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Biomedical Engineering (BME) Course Descriptions

BME 6011  Research Seminar
(1-0) 1 hour credit. Prerequisites: Graduate student standing; consent of the instructor and the Graduate Advisor of Record.
The seminar coordinator may require students to present their research. May be repeated for credit. The grade report for the course is either “CR” (satisfactory performance) or “NC” (unsatisfactory performance). (Formerly BME 5011 and BME 6991. Same as ORTO 6090 at UTHSCSA.)

BME 6021-3  Supervised Teaching
1 to 3 hours credit. Prerequisites: Doctoral student standing; consent of the instructor and the Graduate Advisor of Record.
Supervised teaching of undergraduate or graduate students will be required for at least one semester. Students may be required to lecture at undergraduate courses or graduate courses in the field of their expertise. Students will work with the instructor of the course or with their research supervisor on the number of classes to be taught. (Same as ORTO 6071 at UTHSCSA.)

BME 6033  BME Engineering Analysis
(3-0) 3 hours credit. Prerequisite: Graduate standing in engineering or consent of the instructor.
This course is designed to introduce students to advanced mathematical and numerical methods necessary to solve problems frequently encountered in biomedical engineering. Topics covered include vector differential and integral calculus, linear algebraic equations, and ordinary and partial differential equations. (Same as EGR 6013. Same as BME 6093 offered in Fall 2007. Credit can be earned for only one of the following: BME 6033, BME 6093 taken Fall 2007, or EGR 6013.)

BME 6043  Critical Thinking & Writing for BME
(3-0) 3 hours credit. Prerequisites: Doctoral students who are either taking their qualifying examinations or have been admitted to candidacy; consent of the instructor and of the Graduate Advisor of Record.
This course introduces students to grant applications and manuscript writing, and provides the opportunity to learn through writing and critiquing research proposals, manuscripts, abstracts, and scientific presentations.

BME 6051-3  Independent Study in Biomedical Engineering
1 to 3 hours credit. Prerequisites: Graduate standing; consent of the instructor and of the Graduate Advisor of Record.
Independent reading, research, discussion, and/or writing under the direction of a faculty member. For students needing specialized work not normally or not often available as part of regular course offerings. May be repeated for credit on a different topic of study, but no more than 6 credit hours, regardless of discipline, will apply toward the degree.

BME 6063  Introduction to Scientific Computing and Visualization
(3-0) 3 hours credit. Prerequisites: Graduate standing; consent of the instructor.
This is an introductory course covering the basic concepts and tools of scientific computing and visualization. It will cover basic UNIX operations (shell scripts and editors), UNIX tools (grep, awk, sed), basic visualization concepts and software tools (ParaView and VisIt). It will also cover parallel programming using Fortran/C/C++ with Message Passing Interface (MPI) and public domain libraries. (Credit can be earned for only one of the following: BME 6063, ME 4953 or ME 5013.)

BME 6073  Professional Science Master’s Practicum
3 hours credit. Prerequisites: Graduate standing and consent of the Program Director.
An internship in a Biomedical Engineering company. Students must have completed all required core courses and electives, and be in the writing phase of their thesis. May not be repeated for credit.

BME 6093  Topics in Biomedical Engineering
(3-0) 3 hours credit. Prerequisites: Graduate standing; consent of the instructor and of the Graduate Advisor of Record.
May be repeated for credit on a different topic of study.

BME 6203  Physiology for Engineers
(3-0) 3 hours credit. Prerequisite: Consent of the instructor or completion of ORTO 6004 (UTHSCSA).
Designed to provide students with the essential graduate-level background for applications and practices of biomedical engineering. Integration of the nervous, skeletal, muscle, cardiovascular, and other systems from the sub-cellular to the whole-organism level will be emphasized.

BME 6213  Cellular Engineering
(3-0) 3 hours credit. Prerequisites: Consent of the instructor and completion of ORTO 6004 (UTHSCSA).
This course will focus on the use of engineering skills and principles in the analysis and design of cellular function including protein engineering, enzyme kinetics, drug design, receptor-ligand interactions, cell signaling, metabolism, growth, adhesion and migration.

BME 6223  Transport Processes in Biological Systems
(3-0) 3 hours credit. Prerequisites: Consent of the instructor and completion of ORTO 6004 (UTHSCSA).
This course will introduce the concepts of quantitative modeling of biological systems, particularly with respect to mass, momentum and energy transport, and reaction kinetics. Areas of study will include the use of conservation laws in quantifying cardiopulmonary, renal, and thermal systems of the human physiology, and also apply these principles in developing artificial and extracorporeal devices, drug delivery systems and pharmacokinetic analysis.

