Graduate Courses

Note: Students may also take courses from other engineering departments within Duke's Pratt School of Engineering, and courses from other schools at Duke with the permission of the adviser and the Director of Graduate Studies.

Approved Life Science Electives

CBB 520 Genome Tools and Technologies

 

CELLBIO 730 Stem Cell Course
CMB 797 Modern Techniques in Molecular Biology
MGM 701 Foundations of Molecular Genetics and Microbiology
MGM 732 Human Genetics

BIOCHEM 536 Bioorganic Chemistry
BIOCHEM 622 Structure of Biological Macromolecules
BIOCHEM 681 Physical Biochemistry

CELLBIO 503 Introduction to Physiology
EVANTH 530 Human Functional Anatomy
MEDPHY 505 Anatomy and Physiology for Medical Physicists

Neurobiology 719: Concepts in Neuroscience I
Neurobiology 720 - Concepts in Neuroscience II
Neurobiology 759S - PRINCIPLES COGNITV NEUROSCI I
Neurobiology 760S - PRINCIPLES COGNITV NEUROSCI II

IMM 544 Principles of Immunology
IMM 800 Comprehensive Immunology

Approved Advanced Math Courses

BME 790L Signal Processing and Applied Mathematics

CEE 530 Introduction to the Finite Element Method
CEE 630 Nonlinear Finite Element Analysis
COMPSCI 520 Numerical Analysis
MATH 561 Numerical Linear Algebra, Optimization, and Monte Carlo Simulation
MATH 563 Applied Computational Analysis
MATH 565 Numerical Analysis
MATH 660 Numerical Partial Differential Equations

MATH 551 Applied Partial Differential Equations and Complex Variables
MATH 577 Mathematical Modeling
MATH 721 Linear Algebra and Applications
MATH 753 Ordinary and Partial Differential Equations
PHYSICS 760 Mathematical Methods in Physics

CBB 540 Statistical Methods for Computational Biology
MATH 545 Introduction to Stochastic Calculus
STA 601 Bayesian and Modern Statistical Data Analysis
STA 611 Introduction to Mathematical Statistics

Biomedical Engineering GRADUATE Course Descriptions

Examples of BME graduate level courses are listed below. To find a complete list of the BME courses, please visit the Graduate School Bulletin at

https://registrar.duke.edu/sites/default/files/graduate/2018-19/134/inde...

503(253). Computational Neuroengineering (GE, EL). This course introduces students to the fundamentals of computational modeling of neurons and neuronal circuits and the decoding of information from populations of spike trains. Topics include: integrate and fire neurons, Spike Response Models, Homogeneous and Inhomogeneous Poisson processes, neural circuits, Weiner (optimal), Adaptive Filters, neural networks for classification, population vector coding and decoding. Programming assignments and projects will be carried out using MATLAB. Prerequisites: BME 101/201 or equivalent. Instructor: Henriquez. 3 units. C-L: Neuroscience 503(253).

504(254). Fundamentals of Electrical Stimulation of the Nervous System (GE, EL). This course presents a quantitative approach to the fundamental principles, mechanisms, and techniques of electrical stimulation required for non-damaging and effective application of electrical stimulation. Consent of instructor required. Instructor: Grill. 3 units.

506(204). Measurement and Control of Cardiac Electrical Events (GE, IM, EL). Design of biomedical devices for cardiac application based on a review of theoretical and experimental results from cardiac electrophysiology. Evaluation of the underlying cardiac events using computer simulations. Examination of electrodes, amplifiers, pacemakers, and related computer apparatus. Construction of selected examples. Prerequisites: Biomedical Engineering 253L(153L) or equivalents. Instructor: Wolf. 3 units.

511(211). Theoretical Electrophysiology (GE, EL). Advanced topics on the electrophysiological behavior of nerve and striated muscle. Source-field models for single-fiber and fiber bundles lying in a volume conductor. Forward and inverse models for EMG and ENG. Bidomain model. Model and simulation for stimulation of single-fiber and fiber bundle. Laboratory exercises based on computer simulation, with emphasis on quantitative behavior and design. Readings from original literature. Prerequisite: Biomedical Engineering 301L(201L) or equivalent. Instructor: Barr or Neu. 4 units. C-L: Neuroscience 511(241)

512L(212L). Theoretical Electrocardiography (GE, EL). Electrophysiological behavior of cardiac muscle. Emphasis on quantitative study of cardiac tissue with respect to propagation and the evaluation of sources. Effect of junctions, inhomogeneities, anisotropy, and presence of unbounded extracellular space. Bidomain models. Study of models of arrhythmia, fibrillation, and defibrillation. Electrocardiographic models and forward simulations. Laboratory exercises based on computer simulation, with emphasis on quantitative behavior and design. Readings from original literature. Prerequisite: Biomedical Engineering 301L(201L) or equivalent. Instructor: Barr. 4 units.

