Course Schedule and Catalog

Long Title: CAREERS IN BIOENGINEERING

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Seminar

Credit Hours: 1

Description: This seminar is suitable for freshman, sophomores, and non-majors. A series of guest lectures will introduce students to a variety of career options in bioengineering. Students will participate in at least one field trip to an industry partner or hospital to learn more about careers in bioengineering.

Long Title: BIOENGINEERING FUNDAMENTALS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): MATH 101 AND MATH 102 AND CHEM 122 AND CAAM 210 AND (PHYS 101 OR PHYS 125 OR PHYS 111) AND (PHYS 102 OR PHYS 126 OR PHYS 112)

Description: Introduction to material, energy, charge, and momentum balances in biological systems. Steady state and transient conservation equations for mass, energy, charge and momentum will be derived and applied using basic mathematical principles, physical laws, stoichiometry, and thermodynamic properties. Problem based learning groups will solve open-ended problems. Required for students intending to major in bioengineering. Recommended Co or Prerequisite(s): MATH 211.

Long Title: SYSTEMS PHYSIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOC 201 AND (PHYS 101 AND PHYS 102) OR (PHYS 125 AND PHYS 126)

Description: This course will teach the fundamentals of human physiology with a specific focus on the nervous, cardiovascular, respiratory, and urinary systems. Basic introductory engineering principles will be applied to the study of physiological systems. The course is aimed to be accessible to students with non-engineering backgrounds. Students may receive credit for only one of BIOE 302, BIOE 322, and BIOC 332. Cross-list: BIOC 332. Mutually Exclusive: Cannot register for BIOE 302 if student has credit for BIOE 322.

Long Title: SYSTEMS BIOLOGY OF BLOOD VESSELS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252

Description: How blood vessels respond to hypoxia is a process critical to the progression of many diseases and conditions including cardiovascular disease, cancer, cerebrovascular disease, diabetes, obesity and arthritis. Physiological processes such as exercise, aging, and wound healing also depend on hypoxia-induced microvessel changes. This course introduces engineering concepts of hypoxic response, angiogenesis, and capillary remodeling - from the effects at the intracellular level to the whole body. Topics covered include computational systems biology modeling of hypoxia and angiogenesis, the use of angiogenesis in tissue engineering and regenerative medicine, imaging of blood vessel dynamics, capillaries of the brain, and the design of new blood vessels. Graduate/Undergraduate Equivalency: BIOE 507. Mutually Exclusive: Cannot register for BIOE 307 if student has credit for BIOE 507.

Long Title: SYSTEMS PHYSIOLOGY LAB MODULE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): BIOE 252 AND (BIOS 332 OR BIOE 322 OR BIOC 332)

Description: Exploration of physiologic systems through measurement of biologic signals. EEG, ECG, EMG pulmonary function tests, etc. are performed and analyzed. Students will explore physiologic concepts through computer simulations, data collection, and analysis. Enrollment in or completion of BIOE 322/BIOC 332 is expected and maybe taken the same semester as BIOE 320. For students intending to major in Bioengineering. Instructor Permission Required.

Long Title: CELLULAR ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 or permission of instructor

Description: Introduction to engineering principles and modeling regulation and circuitry at the cellular level. Topics include genetic metabolic networks and cell surface interactions.

Long Title: FUNDAMENTALS OF SYSTEMS PHYSIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND MATH 211

Description: This course will teach the fundamentals of human physiology from an engineering perspective, with specific focus on the nervous, cardiovascular, respiratory and urinary systems. Lectures, assignments and exams will be quantitative and will introduce engineering principles, such as conservation of mass and energy, controls and system analysis, thermodynamics and mass transport, and apply them to the study of physiologic systems. This course is limited to undergraduates. Students may receive credit for only one of BIOE 302, BIOE 322, and BIOC 332 Mutually Exclusive: Cannot register for BIOE 322 if student has credit for BIOC 332/BIOE 302.

Long Title: BIOREACTION ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND (BIOC 201 OR BIOS 201)

Description: Application of engineering principles to biological processes. Mathematical and experimental techniques for quantitative descriptions of enzyme kinetics, metabolic and genetic networks, cell growth kinetics, bioreactor design and operation.

Long Title: BIOENGINEERING THERMODYNAMICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND MATH 212

Description: This course provides a mathematically rigorous and quantitative coverage of the fundamentals of thermodynamics with applications drawn from contemporary bioengineering problems. Fundamental topics will include the Zeroth, First and Second Law, Entropy Inequality, Gibbs and Helmholtz Free Energies, The Third Law, Maxwell Relations, chemical potential, equilibrium, phase transitions, solution thermodynamics, protein-ligand binding and statistical mechanics. Advanced topics will include transcription factor-DNA binding, nucleic acid hybridization, translation initiation and genetic circuits. The course will cover the role that thermodynamics plays in molecular engineering and synthetic biology.

Long Title: LABORATORY IN TISSUE CULTURE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): BIOE 440 OR STAT 440 OR BIOC 311 OR BIOS 311

Description: Introduction to tissue culture techniques, including cell passage, cell viability, and cell attachment and proliferation assays. Students complete quantitative analysis of their data. Engineering design and applications are featured in graded work. Sections 1 and 2 are taught during the first half of the semester. Sections 3 and 4 are taught during the second half of the semester. Students may be required to attend lab on a university holiday. Instructor Permission Required.Cross-list: BIOC 320.

Long Title: MOLECULAR TECHNIQUES IN BIOENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOC 341 AND (BIOE 342 OR BIOC 320)

Description: Introduction to the fundamental physical principles of light interaction with matter, separation (by charge, size, confirmation) and detection techniques utilized in the field of bioengineering. These include absorbance and fluorescence spectroscopy, light and fluorescence microscopy, flow cytometry, electrophoresis, PCR, Blotting, and ELISA. BIOE 342/BIOC 320 may be taken concurrently with BIOE 348.

Long Title: APPROPRIATE DESIGN FOR GLOBAL HEALTH

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 3

Prerequisite(s): GLHT 201

Description: Seminar-style introductory design course covering epidemiology, pathophysiology, health systems, health economics, medical ethics, humanitarian emergencies, scientific and engineering design methods, and appropriate health technology case studies. To register, you must be enrolled in the GLHT minor and submit a 250 statement to beyondtraditionalborders@rice.edu by Monday of preregistration. The minor and course prerequisite is waived for students majoring in Bioengineering. Instructor Permission Required.Cross-list: GLHT 360.

Long Title: METABOLIC ENGINEERING FOR GLOBAL HEALTH ENVIRONMENTS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): (BIOE 362 OR GLHT 362) AND (PHYS 126 OR PHYS 102 OR PHYS 112 OR PHYS 142) AND MATH 102

Description: Importance of nutritional and pharmaceutical compounds, impact of cost of compounds on global health; Overview of biochemical pathways; metabolite analysis; Genetic engineering and molecular biology tools for ME; Pharmaceuticals and drug discovery approaches (antibiotics, antivirals; anti-parasite compounds); anti-diarrhea treatments; vaccines. Cross-list: BIOC 361, GLHT 361.

Long Title: SUSTAINABLE WATER PURIFICATION FOR THE DEVELOPING WORLD

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 1

Description: This course is an introduction to several innovative methods of small-scale water purification which are appropriate for implementation in the developing world. Through the different components of the course, students will acquire and hone a sustainable methodology for addressing global health problems at the local level. Cross-list: CEVE 314.

