Graduate Courses

The faculty has approval to offer the following courses in the academic years 2017–2018 and 2018–2019; however, not all courses are taught each semester or summer session. Students should consult the Course Schedule to determine which courses and topics will be offered during a particular semester or summer session. The Course Schedule may also reflect changes made to the course inventory after the publication of this catalog.

Biomedical Engineering: BME

BME 180J, 380J. Fundamentals of Biomedical Engineering.

One or three lecture hours a week for one semester, or as required by the topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing.

Topic 1: Mathematical Modeling in Biomedical Engineering. Conservation of mass, momentum, energy, and charge; first and second laws of thermodynamics; first- and second-order differential equations; nonlinear differential equations; partial differential equations as applied to biomedical engineering problems.
Topic 2: Quantitative Systems Physiology and Pathophysiology. Modeling of physiological systems from the molecular and cellular levels to the systems level; focus on the neuromuscular and cardiovascular systems. Prerequisite: An undergraduate physiology course or the equivalent, and consent of instructor.
Topic 3: Principles of Biomeasurement. Principles of signal measurement in the biomedical field; survey of transducers used for chemical, mechanical, electrical, and thermal biomedical measurements; analysis of how signals are converted into digital form; analysis of noise; aliasing; data storage.
Topic 4: Fields, Forces, and Flows. Introduction to mathematical models that integrate different energy domains and length scales, with an emphasis on the coupling between them. Prerequisite: Biomedical Engineering 380J (Topic 1) and 380J (Topic 2).
Topic 5: Biostatistics, Study Design, and Research Methodology. Principles for hypothesis testing; confidence limits; regression analysis; correlation; analysis of variance; experimental design and factorial analysis; discriminate analysis; applications of statistics. Prerequisite: An undergraduate probability theory course or the equivalent, and consent of instructor.
Topic 6: Analysis of Biomedical Engineering Systems I. Quantitative examination of the cardiovascular and respiratory systems from the cell to system levels. Presents the cardiovascular and respiratory systems in three phases: (1) anatomy and physiology; (2) energetics (thermodynamics), cellular processes, and engineering analysis; and (3) engineered devices, instrumentation, and imaging for therapeutics and diagnosis. Additional prerequisite: A course in physiology, proficiency in MATLAB, and consent of the graduate adviser.
Topic 7: Analysis of Biomedical Engineering Systems II. Computational techniques used in biomedical engineering. Students propose and conduct an engineering design study relevant to a selected medical problem. Additional prerequisite: Biomedical Engineering 380J (Topic 6).

BME 080M. Dual MD/PhD Program with UT Medical Branch.

Preclinical medical study at the University of Texas Medical Branch at Galveston. May not be taken concurrently with another course at the University of Texas at Austin. Prerequisite: Graduate standing and admission to the MD/PhD dual degree program in biomedical engineering.

BME 381J. Topics in Cell and Molecular Imaging.

Three lecture hours a week for one semester, or as required by the topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing in engineering and consent of instructor; additional prerequisites vary with the topic.

