BIOMEDICAL ENGINEERING

580.111 (E,N)

BME MODELING & DESIGN (2) Haase   Limit 4 5 per section BME Freshmen only (Formerly BME Design Group) Working in teams with upperclassmen this course (1) introduces biomedical engineering freshmen to an orderly method for analyzing and modeling biological systems and (2) introduces engineering principles to solve design problems that are biological, physiological, and/or medical. Freshmen are expected to use the informational content being taught in calculus, physics and chemistry and to apply this knowledge to the solution of practical problems encountered in biomedical engineering.

Lec.

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Th 12-12:50

Th 8:30-10:20

Th 8:30-10:20

Th 8:30-10:20

Th 8:30-10:30

Th 1-2:50

Th 1-2:50

Th 1-2:50

Th 1-2:50

Th 3-4:50

Th 3-4:50

Th 3-4:50

Th 3-4:50

Th 5-6:50pm

Th 5-6:50pm

Th 5-6:50pm

Th 5-6:50pm

F 12-1:50

F 12-1:50

F 12-1:50

F 12-1:50

F 2-3:50

F 2-3:50

F 2-3:50

F 2-3:50

580.211 (E,N)

BME DESIGN GROUP (3) Allen     Limit 20   Sophomore-level version of 580.311-312 or Perm. Req’d

Sec. 01

T 6-6:50pm

580.221 (N)

MOLECULES AND CELLS (4) Haase Limit 35 30 per section  Prereq: 030.101, 030.104  An introduction to modern molecular and cellular biology in the context of potential biomedical engineering applications. Topics covered: reactions between molecules, including receptor-ligand and antigen-antibody specificity, protein structure, enzyme catalysis, genetic information, protein processing and secretion, cell physiology and cell functions. Advanced quantitative treatment including multi-state kinetics, Monte Carlo simulations of biochemical reactions, and transport phenomena.

Secs. 01 & 04 canceled 9/03/08

Lec.

Sec. 01

02

03

04

05

06

MW 1:30-2:45

F 9-9:50

F 10-10:50

F 11-11:50

F 12-12:50

F 1-1:50

F 2-2:50

580.311 (E,N)

BME DESIGN GROUP (3) Allen  Limit 30   Perm. Req’d.  A two-semester course sequence where sophomores, juniors and seniors work with a team leader and a group of BME freshmen and sophomores, to solve open-ended problems in biomedical engineering. Upperclassmen are expected to apply their general knowledge and experience, and their knowledge in their concentration area, to teach lower classmen and to generate the solution to practical problems encountered in biomedical engineering.

Sec. 01

T 6-6:50pm

580.321 (E,N)

STATISTICAL MECHANICS AND THERMODYNAMICS (4) (3) Beer Limit 35 per section   Prerequisites: 110.108-109, 030.101-102, 171.101-102. Basic principles of statistical physics and thermodynamics with application to biological systems. Topics include fundamental principles of thermodynamics, chemical equilibrium and thermodynamics of reactions in solutions, and elementary statistical mechanics.

Lec.

Sec. 01

02

03

04

 MWF 11-11:50

T 11-11:50

T 12-12:50

T 1:30-2:20

T 3-3:50

580.410

BME TEACHING PRACTICUM (2) Haase   Limit 20   Senior biomedical engineering students will assist the BME Modeling & Design course instructor in managing the laboratory component of the class.

Sec. 01

TBA

580.411 (E)

BME DESIGN GROUP (3) Allen
Limit 30 Perm. Req’d.    
Senior-level version of 580.311-312.

Sec. 01

T 6-6:50pm

580.413 (E)

DESIGN TEAM - TEAM LEADER (4) Allen   Limit 30 Perm. Req’d. A two-semester sequence where leaders direct a team of undergraduate biomedical engineering students in a series of design problems. Prior design team experience and permission of course director required.

Sec. 01

T 6-6:50pm

580.420 (N)

BUILD-A-GENOME (4) Bader Limit 8  Must understand fundamentals of DNA structure, DNA electrophoresis and analysis, Polymerase Chain Reaction (PCR) and must be either a) Experienced with molecular biology lab work or b) Adept at programming with a biological twist. In this combination lecture/laboratory "Synthetic Biology" course students will learn how to make DNA building blocks used in an int'l. project to build the world's first synthetic eukaryotic genome, Saccharomyces cerevisiae v. 2.0. Please study the wiki www.syntheticyeast.org for more details about the project. Following a biotechnology boot-camp, students will have 24/7 access to computational and wet-lab resources and will be expected to spend 15-20 hours per week on this course. Advanced students will be expected to contribute to the computational and biotech infrastructure.Successful completion of this course provides 3 credit hours toward the supervised research requirement for Molecular and Cellular Biology majors, or 2 credit hours toward the upper level elective requirement for Biology or Molecular and Cellular Biology majors. Co-listed with 020.420 & 540.420

