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

• ENG BE 602: Ordinary Differential Equations
  This math module will focus on four key ODE concepts: Linear dynamical systems, nonlinear conservative and excitable systems, discrete- time state machines, and generalized Fourier series solutions to Sturm- Liouville problems. Topics include: Filters, enzymatic networks, mechanical models for biomaterials, oscillators and limit cycles, phase- locked loops, nonlinear Leslie matrices, Legendre polynomials, Bessel functions, and a prelude to solving PDE problems associated with heat transfer, diffusion, and electrostatics. Prior exposure to linear algebra (BE 601 equivalent), and working knowledge of a programming language (Matlab, Python, etc.) is helpful. 2 cr.
• ENG BE 603: Partial Differential Equations
  This math module will focus on elliptical and parabolic PDEs associated with transport phenomenon problems in biomedical engineering. We will visit four PDE concepts: Separation of variables, integral transform solutions, superposition principles, and numerical approximations using finite-difference schemes. Topics include: 2D and 3D anisotropic Laplace's, Poisson's, and the heat equations in different coordinate systems, Fourier and Laplace transform solutions, 2D ADI methods, Green's functions, and the method of images. Prior exposure to linear algebra (BE 601 equivalent), ODEs (BE 602 or MA 226 equivalent), Fourier series, Fourier and Laplace transforms (BE 401 equivalent), and working knowledge of a programming language (Matlab, Python, etc.) is highly recommended. 2 cr.
• ENG BE 604: Statistics & Numerical Methods
  In the final math module, we will focus on how linear algebra, ODEs, statistics, and signals & systems techniques can be used to interrogate data from biological and engineering experiments. The lecture topics include: Jacobi, Gauss-Seidel, and SOR iterative solvers for large linear systems; Gauss-Newton iterations (nonlinear least-squares); the ANOVA table, multi- factor regression, and intro to the general linear model (GLM); data deconvolution; Monte Carlo, bootstrap, and kernel density estimation. Prior exposure to linear algebra (BE 601 equivalent), basic probability and statistics (BE 200 equivalent), and working knowledge of a programming language (Matlab, Python, etc.) is highly recommended. 2 cr.
• ENG BE 605: Molecular Bioengineering
  Provides engineering perspectives on the building blocks of living cells and materials for biotechnology. Focuses on origins and synthesis in life and the laboratory, including 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; energetics of protein folding and trafficking; mechanisms of enzymatic catalysts and receptor-ligand binding; cooperative proteins, multi- protein complexes and control of metabolic pathways; generation, storage, transmission and release of biomolecular energy; and methods for study and manipulation of molecules which will include isolation, purification, detection, chemical characterization, imaging and visualization of structure. 4 cr
• ENG BE 606: Quantitative Physiology for Engineers
  Course in human physiology for biomedical engineering students. Fundamentals of cellular and systems physiology, including the nervous , muscular, cardiovascular, respiratory, renal, gastrointestinal, endocrine and immune systems. Quantitative and engineering approaches will be applied to understanding physiological concepts. 4 cr
• ENG BE 694: Biomedical and Clinical Needs Finding
  This course requires students to directly observe clinical procedures in selected medical specialties in appropriate hospital settings. Students will document biomedical technologies associated with the current standard of care, evaluate clinical needs and identify opportunities for developing new biomedical technologies. This course compliments and requires co-registration in BE695: Advanced Biomedical Design and Development. Fall only. 1cr.
• ENG BE 695: Advanced Biomedical Design and Development
  This two-semester 8-credit course is a required sequence for students enrolled in the BME Master of Engineering program. Students will work with leading clinicians to observe and identify unmet clinical challenges, design and develop innovative engineering solutions to those challenges, and explore the regulatory, intellectual property, and reimbursement pathways that will ultimately advance the standard of patient care through the deployment of their innovations. During the first semester, students will qualify for Medical Observer Status and the Boston Medical Center and project teams will conduct formal Needs Finding protocols, select projects, and design alternative solutions. During the second semester, project teams will develop their designs, and make multiple prototypes. Formal Design Control, Life Cycle, Risk Analysis, Project Management, and Intellectual Property Strategies will be introduced. Using formal Product Develop Protocols, students will prepare a detailed regulatory and implementation pathway analysis for completing the commercialization process needed to eventually bring their innovations into clinical practice. 8 credits over 2 semesters - must enroll for both semesters
• ENG BE 700: Advanced Topics in Biomedical Engineering
  Advanced study of a specific research topic in biomedical engineering. Intended primarily for advanced graduate students. Variable cr.
• ENG BE 704: Cancer Biology and Oncology for Engineers
  This course is designed to be an introduction to cancer biology and oncology from the perspective of the engineer. The course will cover basic cancer biology including cancer genetics, tumor metabolism, angiogenesis, and the metastastic cascade, and then discuss how new technologies enable better diagnosis, prognosis, and treatment. The class will explore how engineering principles can be applied to the design and fabrication of new technologies for cancer care, with an emphasis on signal processing, image formation (i.e. tomography), and data analysis. There will be a strong imaging component relevant to both cancer biology and clinical treatment, including optical, MRI, mammography, and PET-CT modalities. The course will be a combination of traditional lectures, class discussions, and journal club, and each student will be expected to present several times during the semester.
