BIOENGINEERING (EG) {BE}
099. Independent Study in Bioengineering. (C) Prerequisite(s): Freshman or Sophomore standing in BE (Both BAS and BSE). An individualized research-based learning experience on a biomedical research
problem. Requires preparation of a proposal, literature evaluation, and preparation of a research paper and presentation.
Regular progress reports and meetings with a faculty advisor are required.
L/L 100. Introduction to Bioengineering. (A) Corequisite(s): MATH 104, PHYS 140 or 150. Open to Freshmen only. Survey course introducing students to the breadth of bioengineering. Course
consists of weekly guest lectures and a series of small projects and reports that allow students to explore different
facets of bioengineering.
L/R 200. Bioengineering I: Introduction to Biomechanics and Biomaterials. (A) Prerequisite(s): Sophomore standing, MATH 104, 114, PHYS 140, 141 or PHYS 150, 151. Corequisite(s): MATH
240. Application of statics and dynamics to simple
force analyses of the musculoskeletal system. Introduction
to the fundamentals of strength of materials. Biomechanics
of soft and hard tissues: microstructure and mechanical
properties. This course is intended to provide a
solid foundation in statics and mechanics of materials
with particular focus on human joint biomechanics.
The first portion of the course will present fundamental
concepts of force and mechanics of rigid and deformable
bodies. The remainder of the course will consist
of an introduction of materials science and engineering,
including the classification and bulk properties
of implantable materials, and will also address specific
topics including torsional loading and bending. By
the end of the course, it is anticipated that students
will be able to integrate the origin of tissue mechanical
properties with structure/function analyses of load-bearing
tissues in the human body.
209. Bioengineering Lab I. (A) Corequisite(s): BE 200. Students taking BE 209 are required to be enrolled
in BE 200 and to have completed the physics and chemistry laboratories scheduled during
the freshmen year. BE 209 is the first laboratory course in the Bioengineering curriculum. It is
required for both BSE and BAS majors. It is intended for the fall semester of the semester. Bioengineering Lab II. (B) Prerequisite(s): BE 209. Corequisite(s): Math 241.Second term of a two-year sequence designed to integrate real world experiences
into various Bioengienering Science courses. Experiments and projects in mechanics, material and chemical applications
to Biomedical Engineering.
L/R 220. (MSE 220) Structure and Properties of Biomaterials. (B) Prerequisite(s): CHEM 101, BE 209. Corequisite(s): MATH 241, BE 210. An examination of the structure of property, performance relationship for materials
used in surgical implants and medical devices. Consideration is given to issues of biocompatibility, degradation
of materials by biological systems, and biological response to artificial materials. Particular attention will be
given to the materials of the total hip prosthesis and their relationship to the long-term outcomes for total hip arthoplasty.
SM 225. Technology and Engineering in Medicine. (C) Prerequisite(s): First year college physics, chemistry and biology or AP credit; Sophmore and higher standing only. This course will provide an in-depth examination of technology and its impact
on medicine, with an emphasis on the intersection of engineering with medicine and health. Basic foundations of historical
perspective, constraints on technological development., and the promise and peril of technological impact
on medicine will be discussed. Modules will also focus on specific tehnological advanceswhich have had significant
impact on the field of medicine. These include: imaging and diagnosis of disease, genetic therapy and pharmacology,
and rehabilitative devices, assistive devices and transplantation.
L/R 301. Bioengineering Signals and Systems. (A) Prerequisite(s): BE 210, MATH 241. Properties of signals and systems and examples of biological and biomedical
signals and systems; linear, time invariant systems; Fourier analysis of signals and systems with applications to biomedical
signals such as ECG and EEG; frequency analysis of first and second order systems; the frequency response;
of systems characterized by linear constant-coefficient differential equations; introduction to digital and analog
filtering, sampling and sampling theorem and aliasing.
L/R 303. (EAS 303) Ethics, Social and Professional Responsibility for Engineers.
(A) Prerequisite(s): Junior Standing. Provides an overview of the ethical and professional responsibilities
of engineers, as engineerng professionals, as members
of engineering organizations, and as participants
in medical or scientific research. The course will
make extensive use of student group presentations
and role playing in the analysis of cases based on
real-world problems with ethical dimensions. The
case studies will vary from year to year, but will
be chosen to reflect the full range of engineering
fields and disciplines including areas of Bioengineering
and Biomedical research.