Sec. 01

MWF 5-6:30pm

580.421 (E,N)

SYSTEMS BIOENGINEERING I (4) Trayanova   Prereq: 580.221 & 580.222  Limit 35 28 per section A quantitative, model-oriented investigation of the cardiovascular system. Topics are organized in three segments. (1) Molecular/cellular physiology, including electrical signaling and muscle contraction. (2) Systems cardiovascular physiology, emphasizing circuit-diagram analysis of hemodynamics. (3) Cardio-vascular horizons and challenges for biomedical engineers, including heart failure and its investigation/treatment by computer simulation, by gene-array analysis, by stem-cell technology, and by mechanical devices (left-ventricular assist and total-heart replacement).

Sec. 06 canceled 6/16/08
Sec. 05 canceled 9/05/08

Lec.

Sec. 01

02

03

04

05

06

MW 3-4:15

F 11-11:50

F 12-12:50 11-11:50

F 1:30-2:20

F 1:30-2:20

F 3-3:50

F 3-3:50

580.423

SYSTEMS BIOENGINEERING LAB I (2) Haase   Limit 36 38 per section  Coreq: 580.421 Priority to Junior BME majors   A two-semester laboratory course in which various physiological preparations are used as examples of problems of applying technology in biological systems. The emphasis in this course is on the design of experimental measurements and on physical models of biological systems.

Sec. 01
Lab

Sec. 02
Lab

Sec. 03
Lab

Sec. 04
Lab

Th 4:30-5:20
Th 9-12:50

Th 4:30-5:20
Th 1-4:50

F 9-9:50
F10 T 9-12:50

F 9-9:50
F T 1-3:50 4:50

580.429 (E,N)

SYSTEMS BIOENGINEERING III (4) Bader   Limit 38 per section  Prereq: 580.221 & 580.222 or Perm. Req’d    Computational and theoretical systems biology at the cellular and molecular level.  Topics include organizational patterns of biological networks; analysis of metabolic networks, gene regulatory networks, and signal transduction networks; inference of pathway structure; and behavior of cellular and molecular circuits.

Sec. 04 canceled 9/09/08

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Sec. 01

02

03

04

MW 12-1:15

F 12-12:50 1:30-2:45

F 12-12:50 1:30-2:45

F 1:30-2:20 3-4:15

F 1:30-2:20 3-4:15

580.439 (E,N)

MODELS OF THE NEURON (4) Young   Limit 40   Prereq: 110.301, 580.421-422 or equivalent    Single-neuron modeling, emphasizing the use of computational models as links between the properties of neurons at several levels of detail. Topics include thermodynamics of ion flow in aqueous environments, biology and biophysics of ion channels, gating, nonlinear dynamics as a way of studying the collective properties of channels in a membrane, synaptic transmission, integration of electrical activity in multi-compartment dendritic tree models, and properties of neural networks. Students will study the properties of computational models of neurons; graduate students will develop a neuron model using data from the literature.  Meets with 580.639

Sec. 01

MTWF 9-9:50

580.440

CELLULAR AND TISSUE ENGINEERING (3) Elisseef/Yarema   Limit 40  Prereq: 580.421-422  Junior, Senior, Graduate students only
Lectures provide an overview of molecular biology fundamentals, an extensivereview on extracellular matrix and basics of receptors, followed by topics on cell-cell and cell-matrix interactions at both the theoretical and experimental levels. Subsequent lectures will cover the effects of physical (shear, stress, strain), chemical (cytokins, growth factors), and electrical stimuli on cell function, emphasizing topics on gene regulation and signal transduction processes. Material on cell-cycle, apoptosis, metabolic engineering and gene therapy will also be incorporated into the course.

Sec. 01

TTh 9-10:15

580.445 (E)

INTRODUCTION TO SPEECH AND AUDIO PROCCESSING (3) Elhilali   Limit 30   Prereq: 520.214 or equiv. (580.222 )     This course gives a foundation in current audio and speech technologies, and covers techniques for sound processing and pattern recognition, acoustics, auditory perception, speech production and synthesis, speech estimation.  The course will explore applications of speech and audio processing in human computer interfaces such as speech recognition, speaker identification, coding schemes (e.g. MP3), music analysis, noise reduction.