Long Title: BIOMATERIALS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND CHEM 211 AND (MECH 211 OR CEVE 211) or permission of instructor

Description: This course will introduce both basic materials science and biological concepts with an emphasis on application of basic quantitative engineering principles to understanding the interactions between materials and biological systems. Topics covered include chemical structure of biomaterials, physical, mechanical, and surface properties of biomaterials, biomaterial degradation, and biomaterial processing. Additional topics include protein and cell interactions with biomaterials, biomaterial implantation, and acute inflammation, wound healing and the presence of biomaterials immune responses to biomaterials, biomaterials, immune responses to biomaterials, biomaterials and thrombosis, as well as infection, tumorigenesis, and calcification of biomaterials that can collectively apply to design of biomaterials for myriad applications. MECH 211 or CEVE 211 may be taken concurrently with BIOE 370.

Long Title: BIOMECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND MATH 212 AND (MECH 211 OR CEVE 211) or permission of instructor

Description: This course introduces the fundamental principles of mechanics applied to the analysis and characterization of biological systems. Topics covered include normal and shear stresses, normal and shear strains, mechanical properties of materials, load, deformation, elasticity and elastoplastic behavior. Quantitative analysis of statically determinate and indeterminate structures subjected to tension, compression, torsion and bending will be covered. Additionally, aspects of blood rheology, viscoelasticity, and musculoskeletal mechanics will be addressed.

Long Title: FUNDAMENTALS OF NERVE AND MUSCLE ELECTROPHYSIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: An introduction to cellular electrophysiology. Includes development of whole-cell models for neurons and muscle (cardiac and skeletal muscle) cells, based on ion channel currents obtained from whole-cell voltage-clamp experiments. Material balance equations are developed for various ions and chemical signaling agents (e.g., second messengers). Numerical methods are introduced for solving the ordinary and partial differential equations associated with these models. Several types of cell models are discussed ranging from neurons and muscle cells to sensory cells of mechanoreceptors, auditory hair cells and photoreceptor cells. Volume conductor boundary-value problems frequently encountered in electrophysiology are posed. Course provides a cellular basis for the interpretation of macroscopic bioelectric signals such as the electrocardiogram (ECG), electromyogram (EMG), electroretinogram (ERG) and electroencephalogram. Cross-list: ELEC 381. Knowledge of ordinary differential equations, electrical circuits and electromatgnetic field theory at the level of elementary physics.

Long Title: BIOMEDICAL ENGINEERING INSTRUMENTATION

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): MATH 211 AND ELEC 243 AND (BIOC 201 OR BIOS 201) AND (PHYS 102 OR PHYS 126 OR PHYS 112)

Description: This is an introductory level course on fundamentals of biomedical engineering instrumentation and analysis. Topics include measurement principles; fundamental concepts in electronics including circuit analysis, data acquisition, amplifiers, filters and A/D converters; Fourier analysis; temperature, pressure, and flow measurements in biological systems.

Long Title: BIOMEDICAL INSTRUMENTATION LAB

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Description: Students will gain hands on experience with building biomedical instrumentation circuits and systems. Students will learn the basics of lab view programming and signal analysis. Instructor Permission Required.

Long Title: NUMERICAL METHODS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252 AND CAAM 210 AND MATH 211 AND MATH 212

Description: Introduction to numerical approximation techniques with bioengineering applications. Topics include error propagation, Taylor's Series expansions curre fitting, roots of equations, optimization numerical differentiation and integration, ordinary differential equations, and partial differential equations. Matlab and other software will be used for solving equations. Math 212 may be taken concurrently with BIOE 391.

Long Title: ENGINEERING UNDERGRADUATE RESEARCH

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Research

Credit Hours: 1 TO 4

Description: Independent investigation of a specific topic or problem in modern bioengineering research under the direction of a selected faculty member. Research project has a strong engineering component. Repeatable for Credit.

Long Title: UNDERGRADUATE RESEARCH

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Research

Credit Hours: 1 TO 3

Description: Independent investigation of a specific topic or problem in modern bioengineering research under the direction of a selected faculty member. Repeatable for Credit.

Long Title: ADVANCES IN BIONANOTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 3

Prerequisite(s): BIOE 370

Description: This course covers nanotechnology applications in bioengineering. Students learn about cutting edge research that uses the tools of nanotechnology to tackle medical problems. Topics include bionanotechnology - related research for diagnosis, detection, and treatment of disease; cell targeting; drug design and delivery; gene therapy; prostheses and implants and tissue regeneration. (REGISTRATION NOTE: The prerequisite BIOE 370 can also be taken concurrently with BIOE 403)

Long Title: INDEPENDENT RESEARCH/INTERNSHIP PROGRAM

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Research

Credit Hours: 0

Description: This independent research course offers multi-disciplinary training in the area of cellular engineering within the Departments of Bioengineering and Biochemistry & Cell Biology. Areas of research will include engineering of hard and soft tissue formation, cardiovascular tissue engineering, engineering cell surface interactions regulating movement and metabolic engineering. Students will conduct independent research under the supervision of a faculty mentor.

Long Title: SYNTHETIC BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 332

Description: Design of biology at scales from molecules to multicellular organisms will be covered by lecture, primary literature, and student presentations. Students will execute a team based design challenge. Graduate/Undergraduate Equivalency: BIOE 508. Mutually Exclusive: Cannot register for BIOE 408 if student has credit for BIOE 508.

Long Title: BIOSYSTEMS TRANSPORT AND REACTION PROCESSES

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): MATH 211 AND MATH 212 AND (BIOE 332 OR CHBE 411)

Description: This course will cover transport phenomena as applied to biological systems. In particular, equations that describe momentum and mass transfer will be derived and applied to biological and physiological systems as well as to the design of biomedical devices. Cross-list: CHBE 420.

Long Title: MICROCONTROLLER APPLICATONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Prerequisite(s): BIOE 385

Description: This class covers the usage of microcontrollers in a laboratory setting. We will start with basic electronics and, in the lab component, design, program, and build systems utilizing widely-available microcontrollers (e.g. Arduino, Raspberry Pi). Units in motion control, sensors (light, temperature, humidity, UV/Vis absorbance), and actuation (pneumatics, gears, and motors) will provide students with functional knowledge to design and prototype their own experimental systems for laboratory-scale automation. Instructor Permission Required.Graduate/Undergraduate Equivalency: BIOE 521. Mutually Exclusive: Cannot register for BIOE 421 if student has credit for BIOE 521.

Long Title: GENE THERAPY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): CHEM 211 AND (BIOS 201 OR BIOC 201) or permission of instructor

Description: This course will examine the gene therapy field, with topics ranging from gene delivery to vectors to ethics of gene therapy. The design principles for engineering improved gene delivery vectors, both viral and nonviral, will be discussed. The course will culminate in a design project focused on engineering a gene delivery device for a specific therapeutic application. Graduate/Undergraduate Equivalency: BIOE 522. Mutually Exclusive: Cannot register for BIOE 422 if student has credit for BIOE 522.