305. Engineering Principles of Human Physiology. (B) Prerequisite(s): Junior Standing. Analysis of cellular and systems-level human physiology with an emphaisis on
clinical applications. Particular emphasis is on
mechanisms of function in the neural and cardiovascular
systems.
309. Bioengineering Lab III. (A) All students taking BE 309 are required to have satisfactorily completed BE
210 and be familiar with the operation and rules
of the laboratory, use of the computer facilities
and software, and safety regulations. BE 309 is the first half of the third year continuation of BE 209 and BE 210.
It is required for BSE majors and may be taken as
an elective by BAS majors.
310. Bioengineering Lab IV. (B) Corequisite(s): BE 350. Fourth semester of a two year sequence designed to integrate real world experiences
into various Bioengineering and Bioengineering Science
courses. Laboratory emphasizing biotransport and
biomedical instumentaion.
L/R 324. Chemical Basis of Bioengineering II. (A) Prerequisite(s): PHYS 140, 141 or 150, 151, MATH 240, CHEM 101, 102. Advanced topics in physical chemistry including solution and colloid chemistry,
electrochemistry, surface phenomena, and macromolecules applied to biological systems.
330. (MSE 330) Soft Materials. (C)
L/R 350. Transport Processes in Living Systems. (B) Prerequisite(s): MATH 241 or equivalent, PHYS 140 or 150. Introduction to basic principles of fluid mechanics and of energy and mass transport
with emphasis on applications to living systems and
biomedical devices.
400. Preceptorship in Clinical Bioengineering. (B) Introduction to the integration of biomedical engineering in clinical medicine
through lectures and a preceptorship with clinical
faculty. This course is for BE majors ONLY, with
preference given to BSE students.
402. (BE 502) From Biomedical Science to the Marketplace. (C) Prerequisite(s): Senior standing in Bioengineering or permission of the instructor. Course Objectives and Relationship
to Program Education. This course explores the transition
from discovery of fundamental knowledge to its ultimate
application in a clinical device or drug. Emphasis
is placed upon factors that influence this transition
and upon the integrative requirements across many
fields necessary to achieve commercial success. Special
emphasis is placed on entrepreneurial strategies,
intellectual property, financing and the FDA process
of proving safety and efficacy. Current public companies
in the medical device and drug industry are studies
in detail and critiqued against principles developed
in class.
421. (BE 521) Brain-Computer Interfaces. (C) Prerequisite(s): BE 301 (Signals and Systems) or equivalent, computer programming
experience, preferably MATLAB (e.g., as used the
BE labs, BE 209/210/310). Some basic neuroscience
background (e.g. BIOL 215, BE 305, BE 520, INSC core
course), or independent study in neuroscience, is
required. This requirement may be waived based upon
practical experience on a case by case basis by the
instructor. The course is geared to advanced undergraduate and graduate students interested
in understanding the basics of implantable neuro-devices,
their design, practical implementation, approval,
and use. Reading will cover the basics of neuro signals,
recording, analysis, classification, modulation,
and fundamental principels of Brain-Machine Interfaces.
The course will be based upon twic weekly lectures
and "hands-on" weekly assignments that
teach basic signal recording, feature extraction,
classification and practical implementation in clinical
systems. Assignments will build incrementally toward
constructing a complete, functional BMI system. Fundamental
concepts in neurosignals, hardware and software will
be reinforced by practical examples and in-depth
study. Guest lecturers and demonstrations will supplement
regular lectures.
440. (BE 540, CBE 440, CBE 540) Biomolecular and Cellular Engineering. (C) This course provides an introduction to the quantitative methods used in characterizing
and engineering biomolecular properties and cellular
behavior, focusing primarily on receptor-mediated
phenomena. The thermodynamics and kinetics of protein/ligand
binding are covered, with an emphasis on experimental
techniques for measuring molecular parameters such
as equilibrium affinities, kinetic rate constants,
and diffusion coefficients. Approaches for probing
and altering these molecular properties of proteins
are also described, including site-directed mutagenesis,
directed evolution, rational design, and covalent
modification. Equilibrium, kinetic, and transport
models are used to elucidate the relationships between
the aforementioned molecular parameters and cellular
processes such as ligand/receptor binding and trafficking,
cell adhesion and motility, signal transduction,
and gene regulation.