Sec. 01

TTh 10:30-11:45

580.451 (E,N)

CELLULAR AND TISSUE ENGINEERING LAB (2) Haase Limit 4 per section   Senior and Graduate students only; others Perm. Req’d.  
Lab Fee: $100 Cell and tissue engineering is a field that relies heavily on experimental techniques. This laboratory course will consist of three six experiments that will provide students with valuable hands-on experience in cell and tissue engineering. Students will learn basic cell culture procedures and specialized techniques related to faculty expertise in cell engineering, microfluidics, gene therapy, microfabrication and cell encapsulation. Experiments include the basics of cell culture techniques, gene transfection and metabolic engineering, basics of cell-substrate interactions I, cell-substrate interactions II, and cell encapsulation and gel contraction.
Co-listed with 530.451

Sec. 01

02

TF 12-1:50

TF 2-3:50

580.471 (E,N)

PRINCIPLES OF DESIGN OF BIOMEDICAL INSTRUMENTATION (4) Thakor    Limit 16 per section   Prereq: 520.213-214, electronics lab or 580.470   Lab Fee: $125   Students satisfying the design requirement must also register for 580.571
This core design course will cover lectures and hands-on labs. The material covered will include fundamentals of biomedical sensors and instrumentation, FDA regulations, designing with electronics, biopotentials and ECG amplifier design, recording from heart, muscle, brain, etc., diagnostic and therapeutic devices (including pacemakers and defibrillators), applications in prosthetics and rehabilitation, and safety. The course includes extensive laboratory work involving circuits, electronics, sensor design and interface, and building complete biomedical instrumentation. The students will also carry out design challenge projects, individually or in teams (examples include “smart cane for blind,” “computer interface for quadriplegic”).

Lec.

Sec. 01

02

Th 4-5:50pm

F 9-12:50

F 1-4:50

580.472 (E)

MEDICAL IMAGING SYSTEMS (3) Prince   Limit  30 Prereq: 520-214 An introduction to the physics, instrumentation, and signal processing methods used in general radiography, X-ray computed tomography, ultrasound imaging, magnetic resonance imaging, and nuclear medicine. The primary focus is on the methods required to reconstruct images within each modality, with emphasis on the resolution, contrast, and signal-to-noise ratio of the resulting images.  (Note: Beginning Fall ’08 this course will permanently move to the fall semester.)  Co-listed as 520.432

Sec.01

MWF 10-10:50

580.474 (E)

MOLECULAR AND CELLULAR IMAGING (3) Bulte/McVeigh   Limit  20 Recommended Prereq: 520/580.472 Introduction to non-invasive imaging techniques as applied to an early diagnosis of disease, altered gene expression, cellular therapeutics, and fundamental molecular or metabolic changes.  Includes magnetic resonance imaging, radionuclide imaging, and optical imaging techniques.  Covered will be:  principles of specific targeting and non-specific uptake of diagnostic contrast agents; NMR spectroscopy of metabolic changes in cancer; use of cell tracking using exogenous tags; imaging of stem cells, imaging using reporter genes, theranostics (combined therapeutics and diagnostics), imaging cancer, imaging of neurodegenerative disease, and imaging of cardiovascular disease.  The emphasis of the overall course is to learn how molecular/ cellular imaging will change the way future diagnostic radiology and drug development will be practiced.
Meets with 580.774 Course canceled 8/12/08

Sec.01

TTh 9-10:15 10:30- 11:45

580.492 (E,N)

BUILD-A-GENOME MENTOR (4) Bader   Perm. Req’d.     Limit 8 In addition to producing and sequencing DNA segments like regular B-a-G students, mentors will help prepare and distribute reagents, and maintain a Moddle site to track student reagent use and productivity. Mentors will also be expected to mentor specific students who are learning new techniques for the first time, contribute to the computational and biotech infrastructure associated with Build-a-Genome, and pursue at least one independent research project. Successful completion of this course provides 3 credit hours toward the supervised research requirement for Molecular and Cellular Biology majors. Co-listed with 020.451

Sec. 01

MWF 5-6:30pm

580.495

MICROFABRICATION LAB (4) Andreou/Wang   Limit 4 per section Seniors only or Perm. Req’d.
This laboratory course introduces the principles used in the construction of microelectronic devices, sensors, and micromechanical structures. Students will work in the laboratory on the fabrication and testing of a device. Accompanying lecture material covers basic processing steps, design and analysis CAD tools, and national foundry services.
Co-listed with 530.495 and 520.495

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Lab 01

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03

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W 1:30-2:20

Th 1-5

Th 5-8pm

 F 8-12

F 1-5

Th 8-12

580.501

FRESHMAN-SOPHOMORE RESEARCH OR PRACTICUM IN BIOMEDICAL ENGINEERING  Research projects or engineering design projects under the supervision of any member of the BME faculty.