BME 6233  Cardiovascular Bioengineering
(3-0) 3 hours credit. Prerequisites: BME 2103 and BME 6033 or consent of the instructor.
This course introduces the bioengineering principles applied to the understanding and modeling of the cardiovascular system. Topics covered include anatomy of the human cardiovascular system; comparative anatomy; allometric scaling principles; cardiovascular molecular and cell biology; overview of continuum mechanics; form and function of blood, blood vessels, and the heart from an engineering perspective; normal, diseased and engineered replacement tissues and medical devices.

BME 6243  Mechanobiology
(3-0) 3 hours credit. Prerequisites: BME 6803 and ORTO 6004 (UTHSCSA).
The course will explore the role of mechanical forces in modulating molecular and cellular responses and signal transduction in cardiovascular, pulmonary, renal, skeletal and muscular systems, and impact in health and disease including stem cell differentiation and microgravity.

BME 6253  Bioheat Transfer
(3-0) 3 hours credit. Prerequisite: Graduate standing in engineering or consent of the instructor.
Principles and applications of heat transfer in soft tissue. Topics may include fundamental conservation laws and governing equations of heat transfer, coupling of fluid and mass transport, and thermal activated nanoparticle transvascular transport. (Same as ME 6253. Credit cannot be earned for both BME 6253 and ME 6253.)

BME 6303  Computational Oncology and Cancer Treatment Simulations
(3-0) 3 hours credit. Prerequisite: Completion of BME 6033 or consent of the instructor.
The objective of this course is to provide both engineering and medical students an introductory knowledge and skills of computational cancer biology, mathematical modeling and computer simulation, particularly in cancer diagnosis, treatment planning, image-guided control, and prognosis simulation. It will also cover basic methods in visualization and computational analysis of complex data.

BME 6313  Computational Bioengineering and Biomedicine
(3-0) 3 hours credit. Prerequisite: Completion of BME 6033 or consent of the instructor.
The objective of this course is to provide both engineering and medical students an introductory knowledge and skills of mathematical modeling and computer simulation, particularly in bioengineering. The course will consist of three parts: theoretical background, computational methods, and practical applications. (Same as ME 6873. Credit cannot be earned for both BME 6313 and ME 6873.)

BME 6323  Bioinformatics
(3-0) 3 hours credit. Prerequisites: Graduate standing and consent of the instructor.
This course is an introduction to algorithms and methods in bioinformatics, with special emphasis on computational molecular biology. Areas of study include fundamental topics such as sequence alignment, gene prediction, RNA secondary structure prediction, phylogenetic inference, gene regulation, microarray data analysis, and advanced topics such as biological network analysis and next-generation sequencing data analysis. (Same as CS 5263.Credit cannot be earned for both BME 6323 and CS 5263.)

BME 6333  Stochastic Modeling in Bioengineering
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
This course deals with development and application of probabilistic and uncertainty quantification methods in engineering. In particular, it covers random variable definitions, probability distributions, distribution selection, functions of random variables, numerical methods including Monte Carlo sampling, First Order Reliability Methods, component and systems reliability, and decision process under uncertainty. (Same as ME 5543. Credit cannot be earned for both BME 6333 and ME 5543.)

BME 6343  Statistical Pattern Recognition and Data Mining in Biomedical Engineering
(3-0) 3 hours credit. Prerequisites: Completion of BME 6333 and consent of the instructor.
This course introduces the fundamental theories and algorithms of statistical classification, regression, and clustering including Bayesian networks, k-nearest neighbor classifier, linear classifier, decision tree, kernel approach for classification and regression, k-means clustering, and hierarchical clustering. Applications to, among others, modeling and analysis gene regulation, cancer prognosis and diagnosis, and gene functions prediction will be discussed in detail.

BME 6353  Computational Methods in Mass Spectrometry
(3-0) 3 hours credit. Prerequisites: Completion of BME 6333 and consent of the instructor.
This course will introduce basic computational processing methods of Mass Spectrometry (MS) for protein quantification and identification. Background topics includes protein, proteome, and proteomics; protein separation; protein digestion; peptide separation using HPLC; and introduction to Mass Spectrometry. The course will focus on computational methods for protein identification and characterization by MS; tandem MS or MS/MS analysis; de novo sequencing and database searching; and quantitative proteomics.

BME 6363  Multiscale Computational Modeling of Biomedical Systems
(3-0) 3 hours credit. Prerequisites: Completion of EE 3413 or EE 5143 and consent of the instructor.
This course is an introduction to the mathematical modeling, simulation and analysis of biological systems focusing on the cardiovascular system. The proposed topics include: fundamental physical/biochemistry laws to model a biological system, current mathematical modeling methods, introduction to the cardiovascular system with respect to LV functions, cellular functions, and gene expressions, applications of the modeling methods to the cardiovascular system, simulation tools for biological systems, and stability analysis and parameter sensitivity analysis of mathematical models for biological systems. (Same as EE 5243 Topic 1. Credit cannot be earned for BME 6363 and EE 5243 on the same topic.)