Long Title: PHARMACEUTICAL ENGINEERING AND DRUG DELIVERY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 391 or permission of instructor

Description: The course introduces the principles of pharmaceutical design, development and delivery. Topics include drug administration, transport, and the pharmacokinetics of distribution in the human body. We will also cover the use of polymeric biomaterials in the development of controlled delivery devices and discuss manufacturing and regulatory implications of such products.

Long Title: BIOMATERIALS APPLICATIONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): (CHEM 211 OR CHEM 251) AND BIOE 370 or permission of instructor

Description: Emphasis will be placed on issues regarding the design, synthesis, evaluation, regulation and clinical translation of biomaterials for specific applications. An overview of significant biomaterials engineering applications will be given, including topics such as ophthalmologic, orthopedic, cardiovascular and drug delivery applications, with attention to specific case studies. Regulatory issues concerning biomaterial will also be addressed. Assignments for this class will include frequent readings of the scientific literature with occasional homework questions, one midterm and cumulative final, a group project, a seminar report and individual presentations. Graduate/Undergraduate Equivalency: BIOE 631. Mutually Exclusive: Cannot register for BIOE 431 if student has credit for BIOE 631.

Long Title: BIOFLUIDS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252

Description: This course provides an introduction to the basic principles of fluid mechanics, emphasizing their importance in the study of biological systems. The course will cover fluid properties, hydrostatics, boundary layers, flow in pipes, laminar and turbulent flows and other fundamental concepts with biomedical applications.

Long Title: APPLIED STATISTICS FOR BIOENGINEERING AND BIOTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252

Description: Course will cover fundamentals of probability and statistics with emphasis on application t biomedical problems and experimental design. Recommended for students pursuing careers in medicine or biotechnology. BIOE 439 and BIOE 440/STAT 440 cannot both be taken for credit. Prerequisite BIOE 252 may be taken concurrently. Mutually Exclusive: Cannot register for BIOE 439 if student has credit for BIOE 440/STAT 440.

Long Title: STATISTICS FOR BIOENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 1

Prerequisite(s): BIOE 252

Description: Course covers application of statistics to bioengineering. Topics include descriptive statistics, estimation, hypothesis testing, ANOVA, and regression. Offered first five weeks of the semester. BIOE 252 may be taken concurrently with BIOE 440. BIOE 440/STAT 440 and BIOE 439 cannot both be taken for credit. Cross-list: STAT 440. Mutually Exclusive: Cannot register for BIOE 440 if student has credit for BIOE 439.

Long Title: TISSUE ENGINEERING LAB MODULE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): (BIOE 342 OR BIOC 320 OR BIOS 320) AND (BIOE 440 OR STAT 440)

Description: Students design and conduct a series of tests to synthesize PLLA, characterize PLLA and PLGA, monitor PLLA and PLGA degradation, and assess the viability, attachment, and proliferation of HDF cells on PLLA films. The experiments include many of the basic types of experiments that would be required to do a preliminary investigation of a tissue engineered product. Sections 1 and 2 will be taught during the first half of the semester and sections 3 and 4 will be taught during the second half of the semester. In addition sections 1 and 3 will need to come into lab on 2-3 Fridays and sections 2 and 4 will need to come into lab on 2-3 Saturdays. Section sign-up is required by the instructor in Keck 108 during preregistration week.

Long Title: BIOPROCESSING LAB MODULE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): (BIOE 342 OR BIOC 320 OR BIOS 320) AND (BIOE 440 OR STAT 440)

Description: Students design and conduct a series of experiments to observe the growth of E. coli under different conditions, including agar plates, shake flasks, and a small-scale bioreactor. The E. coli has been transformed with a plasmid that produces beta-galactosidase. Engineering applications are emphasized. Some work "off hours" (early evening) is required. Sections 1 and 2 are taught in the first half of the semester and Sections 3 and 4 are taught in the second half of the semester. Section sign-up is required by the instructor in Keck 108 during preregistration week.

Long Title: MECHANICAL TESTING LAB MODULE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): BIOE 372 AND (BIOE 440 OR STAT 440)

Description: Students design and conduct a series of tests to elucidate the mechanical and material properties of animal tissue using the Instron. BIOE 372 may be taken concurrently with BIOE 444.

Long Title: ADVANCED INSTRUMENTATION LAB MODULE

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): BIOE 383 AND BIOE 385 AND (BIOE 440 OR STAT 440)

Description: Students design and build a biomedical instrumentation device. Sign up is required in Keck 108 during preregistration week.

Long Title: COMPUTATIONAL MODELING LAB

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Prerequisite(s): BIOE 391

Description: This course offers a hands-on application to systems biology modeling. Students will learn a range of modeling methods, and apply them directly in class to current bioengineering problems. Weekly tutorials will be offered, and a laptop is required (or can be loaned). Topics covered include in silico drug delivery and design studies, integrating multiscale models with high-resolution imaging, experimental design vial computer modeling, and patient-specific simulations. Modeling methods include protein-protein interaction networks, biocircuits, stochastic differential equations, agent-based modeling, computational fluid dynamics, and finite element modeling.

Long Title: DIGITAL DESIGN & VISUALIZATION

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Laboratory

Credit Hours: 1

Description: Students will acquire basic to intermediate-level digital design proficiency for bioengineering-related applications. Programs for the design of patient-specific therapies including image reconstruction, computer aided design, and parameter modeling will be used to create models. Section sign up is required during pre-registration week. Instructor Permission Required.

Long Title: TROUBLESHOOTING WORKSHOP FOR CLINICALLY-RELEVANT BIOMEDICAL EQUIPMENT

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 1

Prerequisite(s): ELEC 243

Description: Bioengineering course in the troubleshooting, repair, and maintenance of standard biomedical equipment used in hospitals in the developed and developing worlds. Instructor Permission Required.Cross-list: GLHT 449. Repeatable for Credit.

Long Title: BIOENGINEERING DESIGN I

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Prerequisite(s): BIOE 383 AND BIOE 385 AND (BIOE 332 OR BIOE 372)

Description: Senior Bioengineering students will design devices in biotechnology or biomedicine. This project-based course covers systematic design processes, engineering economics, FDA requirements, safety, engineering ethics, design failures, research design, intellectual property rights, environmental impact, business planning and marketing. Students will be expected to compile documentation and present orally progress of their teams. BIOE 451 and 452 must be taken the same academic year. Instructor Permission Required.

Long Title: BIOENGINEERING DESIGN II

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Prerequisite(s): BIOE 451

Description: Senior Bioengineering students will design devices in biotechnology or biomedicine. This project-based course covers systematic design processes, engineering economics, FDA requirements, safety, engineering ethics, design failures, research design, intellectual property rights, environmental impact, business planning and marketing. Students will be expected to compile documentation and present orally progress of their teams. BIOE 451 and 452 must be taken the same academic year. Instructor Permission Required.

Long Title: COMPUTATIONAL FLUID MECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Fundamental concepts of finite element methods in fluid mechanics, including spatial discretization and numerical integration in multidimensions, time-integration, and solution of nonlinear ordinary differential equation systems. Advanced numerical stabilization techniques designed for fluid mechanics problems. Strategies for solution of complex, real-world problems. Topics in large-scale computing, parallel processing, and visualization. Cross-list: CEVE 454, MECH 454, Graduate/Undergraduate Equivalency: BIOE 554. Mutually Exclusive: Cannot register for BIOE 454 if student has credit for BIOE 554.