TBA

580.511

FRESHMAN - SOPHOMORE INDEPENDENT STUDY IN BIOMEDICAL ENGINEERING  Directed readings or other literature research under the direction of any member of the BME faculty.

TBA

580.531

JUNIOR - SENIOR RESEARCH OR PRACTICUM IN BIOMEDICAL ENGINEERING  Research projects or engineering design projects under the supervision of any member of the BME faculty. Prerequisite: junior or senior standing.

TBA

580.541

JUNIOR - SENIOR INDEPENDENT STUDY IN BIOMEDICAL ENGINEERING  Directed readings or other literature research under the direction of any BME faculty member. Prereq: Junior or Senior standing.

TBA

580.571

HONORS INSTRUMENTATION Thakor  Perm. Req'd Coreq: Enrollment in 580.471 Students enrolled jointly in 580.471 and 580.571 will not be required to take exams. Instead, students will develop a term paper and patent application and carry out a hands-on individual or team project throughout the semester and the intersession. Previous projects include design of EEG amplifier, voltage clamp and patch clamp, vision aid of blind, pacemaker/defibrillator, sleep detection and alert device, glucose sensor and regulation, temperature controller, eye movement detection and device control, ultrasound ranging and tissue properties, impedance plethysmography, lie detector, blood alcohol detector, pulse oximeter, etc.

Sec. 01

TBA

580.580

SENIOR DESIGN PROJECT Allen Perm. Req’d.Independent or team design project to design and evaluate a system. The design should demonstrate creative thinking and experimental skills, and must draw upon advanced topics of biomedical and traditional engineering. 

Sec. 01

TBA

580.611

BIOMEDICAL DEVICE, DESIGN AND INNOVATION  Allen  Limit 8 MSE students with instructor’s consent Graduate-level version 580.311-312.  Teams consist of MSE students only.

Sec. 01

T 6-6:50pm

580.625

STRUCTOR AND FUNCTION OF THE AUDITORY AND VESTIBULAR SYSTEMS May  Limit 10  Prereq: 580.421-422 or equivalent   Recommended: 580.222 Physiological mechanisms of hearing and balance. Topics include transmission of sound in the ear, transduction of sound and head orientation by hair cells, biophysics and biochemistry of hair cells, representation of sound and balance in eighth-nerve discharge patterns, anatomy of the central auditory and vestibular systems, and synaptic transmission and signal processing in central neurons. Aspects of hearing and balance such as speech perception, sound localization, vestibular reflexes and vestibular compensation are discussed with an integrated perspective covering perceptual, physiological, and mechanistic data. This course is taught at the School of Medicine.

Sec. 01

TTh 9-10:15

580.628

TOPICS IN SYSTEM NEUROSCIENCE Wang/Zhang  Limit 10  Prereq: Intro. to Neuroscience, 110.302, 520.214, 580.421 or equivalent This course consists of weekly discussions of current literature in systems neuroscience. The selected readings will focus on neural mechanisms for perception, attention, motor behavior, learning, and memory, as studied using physiological, psychophysical, computational, and imaging techniques. Students are expected to give presentations and participate in discussions.

Sec. 01

T 4:30-5:20

580.635

PROJECT TOPICS IN BIOLECTROMAGNETIC PHENOMENA  Tung  Limit 10 This course reviews theoretical concepts and experimentsal approaches used to characterize electric, magnetic, and electromagnetic phenomena that arise in biological tissues.  Topics include volume conductor models of cells and tissues, complex conductive properties of tissue and cell suspensions, bioelectric and biomagnetic measurements, electric and magnetic stimulation, and impedance plethysmography. Selected topics will be chosen for oral presentations by class participants.
Course taught at the School of Medicine

Sec. 01

T 4:30-5:20

580.639

MODELS OF THE NEURON Young  Limit 20  Prereq: 110.301-302, 580.421-422 or equivalent.  See description for 580.439.  Graduate version of 580.439. Differs in that an advanced modeling project using data from the literature is required.  Same prerequisites.

Sec. 01

MTWF 9-9:50

580.640

CELLULAR AND TISSUE ENGINEERING Yarema    Limit 10  Lectures provide an overview of molecular biology fundamentals, an extensivereview on extracellular matrix and basics of receptors, followed by topics on cell-cell and cell-matrix interactions at both the theoretical and experimental levels. Subsequent lectures will cover the effects of physical (shear, stress, strain), chemical (cytokins, growth factors), and electrical stimuli on cell function, emphasizing topics on gene regulation and signal transduction processes. Material on cell-cycle, apoptosis, metabolic engineering and gene therapy will also be incorporated into the course.