BME 6523  Biological Laboratory Techniques in Biomedical Engineering
(1-4) 3 hours credit. Prerequisites: Consent of the instructor and completion of ORTO 6004 (UTHSCSA).
Emphasis for this course will be on optical and fluorescence microscopy of mammalian cells and tissues using sterile technique. Common cell-biomaterial characterization techniques will be performed including live/dead analysis, apoptosis, and quantification of cell signaling markers using immunological and advanced fluorescence assays with practical applications to biomaterial design.

BME 6703  Biomedical Imaging
(3-0) 3 hours credit. Prerequisite: Consent of the BME Program Director.
This course will examine, from a systems perspective, the techniques used in a variety of medical imaging modalities, which include X-ray imaging, computed tomography (CT), magnetic resonance imaging (MRI), nuclear medicine (PET), ultrasound imaging, optical imaging and photoacoustic imaging. The fundamental principles and engineering underlying each imaging modality will be discussed and a performance analysis of each system will be examined. With approval from the BME Program Director, credit for this course can be counted towards satisfying the imaging core course for Ph.D. students. (Credit can be earned for only one of the following: BME 6703 or RADI 5015 at UTHSCSA.)

BME 6713  Biomedical Signal Processing
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
Theory and classification of biological signals such as EEG, EKG, EMG, etc. Data acquisition and analysis procedures for biological signals, including computer applications.

BME 6723  Bioinstrumentations
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
This course will cover fundamental principles of bioinstrumentation used in clinical and research measurements. Topics include: principles of transducer operation, amplifiers and signal processing, recording and display. Overview of specific examples in optical sensors, biological sensors, MRI, ultrasound, pacemakers and defibrillators.

BME 6733  Microfabrication and Application
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
This course describes the science of miniaturization which is essential for nanotechnology development. Microfabrication techniques for micro-electro-mechanical systems (MEMS), bioMEMS, microfluidics, and nanomaterials and their applications in biomedical research will be covered.

BME 6743  Biophotonics
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
This course describes the fundamental principles of biophotonics and their wide range of applications in biomedical research. Topics will include fundamentals of light interactions with molecules, cells, and tissues, optical biosensing (fiber-optic biosensors, evanescent wave biosensors, surface plasmon resonance biosensors), optical imaging (transmission microscopy, fluorescence microscopy, confocal scanning microscopy, multiphoton microscopy, fluorescence lifetime imaging microscopy), flow cytometry, photodynamic therapy, laser tweezers and laser scissors, and nanotechnology for biophotonics.

BME 6753  Biosensors: Fundamentals and Applications
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
This course will cover biosensing basics and in-depth view of device design and performance analysis. Topics include optical, electrochemical, acoustic, piezoelectric, and nano-biosensors. Emphasized applications in biomedical, environmental, and homeland security areas are discussed.

BME 6793  Topics in Image and Signal Processing
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
May be repeated for credit on a different topic of study.

BME 6803  Biomechanics I
(2-3) 3 hours credit. Prerequisites: BME 6033 and graduate standing.
Fundamental applications of engineering mechanics in studying and modeling fluid flow, tissues, organs, and the whole human body will be discussed. This course includes a laboratory. (Formerly BME 6833. Same as ME 6833. Credit can be earned for only one of the following: BME 6803, BME 6833, ME 5833, or ME 6833.)

BME 6823  Biomechanics II
(3-0) 3 hours credit. Prerequisite: Graduate standing.
This course covers biomechanics of biological tissue deformation and their constitutive equations. Topics may include elasticity, viscoelasticity, deformation, stress analysis, strain measurement, stress and strain in organs. Tissues covered may include heart, blood vessels, cartilage, and bone.

BME 6863  Mechanical Behavior of Living Tissues
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
Stress-strain relationships, viscoelasticity, mechanical properties, and mechanical modeling of collagenous and mineralized human tissues will be addressed. (Formerly BME 6513. Credit cannot be earned for both BME 6863 and BME 6513.)

BME 6873  Biofluid Mechanics
(3-0) 3 hours credit. Prerequisite: BME 6803 or ME 3663 or consent of the instructor.
This course is an introduction to the fluid dynamics concepts necessary to design and perform research in physiological and biofluid mechanics, with a special emphasis in the quantitative understanding and fundamental engineering concepts of the human systemic and pulmonary circulation. Computational and experimental techniques will be studied with hands-on research projects based on student interest.

BME 6893  Topics in Biomechanics
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
May be repeated for credit on a different topic of study. (Same as ME 6893. Credit cannot be earned for both BME 6893 and ME 6893 when the topic is the same.)