441. Engineering Microbial Systems. (C) Prerequisite(s): Biol 121, Biol 202, BE 209, BE 210 or permission of the instructor. This course is designed to expose students to the principles
underlying engineering microbial systems. The fundamentals
of DNA, RNA, and proteins will be reviewed. An emphasis
will be placed on recombinant DNA technologies, mutagenesis,
cloning, gene knockouts, altered gene expression
and analysis, with practical real world examples
of their application. Throughout this course we will
also focus on case studies and cricial literature
evaluation.
L/R 444. (BE 555, CBE 444, CBE 555, MEAM555) Nanoscale Systems Biology. Prerequisite(s): Background in Biology, Chemistry or Engineering with coursework in thermodynamics
or permission of the instructor. From single molecule
studies to single cell manipulations, the broad field
of cell and molecular biology is becoming increasingly
quantitative and increasingly a matter of systems
simplification and analysis. The elaboration of various
stresses on cellular structures, influences of interaction
pathways and convolutions of incessant thermal motions
will be discussed via lectures and laboratory demonstration.
Topics will range from, but are not limited to, protein
folding/forced unfolding to biomolecule associations,
cell and membrane mechanics, and cell motility, drawing
from very recent examples in the literature. Frequent
hands-on exposure to modern methods in the field
will be a significant element of the course in the
laboratory. Skills in analytical and professional
presentations, papers and laboratory work will be
developed.
450. (BE 550) Hemodynamics. (A) Prerequisite(s): BE 350 or equivalent, or permission of the instructor. Development of concepts about the operation of the mammalian cardiovascular
system as conceived in the years 198 (by Galenus),
1628 (by Harvey), and 1998 (at Penn by A. Noordergraaf).
455. (MEAM455, MEAM544) Continuum Biomechanics. (A) Continuum mechanics with applications to biological systems. Fundamental engineering
conservation laws are introduced and illustrated
using biological and non-biological examples. Kinematics
of deformation, stress, and conservation of mass,
momentum, and energy. Constitutive equations for
fluids, solids, and intermediate types of media are
described and applied to selected biological examples.
Class work is complemented by hands-on experimental
and computational laboratory experiences.
459. (BE 559) Multiscale Modeling of Biological Systems. (C) This course aims to provide theoretical, conceptual, and hands-on modeling experience
on three different length and time scales that are
crucial to biochemical phenomena in cells and to
nanotechnology applications. Special Emphasis will
be on cellular signal transduction. 60% lectures,
40% computational laboratory. No programming skills
required.
470. Medical Devices. (B) Prerequisite(s): Junior or Senior standing in Bioengineering, or permission
of the instructor. This course discusses the design, development, and evaluation of medical devices.
Emphasis is placed on the process of matching technological opportunities to medical needs. Medical devices are
analyzed from three viewpoints: technology driven applications, competing technologies, and disease-related
technology clusters.
480. Introduction to Biomedical Imaging. (A) Prerequisite(s): BE 301 or ESE 325. Introduction to the mathematical, physical and engineering design principles
underlying modern medical imaging systems including x-ray computed tomography, ultrasonic imaging, and magnetic
resonance imaging. Mathematical tools including Fourier analysis and the sampling theorem. The Radon transform
and related transforms. Filtered backprojection and other reconstruction algorithms. Bloch equations, free induction
decay, spin echoes and gradient echoes. Applications include one-dimensional Fourier magnetic resonance imaging,
three-dimensional magnetic resonance imaging and slice excitation.
483. (BE 583) Molecular Imaging. (C) Prerequisite(s): BIOL 215 or BE 305 or permission of the instructor. This course will provide a comprehensive survey of modern medical imaging modalities
with an emphasis on the emerging field of molecular imaging. The basic principles of X-ray, computed
tomography, nuclear imaging, magnetic resonance imaging, and optical tomography will be reviewed. The emphasis of
the course, however, will focus on the concept of contrast media and targeted molecular imaging. Topics to be covered
include the chemistry and mechanisms of various contrast agents, approaches to identifying molecular markers
of disease, ligand screening strategies, and the basic principles of toxicology and pharmacology relevant
to imaging agents.
490. Research in Bioengineering. (C) Prerequisite(s): Junior/Senior Standing. An intensive independent study experience on an engineering or biological science
problem related to BE. Requires preparation of a proposal, literature evaluation, and preparation of a paper
and presentation. Regular progress reports and meetings with faculty advisor are required.
