Biomedical Engineering (BENG)

* BENG 205a, Discovery and Design in Biomedical ResearchJay Humphrey

Multi-disciplinary and team-based research approach to the study of clinical dilemma. Focus on an important health care problem, bringing to bear concepts and principles from diverse areas to identify possible solutions. Study of precision regenerative medicine as it involves aspects of bioengineering, materials science, immunobiology, mechanobiology, computational modeling, and experimental design, as well as hands-on fabrication and materials testing (i.e., data collection and analysis).  Prerequisites: MATH 115 and MATH 120 or ENAS 151.  SC
TTh 1pm-2:15pm

BENG 230a / MB&B 330a / MCDB 330a / NSCI 324a, Modeling Biological Systems IThierry Emonet and Jing Yan

Biological systems make sophisticated decisions at many levels. This course explores the molecular and computational underpinnings of how these decisions are made, with a focus on modeling static and dynamic processes in example biological systems. This course is aimed at biology students and teaches the analytic and computational methods needed to model genetic networks and protein signaling pathways. Students present and discuss original papers in class. They learn to model using MatLab in a series of in-class hackathons that illustrate the biological examples discussed in the lectures. Biological systems and processes that are modeled include: (i) gene expression, including the kinetics of RNA and protein synthesis and degradation; (ii) activators and repressors; (iii) the lysogeny/lysis switch of lambda phage; (iv) network motifs and how they shape response dynamics; (v) cell signaling, MAP kinase networks and cell fate decisions; and (vi) noise in gene expression. Prerequisites: MATH 115 or 116. BIOL 101-104,  or with permission of instructors. This course also benefits students who have taken more advanced biology courses (e.g. MCDB 200, MCDB 310, MB&B 300/301).  QR, SC0 Course cr
TTh 2:30pm-3:45pm

BENG 249b, Introduction to Biomedical ComputationStaff

Computational and mathematical tools used in biomedical engineering for the simulation of biological systems and the analysis of biomedical data. Basics of computational programming in MATLAB; applications to modeling, design, and statistical and data analysis. Prerequisite: MATH 120 or ENAS 151.  QR0 Course cr
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* BENG 280a, Sophomore Seminar in Biomedical EngineeringKathryn Miller-Jensen

Study of past successes and future needs of the multidisciplinary field of biomedical engineering. Areas of focus include: biomolecular engineering, including drug delivery and regenerative medicine; biomechanics, including mechanobiology and multiscale modeling; biomedical imaging and sensing, including image construction and analysis; and systems biology.   ½ Course cr
T 1pm-2:15pm

* BENG 350a / MCDB 310a, Physiological SystemsStaff

Regulation and control in biological systems, emphasizing human physiology and principles of feedback. Biomechanical properties of tissues emphasizing the structural basis of physiological control. Conversion of chemical energy into work in light of metabolic control and temperature regulation. Prerequisites: CHEM 165 or 167 (or CHEM 113 or 115), or PHYS 180 and 181; MCDB 120, or BIOL 101 and 102.  SC0 Course cr
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BENG 351b / CENG 351b, Biotransport and KineticsStaff

Creation and critical analysis of models of biological transport and reaction processes. Topics include mass and heat transport, biochemical interactions and reactions, and thermodynamics. Examples from diverse applications, including drug delivery, biomedical imaging, and tissue engineering. Prerequisites: MATH 115, ENAS 194; BIOL 101 and 102; CHEM 161, 163, or 167; BENG 249.  QR0 Course cr
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BENG 352b, Biomedical Signals and ImagesJames Duncan and Lawrence Staib

Principles and methods used to represent, model, and process signals and images arising from biomedical sources. Topics include continuous and discrete linear systems analysis, Fourier analysis and frequency response, metrics for signal similarity, and noise filtering. Biomedical examples range from one-dimensional electrical signals in nerves and muscles to two-dimensional images of organs and cells. Prerequisite: MATH 120 or ENAS 151. BENG 249, 350, and ENAS 194 strongly recommended.  QR
TTh 11:35am-12:50pm

BENG 353a / PHYS 353a, Introduction to BiomechanicsMichael Murrell

An introduction to the biomechanics used in biosolid mechanics, biofluid mechanics, biothermomechanics, and biochemomechanics. Diverse aspects of biomedical engineering, from basic mechanobiology to the design of novel biomaterials, medical devices, and surgical interventions. Prerequisites: PHYS 180, 181, MATH 115, and ENAS 194.  QR0 Course cr
TTh 9am-10:15am