Topic 1: Laser-Tissue Interaction: Thermal. Same as Electrical Engineering 385J (Topic 9: Laser-Tissue Interaction: Thermal). The thermal response of random media in interaction with laser irradiation. Calculation of the rate of heat production caused by direct absorption of the laser light, thermal damage, and ablation.
Topic 2: Laser-Tissue Interaction: Optical. Same as Electrical Engineering 385J (Topic 16: Laser-Tissue Interaction: Optical). The optical behavior of random media such as tissue in interaction with laser irradiation. Approximate transport equation methods to predict the absorption and scattering parameters of laser light inside tissue. Port-wine stain treatment; cancer treatment by photochemotherapy; and cardiovascular applications.
Topic 3: Imaging Signals and Systems. Same as Electrical Engineering 385J (Topic 18). Physical principles and signal processing techniques used in thermographic, ultrasonic, and radiographic imaging, including image reconstruction from projections such as CT scanning, MRI, and millimeter wave determination of temperature profiles. Additional prerequisite: Electrical Engineering 371R and consent of instructor.
Topic 4: Optical Spectroscopy. Same as Electrical Engineering 385J (Topic 23: Optical Spectroscopy). Measurement and interpretation of spectra: steady-state and time-resolved absorption, fluorescence, phosphorescence, and Raman spectroscopy in the ultraviolet, visible, and infrared portions of the spectrum.
Topic 5: Therapeutic Heating. Same as Electrical Engineering 385J (Topic 26: Therapeutic Heating). Engineering aspects of electromagnetic fields that have therapeutic applications: diathermy (short wave, microwave, and ultrasound), electrosurgery (thermal damage processes), stimulation of excitable tissue, and electrical safety.
Topic 6: Noninvasive Optical Tomography. Same as Electrical Engineering 385J (Topic 28: Noninvasive Optical Tomography). Basic principles of optical tomographic imaging of biological materials for diagnostic or therapeutic applications. Optical-based tomographic imaging techniques including photothermal, photoacoustic, and coherent methodologies.
Topic 7: Digital Image and Video Processing. Digital image acquisition, processing, and analysis; algebraic and geometric image transformations; two-dimensional Fourier analysis; image filtering and coding. Additional prerequisite: Credit or registration for Biomedical Engineering 335 or Electrical Engineering 351K.
Topic 8: Functional Imaging Laboratory. Explores in vivo functional imaging, including aspects of imaging hardware and instrumentation, contrast agents, image processing, management of large imaging data sets, and applications of physiological modeling. Three lecture hours a week for one semester. Additional hours to be arranged. Biomedical Engineering 381J (Topic: Functional Imaging Laboratory) and 381J (Topic 8) may not both be counted. Additional prerequisite: Graduate standing in engineering.
Topic 9: Fundamentals of Biomedical Optical Imaging. Introduction to the field of biophotonics. Discussion of light scattering theory, tissue optical properties, analytical and numerical techniques for determining light propagation in tissue, light-tissue interactions, and bioheat transfer including solution methods. Biomedical Engineering 381J (Topic: Fundamentals of Biomedical Optical Imaging) and 381J (Topic 9) may not both be counted.
Topic 10: Optics and Lasers. Fundamentals of geometric and physical optics, interaction of light with matter, spectroscopy, and laser and electro-optics applications. Biomedical Engineering 381J (Topic: Optics and Lasers) and 381J (Topic 10) may not both be counted.
Topic 11: Medical Imaging. Biomedical Engineering 381J (Topic: Medical Imaging) and 381J (Topic 11) may not both be counted.
Topic 12: Optical Design. The principles of optical design for imaging and laser delivery systems are given. Students develop and test designs using a commercial optical design software package. Biomedical Engineering 381J (Topic: Optical Design) and 381J (Topic 12) may not both be counted.
Topic 13: Fluorescence Micro- and Spectroscopy. Fundamentals of fluorescence microscopy, spectroscopy, and techniques; single-molecule detection; advanced microscopy, including multi-photon microscopy, super-resolution imaging, and molecular tracking. Other subjects include metal-enhanced fluorescence, optogenetics, nanomedicine and microfluidics. Biomedical Engineering 381J (Topic: Fluorescence Micro-/Spectroscopy) and 381J (Topic 13) may not both be counted. Additional prerequisite: Understanding of biochemistry and biology; lab experience using microscopic technology and tools.

BME 382J. Topics in Cellular and Biomolecular Engineering.

Three lecture hours a week for one semester, or as required by the topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing in engineering and consent of instructor.