Long Title: EXTRACELLULAR MATRIX

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOS 341 OR BIOC 341

Description: This course will address the biology, organization, mechanics, and turnover of extracellular matrix. There will be an emphasis on cells and cell-matrix interactions, matrix distribution within and design of connective tissues and organs techniques for quantitative analysis of matrix, techniques for measurement and modeling of connective tissue biomechanics, changes with growth and aging and tissue/matrix degradation. Cross-list: BIOC 464. Recommended Prerequisite(s): BIOE 372, BIOC/BIOE 341.

Long Title: FROM SEQUENCE TO STRUCTURE: AN INTRODUCTION TO COMPUTATIONAL BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 4

Description: Contemporary introduction to problems in computational biology spanning sequence to structure. The course has three modules: the first introduces students to the design and statistical analysis of gene expression studies; the second covers statistical machine learning techniques for understanding experimental data generated in computational biology; and the third introduces problems in the modeling of protein structure using computational methods from robotics. The course is project oriented with an emphasis on computation and problem-solving. Cross-list: COMP 470, STAT 470. Recommended Prerequisite(s): COMP 280 and (STAT 310 or STAT 331).

Long Title: INTRODUCTION TO NEUROENGINEERING: MEASURING AND MANIPULATING NEURAL ACTIVITY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): (PHYS 101 OR PHYS 111 OR PHYS 125 OR PHYS 141) AND (PHYS 102 OR PHYS 112 OR PHYS 126 OR PHYS 142)

Description: Neuroengineering is an emerging discipline focused on measuring and manipulating the activity of the brain and nervous system. Using the language of physics and engineering, this course serves as an introduction to neuroengineering to students who may have little or no prior biology training. The course begins by describing how ion channels, membrane potentials, action potentials, and synapses represent information within the brain. Students will then learn a variety of techniques to model this behavior, and modern methods to measure and manipulate neural activity using electrical, optical, and genetic techniques. Students will be expected to be familiar with voltage, current, resistance, capacitance, RC circuits, and statistical mechanics. Homework assignments will require the use of Matlab. Cross-list: ELEC 480.

Long Title: COMPUTATIONAL NEUROSCIENCE AND NEURAL ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: An introduction to the anatomy and physiology of the brain. Includes basic electrophysiology of nerve and muscle. Develops mathematical models of neurons, synaptic transmission and natural neural networks. Leads to a discussion of neuromorphic circuits which can represent neuron and neural network behavior in silicon. Recommendation: Knowledge of electrical circuits, operational amplifier circuits and ordinary differential equations. Involves programming Matlab. Cross-list: ELEC 481, NEUR 481. Recommended Prerequisite(s): Knowledge of basic electrical and operational amplifier circuits; and ordinary differential equations.

Long Title: PHYSIOLOGICAL CONTROL SYSTEMS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: A study of the somatic and autonomic nervous system control of biological systems. Simulation methods, as well as, techniques common to linear and nonlinear control theory are used. Also included is an introduction to sensors and instrumentation techniques. Examples are taken from the cardiovascular, respiratory, and visual systems. Cross-list: ELEC 482. Recommended Prerequisite(s): Knowledge of basic electrical and operational amplifier circuits: and ordinary differential equations.

Long Title: BIOPHOTONICS INSTRUMENTATION AND APPLICATIONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 383 or permission of instructor

Description: This course is an introduction to the fundamentals of Biophotonics instrumentation related to coherent light generation, transmission by optical components such as lenses and fibers, and modulation and detection. Interference and polarization concepts and light theories including ray and wave optics will be covered. A broad variety of optical imaging and detection techniques including numerous microscopy techniques, spectral imaging, polarimetry, OCT and others will be covered. The course will guide through the principles and concepts used in a variety of optical instruments and point to special requirements for Biomedical applications with emphasis on principles and concepts used in a variety of optical instruments and point to special requirements for Biomedical applications with emphasis on principles and concepts used in a variety of optical instruments and point out special requirements for bio-medical applications in optical sensing, diagnosis, and biomedical applications. Graduate/Undergraduate Equivalency: BIOE 512. Mutually Exclusive: Cannot register for BIOE 484 if student has credit for BIOE 512.

Long Title: FUNDAMENTALS OF MEDICAL IMAGING I

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course will introduce basic principles of image acquisition, formation and processing of several medical imaging modalities such as X-Ray, CT, MRI, and US that are used to evaluate the human anatomy. The course also includes visits to a clinical site to gain experience with the various imaging modalities covered in class. Cross-list: COMP 485, ELEC 485. Recommended Prerequisite(s): MATH 211 and MATH 212.

Long Title: FUNDAMENTALS OF MEDICAL IMAGING II

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): ELEC 485 OR BIOE 485 OR COMP 485

Description: This course focuses on functional imaging modalities used specifically in nuclear medicine such as Gamma cameras, SPECT, and PET imaging. The course will introduce the basic principles of image acquisition, formation, processing and the clinical applications of these imaging modalities and lays the foundations for understanding the principles of radiotracer kinetic modeling. A trip to a clinical site in also planned to gain experience with nuclear medicine imaging. Cross-list: COMP 486, ELEC 486.

Long Title: INTRO COMPUTATIONAL SYSTEMS BIOLOGY: MODELING & DESIGN PRINCIPLES OF BIOCHEM NETWORKS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): (MATH 212 OR MATH 213) AND (BIOE 252 OR CHBE 310) AND BIOC 341 AND CAAM 210

Description: The course summarizes techniques for quantitative analysis and simulations of basic circuits in genetic regulation, signal transduction and metabolism. We discuss engineering approaches adapted to computational systems biology and aim to formulate evolutionary design principles explaining organization of networks in terms of their physiological demands. We discuss biochemical simulation methodology and software as well as recent advances in the field. Topics include end-product inhibition in biosynthesis, optimality and robustness of the signaling networks and kinetic proofreading. Graduate/Undergraduate Equivalency: BIOE 552. Mutually Exclusive: Cannot register for BIOE 490 if student has credit for BIOE 552.

Long Title: SENSORY NEUROENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 3

Prerequisite(s): BIOE 332 or permission of instructor

Description: This course will explore how bioengineering techniques and principles are applied to understand and model sensory systems, with a focus on the auditory, vestibular, and visual systems. The interaction between the electrical, mechanical and optical aspects of these systems, and ways to modulate these interactions, will be explored. The course will also cover the design of current auditory, visual and somato-sensory neuroprosthetics (i.e. cochlear implants, retinal implants and brain-machine interfaces), as well as emerging technologies for neural stimulation. Graduate/Undergraduate Equivalency: BIOE 592. Mutually Exclusive: Cannot register for BIOE 492 if student has credit for BIOE 592.

Long Title: BIOMEMS AND MEDICAL MICRODEVICES

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Through this interdisciplinary course, students will obtain knowledge of the basic elements and major classes of molecular sensors, nano-devices and biomedical microsystems; achieve an understanding of the fundamental principles behind the operation of these systems; gain an understanding of standard microfabrication techniques and apply knowledge of microfabrication techniques and applications to the design and manufacturing of such medical microdevices. This course will include a hands-on laboratory component to be completed in the Oshman Engineering Design Kitchen that will allow the students to experience real-world challenges related to diagnostic device development. Cross-list: CHEM 498.

Long Title: GRADUATE RESEARCH

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Research

Credit Hours: 1 TO 15

Description:  Repeatable for Credit.