513(213). Nonlinear Dynamics in Electrophysiology (GE, EL). Electrophysiological behavior of excitable membranes and nerve fibers examined with methods of nonlinear dynamics. Phase-plane analysis of excitable membranes. Limit cycles and the oscillatory behavior of membranes. Phase resetting by external stimuli. Critical point theory and its applications to the induction of rotors in the heart. Theory of control of chaotic systems and stabilizing irregular cardiac rhythms. Initiation of propagation of waves and theory of traveling waves in a nerve fiber. Laboratory exercises based on computer simulations, with emphasis on quantitative behavior and design. Readings from original literature. Prerequisite: Mathematics 216(107) or equivalent. Instructor: Neu. 4 units.

515(256). Neural Prosthetic Systems. This course will cover several systems that use electrical stimulation or recording of the nervous system to restore function following disease or injury. For each system the course will cover the underlying biophysical basis for the treatment,the technology underlying the treatment,and the associated clinical applications and challenges. Systems to be covered include cochlear implants, spinal cord stimulation of pain, vagus nerve stim. for epilepsy, deep brain stim. for movement disorders, sacral root stim. for bladder dysfunction, and neuromuscular electrical stim.for restoration of movement. Prerequisites: Biomedical Engineering 253L(153L), and consent of instructor. Instructor: Grill. 3 units.

526(206L). Elasticity (GE, BB). Linear elasticity will be emphasized including concepts of stress and strain as second order tensors, equilibrium at the boundary and within the body, and compatibility of strains. Generalized solutions to two and three dimensional problems will be derived and applied to classical problems including torsion of noncircular sections, bending of curved beams, stress concentrations and contact problems. Applications of elasticity solutions to contemporary problem in civil and biomedical engineering will be discussed. Prerequisites: Engineering 201L(75L); Mathematics 353(108). Instructor: Laursen. 3 units. C-L: Civil Engineering 521(206).

527(217). Cell Mechanics and Mechanotransduction. This course examines the mechanical properties of cells and forces exerted by cells in biological processes of clinical and technological importance and the processes by which mechanical forces are converted into biochemical signals and activate gene expression. Topics covered include measurement of mechanical properties of cells, cytoskeleton mechanics, models of cell mechanical properties, cell adhesion, effects of physical forces on cell function, and mechanotransduction. Students will critically evaluate current literature and analyze models of cell mechanics and mechanotransduction. Prerequisites: Engineering 201L(75) and Biomedical Engineering 307(207) or equivalent, knowledge of cell biology and instructor consent. Instructror: Truskey. 3 units.

528(275). Introduction to Biofluid Mechanics. Methods and applications of fluid mechanics in biological and biomedical systems including: Governing equations and methods of solutions,(e.g. conservation of mass flow and momentum), the nature of biological fluids, (e.g.non Newtonian rheological behavior),basic problems with broad relevance, (e.g. flow in pipes, lubrication theory), applications to cells and organs in different physiological systems, (e.g. cardiovascular, gastrointestinal, respiratory, reproductive and musculoskeletal systems), applications to diagnosis and therapy, (e.g.drug delivery and devices). Prerequisite: Biomedical Engineeering 307(207). Instructor: Katz. 3 units.

529(208). Theoretical and Applied Polymer Science (GE, BB). 3 units. C-L: see Mechanical Engineering and Materials Science 514(211)

530(230). Tissue Biomechanics (GE, BB). Introduction to the mechanical behaviors of biological solids and fluids with application to tissues, cells and molecules of the musculoskeletal and cardiovascular systems. Topics to be covered include static force analysis and optimization theory, biomechanics of linearly elastic solids and fluids, anisotropic behaviors of bone and fibrous tissues, blood vessel mechanics, cell mechanics and behaviors of single molecules. Emphasis will be placed on modeling stress-strain relations in these tissues, and experimental devices used to measure stress and strain. Student seminars on topics in applied biomechanics will be included. Prerequisites: Engineering 201L(75L); Mathematics 353(108). Instructor: Myers or Setton. 3 units.

542(222). Principles of Ultrasound Imaging (GE, IM). Propagation, reflection, refraction, and diffraction of acoustic waves in biologic media. Topics include geometric optics, physical optics, attenuation, and image quality parameters such as signal-to-noise ratio, dynamic range, and resolution. Emphasis is placed on the design and analysis of medical ultrasound imaging systems. Prerequisites: Mathematics 216(107) and Physics 152L(62L). Instructor: von Ramm. 3 units.