Topic 1: Cell and Tissue Engineering. Use of case studies to explore pathologies of tissue, current clinical treatment, and the role of engineers in developing new technologies to diagnose and treat these pathologies. Emphasis on the use of quantitative cellular and molecular techniques. Applications of synthetic and natural biomaterials. Additional prerequisite: Quantitative physiology or pathophysiology course.
Topic 2: Introduction to Biochemical Engineering. Microorganisms in chemical and biochemical synthesis; genetic manipulation of cells by classical and recombinant DNA techniques; enzyme technology; design of bioreactors and microbial fermentations; and separations of biological products.
Topic 3: Molecular Sensors and Nanodevices for Biomedical Engineering Applications. Introduction to a variety of methods used to detect biological molecules with optical and electrical transduction mechanisms. Covers the classical approaches to biosensors for the detection of specific molecules in biological systems.
Topic 4: Advanced Engineering Biomaterials. Overview of biomaterials, including prosthetics, ceramics, metal implants, and polymers, with specific emphasis on properties and applications. The immunology of material-tissue interactions and the issues of biocompatibility.
Topic 5: Structured Surfaces, Fabrication, Characterization, and Application. Introduction to fabrication and characterization techniques used to create and analyze microstructured and nanostructured surfaces for biomedical and biotechnology applications. Focuses on the use of self-assembly processes for the fabrication of biological functionality in surface structures.
Topic 6: Biopolymers and Drug/Gene Delivery. Biomedical polymers and their applications in drug delivery and gene therapy. Emphasis on parenteral, mucosal, and topical delivery of biomolecules, and the role of polymers in genetic therapy and DNA vaccination.
Topic 7: Cellular and Molecular Biomechanics. Introduction to the concepts needed to understand and work in the emerging field of cellular and molecular biomechanics. Examination of dynamic interplay between chemical, thermal, and physical forces in determining the mechanics of cells/tissues and their molecular components. Three lectures hours a week for one semester, with additional hours to be arranged. Biomedical Engineering 382J (Topic: Cellular and Molecular Biomechanics) and 382J (Topic 7) may not both be counted. Additional prerequisite: Graduate standing; and coursework in calculus, physics, solid mechanics, and basic chemical/biological principles.
Topic 8: Molecular Biophysics: Measurements and Methods. In-depth study and development of intuition for thermodynamics and mechanics and application of understanding to molecular-scale problems in cell biology and biomedical engineering. Focus on increasing students' familiarity with modern methods of biophysical measurement, their strengths and limitations, and how they are being applied to address current research problems. Biomedical Engineering 382J (Topic: Molecular Biophysics: Measurements and Methods) and 382J (Topic 8) may not both be counted. Additional prerequisite: Undergraduate biology, calculus, chemistry, and physics is recommended.
Topic 9: Biomimetic Design and Engineering. Introduction to biomimetic reverse engineering, including the weaknesses of animal models to predict human physiology, microphysiological systems, the potential of human organs on chips to accelerate drug development processes, pharmaceutical preclinical testing requirements, human microbiome, disease models to study pathophysiology, and related subjects. Biomedical Engineering 382J (Topic: Biomimetic Design and Engineering) and 382J (Topic 9) may not both be counted.
Topic 10: Immune Engineering. Introduction to the concept of immune engineering. Discussion of vaccine design, cancer immunotherapy, genomics, infection, auto-immune diseases and emerging tools and methodologies. Biomedical Engineering 382J (Topic: Immune Engineering) and 382J (Topic 10) may not both be counted. Additional prerequisite: Understanding of biology.

BME 383J. Topics in Computational Biomedical Engineering and Bioinformatics.

Three lecture hours a week for one semester, or as required by the topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing in engineering and consent of instructor; additional prerequisites may vary with the topic.