* BENG 355La, Physiological Systems LaboratoryStaff

Introduction to laboratory techniques and tools used in biomedical engineering for physiological measurement. Topics include bioelectric measurement, signal processing, and bone mechanics. Enrollment limited to majors in Biomedical Engineering, except by permission of the director of undergraduate studies.  SC0 Course cr
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* BENG 356Lb, Biomedical Engineering LaboratoryStaff

Continuation of BENG 355L, introducing laboratory techniques and tools used in biomedical engineering. Topics include biomaterials and cell interactions, magnetic resonance spectroscopy and imaging, and image processing and machine learning. Enrollment limited.  SC0 Course cr
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* BENG 403b / ECON 463b, The Economics and Science of MedicineGregory Raskin and Yashodhara Dash

This multidisciplinary class is an exploration of the background of today’s bestselling medicines, their huge commercial impact, and the companies that created them. It focuses on the most compelling aspects of drug development and company formation in the context of topical issues like cancer treatment, gene editing, stem cell therapy, the opioid epidemic, and drug pricing controversies. Prerequisite: Introductory or intermediate microeconomics, introductory or intermediate Biology, Molecular Biology, Chemistry or Biomedical Engineering.  SO
Th 3:30pm-5:20pm

BENG 404b / MENG 404b, Medical Device Design and InnovationStaff

The engineering design, project planning, prototype creation, and fabrication processes for medical devices that improve patient conditions, experiences, and outcomes. Students develop viable solutions and professional-level working prototypes to address clinical needs identified by practicing physicians. Some attention to topics such as intellectual property, the history of medical devices, documentation and reporting, and regulatory affairs.  0 Course cr
TTh 9am-10:15am

* BENG 405b / EVST 415b, Biotechnology and the Developing WorldAnjelica Gonzalez

Study of technological advances that have global health applications. Ways in which biotechnology has enhanced quality of life in the developing world. The challenges of implementing relevant technologies in resource-limited environments, including technical, practical, social, and ethical aspects. Prerequisite: MCDB 120, or BIOL 101 and 102.
MW 1pm-2:15pm

* BENG 406b, Medical Software DesignXenophon Papademetris

Software design and implementation for medical applications, with emphasis on how new ideas can be developed within today's healthcare regulatory environment. This project-based course focuses on the interaction of medical imaging and 3D printing. Topics include the methods and design principles to take 3D medical images, and how to image analysis algorithms to create 3D models to guide diagnosis and interventional procedures or build patient-specific medical devices.  Permission of the instructor. Strong programming background in at least one programming language.   SC
MW 11:35am-12:50pm

* BENG 410a, Physical and Chemical Basis of Bioimaging and BiosensingFahmeed Hyder, Ansel Hillmer, and Douglas Rothman

Basic principles and technologies for sensing the chemical, electrical, and structural properties of living tissues and of biological macromolecules. Topics include magnetic resonance spectroscopy, microelectrodes, fluorescent probes, chip-based biosensors, X-ray and electron tomography, and MRI. Prerequisites: BENG 351 and 352 or permission of instructor.  QR, SC
MW 1pm-2:15pm

BENG 411a, BioMEMS and Biomedical MicrodevicesRong Fan

Principles and applications of micro- and nanotechnologies for biomedicine. Approaches to fabricating micro- and nanostructures. Fluid mechanics, electrokinetics, and molecular transport in microfluidic systems. Integrated biosensors and microTAS for laboratory medicine and point-of-care uses. High-content technologies, including DNA, protein microarrays, and cell-based assays for differential diagnosis and disease stratification. Emerging nanobiotechnology for systems medicine. Prerequisites: CHEM 161, 165, or 167 (or CHEM 112, 114, or 118), and ENAS 194.  SC
TTh 2:30pm-3:45pm

* BENG 422a, Engineering and Biophysical Approaches to CancerMichael Mak

This course focuses on engineering and biophysical approaches to cancer. The course examines the current state of the art understanding of cancer as a complex disease and the advanced engineering and biophysical methods developed to study and treat this disease. All treatment methods are covered. Basic quantitative and computational backgrounds are required. Prerequisites: BENG 249 or equivalent, MATH 120 or equivalent.  QR, SC
W 3:30pm-5:20pm

* BENG 435b, Biomaterial-Tissue InteractionsThemis Kyriakides

Study of the interactions between tissues and biomaterials, with an emphasis on the importance of molecular- and cellular-level events in dictating the performance and longevity of clinically relevant devices. Attention to specific areas such as biomaterials for tissue engineering and the importance of stem/progenitor cells, as well as biomaterial-mediated gene and drug delivery. Prerequisites: CHEM 161, 165, or 167 (or CHEM 112, 114, or 118); MCDB 120, or BIOL 101 and 102; or equivalents.  SC
TTh 9am-10:15am