Long Title: GRADUATE RESEARCH FOR MED-INTRO-GRAD PROGRAM

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Research

Credit Hours: 1 TO 6

Description: Graduate Research for students participating in the HHMI Med-Intro-Grad program. Med-Into-Grad students should enroll in this course during summer internship. Department approval required for enrollment. Department Permission Required. Repeatable for Credit.

Long Title: PHYSICAL BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Basic introduction to a biophysical view of living systems, from the subcellular to the multicellular scales. Topics include: biomolecular dynamics, cellular biomechanics, cell motility and cell division, calcium signaling, action potential propagation, and tissue organization. Cross-list: SSPB 501.

Long Title: GRADUATE INDEPENDENT STUDY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Research

Credit Hours: 0 TO 2

Description: Independent investigation of a specific topic in modern bioengineering research under the direction of selected faculty member. Instructor Permission Required. Repeatable for Credit.

Long Title: FIRST YEAR GRADUATE STUDENT LAB ROTATION

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Laboratory

Credit Hours: 3

Description: This course provides students the opportunity to experience different research projects and assists first-year students in choosing an advisor and a lab for conduction thesis research. Students must successfully complete rotations in three labs to receive a satisfactory grade. All new BIOE PhD students must take this course during their first semester.

Long Title: OPTICAL IMAGING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: This course includes a theoretical portion which will introduce the fundamentals of optical imaging of neural activity, present the devices that are employed, and review applications and discuss their results. In addition, in a practical part, students will design, set up, and perform simple in vitro experiments to gain practical experience with this exciting and powerful technology. Course meets in S744, Vivian Smith Res. Bldg., Baylor College of Medicine

Long Title: GRADUATE INDEPENDENT STUDY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Independent Study

Credit Hours: 1 TO 6

Description: Independent investigation of a specific topic in modern bioengineering research under the direction of a faculty member. Department Permission Required. Repeatable for Credit.

Long Title: SYSTEMS BIOLOGY OF BLOOD VESSELS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 252

Description: How blood vessels respond to hypoxia is a process critical to the progression of many diseases and conditions including cardiovascular disease, cancer, cerebrovascular disease, diabetes, obesity and arthritis. Physiological processes such as exercise, aging, and wound healing also depend on hypoxia-induced microvessel changes. This course introduces engineering concepts of hypoxic response, angiogenesis, and capillary remodeling - from the effects at the intracellular level to the whole body. Topics covered include computational systems biology modeling of hypoxia and angiogenesis, the use of angiogenesis in tissue engineering and regenerative medicine, imaging of blood vessel dynamics, capillaries of the brain, and the design of new blood vessels. Graduate students will be required to complete a term research project and present a related short seminar. Graduate/Undergraduate Equivalency: BIOE 307. Mutually Exclusive: Cannot register for BIOE 507 if student has credit for BIOE 307.

Long Title: SYNTHETIC BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Design of biology at scales from molecules to multicellular organisms will be covered by lecture, primary literature, and student presentations. Students will write a research proposal at the end of the course. Cross-list: SSPB 503, Graduate/Undergraduate Equivalency: BIOE 408. Mutually Exclusive: Cannot register for BIOE 508 if student has credit for BIOE 408.

Long Title: POINT-OF-CARE DIAGNOSTICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: This course provides an overview of diagnostic technologies that can be used at the point-of-care, including lateral flow assays, 2- and 3-D paper-based assays, and imaging based assays. Topics include the principles of assay design, validation and commercial development, with a focus on diagnostics for low-resource settings. The course includes a lecture and laboratory component, along with a team-based design project. Only graduate students may register for this course.

Long Title: SEMINAR IN TROPICAL MEDICINE

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Seminar

Credit Hours: 1

Description: 8 week lecture series on topics in global health. The theme for this offering is one health; integrating efforts to obtain optimal health for humans, animals, and the environment. Offered in conjunction with the new National School of Tropical Medicine, the course will feature lectures by various experts on the public health issues most pressing in poor populations in the world today. Course open to all undergraduates and graduate students. Cross-list: GLHT 510. Repeatable for Credit.

Long Title: BIOPHOTONICS INSTRUMENTATION AND APPLICATIONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course is an introduction to the fundamentals of Biophotonics instrumentation related to coherent light generation, transmission by optical components such as lenses and fibers, and modulation and detection. Interference and polarization concepts and light theories including ray and wave optics will be covered. A broad variety of optical imaging and detection techniques including numerous microscopy techniques, spectral imaging, polarimetry, OCT and others will be covered. The course will guide through the principles and concepts used in a variety of optical instruments and point to special requirements for Biomedical applications with emphasis on principles and concepts used in a variety of optical instruments and point to special requirements for Biomedical applications with emphasis on principles and concepts used in a variety of optical instruments and point out special requirements for bio-medical applications in optical sensing, diagnosis, and biomedical applications. In addition to the undergraduate requirements in BIOE 484, graduate students will be required to complete more complex problems on both homework and tests. Graduate students will also be required to submit a research paper with oral presentations. Graduate/Undergraduate Equivalency: BIOE 484. Mutually Exclusive: Cannot register for BIOE 512 if student has credit for BIOE 484.

Long Title: INTRODUCTION TO BIOSTATISTICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: Presents basic and advanced methods of statistics as applied to problems in bioengineering. Demonstrates techniques for data organization, exploration, and presentation. Foundations of statistical estimation, inference, and testing are reviewed. Optimal planning of experiments is explored. Advanced techniques include multiple regression, variable selection, logistic regression, analysis of variance, survival analysis, multiple measurements and measurements over time. Additional topics, such as Bayesian methods, will be discussed as time allows. Labs will use the statistical software JMP and/or R. Cross-list: STAT 514.

Long Title: MECHANICS, TRANSPORT, AND CELLULAR SIGNALING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course will cover the fundamental principles of mechanics, thermodynamics, and transport in the context of classical and contemporary bioengineering problems. An overall goal will be to expose students to the integrated approaches that are necessary to solve complex research problems. Topics covered will include membrane transport, cell signaling, and mechanotransduction. This course is intended for first year BIOE PhD students only.

Long Title: INSTRUMENTATION AND MOLECULAR ANALYSIS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course will cover the basic principles of optics, optical instrumentation, microscopy and molecular detection technologies. Emphasis will be placed on the application of advance microscopy techniques to imaging problems in biology and medicine. This course is intended for first year BIOE PhD students only.

Long Title: INTRODUCTION TO COMPUTATIONAL BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Provides students with the ability to use computational methods to understand and analyze biological data. This course will introduce students to advances in computational cell biology from an engineering perspective, and equip them with a suite of tools emerging from systems biology. Topics covered include computational cell engineering, high-throughput analysis, modeling of signaling pathways, network analysis, imaging coupled to modeling, and multi scale modeling. This course is intended for first year BIOE PhD students only.

Long Title: BIOMATERIALS SYNTHESIS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Biomaterials covers the design and synthesis of materials which interact with biologic phenomena such as cell-free, microbial, and mammalian systems. Topics covered include: surfaces and surface fractionalization, biomedical implants and them immune response, three dimensional cell culture systems, and regulatory hurdles (e.g., FDA clearance). The class will be rooted in a historical perspective, with a particular emphasis on the latest techniques in synthetic chemistry relating to biomaterials. This course is intended for first year BIOE PhD students only.

