Biomedical Engineering (BME)

BME 500
Introduction to Biomedical Engineering

Introduction to the concepts and research in biomedical engineering. Provides an overview of current biomedical engineering research areas, emphasis on application of an engineering approach to medicine and physiology signals. The focus is on connecting theory with practice: students are expected to critically analyze research manuscripts and perform corresponding analysis on relevant biomedical data.

Lecture: 2 Lab: 0 Credits: 2
BME 501
Communication Skills in BME

Students will be taught to communicate biomedical engineering research findings through written, poster, and oral presentation formats. Masters of Science with Thesis and PhD program students will be required to present their own research annually at the BME Seminar while enrolled in their thesis program.

Lecture: 1 Lab: 0 Credits: 1
BME 502
Introduction to Regulatory Science for Engineers

Engineers must be equipped to answer the growing demands for new medical technologies. Introduction to Regulatory Science teaches engineers how the regulated environment impacts the design, testing. and delivery of medical devices. It will equip students with the essential skills and tools critical to the practice of engineering in the medical device industry. In this course, students will be exposed to the core concepts, processes, and tools surrounding the global medical device regulatory framework, and will gain foundational knowledge for the practical application of regulations throughout the product development lifecycle. From knowledge gained in the class, students will be expected to work in teams and use critical thinking, data analysis and interpretation skills to research, evaluate, and present a scientific, technical, and legally justifiable approach for the global introduction of a new medical device.

Lecture: 3 Lab: 0 Credits: 3
BME 503
Mathematical and Statistical Methods for Neuroscience I

This quarter introduces mathematical ideas and techniques in a neuroscience context. Topics will include some coverage of matrices and complex variables; eigen value problems, spectral methods and Greens functions for differential equations; and some discussion of both deterministic and probabilistic modeling in the neurosciences. Instructor permission required.

Lecture: 2 Lab: 0 Credits: 2
BME 504
Neurobiology

This course is concerned with the structure and function of systems of neurons, and how these are related to behavior. Common patterns of organization are described from the anatomical, physiological, and behavioral perspectives of analysis. The comparative approach is emphasized throughout. Laboratories include exposure to instrumentation and electronics, and involve work with live animals. A central goal of the laboratory is to expose students to in vivo extracellular electrophysiology in vertebrate preparations. Laboratories will be attended only on one day a week but may run well beyond the canonical period. Instructor permission required.

Lecture: 2 Lab: 0 Credits: 2
BME 505
Mathematical and Statistical Methods for Neuroscience II

This quarter treats statistical methods important in understanding nervous system function. It includes basic concepts of mathematical probability; information theory, discrete Markov processes, and time series. Instructor permission required.

Prerequisite(s): BME 503 with min. grade of C
Lecture: 2 Lab: 0 Credits: 2
BME 506
Computational Neuroscience II: Vision

This course considers computational approaches to vision. It discusses the basic anatomy and physiology of the retina and central visual pathways, and then examines computational approaches to vision based on linear and non-linear systems theory, and algorithms derived from computer vision.

Lecture: 3 Lab: 0 Credits: 3
BME 507
Cognitive Neuroscience

This course is concerned with the relationship of the nervous system to higher order behaviors such as perception and encoding, action, attention and learning and memory. Modern methods of imaging neural activity are introduced, and information theoretic methods for studying neural coding in individual neurons and populations of neurons are discussed. Instructor permission required.

Lecture: 2 Lab: 0 Credits: 2
BME 508
Mathematics and Statistics for Neuroscience III

This course covers more advanced topics including perturbation and bifurcation methods for the study of dynamical systems, symmetry methods, and some group theory. A variety of applications to neuroscience with be described. Instructor permission required.

Prerequisite(s): BME 505 with min. grade of C and BME 503 with min. grade of C
Lecture: 2 Lab: 0 Credits: 2
BME 509
Vertebrate Neural Systems

This lab-centered course teaches students the fundamental principles of mammation neuroanatomy. Students learn the major structures and the basic circuitry of the CNS and PNS. Students become practiced at recognizing the nuclear organization and cellular architecture of many regions in animal brain models. This course is taught at the University of Chicago. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 510
Neurobiology of Disease I

This seminar course is devoted to basic clinical and pathological features and pathogenic mechanisms of neurological diseases. The first semester is devoted to a broad set of disorders ranging from developmental to acquired disorders of the central and peripheral nervous system. Weekly seminars are given by experts in the clinical and scientific aspects of the disease under discussion. For each lecture, students are given a brief description of clinical and pathological features of a given set of neurological diseases followed by a more detailed description of the current status of knowledge of several of the prototypic pathogenic mechanisms.

