Biomedical Engineering

E62 BME 501C BME Doctoral Seminar Series

This is a 1-unit credit option for BME students who attend regularly scheduled BME seminars (or approved substitute seminars). A satisfactory grade is obtained by submission of a two-page peer-reviewed paper written by one of the regularly scheduled BME seminar speakers whose seminar the student attended. Papers are to be submitted to the Graduate Student Administrator for review by the Director of Doctoral Studies. Prerequisite: current BME student in the second year or beyond.

Credit 1 unit.

E62 BME 506 Seminar in Imaging Science and Engineering

This seminar course consists of a series of tutorial lectures on Imaging Science and Engineering with emphasis on applications of imaging technology. Students are exposed to a variety of imaging applications that vary depending on the semester, but may include multispectral remote sensing, astronomical imaging, microscopic imaging, ultrasound imaging, and tomographic imaging. Guest lecturers come from several parts of the university. This course is required of all students in the Imaging Science and Engineering program; the only requirement is attendance. This course is graded pass/fail. Prerequisite: admission to Imaging Science and Engineering program.
Same as E35 ESE 596

Credit 1 unit.

E62 BME 507 Radiological Physics and Dosimetry

This class is designed to construct a theoretical foundation for ionizing radiation dose calculations and measurements in a medical context and prepare graduate students for proper scientific presentations in the field of x-ray imaging and radiation therapy. Specifically, a student completing this course will be able to do the following: 1. Understand and apply key concepts specific to energy deposition for both ionizing photon interactions and transport in matter and for energetic charged particle interactions and transport in matter. Radiation sources include radioactivity, x-ray tubes, and linear accelerators. 2. Understand the theoretical details of ion-chamber based dosimetry and of both cavity-theory based (TG-21) and Monte-Carlo based (TG-51) clinical protocols. 3. Perform and present real-world style research projects as a group, and present these projects in a typical professional scientific format and style. 4. Achieve an appreciation of the history and potential future developments in ionizing radiation detection and dosimetry. Prerequisites: BS in physics or engineering and instructor approval.

Credit 3 units.

E62 BME 5071 Radiobiology

Effects of ionizing radiations on living cells and organisms, including physical, chemical, and physiological bases of radiation cytotoxicity, mutagenicity and carcinogenesis. Textbook: Radiobiology for the Radiologist. Eric Hall and Amato Giaccia. Two lectures per week. Prerequisites: graduate student standing and one year each of biology, physics and organic chemistry, or approval of instructor.

Credit 2 units.

E62 BME 5072 Radiation Therapy Physics

Ionizing radiation use in radiation therapy to cause controlled biological effects in cancer patients. Physics of the interaction of the various radiation modalities with body-equivalent materials, and physical aspects of clinical applications. Lecture and lab. Prerequisites: graduate student standing or permission of instructor.

Credit 3 units.

E62 BME 5073 Radiation Protection and Safety

This course will introduce concepts of radiation protection and safety. The focus will be on how to protect humans and environment from ionizing radiation. Special emphasis will be on radiological protection in clinics. Prerequisite: graduate student standing or permission of the instructor.

Credit 2 units.

E62 BME 523 Biomaterials Science

An understanding of the interactions between biological systems and artificial materials is of vital importance in the design of medical devices. This course will introduce the principles of biomaterials science, unifying knowledge from the fields of biology, materials science, surface science, and colloid science. The course will be taught from the primary scientific literature, focusing on the study of protein/surface interactions and hydrogel materials.

Credit 3 units. EN: TU

E62 BME 524 Tissue Engineering

This course integrates the principles and methods of engineering and life sciences toward the fundamental understanding of normal and pathological mammalian tissues especially as they relate to the development of biological substitutes to restore or improve tissue function. Current concepts and strategies including drug delivery, tissue and cell transplantation, and in vivo tissue regeneration will be introduced as well as their respective clinical applications. Prerequisites: BME 366; or MEMS 3410, Biol 2960 and 2970; or permission of the instructor.