Topic 1: Network Thermodynamics in Biophysics. Modeling and simulation methods for nonlinear biological processes, including coupling across multienergy domains; practical implementation by bond graph techniques. Additional prerequisite: Mechanical Engineering 344 or consent of instructor.
Topic 2: Musculoskeletal Biomechanics. Synthesis of properties of the musculotendon and skeletal systems to construct detailed computer models that quantify human performance and muscular coordination. Additional prerequisite: Mathematics 341 and Kinesiology 395 (Topic 36: Biomechanics of Human Movement).
Topic 4: Biomechanics of Human Movement. Same as Kinesiology 395 (Topic 36: Biomechanics of Human Movement). Additional prerequisite: Kinesiology 326K, two semesters of calculus, one semester of college physics (mechanics), and consent of instructor.
Topic 5: Introduction to Nonlinear Dynamics in Biological Systems. Same as Kinesiology 395 (Topic 63: Introduction to Nonlinear Dynamics in Biological Systems). Basic concepts of nonlinear mathematics and their application to biological systems. Additional prerequisite: Two semesters of college-level calculus and consent of instructor.
Topic 7: Data Mining. Analyzing large data sets for interesting and useful information; online analytical processing, finding association rules, clustering, classification, and function approximation; scalability of algorithms and real-life applications.
Topic 8: Systems Biology. The biological function of genetic and biochemical networks from a quantitative perspective. Students use mathematical tools to model network modules, such as biological switches, oscillators, and amplifiers. Discusses recent papers on a variety of biological problems that can be addressed with a systems biology approach. Additional prerequisite: Biology 311C and Mathematics 427K; Chemistry 369 or an introductory course in biochemistry, and knowledge of MATLAB, are recommended.
Topic 9: Computational Methods for Biomedical Engineers. Study of and hands-on experiences with computational methods commonly employed in biomedical engineering research. Three lecture hours a week for one semester. Biomedical Engineering 383J (Topic: Computational Methods for Biomedical Engineers I) and 383J (Topic 9) may not both be counted. Additional prerequisite: Graduate standing in engineering.
Topic 10: Computational Biomolecular Engineering. Provides an introduction to the principles and applications of biomolecular modeling and simulation, including the theoretical background of molecular thermodynamics and molecular mechanics, major simulation/computational techniques and commonly used software tools. Biomedical Engineering 383J (Topic: Computational Biomolecular Engineering) and 383J (Topic 10) may not both be counted. Additional prerequisite: Undergraduate biochemistry coursework, and thermodynamics or physical chemistry coursework; or consent of instructor.
Topic 11: Dynamical Modeling of Biological Signaling and Regulatory Systems. Introduction to various approaches currently used for modeling and simulating cellular signal transduction, metabolic, and gene regulatory networks. Biomedical Engineering 383J (Topic: Dynamical Modeling of Biological Signaling and Regulatory Systems) and 383J (Topic 11) may not both be counted. Additional prerequisite: Understanding of biochemistry and biology; familiarity with a programming environment.

BME 384J. Topics in Instrumentation.

Three lecture hours a week for one semester, or as required by the topic. May be repeated for credit when the topics vary. Prerequisite: Graduate standing in engineering and consent of instructor; additional prerequisites vary with the topic.

Topic 1: Biomedical Instrumentation I. Same as Electrical Engineering 385J (Topic 31: Biomedical Instrumentation I). Application of electrical engineering techniques to analysis and instrumentation in biological sciences: pressure, flow, temperature measurement; bioelectrical signals; pacemakers; ultrasonics; electrical safety; electrotherapeutics.
Topic 2: Biomedical Instrumentation II: Real-Time Computer-Based Systems. Same as Electrical Engineering 385J (Topic 17: Biomedical Instrumentation II: Real-Time Computer-Based Systems). Design, testing, patient safety, electrical noise, biomedical measurement transducers, therapeutics, instrumentation electronics, microcomputer interfaces, and embedded systems. Four structured laboratories and an individual project laboratory.
Topic 3: Biosignal Analysis. Same as Electrical Engineering 385J (Topic 15: Biosignal Analysis). Theory and classification of biological signals such as EEG, EKG, and EMG. Data acquisition and analysis procedures for biological signals, including computer applications.
Topic 4: Bioelectric Phenomena. Same as Electrical Engineering 385J (Topic 3: Bioelectric Phenomena). Examines the physiological bases of bioelectricity and the techniques required to record bioelectric phenomena both intracellularly and extracellularly; the representation of bioelectric activity by equivalent dipoles and the volume conductor fields produced.
Topic 5: Projects in Biomedical Engineering. Same as Electrical Engineering 385J (Topic 32: Projects in Biomedical Engineering). An in-depth examination of selected topics, such as optical and thermal properties of laser interaction with tissue; measurement of perfusion in the microvascular system; diagnostic imaging; interaction of living systems with electromagnetic fields; robotic surgical tools; ophthalmic instrumentation; noninvasive cardiovascular measurements. Three lecture hours and six laboratory hours a week for one semester. Additional prerequisite: Biomedical Engineering 384J (Topic 1) or Electrical Engineering 385J (Topic 31).
Topic 6: Neurophysiology/Prosthesis Design. Same as Electrical Engineering 385J (Topic 33: Neurophysiology/Prosthesis Design). The structure and function of the human brain. Discussion of selected neurological diseases in conjunction with normal neurophysiology. Study of neuroprosthesis treatments and design philosophy, functional neural stimulation, and functional muscular stimulation.