492. Research in Biomedical Science. (C) Prerequisite(s): Junior or Senior Standing. Second semester of a year-long project.
495. Senior Design Project. (A) Prerequisite(s): BE Senior Standing. Design projects in various areas of bioengineering; projects are chosen by the
students with approval of the instructor in the Spring semester of the Junior year; a proposal, three interim reports, a
final report, and a presentation are required. Also emphasized are proposal and report writing, scheduling, project risk assessment,
multidisciplinary environments and ethics.
496. Senior Design Project. (B) Prerequisite(s): BE Senior Standing. Second semester of a year-long design project.
497.Senior Thesis in Biomedical Science. (C) Prerequisite(s): Senior Standing in Applied Science Biomedical Science Program (BAS students only). An intensive independent project experience incorporating both technical and
non-technical aspects of the student's chosen career path. Chosen topic should incorporate elements from the student's
career path electives, and may involve advisors for both technical and non-technical elements. Topics may range from
biomedical research to societal, technological and business aspects of Bioengineering. A proposal, regular progress
reports and meetings with a faculty advisor, a written thesis, and a presentation are required.
498. Senior Thesis in Biomedical Science. (A) Prerequisite(s): Senior Standing in Applied Science Biomedical Science Program (BAS students only). Second semester of a year-long project.
502. (BE 402) From Biomedical Science to the Marketplace. (A) Prerequisite(s): First year graduate level, or Senior standing in Bioengineering, or permission of the instructor. This course explores the transition from discovery of fundamental knowledge
to its ultimate application in a clinical device or drug. Emphasis is placed upon factors that influence this transition
and upon the integrative requirements across many fields necessary to achieve commercial success. Special emphasis
is placed on entrepreneurial strategies, intellectual property, financing and the FDA process of proving safety and efficacy.
Current public companies in the medical device and drug industry are studies in detail and critiqued against
principles developed in class.
505. Quantitative Human Physiology. (B) Prerequisite(s): BE 305. Introduction to human physiology using the quantitative methods of engineering
and physical science. Emphasis is on the operation of the major organ systems at both the macroscopic and cellular
level.
510. Biomechanics and Biotransport. (A) Prerequisite(s): Math through 241; BE 350, BE 324 as pre-or corequisites. The course is intended as an introduction to continuum mechanics in both solid
and fluid media, with special emphasis on the application to biomedical engineering. Once basic principles are established,
the course will cover more advanced concepts in biosolid mechanics that include computational mechanics
and bio-constitutive theory. Applications of these advanced concepts to current research problems will be
emphasized.
511. Analysis and Design of Bioengineering Signals. (B) Prerequisite(s): BE 301 or graduate status. Not intended for students with previous courses in digital signal processing. This
is a practically-oriented course in the analysis
of biomedical signals focusing on medically significant
applications. The specific applications will vary
from year to year, but lectures will include the
nature of major signals of biomedical importance, diginal signal processing including convolution, digital
filtering, wavelet analysis. The course will include
student experiments using Matlab and independent
projects.
L/R 512. Bioengineering III: Biomaterials. (B) This course provides a comprehensive background in biomaterials. It covers surface
properties, mechanical behavior and tissue response
of ceramics, polymers and metals used in the body.
It also builds on this knowledge to address aspects
of tissue engineering, particularly the substrate
component of engineering tissue and organs.
513. Cell Biology. (A) Prerequisite(s): Graduate Standing or permission of the instructor. Introduction to cell and molecular biology with emphasis on quantitative concepts
and applications to multicellular systems.
517. (ESE 517) Optical Imaging. (C) Prerequisite(s): ESE 310 and ESE 325 or equivalent. A modern introduction to the physical principles of optical imaging with biomedical
applications. Propagation and interference of electromagnetic waves. Geometrical optics and the eikonal. Plane-wave
expansions, diffraction and the Rayleigh criterion. Scattering theory and the Born approximation. Introduction
to inverse problems. Multiple scattering and radiative transport. Diffusion approximation and physical optics
of diffusing waves. Imaging in turbid media. Introduction to coherence theory and coherence imaging. Applications
will be chosen from the recent literature in biomedical optics.
519. Cellular-Level Neural Simulation and Modeling. (M) Finkel. Cellular level simulation of neurons at the biophysical level. Topics include
cable theory, the Hodgkin-Huxley formalism for different channelspecies , synaptic interactions and plasticity,
information measures in network activity, neuromodulation, and applications to modeling neurological disease.