Credit 3 units. EN: TU

E62 BME 527 Design of Artificial Organs

Medical devices that replace the function of one of the major organs in the body must usually interface with flowing blood. Examples include total artificial hearts, left ventricular assist devices, membrane oxygenators, hemodialysis systems and encapsulated endocrine cells. The design of these devices relies on integration of knowledge from a variety of fields, in particular computational fluid dynamics and blood rheology. We will study the process by which a concept for a device eventually leads to a functioning, blood-contacting medical device, with most of the focus on the design of left ventricular assist devices. Students will learn to use CAD to design blood pumping devices, test their designs via computational fluid dynamics, and 3D print and test their pumps with water. Prerequisites: BME 366 or equivalent course in transport phenomena (including momentum and mass transfer).

Credit 3 units. EN: TU

E62 BME 528 Translational Regenerative Medicine

This course provides students with an opportunity to connect basic research with applications in translation for several tissues/disease models. Course sessions will alternate between literature on basic mechanisms of development/stem cell biology and applications led by researchers or clinicians working in each area. Areas of focus will include cardiovascular development/congenital heart disease and arrhythmia, lung, endocrinology/diabetes, gut/intestinal disorders, musculoskeletal, neural (peripheral and brain), liver, hematology and eye. Emphasis on how discovery can be translated will be a major focus of the course. Students will be expected to review and present on primary literature in the field. Graduate standing is required. Prerequisites: graduate standing Engineering or DBBS.

Credit 3 units.

E62 BME 530A Molecular Cell Biology for Engineers

This course is designed for upper level undergraduates and first year graduate students with a background in engineering. This course covers the biology of cells of higher organisms: protein structure and function; cellular membranes and organelles; cell growth and oncogenic transformation; cellular transport, receptors and cell signaling; the cytoskeleton, the extracellular matrix, and cell movement. Emphasis will be placed on examples relevant to biomedical engineering. In addition to lecture material, an emphasis will be placed on understanding experimental techniques used in cell biology and critical analysis of primary literature. Note this course does not count for engineering topics credits and is meant to fulfill a life science requirement for engineering or physical sciences graduate students. Prereq: Completion of Biol 2960 and 2970 or graduate standing.

Credit 3 units.

E62 BME 532 Physics of Biopolymers and Bioinspired Polymers

This course will cover physics concepts from the statistical physics of polymers and polymer solutions to describe proteins, nucleic acids, and bioinspired polymers. Topics include statistical physics concepts, theoretical and numerical descriptions of polymers, applying these descriptions to biopolymers, the thermodynamics of polymer solutions, concepts of polymer dynamics, descriptions of polymeric materials and advanced topics in phase transitions and molecular design. The material will be fast-paced and involve rigorous mathematical descriptions, experimental design, interpretations of experimental data, and some numerical simulations. The course will be heavy on individual homework and team-based project work. Direct connections between concepts and modern topics in biology and biomaterials will be emphasized. Prerequisites: BME 320B or equivalent and a first course in transport phenomena.
Same as E62 BME 432

Credit 3 units. EN: TU

E62 BME 533 Biomedical Signal Processing

Course designed for graduate students with little or no background in signal processing. Continuous-time and discrete-time application of signal processing tools to a variety of biomedical problems. Course topics include review of linear signals and systems theory, frequency transforms, sampling theorem, basis functions, linear filtering, feature extraction, parameter estimation and biological system modeling. Special emphasis will be placed on signal transduction and data acquisition. Additional topics include noise analysis of real-world biosignals, biological system identification, stochastic/chaotic/fractal/nonlinear processes in biological systems. Concepts learned in class will be applied using software tools to 1D biomedical signals such as biological rhythms, chemical concentrations, blood pressure, speech, EMG, ECG, EEG. Prerequisites: graduate standing or consent of instructor.