BME 385J. Topics in Biomedical Engineering.

Three lecture hours a week for one semester, or as required by the topic. Biomedical Engineering 385J and 387J may not both be counted unless the topics vary. May be repeated for credit when the topics vary. Prerequisite: Graduate standing in engineering and consent of instructor.

Topic 6: Analysis of Biological Systems. Biomedical Engineering 383J (Topic: Analysis of Biological Systems I) and 385J (Topic 6) may not both be counted.
Topic 7: Tissue and Cell Biomechanics Applications. Analysis of biosolid mechanics via the mechanical behavior of scaffolds and living tissues and cells. Emphasis on biomechanical application areas, including cell mechanics, engineered materials, hard and soft tissues, and organs. Biomedical Engineering 385J (Topic: TISSUE/SCAFFOLD BIOMECHANICS) and 385J (Topic 7) may not both be counted.
Topic 12: Biomedical Heat Transfer. Application of the principles of heat transfer to the solution of a series of advanced, open-ended problems in medicine and biology. Inquiry learning format in which students take personal responsibility for identifying and pursuing solution strategies for a range of cutting edge problems in bioheat transfer. Additional prerequisite: Biomedical Engineering 353, Chemical Engineering 319 (or 353), or another course in transport phenomena.
Topic 39: Medical Decision Making. Selected subjects from cognitive psychology and human-machine interaction for engineering students to design more effective systems for supporting medical decision making. Biomedical Engineering 385J (Topic: Medical Decision Making) and 385J (Topic 39) may not both be counted.

BME 396. Research Internship.

Students participate in research in an industry, clinic, or academic laboratory setting selected with the approval of the faculty adviser. At least twenty hours of fieldwork a week for one semester. May be counted only once toward either the master's or the doctoral degree. Offered on the credit/no credit basis only. Prerequisite: Graduate standing.

BME 197, 297, 397, 597, 697. Research Problems.

Problems selected by the student with approval of the faculty adviser. For each semester hour of credit earned, three laboratory hours a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing in biomedical engineering.

BME 197E. Professional Responsibilities in Imaging.

One lecture hour a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing.

BME 197N. Integrated Biomedical Engineering Seminar.

Designed to support students' professional development as well as their broad understanding of the biomedical engineering research enterprise. One lecture hour a week for one semester. Prerequisite: Graduate standing.

BME 197P, 297P, 397P. Graduate Professional Development Seminar.

Explores professional development goals of biomedical engineers. Subjects include an individual development plan, careers in academia, entrepreneurship, careers in industry, and more. For each semester hour of credit earned, one lecture hour a week for one semester. Offered on the credit/no credit basis only.

BME 197S. Graduate Seminar in Biomedical Engineering.

The equivalent of one lecture hour a week for one semester. May be repeated for credit. Offered on the credit/no credit basis only. Prerequisite: Graduate standing.

BME 698. Thesis.

The equivalent of three lecture hours a week for two semesters. Offered on the credit/no credit basis only. Prerequisite: For 698A, graduate standing in biomedical engineering and consent of the graduate adviser; for 698B, Biomedical Engineering 698A.

BME 398R. Master's Report.

Preparation of a report to fulfill the requirement for the master's degree under the report option. The equivalent of three lecture hours a week for one semester. Offered on the credit/no credit basis only. Prerequisite: Graduate standing in biomedical engineering and consent of the graduate adviser.

BME 399R, 699R, 999R. Dissertation.

Offered on the credit/no credit basis only. Prerequisite: Admission to candidacy for the doctoral degree.

BME 399W, 699W, 999W. Dissertation.

Offered on the credit/no credit basis only. Prerequisite: Biomedical Engineering 399R, 699R, or 999R.