Biomedical Engineering (BME)

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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)

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.

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.

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.

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.

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

Special projects.

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

Special problems.

Research and Thesis for PhD degree. (variable credit)