Long Title: MICROCONTROLLER APPLICATIONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Prerequisite(s): BIOE 385

Description: This class covers the usage of microcontrollers in a laboratory setting. We will start with basic electronics and, in the lab component, design, program, and build systems utilizing widely-available microcontrollers (e.g. Arduino, Raspberry Pi). Units in motion control, sensors (light, temperature, humidity, UV/Vis absorbance), and actuation (pneumatics, gears, and motors) will provide students with functional knowledge to design and prototype their own experimental systems for laboratory-scale automation. BIOE 521 students will be expected to complete a final research paper. Instructor Permission Required.Graduate/Undergraduate Equivalency: BIOE 421. Mutually Exclusive: Cannot register for BIOE 521 if student has credit for BIOE 421.

Long Title: GENE THERAPY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): CHEM 212 AND (BIOS 201 OR BIOC 201) or permission of instructor

Description: This course will examine the gene therapy field, with topics ranging from gene delivery to vectors to ethics of gene therapy. The design principles for engineering improved gene delivery vectors, both viral and nonviral, will be discussed. The course will culminate in a design project focused on engineering a gene delivery device for a specific therapeutic application. Graduate/Undergraduate Equivalency: BIOE 422. Mutually Exclusive: Cannot register for BIOE 522 if student has credit for BIOE 422.

Long Title: CONTROL THEORY AND SYSTEMS/SYNTHETIC BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: An overview of the interplay between control theory and systems/synthetic biology. Topics include introduction to basic control theory and methods and tools for analyzing the dynamics of biological systems.

Long Title: MEDICAL INNOVATION I

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: This course will explore the front half of the medical innovation process through instruction in upstream marketing, finding and screening unmet clinical needs, and generating concepts and prototypes. Students will participate in a medical technology design project to apply the principles they are learning. Students in this course will be expected to continue their projects with BIOE 532 in the spring semester. Currently, the course is limited to MBE students. Department Permission Required.

Long Title: MEDICAL INNOVATION II

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This one semester course for Masters of Bioengineering (MBE) students will cover systematic design processes, market evaluation, innovation, and FDA requirements relevant to the medical device and biotechnology industry. Enrollment is limited to students enrolled in the MBE program. Department Permission Required. Repeatable for Credit.

Long Title: INTRODUCTION TO SYSTEMS BIOLOGY AND SYSTEMS BIOTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Systems biology is an integrated experimental and mathematical approach to study the complex dynamic interactions between various components of a biological system. The course is designed to explore the basic concepts of systems biology. The course will introduce "systems" approaches based on genomics, transcriptomics, proteomics and metabolomics.

Long Title: MACROMOLECULAR SYSTEMS BIOENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Multi-component complexes of biological macromolecules form the basis of many cellular processes including signaling, metabolism, and biomolecular transport. This course will examine the impact of supramolecular architecture on these processes by discussing the self-assembly, dynamic properties and physiological function of non-covalently coupled macromolecules and interacting proteins. The course will cover fundamental models of protein-protein interactions, cooperativity, instrumentation, and potential technological applications.

Long Title: DNA BIOTECHNOLOGY, BIOPHYSICS, AND MODELING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: Semester-long course on fundamental properties of DNA, and their role in DNA biotechnology. Students will develop, analyze, and simulate simple biophysical models of DNA reactions, as well as learn and model methods of modern DNA biotechnology. Proficiency with MATLAB required.

Long Title: MACHINE LEARNING AND SIGNAL PROCESSING FOR NEURO ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: The activity of a complex network of billions of interconnected neurons underlies our ability to sense, represent and store the details of experienced life, and enables us to interact with our environment and other organisms. Modern neuroscience techniques enable us to access this activity, and thus to begin to understand the processes whereby individual neurons enable complex behaviors. In order to increase this understanding and to design biomedical systems which might therapeutically interact with neural circuits, advanced statistical signal processing and machine learning approaches are required. This class will cover a range of techniques and their application to basic neuroscience and neural interfaces. Topics include latent variable models, point processes, Bayesian inference, dimensionality reduction, dynamical systems, and spectral analysis. Neuroscience applications include modeling neural firing rates, spike sorting, decoding, characterization of neural systems, and field potential analysis. Cross-list: ELEC 548.

Long Title: INTRO COMPUTATIONAL SYSTEMS BIOLOGY: MODELING & DESIGN PRINCIPLES OF BIOCHEM NETWORKS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: The course summarizes techniques for quantitative analysis and simulations of basic circuits in genetic regulation, signal transduction and metabolism. We discuss engineering approaches adapted to computational systems biology and aim to formulate evolutionary design principles explaining organization of networks in terms of their physiological demands. We discuss biochemical simulation methodology and software as well as recent advances in the field. Topics include end-product inhibition in biosynthesis, optimality and robustness of the signaling networks and kinetic proofreading. Same as 490 but with more emphasis on recent advances in the field - paper reading and presentations. Cross-list: SSPB 502, Graduate/Undergraduate Equivalency: BIOE 490. Recommended Prerequisite(s): Basic knowledge of biochemistry, cell biology, linear algebra, and ordinary differential equations is expected. Mutually Exclusive: Cannot register for BIOE 552 if student has credit for BIOE 490.

Long Title: COMPUTATIONAL FLUID MECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Graduate version of BIOE 454. Additional work required. Cross-list: CEVE 554, MECH 554, Graduate/Undergraduate Equivalency: BIOE 454. Mutually Exclusive: Cannot register for BIOE 554 if student has credit for BIOE 454.

Long Title: CANCER BIOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Provides an integrated lecture series summarizing current knowledge in cancer biology and integrating current literature with basic concepts. Topics include: statistics of incidence/survival, types of cancer, pathology, the process of carcinogenesis and sources of carcinogens, genetic and epigenetic mechanisms and consequences, cancer progression, metastasis and current treatment options. Students will learn to use online databases to develop independent strategies for analyzing datasets. There will be several writing assignments and in class oral presentations of research articles. This course requires instructor permission to enroll. Please send all enrollment requests to Monica Roberts, mr19@rice.edu. All requests will be reviewed and you will be notified of enrollment decision by December 5th. Instructor Permission Required.Cross-list: BIOC 560.

Long Title: BIOINFORMATICS: NETWORK ANALYSIS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course covers computational aspects of biological network analysis, a major theme in the area of systems biology. The course addresses protein-protein interaction networks, signaling, and metabolic networks, and covers issues related to reconstructing, analyzing, and integrating various types of networks. Cross-list: BIOC 572, COMP 572.

Long Title: CONTINUUM BIOMECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 372

Description: This course deals with elements of continuum mechanics relevant to bioengineering. The course covers important concepts in tensor calculus, kinematics, stress and strain, and constitutive theories of continua. Selected topics in bone, articular cartilage, blood and circulation, and cell biomechanics will be discussed to illustrate the application of continuum mechanism to bioengineering problems.

Long Title: FOUNDATIONS OF BIOTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 1

Description: Graduate level introduction to a wide range of research methods in biosciences and bioengineering. Individual faculty members from the Biosciences and Bioengineering will each present practices and techniques for their areas of expertise. A web-based methods database will be constructed, with student involvement, from the library of lectures. Cross-list: BIOC 576.