Credit 3 units. EN: TU

E62 BME 537 Computational Molecular Biology

This course is a survey of algorithms and mathematical methods in biological sequence analysis (with a strong emphasis on probabilistic methods) and systems biology. Sequence analysis topics include introduction to probability, probabilistic inference in missing data problems, hidden Markov models (HMMs), profile HMMs, sequence alignment, and identification of transcription-factor binding sites. Systems biology topics include discovery of gene regulatory networks, quantitative modeling of gene regulatory networks, synthetic biology, and (in some years) quantitative modeling of metabolism. Prerequisites: CSE 131 or CSE 501N.
Same as E81 CSE 587A

Credit 3 units. EN: TU

E62 BME 538 Cell Signal Transduction

This course will cover the elements of cell signal transduction important to human development, homeostasis and disease. Lectures will be combined with primary literature review to cover canonical signaling and current topics within the field. Spatial, time and dose-dependent aspects of signaling will be of particular focus. Topics include G protein-coupled receptors, receptor tyrosine kinases, adhesion signaling, the MAPK cascade, lipid signaling, the DNA damage response, and autocrine, paracrine and juxtacrine signaling. Prerequisite: BME 530A or BME 5068.

Credit 3 units.

E62 BME 542 Biomacromolecules Design and Engineering

Biological macromolecules (i.e., carbohydrates, lipids, proteins, and nucleic acids) are important components of the cell and its supporting matrix that perform a wide array of functions. This course will introduce the principles and recent advances in nucleic acid/gene engineering, protein/peptide engineering, and chemical/enzymatic conjugation technologies; it will also discuss the application of engineered biomacromolecules in clinical therapeutics/diagnostics, biosensing, bioimaging, and biocatalysis. Students will learn material through lectures, reading, homework, scientific publications, and molecular visualization tools. Students will work individually or in pairs/groups to develop and lead discussions on engineering biomacromolecules and molecular characterization techniques. Prerequisites: basic knowledge of genes and cloning.
Same as E62 BME 442

Credit 3 units. EN: TU

E62 BME 543 Molecular and Cellular Engineering

The ability to engineer biological function at the cellular level holds tremendous potential for both basic and applied science. This course aims to provide knowledge and practical proficiency in the methods available for measuring and controlling the molecular organization of eukaryotic cells. Topics to be covered include genome engineering using viral- and CRISPR-Cas systems; spatial and temporal control of proteins and their interactions; methods for characterizing and engineering post-translational modifications; and the relationship between cellular organization and function in migration, immune cell target recognition, and differentiation. Examples from recent scientific literature will provide the foundation for these topics.
Same as E62 BME 443

Credit 3 units. EN: TU

E62 BME 5430 Systems Analysis of Biological Signaling

This course covers biochemical and computational methods of cellular signaling pathway analysis. Topics include kinetics, differential equations, and sensitivity analysis, with emphasis on cellular and molecular vascular signaling in health and disease. Prerequisites: Biol 2960 and Math 217.

Credit 3 units. EN: TU

E62 BME 544 Biomedical Instrumentation

This course will include operational and instrumentation amplifiers for bioelectric event signal conditioning, interfacing and processing; instrumentation noise analysis and filter design; A/D converters and hardware and software principles as related to sampling, storing, processing, and display of biosignals; modeling, analysis, and operation of transducers, sensors, and electrodes, for physiological and imaging systems; and an introduction to ultrasound, X-ray, and optical imaging systems. In addition, students will be involved in three projects of designing and building instrumentation amplifier and filter systems, ultrasound systems, and optical systems. Prerequisites: BME 301A and BME 301B.
Same as E62 BME 444

Credit 3 units. EN: TU

E62 BME 550 Numerical Methods for Computational Modeling in Biomedicine

Advanced computational methods are required for the creation of biological models. Students will be introduced to the process of model development from beginning to end, which includes model formulation, how to solve and parameterize equations, and how to evaluate model success. To illustrate the potential of these methods, participants will systematically build a model to simulate a "real-life" biological system that is applicable to their research or interest. A mechanistic appreciation of the methods will be gained by programming the methods in a low-level language (C++) in a Linux environment. While extensive programming knowledge is not required, participants are likely to find that some programming background will be helpful. Students enrolled in the 550 graduate class will be required to complete a final project that incorporates the methods taught in class. Prerequisites: introductory programming course similar to E81 CSE 131.
Same as E62 BME 450