561L(258L). Genome Science & Technology Lab (GE, MC). Hands-on experience on using and developing advanced technology platforms for genomics and proteomics research. Experiments may include nucleic acid amplification and quantification, lab-on-chip, bimolecular separation and detection, DNA sequencing, SNP genotyping, microarrays, and synthetic biology techniques. Laboratory exercises and designing projects are combined with lectures and literature reviews. Prior knowledge in molecular biology and biochemistry is required. Instructor consent required. Instructor: Tian. Variable credit. C-L: Computational Biology and Bioinformatics 542(222)

562. Biology by Design (GE, MC). Engineering biological systems emphasizing synthetic biology and the application of biological/chemical principles to the design of new biomolecules and cellular pathways. Review of primary scientific literature, highlighting contemporary research in this area, including artificial amino and nucleic acids, gene regulatory systems, directed molecular evolution, recombinant antibodies, novel biosynthesis pathways, cell communication, and the design of minimal organisms. Topics are presented with applications such as drug design, discovery, productions, regenerative medicine, and bioremediation. Prerequisite: Biomedical Engineering 244L. Organic chemistry or biochemistry suggested. Instructor consent required. Instructor: Gersbach. 3 units.

563. Transport Processes in HIV Transmission and Prevention (GE, BB, MC). Application of transport theory to analyze processes of HIV migration to target cells in the mucosa of the lower female reproductive tract. Analysis of the introduction, transport and bioactivity of molecules that inhibit these HIV-infection processes, including those acting topically (microbicides) and those introduced in a variety of drug delivery vehicles: semi-solid materials (gels, films) and solid materials (intravaginal rings). A succession of mathematical models will describe elements of the fundamental biology of this system and analyze the performance of specific products that act prophylactically against HIV infection. Prerequisite: BME 307 or instructor consent. Instructor: Katz. 3 units.

565L(240L). Environmental Molecular Biotechnology (GE, MC). 3 units. C-L: see Civil Engineering 661L(239L)

567(237). Biosensors (GE, IM, MC). Biosensors are defined as the use of biospecific recognition mechanisms in the detection of analyte concentration. The basic principles of protein binding with specific reference to enzyme-substrate, lectin-sugar, antibody-antigen, and receptor-transmitting binding. Simple surface diffusion and absorption physics at surfaces with particular attention paid to surface binding phenomena. Optical, electrochemical, gravimetric, and thermal transduction mechanisms which form the basis of the sensor design. Prerequisites: Biomedical Engineering 260L(100L) or equivalent and consent of instructor. Instructor: Reichert or Vo-Dinh. 3 units.

570L(220L). Introduction to Biomolecular Engineering (GE, BB, MC). Structure of biological macromolecules, recombinant DNA techniques, principles of and techniques to study protein structure-function. Discussion of biomolecular design and engineering from the research literature. Linked laboratory assignments to alter protein structure at the genetic level. Expression, purification, and ligand-binding studies of protein function. Consent of instructor required. Instructor: Chilkoti. 3 units.

574(221). Modeling and Engineering Gene Circuits. This course discusses modeling and engineering gene circuits, such as prokaryotic gene expression, cell signaling dynamics, cell-cell communication, pattern formation, stochastic dynamics in cellular networks and its control by feedback or feedforward regulation, and cellular information processing. The theme is the application of modeling to explore "design principles" of cellular networks, and strategies to engineer such networks. Students need to define an appropriate modeling project. At the end of the course, they're required to write up their results and interpretation in a research-paper style report and give an oral presentation. Prerequisites: Biomedical Engineering 260L(100L) or consent of instructor. Instructor: You. 3 units.

577(247). Drug Delivery (GE, BB, MC). Introduction to drug delivery in solid tumors and normal organs (for example, reproductive organs, kidney, skin, eyes). Emphasis on quantitative analysis of drug transport. Specific topics include: physiologically-based pharmacokinetic analysis, microcirculation, network analysis of oxygen transport, transvascular transport, interstitial transport, transport across cell membrane, specific issues in the delivery of cells and genes, drug delivery systems, and targeted drug delivery. Prerequisite: Biomedical Engineering 307(207) and Engineering 110L(53). Instructor: Yuan. 3 units.