Lecture: 2 Lab: 0 Credits: 2
BME 511
Extracellular Matrices: Chemistry and Biology

Advanced topics dealing with the biology and chemistry of the extracellular matrix, cell-matrix interactions, and current methodologies for engineering these interfaces.

Lecture: 2 Lab: 0 Credits: 2
BME 512
Behavioral Neurosciences

This course is concerned with the structure and function of systems of neurons and how these are related to behavior. Common patterns of organization are described from the anatomical, physiological, and behavioral perspectives of analysis. The comparative approach is emphasized throughout. Laboratories include exposure to instrumentation and electronics and work involvement with live animals.

Lecture: 2 Lab: 0 Credits: 2
BME 513
Methods of Computational Neuroscience: Single Neurons

Topics include, but are not limited to, Hodgkin-Huxley equations, cable theory, single neuron models, information theory, signal detection theory, reverse correlation, relating neural responses to behavior, and rate versus temporal codes. Instructor permission is required.

Lecture: 3 Lab: 0 Credits: 3
BME 516
Biotechnology for Engineers

This course will provide students opportunity to learn about the field of biotechnology and how to apply engineering principles to biological systems and living organisms for betterment of medicines as well as agricultural products. The course covers the introduction to biotechnology with information about cell and molecular biology, the role of enzyme and growth kinetics, media preparations for cell culture and various chromatographic techniques, and antibiotics and its role in secondary metabolic production. Biological effluent treatment and regulatory issues to obtain FDA will be taught. Instructor permission is required.

Lecture: 3 Lab: 0 Credits: 3
BME 517
Technologies for Treatment of Diabetes

Study of physiological control systems and engineering of external control of biological systems by focusing on an endocrine system disorder -- diabetes. The effects of type 1 diabetes on glucose homeostasis and various treatment technologies for regulation of glucose concentration. Development of mathematical models describing the dynamics of glucose and insulin concentration variations, blood glucose concentration measurement and inference techniques, insulin pumps, and artificial pancreas systems.

Lecture: 3 Lab: 0 Credits: 3
BME 518
Reaction Kinetics for Biomedical Engineering

This course is an introduction to the fundamentals of chemical kinetics. Analysis of rate data; single and multiple reaction schemes. Biomedical topics include biological systems, enzymatic pathways, enzyme and receptor-ligand kinetics, pharmacokinetics, heterogeneous reactions, microbial cell growth and product formation, and the design and analysis of biological reactors.

Corequisite(s): BME 482
Prerequisite(s): BME 301 and MATH 252 and BME 335
Lecture: 3 Lab: 0 Credits: 3
BME 519
Cardiovascular Fluid Mechanics

Anatomy of the cardiovascular system. Scaling principles. Lumped parameter, one-dimensional linear and nonlinear wave propagation, and three-dimensional modeling techniques applied to simulate blood flow in the cardiovascular system. Steady and pulsatile flow in rigid and elastic tubes. Form and function of blood, blood vessels, and the heart from an engineering perspective. Sensing, feedback, and control of the circulation. Includes a student project.

Lecture: 3 Lab: 0 Credits: 3
BME 521
Medical Imaging

Study of modern technology for medical imaging. Theory and operation of CAT, SPECT, PET, MRI, X-ray and echo imaging modalities.

Lecture: 3 Lab: 0 Credits: 3
BME 522
Mathematical Methods in Biomedical Engineering

Graduate standing in BME or consent of instructor This course is an introductory graduate level course that integrates mathematical and computational tools that address directly the needs of biomedical engineers. The topics covered include the mathematics of diffusion, pharmacokinetic models, biological fluid mechanics, and biosignal representations and analysis. The use of MATLAB will be emphasized for numerically solving problems of practical relevance.

Lecture: 3 Lab: 0 Credits: 3
BME 523
Cell Biomechanics: Principles and Biological Processes

This course will provide students an opportunity to learn about mechanical forces that develop in the human body and how they can influence cell functions in a range of biological processes from embryogenesis, wound healing, and regenerative medicine to pathological conditions such as cancer invasion. Examples of research methods for investigating cell biomechanics in various biological systems will be discussed. Permission of instructor is required.