Credit 3 units. EN: TU

E62 BME 5565 Mechanobiology of Cells and Matrices

At the interface of the cell and the extracellular matrix, mechanical forces regulate key cellular and molecular events that profoundly affect aspects of human health and disease. This course offers a detailed review of biomechanical inputs that drive cell behavior in physically diverse matrices. In particular, cytoskeletal force-generation machineries, mechanical roles of cell-cell and cell-matrix adhesions, and regulation of matrix deformations are discussed. Also covered are key methods for mechanical measurements and mathematical modeling of cellular response. Implications of matrix-dependent cell motility in cancer metastasis and embryonic development are discussed. Prerequisite: graduate standing or permission of the instructor.
Same as E37 MEMS 5565

Credit 3 units. EN: BME T, TU

E62 BME 559 Intermediate Biomechanics

This course covers several of the fundamental theories of solid mechanics that are needed to solve problems in biomechanics. The theories of nonlinear elasticity, viscoelasticity and poroelasticity are applied to a large range of biological tissues including bone, articular cartilage, blood vessels, the heart, skeletal muscle, and red blood cells. Other topics include muscle activation, the biomechanics of development and functional adaptation, and the mechanics of hearing. Prerequisites: BME 240 and ESE 318 and ESE 319 or equivalent, or permission of instructor.

Credit 3 units. EN: TU

E62 BME 562 Mechanics of Growth and Development

This course applies the fundamental principles of solid mechanics to problems involving growth, remodeling and morphogenesis of cells, tissues and organs. Introduction to developmental biology, nonlinear elasticity, viscoelasticity and active contraction. Particular topics include cellular morphogenetic mechanisms, growth and development of the cardiovascular system, and adaptive remodeling of bone. Prerequisites: BME 240 or MEMS 241 or equivalent.

Credit 3 units. EN: BME T, TU

E62 BME 564 Orthopaedic Biomechanics — Cartilage/Tendon

Basic and advanced viscoelasticity and finite strain analysis applied to the musculoskeletal system, with a primary focus on soft orthopaedic tissues (cartilage, tendon and ligament). Topics include: mechanical properties of cartilage, tendon and ligament; applied viscoelasticity theory for cartilage, tendon and ligament; cartilage, tendon and ligament biology; tendon and ligament wound healing; osteoarthritis. This class is geared to graduate students and upper-level undergraduates familiar with statics and mechanics of deformable bodies. Prerequisite: BME 240 or equivalent. Note: BME 590Z (BME 463/563) Orthopaedic Biomechanics — Bones and Joints is not a prerequisite.
Same as E37 MEMS 5564

Credit 3 units. EN: TU

E62 BME 565 Biosolid Mechanics

Introduction to the mechanical behaviors of biological tissues of musculoskeletal, cardiac and vascular systems. Topics to be covered include static force analysis and nonlinear optimization theory; linearly elastic models for stress-strain analysis and solutions to relevant problems in bioelasticity; models of active structures (e.g., muscles); strain energy methods and nonlinear tissue behaviors; and introductory theory for finite element analysis. Emphasis will be placed on modeling stress-strain relations with relevance to biological tissues. Prerequisites: BME 240 or equivalent and ESE 318 and ESE 319.
Same as E62 BME 465

Credit 3 units. EN: TU

E62 BME 570 Mathematics of Imaging Science

This course will expose students to a unified treatment of the mathematical properties of images and imaging. This will include an introduction to linear vector space theory, operator theory on Hilbert spaces, and concepts from applied functional analysis. Further, concepts from generalized functions, Fourier analysis, and radon transform will be discussed. These tools will be applied to conduct deterministic analyses of imaging systems that are described as continuous-to-continuous, continuous-to-discrete, and discrete-to-discrete mappings from object properties to image data. In addition, imaging systems will be analyzed in a statistical framework where stochastic models for objects and images will be introduced. Prerequisite: senior standing or permission of instructor.

Credit 3 units.

E62 BME 572 Biological Neural Computation

This course considers the computations performed by the biological nervous system with a particular focus on neural circuits and population-level encoding/decoding. Topics include Hodgkin-Huxley equations; phase-plane analysis; reduction of Hodgkin-Huxley equations; models of neural circuits; plasticity and learning; and pattern recognition and machine learning algorithms for analyzing neural data. Note: Graduate students in psychology or neuroscience who are in the Cognitive, Computational and Systems Neuroscience curriculum pathway may register in Biol 5657 for 3 credits. For non-BME majors, conceptual understanding, and selection/application of right neural data analysis technique are stressed. Hence homework assignments/examinations for the two sections are different, however all students are required to participate in a semester-long independent project as part of the course. Prerequisites: calculus, differential equations, basic probability and linear algebra. Undergraduates need permission of the instructor. Biol 5657 prerequisites: permission from the instructor.