• ENG BE 709: From Cells to Tissue: Engineering Structure and Function
  This course is a primary literature-based course that will introduce students to engineering concepts in understanding and manipulating the behavior of biological cells. We will try to understand the interplay between cells, the extracellular environment, and intracellular signaling pathways in regulating cellular and multicellular structure and function. In particular, we will explore the use of modern experimental approaches to characterize and manipulate cells for bioengineering applications, and the concepts in scaling cellular engineering to functional issues. In this context, we will focus on several topics, including signal transduction and the molecular regulation of cell function, cellular microenvironment, cell adhesion and mecghanics, stem cells, multicellularity, and experimental models of tissue development. We will introduce both classic approaches and those that are still in early development. Due to the expansive nature of this area of science, we will only be able to introduce a sampling of the space.
• ENG BE 710: Neural Plasticity and Perceptual Learning
  This course explores the capacity of cortical sensory and motor maps in the adult brain to change as a result of alterations in the effectiveness of the input, direct damage, or practice. The lectures will describe and discuss (1) the physiology and anatomy underlying adult dynamics; (2) psychophysical methods and experimental paradigms that have been used to study cortical plasticity in the early stages of the sensory and motor pathways; (3) evidence for perceptual learning; and (4) biologically plausible computational models of learning. We will discuss applications of functional neuroimaging to study perceptual learning and restorative plasticity in the human brain. 4 cr
• ENG BE 716: Quantitative Medical Imaging: Theory and Methods
  The theory of quantitative medical imaging is studied systematically using the pixel value equation as the unifying mathematical concept. The physics foundations of electromagnetism, quantum mechanics, and NMR dynamics are studied at an intermediate level thus providing a solid foundation for the development of quantitative techniques as applicable to x-ray CT and MRI.
• ENG BE 726: Fundamentals of Biomaterials
  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 and hydrogels). Same as ME/MS 726. Students may not receive credit for both. 4 cr
• ENG BE 727: Principles and Applications of Tissue Engineering
  Provides the chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on cell-biomaterial interactions, soft tissue mechanics and specific research topics. Students will write a NIH-style grant proposal on a specific research topic. Same as ME/MS 727. Students may not receive credit for both. 4 cr
• ENG BE 745: Nanomedicine- Principles and Applications
  The use of nanoscience and technology for biomedical problems has spawned a field of applications ranging from nanoparticles for imaging and therapeutics, to biosensors for disease diagnostics. Nanomedicine is a rapidly growing field that exploits the novel properties of nanoscale materials and techniques to rapidly advance our understanding of human biology and the practice of medicine. This course focuses on the fundamental properties, synthesis and characterization of nanomaterials, coupled with their applications in nanomedicine, including: micro- and nano-particles for drug delivery and imaging, microfluidics for in vitro diagnostics, nanomaterials and platforms for biological applications. The biomedical applications include cancer, cardiovascular disease, and infectious diseases. 4 cr
• ENG BE 747: Advanced Signals and Systems Analysis for Biomedical Engineering
  Introduction to advanced techniques for signals and systems analysis with applications to problems in biomedical engineering research. Time-domain and frequency-domain analysis of multiple input, multiple output systems using the fundamental matrix approach. Hilbert transform relations; applications to head- related transfer functions. Second-order characterization of stochastic processes: power density spectra, cross-spectra, auto-and cross-correlation functions. Gaussian and Poisson processes. Models of neural firing patterns. Effects of linear systems on spectra and correlation functions. Applications to models of the peripheral auditory system. Optimum processing applications. Applications to psychophysical modeling. Introduction to wavelets and wavelet transforms. Wavelet filter banks and wavelet signal processing. 4 cr
• ENG BE 755: Molecular Systems and Synthetic Biology Laboratory
  Molecular Systems and Synthetic Biology Laboratory
• ENG BE 765: Biomedical Optics and Biophotonics
  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 applications. The course teaches only those aspects of biology itself that are necessary to understand the purpose of the application. 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 diseases; 2) Photon migration and optical imaging of subsurface structures in tissue; and 3) Laser-tissue interactions and other applications of light for therapeutic purposes. In addition to formal lectures, recent publications from the literature will be selected as illustrative of various topical areas, and for each publication one student will be assigned to prepare an informal presentation (with overhead slides or PowerPoint) reviewing for the class the underlying principles of that paper and outlining the research results. Same as ENG EC 765; students may not receive credit for both. 4 cr
• ENG BE 771: Introduction to Neuroengineering
  This course covers existing and future neurotechnologies for analyzing brain signals and for treating neurological and psychiatric diseases. It focuses on the biophysical, biochemical, anatomical principles governing the design of current neurotechnologies, with a goal of encouraging innovations of a 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, gene therapy, and stem-cell therapy. Discussions of related literatures and design projects will be involved. This course is open to graduate students only and it meets with BE571. 4 cr.
• ENG BE 773: Advanced Optical Microscopy and Biological Imaging
  This course will present a rigorous and detailed overview of the theory of optical microscopy starting from basic notions in light propagation and covering advanced concepts in imaging theory such as Fourier optics and partial coherence. Topics will include basic geometric optics, photometry, diffraction, optical transfer functions, phase contrast microscopy, 3D imaging theory, basic scattering and fluorescence theory, imaging in turbid media, confocal microscopy, optical coherence tomography (OCT), holographic microscopy, fluorescence correlation spectroscopy (FCS), fluorescence resonant energy transfer (FRET), and nonlinear-optics based techniques such as two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) microscopy. Biological applications such as calcium and membrane-potential imaging will be discussed. A background in optics is preferable. A background in signals and analysis is indispensable. In particular, the student should be comfortable with Fourier transforms, complex analysis, and transfer functions. Meets with ENGEC773. Students may not receive credit for both. 4 cr

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