520. (INSC594) Computational Neuroscience and Neuroengineering. (B) Finkel. Computational modeling and simulation of the structure and function of brain
circuits. A short survey of the major ideas and techniques in the neural network literature. Particular emphasis on
models of hippocampus, basal ganglia and visual cortex. A series of lab exercises introduces techniques of neural
simulation.
521. (BE 421) Brain-Computer Interfaces. (C) Prerequisite(s): BE 301 (Signals and Systems) or equivalent, computer programming
experience, preferably MATLAB (e.g., as used the
BE labs, BE 209/210/310). Some basic neuroscience
background (e.g. BIOL 215, BE 305, BE 520, INSC core
course), or independent study in neuroscience, is
required. This requirement may be waived based upon
practical experience on a case by case basis by the
instructor.The course is geared to advanced undergraduate
and graduate students interested in understanding
the basics ofimplantable neuro-devices, their design,
practical implementation, approval, and use. Reading
will cover the basics of neuro signals, recording,
analysis, classification, modulation, and fundamental
principels of Brain-Machine Interfaces. The
course will be based upon twic weekly lectures
and "hands-on" weekly
assignments that teach basic signal recording,
feature extraction, classification and
practical implementation in clinical systems.
Assignments will build incrementally toward
constructing a complete, functional BMI
system. Fundamental concepts in neurosignals, hardware
and software will be reinforced by practical
examples and in-depth study. Guest lecturers
and demonstrations will supplement regular
lectures.
537. (CIS 537) Biomedical Image Analysis. (C) Prerequisite(s): Math through multivariate calculus (MATH 241), programming experience, as well as some familiarity with linear algebra,
basic physics, and statistics.
539. (ESE 539) Neural Networks, Chaos, and Dynamics: Theory and Application. (B) Physiology and anatomy of living neurons and neural networks; Brain organization;
Elements of nonlinear dynamics, the driven pendulum
as paradigm for complexity, synchronicity, bifurcation,
self-organization and chaos; Iterative maps on the
interval, period-doubling route to chaos, universality
and the Feigenbaum constant, Lyapunov exponents,
entropy and information; Geometric characterization
of attractors; Fractals and the Mandelbrot set; Neuron
dynamics: from Hudgkin-Huxley to integrate and fire,
bifurcation neuron; Artificial neural networks and
connectionist models, Hopfield (attractor-type) networks,energy
functions, convergence theorems, storage capacity,
associative memory, pattern classification, pattern
completion and error correction, the Morita network;
Stochastic networks, simulated annealing and the
Boltzmann machine, solution of optimization problems,
hardware implementations of neural networks; the
problem of learning, algorithmic approaches: Perception
learning, back-propagation, Kohonnen's self-organizing
maps and other networks; Coupled-map lattices; Selected
applications including financial markets.
540. (BE 440, CBE 440, CBE 540) Biomolecular and Cellular Engineering. This course provides an introduction to the quantitative methods used in characterizing
and engineering biomolecular properties and cellular
behavior, focusing primarily on receptor-mediated
phenomena. The thermodynamics and kinetics of protein/ligand binding are covered, with an emphasis on experimental
techniques for measuring molecular parameters such
as equilibrium affinities, kinetic rate constants,
and diffusion coefficients. Approaches for probing
and altering these molecular properties of proteins
are also described, including site-directed mutagenesis,
directed evolution, rational design, and covalent
modification. Equilibrium, kinetic, and transport
models are used to elucidate the relationships between
the aforementioned molecular parameters and cellular
processes such as ligand/receptor binding and trafficking,
cell adhesion and motility, signal transduction,
and gene regulation.
546. (BMB 546) Fundamental Techniques of Imaging I. (H) This course covers the fundamentals of modern techniques in biological and in
vivo biomedical imaging. This practical course consists
of a series of hands-on lab exercises, covering major
imaging modalities, but also extends to non-radiology
modalities of interest in biological, pathological
or animal imaging (e.g., optical imaging). Topics
include x-ray, mammography, MRS, MRI, PET, and ultrasound.
The emphasis will be on hands-on aspects of all areas
of imaging and imaging analysis. Small groups of
students will be led by a faculty member with technical
assistance as appropriate.