BME 6903  Biomaterials
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
Fundamentals of biomaterials science and engineering principles and concepts in repairing, replacing, and protecting human tissues and organs will be discussed. (Formerly BME 5903 and BME 6813. Same as ME 6813. Credit can be earned for only one of the following: BME 5903, BME 6903, BME 6813, ME 5813 or ME 6813.)

BME 6913  Biomaterials II
(3-0) 3 hours credit. Prerequisites: BME 6903 and consent of the instructor.
Application of biomaterials in medicine and dentistry will be emphasized.

BME 6923  Tissue Engineering
(3-0) 3 hours credit. Prerequisite: Graduate standing.
This course is an introduction to the principles and current practice of tissue engineering endeavors. Strategies for choosing and using mammalian cells and scaffold biomaterials as well as select chemical and biophysical stimuli in order to obtain neotissue formation are reviewed in detail. Case studies are discussed to illustrate successful tissue engineering solutions of clinical problems pertinent to tissue regeneration. (Formerly BME 5923 and BME 6853. Credit can be earned for only one of the following: BME 5923, BME 6853, or BME 6923.)

BME 6933  Tissue-Biomaterials Interactions
(3-0) 3 hours credit. Prerequisite: Graduate standing.
This course is an introduction to biocompatibility with special emphasis on the interaction of proteins, cells and tissues with biomaterials. Blood-material interactions are reviewed in detail. Case studies of implants are discussed to illustrate biomaterial selection as a key aspect to successful design of implant materials and prosthetic devices.

BME 6943  Biomaterials & Cell Signaling
(2-3) 3 hours credit. Prerequisite: Graduate standing.
Develop current understanding of topics in cell receptors and signaling mechanisms with application for biomaterial design. Focus will emphasize receptor-ligand communication, methods of identification and quantification, and pathways involved for cell to material stress response.

BME 6953  Biomaterials for Drug-Delivery/Pharmacology
(2-3) 3 hours credit. Prerequisite: Graduate standing.
Provides conceptual understanding of therapeutic agents used to regulate physiological function of cells comprising organ systems with relevance to biomaterials. Interpretation of drug mechanisms at a molecular, cellular and tissue level. Traditional reviews of pharmacodynamics and pharmacokinetics will be addressed with particular application to biomaterial interaction and drug-delivery systems.

BME 6961  Comprehensive Examination
1 hour credit. Prerequisite: Approval of the Biomedical Engineering Committee on Graduate Studies to take the Comprehensive Examination.
Independent study course for the purpose of taking the Comprehensive Examination for M.S. students in the nonthesis option.  May be repeated once if approved by the Biomedical Engineering Committee on Graduate Studies and if the student received an “unsatisfactory performance” on his/her previous attempt on the Comprehensive Examination. Enrollment is required each term in which the Comprehensive Examination is taken if no other courses are being taken that term. The grade report for the course is either “CR” (satisfactory performance on the Comprehensive Examination) or “NC” (unsatisfactory performance on the Comprehensive Examination).

BME 6963  Fundamentals to Polymer Science with Select Biomedical Applications
(3-0) 3 hours credit. Prerequisites: Graduate standing and BME 6903; or consent of the instructor.
This course introduces the fundamentals of polymer chemistry, characterization of the chemical and material properties, and determination of the biocompatibility of polymer formulations. Current applications of polymeric biomaterials in diagnostic and therapeutic devices, implants, tissue engineering and regenerative medicine are highlighted and discussed in detail.

BME 6973  Current Analytical Tools for Biomaterials Characterizations
(1-4) 3 hours credit. Prerequisites: Graduate standing and BME 6903; or consent of the instructor.
This course introduces the fundamentals of biomaterials characterizations and its limitations.

BME 6981,2,3,6  Master’s Thesis Research
1, 2, 3, or 6 hours credit. Prerequisites: Master’s student standing; consent of the instructor and of the Graduate Advisor of Record.
May be repeated for a maximum of 9 credit hours. (Formerly BME 5953,6.)

BME 6993  Topics in Biomaterials
(3-0) 3 hours credit. Prerequisite: Consent of the instructor.
May be repeated for credit on a different topic of study.

BME 7951,2,3,6  Doctoral Research
1, 2, 3, or 6 hours credit. Prerequisites: Doctoral student standing; consent of the instructor and of the Graduate Advisor of Record.
This course consists of independent, original research under the direction of a faculty advisor. May be repeated for a maximum of 18 credit hours. (Same as ORTO 6097 at UTHSCSA.)

BME 7991,2,3,6  Doctoral Dissertation
1, 2, 3, or 6 hours credit. Prerequisites: Admission to Doctoral candidacy; consent of the Graduate Advisor of Record and Dissertation Advisor.
May be repeated for a maximum of 18 credit hours. (Same at ORTO 7099 at UTHSCSA.)

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