BENG 444a, Modern Medical Imaging: Lecture and DemonstrationsChi Liu, Dana Peters, and Gigi Galiana

Survey of engineering and physics foundations of modern medical imaging modalities with an emphasis on immersive and interactive experiences. Traditional lectures are balanced with guest lectures on state-of-the-art techniques and opportunities to observe procedures, acquire imaging data and reconstruct images. Modalities include MRI, X-ray, CT, SPECT, PET, optical and ultrasound methods. Prerequisite: BENG 352 or similar background.  QR, SC
MW 11:35am-12:50pm

BENG 445a / EENG 445a, Biomedical Image Processing and AnalysisJames Duncan and Lawrence Staib

This course is an introduction to biomedical image processing and analysis, covering image processing basics and techniques for image enhancement, feature extraction, compression, segmentation, registration and motion analysis including traditional and machine learning techniques. Student learn the fundamentals behind image processing and analysis methods and algorithms with an emphasis on biomedical applications.   Prerequisite: BENG 352 or EENG 310 or permission of instructors. Recommended preparation: familiarity with probability theory.
TTh 11:35am-12:50pm

BENG 449b, Biomedical Data AnalysisStaff

Study of biological and medical data analysis associated with applications of biomedical engineering. Provides basics of probability and statistics, as well as analytical approaches for determination of quantitative biological parameters from experimental data. Includes substantial programming in MATLAB. Prerequisite: MATH 120 or ENAS 151. After or concurrently with ENAS 194.  QR0 Course cr
TTh 1pm-2:15pm

BENG 455b, Vascular MechanicsJay Humphrey

Methods of continuum biomechanics used to study diverse vascular conditions and treatments from an engineering perspective. Topics include hypertension, atherosclerosis, aneurysms, vein grafts, and tissue engineered constructs. Emphasis on mechanics driven by advances in vascular mechanobiology. Prerequisite: BENG 353.  QR
TTh 1pm-2:15pm

* BENG 456b, Molecular and Cellular BiomechanicsMichael Murrell

The basic mechanical principles at the molecular and cellular level that underlie the major physical behaviors of the cell, from cell division to cell migration. Basic cellular physiology, methodology for studying cell mechanical behaviors, models for understanding the cellular response under mechanical stimulation, and the mechanical impact on cell differentiation and proliferation. Prerequisites: MENG 211 and 280 or equivalents, and experience with MATLAB. Recommended preparation: BENG 353 and MCDB 205.  QR, SC
W 3:30pm-5:20pm

BENG 458b, Multiscale Models of Biomechanical SystemsStuart Campbell

Current methods for simulating biomechanical function across biological scales, from molecules to organ systems of the human body. Theory and numerical methods; case studies exploring recent advances in multiscale biomechanical modeling. Includes computer laboratory sessions that introduce relevant software packages. Prerequisites: BENG 249, 351, and 353, or permission of instructor.  QR
MW 1pm-2:15pm

BENG 459b / MENG 459b, Neuromuscular BiomechanicsStaff

Mechanics and control of animal movement, including skeletal muscle mechanics, systems-level neural and sensory physiology, elements of feedback control, and optimal control. Deriving equations of motion for multibody mechanical systems that are actuated by muscles or muscle-like motors; incorporating sensory feedback; analyzing system properties such as stability and energetics. Prerequisites: MENG 383 and MATH 222 or equivalents, and familiarity with MATLAB or a similar scientific computing environment.  QRRP
MW 4pm-5:15pm

BENG 463a, ImmunoengineeringTarek Fahmy

Immuno-engineering uses engineering and applied sciences to better understand how the immune system works. It also uses immunity to build better models and biomaterials that help fight diseases such as cancer, diabetes, lupus, MS, etc. This is an integrative class. It integrates what we know in ENAS with what we know in Immunity to address critical and urgent concerns in health and disease. Students learn that analytical tools and reagents built by engineers address some extremely significant problems in immunity, such as optimal vaccine design. Students also have the opportunity to apply new understandings towards gaping holes in immunotherapy and immunodiagnostics.  Prerequisite: A basic understanding of biochemistry, biophysics, cell biology; calculus and differential equations.  QR, SC
TTh 11:35am-12:50pm

BENG 465b / MB&B 361b / MCDB 361b / NSCI 325b, Modeling Biological Systems IIJonathan Howard, Thierry Emonet, and Damon Clark