Long Title: FOUNDATIONS OF BIOTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 1

Description: Graduate level introduction to a wide range of research methods in biosciences and bioengineering. Individual faculty members from the biosciences and bioengineering will each present practices and techniques for their areas of expertise. A web-based methods database will be constructed, with student involvement, from the library of lectures. Cross-list: BIOC 577.

Long Title: BIOTECHNOLOGY PRACTICUM

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Internship/Practicum

Credit Hours: 1

Description: This course is part of the NIH Biotechnology Training Program and is limited to program participants. Students will receive exposure and training in cutting edge concepts and technologies. Cross-list: BIOC 578.

Long Title: PROTEIN ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Manipulation of gene expression in prokaryotic and eukaryotic cells. Rational design and directed evolution for cell and protein engineering. Selection and screening technologies and process optimization. Synthetic Biology: engineering and application of gene circuits. Molecular biotechnology applications: Diagnosis, Therapeutics and Vaccines. Cross-list: BIOC 580, CHBE 580. Recommended Prerequisite(s): CHBE 310/510 or equivalent is highly recommended.

Long Title: CARDIOVASCULAR AND RESPIRATORY SYSTEM DYNAMICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Autonomic nervous system control of the cardiovascular and respiratory systems. Development of models of neuron and cardiac cell activity; models of ventricular and vascular system mechanics; models of pulmonary mechanics and gas transport. Includes a study of instrumentation and techniques used in the cardiac catherization laboratory. Discussions of different types of ventricular assist devices is also included. The course serves as an introduction to engineering in cardiovascular and respiratory system diagnosis and critical care medicine. Cross-list: ELEC 581. Recommended Prerequisite(s): Knowledge of ordinary differential equations; electricity and magnetism, and solid mechanics form elementary physics; linear control theory and elementary physiology of the cardiovascular and respiratory systems. Repeatable for Credit.

Long Title: TRANSLATIONAL BIOENGINEERING SEMINAR

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 1.5

Description: A seminar series focused on translational research opportunities to be held each semester. Each seminar will be jointly presented by a clinical faculty member, a basic science faculty member, and bioengineering faculty member to integrate focused discussion of clinical cancer needs, advances in cancer biology, and new diagnostic and therapeutic technologies which build on these advances to meet clinical needs. Seminars held at MDACC.

Long Title: RESPIRATORY SYSTEM MECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Mechanics of ventilation, respiratory muscle mechanics, rib cage mechanics, mechanical coupling between the respiratory muscles and the rib cage, and inferences on mechanics from respiratory muscle anatomy. The class will meet in the Pulmonary Division at Baylor College of Medicine in the Texas Medical Center. Cross-list: MECH 586.

Long Title: OPTICAL IMAGING AND NANOBIOPHOTONICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course focuses on diagnostic and therapeutic applications of photonics-based technologies with particular emphasis on nanotechnology enabled optical approaches. This course emphasizes biomedical applications of optics and complements BIOE 484 which introduces fundamental principles of optics to bioengineers.

Long Title: COMPUTATIONAL MOLECULAR BIOENGINEERING/BIOPHYSICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This is a course designed for students in computationally-oriented biomedical and bioengineering majors to introduce the principles and methods used for the simulations and modeling of macromolecules of biological interest. Protein conformation and dynamics are emphasized. Empirical energy function and molecular dynamics calculations are described. Specific biological problems are discussed to illustrate the methodology. Classic examples such as the cooperative mechanism of hemoglobin and more frontier topics such as the motional properties of molecular motors and ion channels as well as results derived from the current literature are covered. Cross-list: BIOC 589. Recommended Prerequisite(s): MATH 212, (BIOS 301 or BIOC 301), BIOE 332.

Long Title: SENSORY NEUROENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 3

Prerequisite(s): BIOE 332 AND BIOE 384

Description: This course will explore how bioengineering techniques and principles are applied to understand and model sensory systems, with a focus on the auditory, vestibular, and visual systems. The interaction between the electrical, mechanical and optical aspects of these systems, and ways to modulate these interactions, will be explored. The course will also cover the design of current auditory, visual and somato-sensory neuroprosthetics (i.e. cochlear- implants, retinal implants and brain-machine interfaces), as well as emerging technologies for neural stimulation. Graduate/Undergraduate Equivalency: BIOE 492. Mutually Exclusive: Cannot register for BIOE 592 if student has credit for BIOE 492.

Long Title: MODELING TISSUE MECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Independent Study

Credit Hours: 3

Description: Independent study and seminar course which focuses on modeling the mechanical properties of biological tissues. Data from experiments will be used to refine the predictions of nonlinear mathematical computer models. Aimed at juniors, seniors, and graduate students. Laboratory work performed at Baylor College of Medicine, computer work at Rice University. Cross-list: MECH 595.

Long Title: FUNDAMENTALS AND APPLICATIONS OF MEDICAL MICRODEVICES

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Through this interdisciplinary graduate course, students will obtain a basic understanding of the fundamental principles behind the operation of molecular sensors, nano-devices and biomedical microsystems. The students will be exposed to standard and novel microfabrication techniques as they are being applied to the next generation of medical microdevices. Further, class participants will secure an appreciation of the unmet clinical needs that may be serviced by the next generation of powerful, yet affordable mini-medical devices. Expected to be offered Spring 2016. Cross-list: CHEM 598.

Long Title: GRADUATE BIOENGINEERING INDUSTRY INTERNSHIP

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Internship/Practicum

Credit Hours: 3 TO 6

Description: Students will participate in an industry internship or industry-sponsored project under the direction of Bioengineering faculty. This course may be taken in the summer for six credits or in the fall and spring for three credits each semester. Enrollment is limited to students in the Global Medical Innovation track of the MBE degree. Instructor permission is required. Instructor Permission Required. Repeatable for Credit.

Long Title: METHODS OF MOLECULAR SIMULATION

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): CHBE 611 OR BIOC 589 OR BIOE 589 OR BIOS 589 OR CHEM 520 OR PHYS 526 or permission of instructor

Description: Modern simulation techniques for classical atomistic systems. Review of statistical mechanical systems. Monte Carlo and molecular dynamics simulation techniques. Extensions of the basic methods to various ensembles. Applications to simulations of large molecules such as proteins. Advanced techniques for simulation of complex systems, including constraint satisfaction, cluster moves, biased sampling, and random energy models. Cross-list: PHYS 610.

Long Title: BIOENGINEERING AND CARDIAC SURGERY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This course will address biomaterials and medical devices relevant to cardiac and vascular surgery and interventional cardiology in adult and pediatric patients. Mechanical and design considerations, notable successes and failures, and ethical issues will also be discussed, as will differences in cardiac disease and care due to health disparities.

Long Title: TISSUE ENGINEERING

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Study of cell-cell interactions and the role of the extracellular matrix in the structure and function of normal and pathological tissues. Includes strategies to regenerate metabolic organs and repair structural tissues, as well as cell-based therapies to deliver proteins and other therapeutic drugs, with emphasis on issues related to cell and tissue transplantation such as substrate properties, angiogenesis, growth stimulation, cell differentiation, and immunoprotection. Cross-list: CHBE 620.