547. Fundamental Techniques of Imaging 2. (C) This course is a continuation of the course Fundamental Techniques of Imaging
1 (BE546). It builds upon the fall course instruction
and continues to expose students to the fundamentals
of modern techniques in biological and in vivo biomedical
imaging. This course consists of a series of hands-on
lab exercises, covering major imaging modalities,
but also extends to non-radiology modalities of interest
in biological, pathological or animal imaging (e.g.,
optical imaging). Topics include SPECT, Micro-CT,
diffuse optical spectroscopy, in vivo fluorescence
imaging, and computed tomography. The course will
continue to emphasize the hands-on aspects of all
areas of imaging and imaging analysis. Small groups
of students will be led by a faculty member with
technical assistance as appropriate.
550. (BE 450) Hemodynamics. (A) Prerequisite(s): BE 350 or equivalent, or permission of the instructor. Development of concepts about the operation of themammalian cardiovascular system
as conceived in the years 198 (by Galenus), 1628
(by Harvey), and 1998 (at Penn by A. Noordergraaf).
L/R 552. (CBE 552) Cellular Engineering. (M) Prerequisite(s): Math through 241; BE 350, BE 324 as pre- or corequisites. Molecular & cellular biology. The goal of this course is to
introduce students quantitative concepts in understanding
and manipulating the behavior of biological cells.
We will try to understand the interplay between molecules
in cells and cell function. A particular focus is
on receptors - cell surface molecules that mediate
cell responses. We will also try to understand processes
such as adhesion, motility, cytoskeleton, signal
transduction, differentiation, and gene regulation.
553. Principles, Methods, and Applications of Tissue Engineering. (B) Prerequisite(s): Graduate Standing or instructor's permission. Tissue engineering demonstrates enormous potential
for improving human health. While there is an extensive
body of literature discussing the state of the art
of tissue engineering, the majority of this literature
is descriptive and does little to address the principles
that govern the success or failure of an engineering
tissue. This course explores principles of tissue
engineering, drawing upon diverse fields such as
developmental biology, immunology, cell biology,
physiology, transport phenomena, material science,
and polymer chemistry. Current and developing methods
of tissue engineering as well as specific applications
will be discussed in the context of these principles.
554. (CBE 554) Engineering Biotechnology. (M) Advanced study of re DNA techniques; bioreactor design for bacteria, mammalian
and insect culture; separation methods; chromatography;
drug and cell delivery systems; gene therapy; and
diagnostics.
L/R 555. (BE 444, CBE 444, CBE 555, MEAM555) Nanoscale Systems Biology. (A) Prerequisite(s): Background in Biology, Chemistry or Engineering with coursework in thermodynamics
or permission of the instructor. From single molecule
studies to single cell manipulations, the broad field
of cell and molecular biology is becoming increasingly
quantitative and increasingly a matter of systems
simplification and analysis. The elaboration of various
stresses on cellular structures, influences of interaction
pathways and convolutions of incessant thermal motions
will be discussed via lectures and laboratory demonstration.
Topics will range from, but are not limited to, protein
folding/forced unfolding to biomolecule associations,
cell and membrane mechanics, and cell motility, drawing
from very recent examples in the literature. Frequent
hands-on exposure to modern methods in the field
will be a significant element of the course in the
laboratory. Skills in analytical and professional
presentations, papers and laboratory work will be
developed.
556. Mechanical Forces: Cells/Tissue. (M) This course will explore the biological effects of mechanical forces at the
molecular, cellular and tissue level in specific
tissues (blood vessels, cartilage, bone, brain, lung,
and skeletal and cardiac muscle). The importance
of physical forces in the health, disease, development,
remodeling and injury of these tissues will be highlighted.
An understanding of these specific systems will provide
a foundation for discussions of the molecular basis
of mechanotransduction, mechanically induced trauma,
as well as the manipulation of the mechanical environment
in biotechnology and tissue engineering applications.
Throughout the course, the use of engineering principles
and methods to understand and model mechanically
induced biological phenomena will be stressed.
L/R 557. From Cells to Tissue: Engineering Structure and Function. (C) Faculty. Prerequisite(s): Math through 241; BE350, BE324 as pre- or corequisites; Molecular & cellular
biology. The goal of this course is to introduce
students to quantitative concepts in understanding
and manipulating the behavior of biological cells.
We will try to understand the interplay between molecules
in cells and cell function. A particular focus is
on receptors - cell surface molecules that mediate
cell responses. We will also try to understand processes
such as adhesion, motility, cytoskeleton, signal
transduction, differentiation, and gene regulation.