Advanced topics related to dynamical processes in biological systems. Processes by which cells compute, count, tell time, oscillate, and generate spatial patterns. Time-dependent dynamics in regulatory, signal-transduction, and neuronal networks; fluctuations, growth, and form. Comparisons between models and experimental data. Dynamical models applied to neurons, neural systems, and cellular biophysical processes. Use of MATLAB to create models. Prerequisite: MCDB 330 or equivalent, or a 200-level biology course, or with permission of instructor.  QR
TTh 2:30pm-3:45pm

BENG 467b, Systems Biology of Cell SignalingAndre Levchenko

Approaches from systems biology to the fundamental processes underlying both the sensory capability of individual cells and cell-to-cell communication in health and disease. Prerequisites: BENG 249 and ENAS 194, or equivalents.  QR, SC
MW 4pm-5:15pm

BENG 468b, Topics in ImmunoEngineeringTarek Fahmy

This course addresses the intersection of Immunobiology with Engineering and Biophysics. It invokes engineering tools, such as biomaterials, solid-state devices, nanotechnology, biophysical chemistry, and chemical engineering towards developing newer and effective solutions to cancer immunotherapy, autoimmune therapy, vaccine design, transplantation, allergy, asthma, and infections. The central theme is that dysfunctional immunity is responsible for a wide range of disease states and that engineering tools and methods can forge a link between the basic science and clinically translatable solutions that will potentially be "modern cures" to disease. This course is a follow-up to BENG 463, Immunoengineering  and focuses more on the clinical translation aspect as well as new understandings in immunology and how they can be translated to the clinic and eventually to the market.  Prerequisites: BENG 463, Differential Equations, Advanced Calculus.  SC
MW 4pm-5:15pm

BENG 469b, Single-Cell Biology, Technologies, and AnalysisRong Fan

This course is to teach the principles of single-cell heterogeneity in human health and disease as well as computational techniques for single-cell analysis, with a particular focus on the omics-level data. Topics to be covered include single-cell level morphometric analysis, genomic alteration analysis, epigenomic analysis, mRNA transcriptome sequencing, small RNA profiling, surface epitope, intracellular signaling protein, and secreted protein analysis, metabolomics, multi-omics, and spatially resolved single-cell omics mapping. The students are expected to perform computational analysis of single-cell high-dimensional datasets to identify population heterogeneity, identify cell types, states, and differentiation trajectories. Finally, case studies are provided to show the power of single-cell analysis in therapeutic target discovery, biomarker research, clinical diagnostics, and personalized medicine. Lab tours may be provided to show how single-cell omics data are generated and how high-throughput sequencing is conducted.   SC
TTh 2:30pm-3:45pm

* BENG 471a and BENG 472b, Special ProjectsLawrence Staib

Faculty-supervised individual or small-group projects with emphasis on research (laboratory or theory), engineering design, or tutorial study. Students are expected to consult the director of undergraduate studies and appropriate faculty members about ideas and suggestions for suitable topics. This course, offered Pass/Fail, can be taken at any time during a student's career, and may be taken more than once. For the Senior Project, see BENG 473, 474. Permission of both the instructor and the director of undergraduate studies is required.
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* BENG 473a and BENG 474b, Senior ProjectLawrence Staib

Faculty-supervised biomedical engineering projects focused on research (laboratory or theory) or engineering design. Students should consult with the director of undergraduate studies and appropriate faculty mentors for suitable projects. BENG 473 is taken during the fall term of the senior year and BENG 474 is taken during the spring term of the senior year. Permission of both the faculty mentor and the director of undergraduate studies is required.
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BENG 475a / CPSC 475a / EENG 475a, Computational Vision and Biological PerceptionSteven Zucker

An overview of computational vision with a biological emphasis. Suitable as an introduction to biological perception for computer science and engineering students, as well as an introduction to computational vision for mathematics, psychology, and physiology students. Prerequisite: CPSC 112 and MATH 120, or with permission of instructor.  QR, SCRP
MW 2:30pm-3:45pm

* BENG 480a, Seminar in Biomedical EngineeringAndre Levchenko

Oral presentations and written reports by students analyzing papers from scientific journals on topics of interest in biomedical engineering, including discussions and advanced seminars from faculty on selected subjects. (For Class of 2020 and beyond this course is worth .5 credit.)  ½ Course cr
TTh 1pm-2:15pm

* BENG 485b, Fundamentals of NeuroimagingFahmeed Hyder and Douglas Rothman

The neuroenergetic and neurochemical basis of several dominant neuroimaging methods, including fMRI. Technical aspects of different methods, interpretation of results, and controversies or challenges regarding the application of fMRI and related methods in medicine.  WR, SC
W 3:30pm-5:20pm