Long Title: BIOVENTURES

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Seminar

Credit Hours: 2

Prerequisite(s): MGMT 633 OR BIOE 633

Description: A hands-on immersion into life science entrepreneurship through practical lessons that are applied to students' group projects throughout the course. This practical course will provide the skills and resources to facilitate scientist-driven entrepreneurship in conceiving new life science ventures and translating research ideas into commercial ventures. This course will be taught in conjunction w/UTMB faculty on the Rice campus (BRC) and will meet from Feb 26 - April 30, 2015. To apply for the course, Rice students should fill out the online application located on the URL site listed above. Instructor Permission Required. Repeatable for Credit.

Long Title: BIOMATERIALS APPLICATIONS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 519 OR BIOE 370 or permission of instructor

Description: Emphasis will be placed on issues regarding the design, synthesis, evaluation, regulation and clinical translation of biomaterials for specific applications. An overview of significant biomaterials engineering applications will be given, including topics such as ophthalmologic, orthopedic, cardiovascular and drug delivery applications, with attention to specific case studies. Regulatory issues concerning biomaterial will also be addressed. Assignments for this class will include frequent readings of the scientific literature with occasional homework questions, one midterm and cumulative final, a group project, a seminar report and individual presentations. In addition, graduate students in BIOE 631 will have additional exam problems and an additional research paper. Graduate/Undergraduate Equivalency: BIOE 431. Mutually Exclusive: Cannot register for BIOE 631 if student has credit for BIOE 431.

Long Title: LIFE SCIENCE ENTREPRENEURSHIP AND THE ROLES OF FOUNDERS AND VENTURE CAPTIAL ON HIGH TECH STARTUP

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 1.5

Description: The roles of physicians, scientists, engineers, and MBA’s in biotech, medical device, and other life science companies will be described and characterized. The major trends and innovations driving the creation of new products in large established companies and venture-capital-backed startup companies are discussed. This pragmatic, experienced-based course describes the venture capital process, formation, and capitalization of high-tech companies, sources of technologies, role of tech transfer at universities and medical schools, startup operational issues, role of VCs and board members, execution time frames, liquidity process, IPOs and mergers, and payout prospects for founders and investors. Live, ongoing case studies are presented by guest entrepreneurs. These case studies of ongoing biotech, medical device, and healthcare informatics companies are presented by many notable M.D. and Ph.D. founders and CEOs. Rules of professional and ethical conduct of M.D.s, Ph.D.s, scientific advisory boards, clinical advisory boards, and boards of directors are reviewed. In the final classes, a high-tech, career-planning guide is discussed, plus a special lecture on leadership, intelligence, and entrepreneurship will be presented. Insider secrets and success stories from decades of highly successful VC practice in medical, biotech and infotech companies will be shared. Cross-list: MGMT 633. Repeatable for Credit.

Long Title: CELL MECHANICS, MECHANOTRANSDUCTION AND THE CELL MICROENVIRONMENT

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Mechanotransduction is a fundamental process essential for living systems and plays a fundamental role in cell signaling, cancer metastasis and stem cell differentiation. Additionally, fundamental biological processes such as endocytosis cell fusion and cell migration are driven by a coordinated interplay of molecular interactions that drive membrane deformation. This course will survey the current understanding of mechanotransduction and the mechanical properties of cells and their microenvironment, including membrane and cytoskeletal mechanics. Experimental approaches for measuring and manipulating the material properties of cells and their environment; including optical, electrical and magnetic techniques will be covered. A variety of application will be covered, including manipulation in engineering of mechanotransduction pathways to drive cell migration and stem cell differentiation. Instructor Permission Required.Cross-list: BIOC 643, PHYS 643.

Long Title: ADVANCED COMPUTATIONAL MECHANICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Prerequisite(s): BIOE 554 OR CEVE 554 OR MECH 554 OR BIOE 454 OR CEVE 454 OR MECH 454 or permission of instructor

Description: Advanced topics in computational mechanics with emphasis on finite element methods and fluid mechanics. Stabilized formulations. Fluid-particle and fluid-structure interactions and free-surface and two-fluid flows. Interface tracking and interface-capturing techniques, space-time formulations, and mesh update methods. Enhanced discretization and solution techniques. Iterative solution methods, matrix-free computations, and advanced preconditioning techniques. Cross-list: CEVE 654, MECH 654.

Long Title: ONCOLOGY FOR BIOENGINEERS: MOLECULES TO ORGANS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture/Laboratory

Credit Hours: 3

Description: Students will develop and work through patient cases that emphasize the informational needs of graduate bioengineering students interested in cancer-related translational research. The class will review and discuss the initial case, decide on relevant learning issues, gather information, present findings for further review and discussion, and submit a case-specific written assignment. Using the same model, each student will then develop and lead his/her own patient case for class study. Instructor Permission Required. Required: Admission to Med Into Grad Program.

Long Title: NEW TECHNIQUES FOR CANCER DIAGNOSIS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 1

Description: This course will provide an overview of promising cancer-related biomarkers, and biomarker identification techniques, molecular targeting technologies, sensing and transducing technologies, and imaging technologies. Prerequisites: Admission to BIOE Graduate Program. Instructor Permission Required.

Long Title: NANO-NEUROTECHNOLOGY

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Seminar

Credit Hours: 3

Description: This course will review current nanofabricated technologies for measuring, manipulating, and controlling neural activity. The course will be based on reviewing current academic literature and topics will include nano-electronic, -photonic, -mechanical, and -fluidic neural devices. Cross-list: ELEC 680.

Long Title: SYSTEMS BIOLOGY OF HUMAN DISEASES

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: Introduction to concepts necessary for application of systems - Biology Approaches to Human Diseases. Topics include transcriptional and metabolic design principles, introduction to various regulatory network motifs in diseases and potential treatments using embryonic stem cells. Analysis of complex diseases using engineering concepts such as optimality, nonequilibrium thermodynamics, multiscale analysis and spatiotemporal transport. Cross-list: CHBE 682.

Long Title: ADVANCED BIOPHOTONICS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: This advanced topics course focuses on novel technologies for optical spectroscopy, microscopy, and in vivo imaging with an emphasis on applications in clinical medicine. Previous course work in optics is required.

Long Title: PROFESSIONAL DEVELOPMENT FOR BIOENGINEERS

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 1.5

Description: Professional development topics relevant to academic careers including applying for faculty positions, interviewing , negotiating offers, building a lab, obtaining funding and balancing professional obligations. Designed for graduate students planning academic careers in research-intensive bioengineering departments.

Long Title: BIOENGINEERING COLLOQUIA

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Seminar

Credit Hours: 1

Description: Recent research in bioengineering will be presented in this colloquium series. These colloquia provide an opportunity to learn about the research at other institutions, oftentimes in an area outside students' specific dissertation specialty, and are an important part of graduate education. Graduate students in BIOE are expected to attend all regular Bioengineering colloquia. Repeatable for Credit.

Long Title: BIOENGINEERING COLLOQUIA

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Seminar

Credit Hours: 1

Description: Recent research in bioengineering will be presented in this colloquium series. These colloquia provide an opportunity to learn about the research at other institutions, oftentimes in an area outside students' specific dissertation specialty, and are an important part of graduate education. Graduate students in BIOE are expected to attend all regular Bioengineering colloquia. Repeatable for Credit.

Long Title: VISITING RESEARCH TRAINEE

Department: Bioengineering

Grade Mode: Satisfactory/Unsatisfactory

Course Type: Research

Credit Hours: 0