578(248). Tissue Engineering (GE, MC). This course will serve as an overview of selected topics and problems in the emerging field of tissue engineering. General topics include cell sourcing and maintenance of differentiated state, culture scaffolds, cell-biomaterials interactions, bioreactor design, and surgical implantation considerations. Specific tissue types to be reviewed include cartilage, skin equivalents, blood vessels, myocardium and heart valves, and bioartificial livers. Prerequisites: Mathmetics 353(108) or consent of instructor. Instructor: Bursac. 3 units.

 

717S(351). Seminars in Medical Physics. Medical physics is the application of the concepts and methods of physics and engineering to the diagnosis and treatment of human disease. This course consists of weekly lectures covering broad topics in medical physics including diagnostic imaging, radiation oncology, radiation safety, and nuclear medicine. Lectures will be given by invited speakers drawn from many university and medical center departments including Biomedical Engineering, radiology, physics, radiation safety, and radiation oncology. Prerequisites: background in engineering or physics. 1 CC (0.5 ES/0.5 ED). Consent of instructor required. Instructor: Lo and Samei. 1 unit.

717S(351). Seminars in Medical Physics. Medical physics is the application of the concepts and methods of physics and engineering to the diagnosis and treatment of human disease. This course consists of weekly lectures covering broad topics in medical physics including diagnostic imaging, radiation oncology, radiation safety, and nuclear medicine. Lectures will be given by invited speakers drawn from many university and medical center departments including Biomedical Engineering, radiology, physics, radiation safety, and radiation oncology. Prerequisites: background in engineering or physics. 1 CC (0.5 ES/0.5 ED). Consent of instructor required. Instructor: Lo and Samei. 1 unit.

785(350). Principles of Research Management. A survey of topics in modern research management techniques that will cover proven successful principles and their application in the areas of research lab organization, resource management, organization of technical projects, team leadership, financial accountability, and professional ethics. Instructor: Staff. 1 unit.

788(362). Invention to Application: Healthcare Research Commercialization. Interdisciplinary teams of students from engineering, medical science, business, and medicine work together to understand and evaluate the commercial potential of Duke faculty research innovations and develop a comprehensive research translation and business plan for one chosen opportunity. Learning includes understanding technology, product development, marketing, finance, regulatory requirements, and reimbursement. In addition to weekly lectures, students are mentored in this real world experience by a team including technology transfer experts, venture capitalists, researchers, physicians, and entrepreneurs. Prerequisites: none. Consent of instructor required. Instructor: Myers. 3 units.

834(331). Viscoelasticity. Viscoelasticity of hard and soft tissue solids and composite structures. Linear and nonlinear one-dimensional viscoelastic behavior, internal damping, and three-dimensional viscoelasticity. Approximation techniques for determination of viscoelastic constitutive equations from experimental data. Mathematical formulations for the characterization of the dynamic behavior of biologic structures. Consent of instructor required. Instructor: Myers. 3 units.

844(321). Advanced Ultrasonic Imaging. This course provides students with a mathematical basis of ultrasonic imaging methods. Topics include K-space, descriptions of ultrasonic imaging, ultrasonic beam-former design, tissue motion and blood flow imaging methods, and novel ultrasonic imaging methods. Students conduct extensive simulations of ultrasonic imaging methods. Prerequisite: BME 303(233). Instructor: Trahey. 3 units.

848L(334L). Radiology in Practice. Designed to complement BME 233 Modern Diagnostic Imaging Systems. Review and real-life exercises on principles of modern medical imaging systems with emphasis on the engineering aspects of image acquisition, reconstruction and visualization, observations of imaging procedures in near clinical settings, and hands-on experience with the instruments. Modalities covered include ultrasound, CT, MRI, nuclear medicine and optical imaging. Prerequisite: BME 303(233) or equivalent. Instructor: Trahey. 3 units. C-L: Medical Physics 738(338)

850(335). Advances in Photonics: An Overview of State-of-the-Art Techniques and Applications. The main goal of this course is to provide and overview of various photonics techniques and their applications. The purpose is to enhance the students' breath of understanding and knowledge of advanced techniques and introduce them to the wide variety of applications in photonics, the science and technology associated with interactions of light with matter. Examples of topics include: High-resolution Luminescence Techniques, Raman Techniques, Optical Coherence Techniques, Ultrafast Laser-base Techniques, Near-Filed and Confocal Optical Techniques, Remote Sensing Techniques, Advanced Light Measurement Techniques, Optical Biosensors, Nano Micro Electrooptics Systems, Highthroughput Assays using Optical Detection, Photonics Meta Materials and Applications, Optics in Telecommunications, and Nanophotonics. The lectures will be presented by faculty members who are leaders in their areas of research in photonics. Instructor: Vo-Dinh. 3 units. C-L: Chemistry 630(335).