559. (BE 459) Multiscale Modeling of Biological Systems. (C) Prerequisite(s): Undergraduates who have taken BE 324 or equivalent courses
in Quantum Mechanics and/or Statistical Physics need
no permission. Others, email instructor for permission. This course aims to provide theoretical, conceptual, and hands-on modeling experience
on three different length and time scales that are
crucial to biochemical phenomena in cells and to
nanotechnology applications. Special Emphasis will
be on cellular signal transduction. 60% lectures,
40% computational laboratory. No programming skills
required.
L/R 562. (CBE 562) Drug Discovery & Development. (B)
L/R 567. (AMCS567, BMB 580) Mathematical Computation Methods for Modeling Biological
Systems. (C) Prerequisite(s): BE 324 and BE 350. This is an introductory course in mathematical biology. The emphasis will be
on the use of mathematical and computational tools for modeling physical phenomena which arise in the study
biological systems. Possible topics include random walk models of polymers, membrane elasticity, electrodiffusion
and excitable systems, single-molecule kinetics, and stochastic models of biochemical networks.
575. Injury Biomechanics. (B) Prerequisite(s): ENM 500 or 510, BE 510 or MEAM 519 or equivalent. A background in physiology and anatomy is also recommended. This course is intended as an introduction to investigating the mechanics of
injury, from the organism to the tissue level. The students will be exposed to both formal didactic instruction and
selected field work. The course will cover principles in continuum and analytical mechanics, and will use application in
injury research to illustrate these concepts. The course will be divided into three major units. The first unit
will be an introduction to variational principles of mechanics and calculus of variations, and will apply these concepts
to injury problems (e.g., occupant kinematics during a collision, vehicle kinematics, impact to padded surfaces).
Special emphasis will be placed on converting a system input into a body response. The second unit of the course
will be used to discuss the effect of gross body motion on tissue and organ mechanical response. Material models of
biological tissue will be discussed, and examples relating body motion to tissue response will be reviewed. In the
final unit of this course, students are required to research and review a problem of their choice and present a report
detailing an engineering based solution to the problem.
580. (PHYS582) Medical Radiation Engineering. (B) Prerequisite(s): Junior standing. This course in medical radiatioin physics investigates electromagnetic and particulate
radiation and its interaction with matter. The theory of radiation transport and the basic concept of dosimetry
will be presented. The principles of radiation detectors and radiation protection will be discussed.
581. (BMB 581) Techniques of Magnetic Resonance Imaging. (M) Detailed survey of the physics and engineering of magnetic resonance imaging
as applied to medical diagnosis. Covered are: history
of MRI, fundamentals of electromagnetism, spin and
magnetic moment, Bloch equations, spin relaxation,
image contrast mechanisms, spatial encoding principles,
Fourier reconstruction,imaging pulse sequences and
pulse design, high-speeding imaging techniques, effects
of motion, non-Cartesian sampling strategies, chemical
shift encoding, flow encoding, susceptibility boundary
effects, diffusion and perfusion imaging.
583. (BE 483) Molecular Imaging. (C) Prerequisite(s): BIOL 215 or BE 305 or permission of the instructor. This course will provide a comprehensive survey of modern medical imaging modalities
with an emphasis on the emerging field of molecular
imaging. The basic principles of X-ray, computed
tomography, nuclear imaging, magnetic resonance imaging, and optical tomography will be reviewed. The emphasis of
the course, however, will focus on the concept of
contrast media and targeted molecular imaging. Topics
to be covered include the chemistry and mechanisms
of various contrast agents, approaches to identifying
molecular markers of disease, ligand screening strategies,
and the basic principles of toxicology and pharmacology
relevant to imaging agents.
584. (MATH584) Mathematics of Medical Imaging and Measurements. (M) Prerequisite(s): Math through 241 as well as some familiarity with linear algebra and basic physics. In the
last 25 years there as has been a revolution in image
reconstruction techniques in fields from astrophysics
to electron microscopy and most notably in medical
imaging. In each of these fields one would like to
have a precise picture of a 2 or 3 dimensional object,
which cannot be obtained directly. The data that
is accessible is typically some collection of weighted
averages. The problem of image reconstruction is
to build an object out of the averaged data and then
estimate how close the reconstruction is to the actual
object. In this course we introduce the mathematical
techniques used to model measurements and reconstruct
images. As a simple representative case we study
transmission X-ray tomography (CT). In this contest
we cover the basic principles of mathematical analysis,
the Fourier transform, interpolation and approximation
of functions, sampling theory, digital filtering
and noise analysis.