Sec. 01

TTh 9-10:15

580.681

ADVANCED TOPICS IN COMPUTER VISION (formerly 580.464)  Vidal  Limit 10Prereq: 110.202 and 600.461 or instructor’s permission State-of-the-art methods in dynamic vision, with an emphasis on segmentation, reconstruction, and recognition of static and dynamic scenes. Topics include reconstruction of static scenes (tracking and correspondence, multiple view geometry, self-calibration), reconstruction of dynamic scenes (2-D and 3-D motion sementation, nonrigid motion analysis), recognition of visual dynamics (dynamic textures, face and hand gestures, human gaits, crowd motion analysis), as well as geometric and statistical methods for clustering and unsupervised learning, such as K-means, Expectation Maximization, and Generalized Principal Component Analysis. Applications in robotics and biomedical imaging are also included.

Sec. 01

MW 1:30-2:45 TTh 10:30-11:45

580.682

COMPUTATIONAL MODELS OF THE CARDIAC MYOCYTE CARDIAC MODELS OF THE MYOCYTE Winslow/Greenstein  Graduate level course open to qualified undergraduate seniors with permission of the instructors. Recommended Prereq: 580.421-422 or equivalent, 110.201 & 110.302 or 550.291, knowledge of C/C++ OR Matlab. Students will need a laptop.
The cardiac myocyte is one of the most extensively studied cells in biology. As such, it serves as an important example of how to develop quantitative, dynamic, computational models of cell function. "Computational Models of the Cardiac Myocyte" will present a comprehensive review of all aspects of modeling of the cardiac myocyte as an introduction to the discipline of computational cell biology. The course will be presented in an innovative way. Students will be expected to review web-based course material prior to weekly lab meetings. Weekly 3 hour lab session will be used to interact with the instructors, and to implement and study computational models. Course added 4/29/08

Sec. 01

TBA

580.701

SENSORIMOTOR SYSTEMS Shadmehr  Limit 20  This course introduces current research in sensorimotor systems, with particular emphasis on the functions of the human brain as inferred from patient work, psychophysics, and computational studies. Students are expected to present two papers per semester and actively engage in discussion of weekly research papers.

Sec. 01

Th 12-12:50

580.771

PRINCIPLES OF BME INSTRUMENTATION  Thakor   Limit 16  Graduate students only
This course is designed for graduate students interested in learning basic biomedical instrumentation design concepets and translating these into advanced projects based on their research on current state-of-the-art. They will first gain the basic knowledge of instrumentation design, explore various applications, and critically gain hands-on experience through laboratory and projects. At the end of the course, students would get an excellent awareness of biological or clinical measurement techniques, design of sensors and electronics (or electromechanical/ chemical, microprocessor system and their use). They will systematically learn to design instrumentation with a focus on the use of sensors, electronics to design a core instrumentation system such as an ECG amplifier. Armed with that knowledge and lab skills, students will be encouraged to discuss various advanced instrumentation applications, such as brain monitor, pacemaker/defibrillator, or prosthetics.  Further, they will be “challenged” to come up with some novel design ideas and implement them in a semester-long design project. Students will take part in reading the literature, learning about the state-of-the-art through journal papers and patents, and discussing, critiquing, and improving on these ideas. Finally, they will be implementing a selected idea into a semester-long advanced group project.
Meets with 580.471

Lec.

Sec. 01

Th 4-5:50pm

F 6-8:50pm

580.774

MOLECULAR AND CELLULAR IMAGING (3) Bulte/McVeigh   Limit 20   Introduction to non-invasive imaging techniques as applied to an early diagnosis of disease, altered gene expression, cellular therapeutics, and fundamental molecular or metabolic changes.  Includes magnetic resonance imaging, radionuclide imaging, and optical imaging techniques.  Covered will be:  principles of specific targeting and non-specific uptake of diagnostic contrast agents; NMR spectroscopy of metabolic changes in cancer; use of cell tracking using exogenous tags; imaging of stem cells, imaging using reporter genes, theranostics (combined therapeutics and diagnostics), imaging cancer, imaging of neurodegenerative disease, and imaging of cardiovascular disease.  The emphasis of the overall course is to learn how molecular/ cellular imaging will change the way future diagnostic radiology and drug development will be practiced.
Meets with 580.474 Course canceled 8/12/08

Sec.01

TTh 9-10:15 10:30-11:45

580.801

RESEARCH IN BIOMEDICAL ENGINEERING
Graduate Students only

TBA