Credit 3 units. EN: TU

E62 BME 574 Quantitative Bioelectricity and Cardiac Excitation

Action potential generation, action potential propagation, source-field relationships in homogeneous and inhomogeneous media, models of cardiac excitation and arrhythmia, quantitative electrocardiography. Prerequisites: differential equations, Laplace transform, electromagnetic field theory (undergraduate level).

Credit 3 units. EN: TU

E62 BME 575 Molecular Basis of Bioelectrical Excitation

Ion channels are the molecular basis of membrane excitability in all cell types, including neuronal, heart and muscle cells. This course presents the structure and the mechanism of function of ion channels at the molecular level. It introduces the basic principles and methods in the ion channel study as well as the structure-function relation of various types of channels. Exemplary channels that have been best studied are discussed to illustrate the current understanding. Prerequisites: knowledge of differential equations, electrical circuits and chemical kinetics.

Credit 3 units. EN: TU

E62 BME 5771 Biomedical Product Development

Advances in science and technology have opened the health care field to innovation now more than any other time in history. Engineers and inventors can make real and rapid improvements to patient treatments, length of hospital stay, procedure time, cost containment, and accessibility to treatment. However, a successful transition from idea to implementation requires careful market analysis and strategy planning. This course will address the steps in this process, including personal and team strength assessment, medical need validation, brainstorming initial solutions, market analysis, solution evaluation, regulatory, patent and intellectual property concerns, manufacturability, risk assessment and mitigation, and global considerations. Students will be expected to review resource material prior to coming to class in order to facilitate active class discussion and team-based application of the material during class; regular attendance will be key to course success. The course will focus on applying product development techniques to several real unmet medical needs; students will thus perform analysis and create reports and presentations for several different product solutions. Peer and faculty evaluations will provide feedback to improve individual technique. In addition, throughout the semester, local biomedical entrepreneurs will visit to share their expertise and experiences. Prerequisites: graduate or professional student standing or permission of the instructor.

Credit 3 units.

E62 BME 5772 Biomedical Business Development

For medical innovators, a successful translation from product to market will require careful strategy and an understanding of the steps needed to form and fund a biotech business, either as a new startup or as an extension of the product line of an existing company. This course will address the steps in this process, including intellectual property concerns, R&D, clinical strategy, regulatory issues, quality management, reimbursement, marketing strategy, sales and distribution, operating plans, and approaches to funding. Prerequisites: graduate or professional student standing or permission of the instructor.

Credit 3 units.

E62 BME 5799 Independent Study for Candidates in the Master of Engineering Program

Independent investigation on a topic of special interest. The student and mentor must justify the requested number of units. The MEng program director must approve the requested number of units.

Credit variable, maximum 6 units.

E62 BME 5820 Fundamentals and Applications of Modern Optical Imaging

Analysis, design, and application of modern optical imaging systems, with emphasis on biological imaging. The first part of the course will focus on the physical principles underlying the operation of imaging systems and their mathematical models. Topics include ray optics (speed of light, refractive index, laws of reflection and refraction, plane surfaces, mirrors, lenses, aberrations), wave optics (amplitude and intensity, frequency and wavelength, superposition and interference, interferometry), Fourier optics (space-invariant linear systems, Huygens-Fresnel principle, angular spectrum, Fresnel diffraction, Fraunhofer diffraction, frequency analysis of imaging systems), and light-matter interaction (absorption, scattering, dispersion, fluorescence). The second part of the course will compare modern quantitative imaging technologies, including but not limited to digital holography, computational imaging, and super-resolution microscopy. Students will evaluate and critique recent optical imaging literature. Prerequisites: ESE 318 and ESE 319 or their equivalents; ESE 330 or Physics 421 or equivalent.
Same as E35 ESE 582