591. Anatomy and Biomechanics of Synovial Joints. (B) Anatomy and Biomechanics of Synovial Joints in Health and Disease.
612. Materials Affecting Cell and Molecular Function. (B) This course provides advanced knowledge regarding the effect of the various
classes of materials on tissues, cells and molecules,
with the emphasis on musculoskeletal tissues. Topics
include the effect of particulate matter, controlled
release carriers and scaffolds for tissue repair.
Emphasis is placed on recent developments in tissue
engineering of bone and cartilage. The course discusses
the use of materials science techniques in the study
of tissue-engineered constructs. Data in the literature
related to the subject matter will be extensively
discussed and the students will write two articles
on selected topics.
619. (BMB 604) Statistical Mechanics. (C) Prerequisite(s): CBE 618 or equivalent. A modern introduction to statistical mechanics with biophysical applications.
Theory of ensembles. Noninteracting systems. Liquid theory. Phase transitions and critical phenomena Nonequilibrium
systems. Applications to reaction kinetics, polymers and membranes.
630. (EE 630) Elements of Neural Computation, Complexity and Learning. (M) Prerequisite(s): A semester course in probability or equivalent exposure to probability (e.g. ESE 530). Non-linear elements and networks: linear and polynomial threshold elements,
sigmoidal units, radial basis functions. Finite (Boolean) problems: acyclic networks; Fourier analysis and efficient
computation; projection pursuit; low frequency functions. Network capacity: Feedforward networks; Vapnik-Chervnenkis
dimension. Learning theory: Valiant's learning model; the sample complexity of learning. Learning algorithms:
Perception training, gradient descent algorithms, stochastic approximation. Learning complexity: the intractability
of learning; model selection.
645. Biological Elasticity. (C) Prerequisite(s): BE 510 or equivalent. Large deformation mechanics of biological materials. Nonlinear elasticity theory,
strain energy functions, constitutive laws of hyperelastic and viscoelastic biological materials. Applications to
heart, lung, and arteries.
655. (MSE 655) Advanced Topics in Biomaterials. (M) Prerequisite(s): BE 512 and MSE 506 or permission of instructor. The effect of nearly inert and bioactive materials on surrounding tissues. Mechanisms
of bone tissue growth enhancement with bioactive ceramics. Elasticity and strength of porous coated
and ceramic coated implants. Tissue remodeling around coated implants.
L/R 662. (CBE 618, MEAM662) Advanced Molecular Thermodynamics. Review of classical thermodynamics. Phase and chemical equilibrium for multicomponent
systems. Prediction of thermodynamic functions from
molecular properties. Concepts in applied statistical
mechanics. Modern theories of liquid mixtures.
SM 699. Bioengineering Seminar. (C)
700. Special Topics in Bioengineering. (M) The research areas discussed will be those of the participating BE faculty who
will direct the discussions and present background
material. The purpose of the course is to present
current research being done in the bioengineering Graduate Group and study relevant literature. The grade will be based on class
participation and a final paper or presentation.
Course content and staffing varies from year to year.
799. Research Rotation. (C)
895. Methods in Bioengineering Education. PHD students only. This course provides training in the practical aspects of teaching. The students
will attend seminars emphasizing basic pedagogical skills. Depending on the course setting for the practicum portion,
student will obtain handson experience developing and delivering lectures, leading recitations, developing and supervising
instructional laboratories, preparing and grading homework, grading laboratory reports, and preparing and grading
examinations. Practicum experiences will be supervised by a faculty mentor. Students will meet during the practicum
portion of the course to discuss difficult situations encountered in the classroom/laboratory and to constructively
review each other. Final evaluations will be based on mentor, peer, and student feedback.
899. Independent Study. (C) Graduate Students Only. For students who are studying a specific advance subject area in fulfillment
of the Bioengineering rotation requirements. Students must submit a proposal outlining the study area along
with the faculty supervisors approval. A paper or presentation is required.
990. Masters Thesis. (C) For students working on a Masters Thesis project leading to the completion of
a M.S.E. degree.
995. Dissertation. (C)
999. Thesis/Dissertation Research. (C) For students working on an advanced research program leading to the completion
of master's thesis or Ph.D. dissertation requirements.
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