Lecture: 3 Lab: 0 Credits: 3
BME 524
Quantitative Aspects of Cell andTissue Engineering

This course is designed to cover fundamentals of cell and tissue engineering from a quantitative perspective. Topics addressed include elements of tissue development, cell growth and differentiation, cell adhesion, migration, molecular and cellular transport in tissues and polymeric hydrogels for tissue engineering and drug delivery applications.

Lecture: 3 Lab: 0 Credits: 3
BME 525
Introduction to Medical Devices, BioMEMS and Microfluidics

This course will present fundamentals and applications of medical devices, BioMEMS, and microfluidic technologies for applications in the broad health and biomedical engineering. It will provide a broad view of the general field and a knowledge of relevant fabrication methods and analysis techniques. Fabrication and analytical techniques, interfacing with biological materials, and techniques for analyte detection will be emphasized. The course will include individual projects and critical paper reviews in which each student will be encouraged to master basic concepts in design and fabrication for devices for specific applications.

Lecture: 3 Lab: 0 Credits: 3
BME 526
Advanced Biomedical Engineering Design

This course aims to educate students on project definition, and on the design, development, and technology transfer of potential biomedical products in the context of the student's major capstone project. Students will learn best practices for designing a marketable medical device, including the design process from the clinical problem definition through prototype and clinical testing to market readiness. Permission from instructor is required.

Lecture: 3 Lab: 0 Credits: 3
BME 527
Extracellular Matrix Biology

This course is a the same as the BME 427 Extracellular Matrix Biology course that has been approved for banner listing for Summer 2020. BME527 is the same class to extend this course to graduate students. The Extra Cellular Matrix (ECM) is that which connects cells in tissues and provides much of the organization and support in almost every tissue and or organ system of the body. Thus the aim of this course is to give students insights into ECM biology and its relevance to modern medicine and biomedical (tissue) engineering. A significant portion of working population is suffering from ECM-related maladies, and the focus of research has shifted into creating ECM implants. The ECM implant market is growing rapidly. For instance, the collagen meniscus implant market was reported to be at $308.6 million in 20181. Understanding the implications of the molecular biology of ECM to feed into this research is highly relevant for students considering careers (academic and industry) in life sciences in industry, academia and healthcare. Extracellular Matrix (ECM) is a highly complex system in mammalian biology responsible for structural support and functional (biochemical) signals for physiology. Specific amino acid sequences on the various ECM elements are responsible to trigger intra- and extracellular cascades leading to cell division, proliferation, tissue regeneration, wound healing and inflammation. This course will focus on the following key concepts: a) Gene expression, structure and function of various ECM proteins and complexes and the physiological processes. b) Etiology and the molecular progression of diseases caused by abnormalities to ECM proteins. c) Mechanobiology of various ECM proteins. d) Structure function and mechanical function of ECM interfaces with other tissues (muscle, bone, skin etc.) e) Implications for tissue engineering and development of novel biomimetic and biological ECM implants.

Lecture: 3 Lab: 0 Credits: 3
BME 528
Engineering World Health

This course covers the major types of medical equipment, including the principles of operation, the physiology underlying the measurement, the major functional (system) pieces for each instrument, and typical problems/applications of each instrument. Special focus is placed on making reliable and safe repairs in a low resource setting: Troubleshooting, creative problem solving, calibration and testing. Laboratory sessions will focus on learning hands on and technical knowledge required for completing basic electronic and mechanical repairs. Basic electronics through simple power supply design will be covered. Over the course of the semester, the class will travel to a hospital or training laboratory to troubleshoot and repair medical equipment as a group.

Prerequisite(s): MATH 152 and PHYS 221
Lecture: 3 Lab: 0 Credits: 3
BME 529
Design of Pharmaceutical Protein Formulations

This course introduces the discovery and development of pharmaceutical proteins and vaccines. The course focuses on understanding protein structure physical and chemical stability and identifying the cause of degradation processes in protein-based pharmaceutical products. Additionally, this course deals with vaccine-based formulations and their manufacturing process.

Lecture: 3 Lab: 0 Credits: 3
BME 530
Inverse Problems in Biomedical Imaging

This course will introduce graduate students to the mathematical theory of inverse problems. Concept from functional analysis will be applied for understanding and characterizing mathematical properties of inverse problems. This will permit for the analysis of the stability and resolution of image reconstruction algorithms for various existing and novel biomedical imaging systems. The singular value decomposition (SVD) is introduced and applied for understanding fundamental properties of imaging systems and reconstruction algorithms. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 532
Medical Imaging Science

This course is an introduction to basic concepts in medical imaging, such as: receiver operating characteristics, the rose model, point spread function and transfer function, covariance and auto covariance, noise, filters, sampling, aliasing, interpolation, and image registration. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 533
Biostatistics

This course is designed to cover the tools and techniques of modern statistics with specific applications to biomedical and clinical research. Both parametric and nonparametric analysis will be presented. Descriptive statistics will be discussed although emphasis is on inferential statistics and experimental design.