Credit 3 units. EN: BME T, TU

E62 BME 589 Biological Imaging Technology

This class develops a fundamental understanding of the physics and mathematical methods that underlie biological imaging and critically examine case studies of seminal biological imaging technology literature. The physics section examines how electromagnetic and acoustic waves interact with tissues and cells, how waves can be used to image the biological structure and function, image formation methods and diffraction limited imaging. The math section examines image decomposition using basis functions (e.g., Fourier transforms), synthesis of measurement data, image analysis for feature extraction, reduction of multidimensional imaging datasets, multivariate regression and statistical image analysis. Original literature on electron, confocal and two photon microscopy, ultrasound, computed tomography, functional and structural magnetic resonance imaging and other emerging imaging technology are critiqued.
Same as E35 ESE 589

Credit 3 units. EN: BME T, TU

E62 BME 5901 Integrative Cardiac Electrophysiology

Quantitative electrophysiology of the heart, integrating from the molecular level (ion channels, regulatory pathways, cell signaling) to the cardiac cell (action potential and calcium transient), multicellular tissue (cell-cell communication) and the whole heart. Prerequisite: permission of instructor.

Credit 3 units. EN: BME T, TU

E62 BME 5902 Cellular Neurophysiology

This course will examine the biophysical concepts of synaptic function, with a focus on the mechanisms of neural signal processing at synapses and elementary circuits. The course combines lectures and discussion sessions of primary research papers. Topics include synaptic and dendritic structure, electrical properties of axons and dendrites, synaptic transmission, rapid and long-term forms of synaptic plasticity, information analysis by synapses and basic neuronal circuits, principles of information coding, mechanisms of learning and memory, function of synapses in sensory systems, and models of synaptic disease states such as Parkinson's and Alzheimer's diseases. In addition, a set of lectures will be devoted to modern electrophysiological and imaging techniques as well as modeling approaches to study synapses and neural circuits. Prerequisite: senior or graduate standing.

Credit 3 units. EN: TU

E62 BME 591 Biomedical Optics I: Principles

This course covers the principles of optical photon transport in biological tissue. This course covers the principles and applications of optical photon transport in biological tissue. Topics include a brief introduction to biomedical optics, single-scatterer theories, Monte Carlo modeling of photon transport, convolution for broad-beam responses, radiative transfer equation, diffusion theory and applications, sensing of optical properties and spectroscopy, and photoacoustic imaging principles and applications. Prerequisite: Differential equations

Credit 3 units. EN: TU

E62 BME 5911 Cardiovascular Biophysics Journal Club

This journal club is intended for beginning graduate students, advanced undergraduates and MSTP students with a background in the quantitative sciences (engineering, physics, math, chemistry, etc.). The subjects covered are inherently multidisciplinary. We review landmark and recent publications in quantitative cardiovascular physiology, mathematical modeling of physiologic systems and related topics such as chaos theory and nonlinear dynamics of biological systems. Familiarity with calculus, differential equations and basic engineering/thermodynamic principles is assumed. Knowledge of anatomy/physiology is optional.

Credit 1 unit.

E62 BME 5913 Molecular Systems Biology: Computation & Measurements for Understanding Cell Physiology and Disease

Systems-level measurements of molecules in cells and tissues harbor the promise of identifying the ways in which tissues develop, maintain, age, and become diseased. This class will introduce the systems-level measurement techniques for capturing molecular information and the mathematical and computational methods for harnessing the information from these measurements to improve our understanding of cell physiology and disease. This is a practical class, which involves implementation of the concepts in MATLAB and will be applied to existing, real data from published journal articles. Molecular topics will include gene expression, microRNA, proteins, post-translational modifications, drugs, and splicing. Computational/mathematical topics covered will include statistical inference, dimensionality reduction techniques, unsupervised and supervised machine learning, and graph-based techniques. Prerequisites: A working knowledge of molecular biology, linear algebra, and statistics is required.

Credit 3 units. EN: TU

E62 BME 594 Ultrasound Imaging

This course will introduce basic principles of ultrasound imaging, diagnostic ultrasound imaging system, clinical applications, and emerging technologies in industry. Prerequisite: ESE 351.
Same as E62 BME 494

Credit 3 units. EN: TU

E62 BME 601C Research Rotation for BME Doctoral Students

Credit 3 units.