolution imaging, etc.. You will be assigned weekly exercises related to image processing. There will be a mid-term exam. Finally, you will be required to present an oral report on a current research topic of their choice involving optical microscopy.
• ENG BE 521: Continuum Mechanics
  Undergraduate Prerequisites: (ENGME303 OR ENGBE436) 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 525: Engineering Tissue Injury, Repair and Foreign Body Responses
  Prerequisites: ENGBE 209. - Tissue injuries and diseases involving foreign bodies such as infection continue to be massive global challenges. Developing appropriate engineering solutions to these challenges requires understanding the pathological mechanisms of tissue injury and foreign bodies as well as knowledge of current state-of-the-art methods used to diagnose and treat the related disorders across the various organ systems of the body. This course will provide the foundational content on the cell and molecular mechanisms of injury and foreign body responses, introduce pathology methods, and explore advanced concepts in the engineering of tissue and organ repair and engineering approaches to regulating foreign body responses. In addition to lectured content, students will dissect and present new multidisciplinary peer-reviewed studies from the literature on emerging topics related to injury, repair and foreign body responses.
• ENG BE 526: Fundamentals of Biomaterials
  Undergraduate Prerequisites: (ENGEK301 & ENGEK424 & CASCH101 & CASCH102 & ENGBE209) - 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: (ENGEK301 & ENGEK424 & CASCH101 & CASCH102 & ENGBE209 & ENGBE526) - 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 549: Structure and Function of the Extracellular Matrix
  Undergraduate Prerequisites: (ENGBE420) - 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 555: Introduction to Biomedical Optics
  Undergraduate Prerequisites: (ENGBE403 OR ENGEC401) 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 tweezers 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; and half of class time will be devoted to solving problems in small groups.
• ENG BE 556: Optical Spectroscopic Imaging
  Undergraduate Prerequisites: PY 212 or equivalent knowledge of lights and waves, EK 122/125 or equi valent 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 557: Programming Fundamentals for Biomedical Engineering Data Analysis
  Prerequisites: ENGEK103, 125 and CASMA226. - A fast-paced bootcamp in the fundamentals of computation and programming for BME students. The course is designed for graduate students and senior undergraduates with minimal programming experience who seek to develop the skills necessary to develop practical software systems. The course will go beyond teaching the Python language to include a broader set of programming concepts including algorithms, data structures, object-oriented programming, and numerical computation. The topics covered will prepare students for downstream classes in machine learning applied to BME problems.
• ENG BE 559: Foundations of Biomedical Data Science and Machine Learning
  ¿Prerequisites: ENGEK103 and EK381. Programming Fundamentals for Biomedical Engineering Data Analysis with Python (BE500) or equivalent programming experience in Python (requires instructor approval). Proficiency in probability, calculus, and linear algebra.¿- This course will cover the conceptual foundations of data science and introductory machine learning for biomedical engineers and serves as a foundational course in data analytics for students in the biomedical sciences. It is designed to follow in depth-study of math (linear algebra, calculus, and probability) and programming and will prepare students for graduate-level classes focusing on more advanced applications of machine learning and data science. This course, taught in Python, will cover the theory and practical applications of hypothesis testing, model fitting and parameter estimation, classification, clustering, dimensionality reduction, and artificial neural networks.
• ENG BE 560: Biomolecular Architecture
  Undergraduate Prerequisites: (CASPY212 & CASCH131) 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 equa tions 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 571: Introduction to Neuroengineering
  Undergraduate Prerequisites: (ENGBE209) - This course covers current and future neurotechnologies for analyzing the brain and for treating neurological and psychiatric diseases. It focuses on the biophysical, biochemical, anatomical principles governing the design of the current neurotechnologies, with a goal of encouraging innovations of new generation of therapies. Topics include basic microscopic and macroscopic architecture of the brain, the fundamental properties of individual neurons and ensemble neural networks, electrophysiology, DBS, TMS, various imaging methods, optical neural control technologies, optogenetics, neuropharmacology, and gene/stem-cell therapies. Discussions of related literatures and design projects will be involved. Enrollment is limited to 30 students. The course is open to MS, MEng, and PhD students, as well as qualified undergraduate seniors. Same as ENG BE 771. Students may not receive credit for both.
• ENG BE 572: Neurotechnology Devices
  Undergraduate Prerequisites: (ENGBE403) - From electro-physiology to optical and MRI, non-invasive to invasive, neuro-sensing to neuro-modulation, and spanning applications in humans and animals; this course will cover the latest developments in devices used to study the brain. The course will center around several recent journal papers that introduces or utilizes novel devices for the advancement of neuroscience. For each paper, there will be one or two lectures on the background behind the specific neurotechnology advanced or utilized in the paper. In the following class, students will be required to critically discuss the given paper, with the discussion led by a group of assigned students who will first present an overview of the paper. Homeworks and the final project will further enhance critial review of the literature and investigation of neurotechnology devices. Same as ENG BE 772. Students may not receive credit for both.
• ENG BE 601: Linear Algebra
  The first of four math modules designed to reinforce basic mathematical and computer programming concepts pertinent to graduate research in biomedical engineering. This course will emphasize the 5 cornerstones of applied linear algebra: Linear combinations, projections & orthogonality, norms, eigenvalues & eigenvectors, and SVD. Topics include linear least-squares, data projections, Fourier series, wavelets, discrete Fourier transform (DFT), solid mechanics, Markov chains, principal component analysis, and signal processing techniques. This course will provide the necessary linear algebra background needed to solve problems in BE 602, 603 and 604.