Lecture: 3 Lab: 0 Credits: 3
BME 535
Magnetic Resonance Imaging

This is an introduction to the Physics and technology of magnetic resonance imaging (MRI). the topics that are covered include: basic MR physics, source of signal, signal acquisition, pulse sequences, hardware, artifacts, spectroscopy, and advanced imaging techniques. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 537
Introduction to Molecular Imaging

This course provides an overview of molecular imaging, a subcategory of medical imaging that focuses on noninvasively imaging molecular pathways in living organisms. Topics include imaging systems, contrast agents, reporter genes and proteins, tracer kinetic modeling. Preclinical and clinical applications will also be discussed with an emphasis on cancer and the central nervous system.

Lecture: 3 Lab: 0 Credits: 3
BME 538
Neuroimaging

This course describes the use of different imaging modalities to study brain function and connectivity. The first part of the course deals with brain function. It includes an introduction to energy metabolism in the brain, cerebral blood flow, and brain activation. It continues with an introduction to magnetic resonance imaging (MRI), perfusion-based fMRI, Bold fMRI, fMRI paradigm design and statistical analysis, introduction to positron emission tomography, (PET) and studying brain function with PET, introduction to magneto encephalography (MEG) and studying brain function with MEG. The second part of the deals with brain connectivity. It includes an introduction to diffusion tensor MRI, explanation of the relationship between the diffusion properties of tissue its structural characteristics, and white matter fiber tractography techniques. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 539
Advanced Medical Imaging

This course introduces advanced clinical imaging modalities, research imaging techniques, and concepts from image science and image perception. The first part of the course introduces the perception of image data by human observers and the visualization of brain structure and function. It includes an introduction to magnetic resonance imaging (MRI) and a survey of neurological imaging via functional MRI (fMRI). The second part of the course covers image science, clinical imaging applications, and novel research imaging techniques. It includes an introduction to radiation detection and image quality evaluation, a survey of clinical cases, and an overview of new imaging methods.

Lecture: 3 Lab: 0 Credits: 3
BME 540
Wave Physics and Applied Optics for Imaging Scientists

This course will introduce students to fundamental concepts in wave physics and the analysis of optical wave fields. These principles will be utilized for understanding existing and novel imaging methods that employ coherent radiation. Solutions to inverse scattering and inverse source problems will be derived and algorithmic realizations of the solutions will be developed. Phase contrast imaging techniques and X-ray imaging systems that employ coherent radiation will be studied. Instructor permission required.

Lecture: 3 Lab: 0 Credits: 3
BME 542
Advanced Concepts in Image Science

This graduate level course introduces students to fundamental concepts in image science that are related to the optimization and evaluation of biomedical imaging systems. Topics covered include: deterministic descriptions of imaging systems, stochastic descriptions of imaging systems, statistical decision theory, and objective assessment of image quality.

Prerequisite(s): BME 532 with min. grade of C and BME 530 with min. grade of C
Lecture: 3 Lab: 0 Credits: 3
BME 543
Bioinstrumentation and Electronics

Principles of circuit analysis are applied to typical transducer and signal recording situations found in biomedical engineering. Basic electrical and electronic circuit theory is reviewed with an emphasis on biomedical measurement applications. a special topic is individually studied by the student and presented to the class electrical physics class or basic circuits.

Lecture: 3 Lab: 0 Credits: 3
BME 545
Quantitative Neural Function

Computational approach to basic neural modeling and function, including cable theory, ion channels, presynaptic potentials, stimulation thresholds, and nerve blocking techniques. Synaptic function is examined at the fundamental level.

Prerequisite(s): BME 453 with min. grade of C or BME 553* with min. grade of C, An asterisk (*) designates a course which may be taken concurrently.
Lecture: 3 Lab: 0 Credits: 3
BME 551
Physiological Signal Processing and Control Theory

This is the first of a 2 part course co-taught at IIT and the University of Chicago. essential elements of signal processing and control theory as it is applied to physiological systems will be covered. Part I will cover data acquisition and sampling, Laplace and Fourier transforms, filtering, time and frequency domains, system descriptions and lumped vs. distributed parameters. Students will use Mat lab to test concepts presented in class.

Lecture: 2 Lab: 0 Credits: 2
BME 552
Control Systems for Biomedical Engineers

Control systems design and analysis in biomedical engineering. Time and frequency domain analysis, impulse vs. step response, open vs. closed loop response, stability, adaptive control, system modeling. Emphasis is on understanding physiological control systems and the engineering of external control of biological systems.

Lecture: 3 Lab: 0 Credits: 3
BME 553
Advanced Quantitative Physiology

The main systems that control the human body functions will be reviewed to enable the students to understand the individual role of each major functional system as well as the need for the integration or coordination of the activities of the various systems.

Lecture: 3 Lab: 0 Credits: 3
BME 560
Methods in Biomedical Data Science

The course provides an overview of predictive and descriptive statistical modeling methods for large biomedical datasets. Building on undergraduate-level knowledge of statistics, the course introduces Bayes and information theory, develops from these modeling algorithms and provides a series of biomedical application areas. Methods include meta-analytic techniques, linear and non-linear dimensionality reduction, traditional “non-deep” predictive tools (e.g. perceptron, support vector machines, logistic regression, decision trees, boosting, etc.), and some applications of deep neural networks. Application areas may include medical imaging (e.g. image segmentation), EEG and ECG signal analysis (e.g. anomaly detection), genetics (e.g. imputation methods, polygenic risk score computation, cell-free DNA analysis, etc.). Each course module involves analysis of real data using existing modeling libraries and students’ own implementation. The predictive results may be compared to the state-of-the-art for each example dataset to assess the usefulness of the models. (3-0-3)

Prerequisite(s): (MATH 225 or BME 433 or CHE 426) and (MATH 332 or MATH 333)
Lecture: 3 Lab: 0 Credits: 3
BME 575
Neuromechanics of Human Movement

This course will explore how we control movement of our extremities, with concepts drawn from mechanics and neurophysiology. The progression from neurological signals to muscle activation and resulting movement of the hand or foot will be modeled, starting at the periphery and moving back toward the central nervous system. Biomechanics of the limbs will be modeled using dynamic simulation software (Working Model) which will be driven by a neural controller, implemented in MATLAB. Issues related to sensory feedback and redundancy will be addresses.

Lecture: 3 Lab: 0 Credits: 3
BME 581
Fluid Mechanics for Biomedical Engineers

This course is primarily focused on the development of theoretical and experimental principles necessary for the delineation of fluid flow in various in vitro chambers and the cardiovascular system. Its content will primarily deal with the basic concepts of flow in various geometries, the heterogeneous nature of blood and the application of such principles in flow chambers designed to expose blood elements to defined flow conditions. The relationship to flow in the normal and diseased vascular system will also be considered. A basic Fluid Dynamics Course is recommended. Instructor permission required.

Prerequisite(s): BME 500 with min. grade of C
Lecture: 3 Lab: 0 Credits: 3
BME 582
Advanced Mass Transport for Biomedical Engineers

This course is primarily focused on the development of theoretical and mathematical principles necessary for the delineation of mass transport processes in biological & medical systems. The content includes heterogeneous reactions that occur at or in the vicinity of cells or vascular structures under applied laminar flow and transport across cell membranes and within tissues.

Lecture: 3 Lab: 0 Credits: 3
BME 585
Computational Models of the Human Cardiovascular System

This course will focus on the use of computational fluid dynamics for the modeling and analysis of the human cardiovascular system. The course will cover both computational methods for fluid dynamics and biomedical aspects of the human cardiovascular system. Computer models for the simulation and analysis of hemodynamic phenomena will be developed. Requires an Introductory fluid dynamics.

Lecture: 3 Lab: 0 Credits: 3
BME 591
Research and Thesis for Master of Science Degree

Research and thesis for master of science degree students. Instructor permission required.

Credit: Variable
BME 594
Special Projects

Special projects.

Credit: Variable
BME 595
Seminar in Biomedical Engineering

Current research and development topics in biomedical engineering as presented by outside speakers, faculty and advanced students.

Lecture: 0 Lab: 1 Credits: 1
BME 597
Special Problems

Special problems.

Credit: Variable
BME 691
Research and Thesis PHD

Research and Thesis for PhD degree. (variable credit)

Credit: Variable