BIOMEDICAL ENGINEERING

Biomedical Engineering

(BME)

Chair: Clinton T. Rubin, Psychology A, Third Floor, (631) 632-2302

Graduate Program Director: Helmut Strey, Psychology A, Third Floor, (631) 632-1957
Administrative Staff Assistant: Anne Marie Dusatko, Health Sciences Center T18-030, (631) 444-2303
Degrees awarded: M.S. in Biomedical Engineering; Ph.D. in Biomedical Engineering

Biomedical engineering is at the forefront

of medicines technologic revolution; its
many successes have raised expectations
for the prevention, diagnosis, and
treatment of disease. Faculty at Stony
Brook University have been active
contributors to the cutting edge of this
technology, and our University is building
on internationally acclaimed strengths in
Bioelectromagnetics, Biomaterials,
Biomechanics, Biotechnology, Instrumentation, Medical Imaging, and Tissue
Engineering. These disciplines thrive
through active interdisciplinary collaborations among the faculty in the College of
Engineering and Applied Sciences, the
School of Medicine, and the College of
Arts and Sciences, all of which are in
close proximity. This ongoing biomedical
research, combined with unique facilities at the University, Brookhaven
National Laboratory, and Cold Spring
Harbor Laboratory have helped distinguish Stony Brook as a superb resource
for education in both the engineering
and health sciences. With these intellectual and physical resources, the program in Biomedical Engineering is positioned to provide a rigorous, cross-disciplinary graduate training and research
environment for our students.
This is a very exciting time for
Biomedical Engineering. New areas are
opening each day, ranging from the engineering of tissues to making outer space
habitable for mankind. It is an excellent
time to begin your studies in Biomedical
Engineering and we believe you will find
Stony Brook a superb place to train. Our
faculty is diverse, our commitment is
high, and our facilities are unique. If there
are any questions we can address, please
contact us directly.
The Graduate Program in Biomedical
Engineering at Stony Brook University
trains individuals with baccalaureate
degrees in engineering, applied mathematics, and the sciences and provides
them with the synthesis, design, and
analysis skills necessary to contribute
effectively to the advancement of technology in health and medical care. The M.S.
and Ph.D. degree programs are specifically designed to provide graduate stu-

dents and engineering professionals

with the knowledge and skills necessary
to transfer recent developments in the
basic sciences into commercially viable
products and processes. Training of the
student is accomplished by exposing the
individual to the biology, engineering,
and business concepts critical to succeeding in the biomedical research and
development environment.
Training in Biomedical Engineering is
directed by faculty from the College of
Engineering and Applied Sciences, School
of Medicine, College of Arts and Sciences,
Health Sciences Center, as well as from
Brookhaven National Laboratory and
Cold Spring Harbor Laboratory. These
diverse faculty provide a spectrum of
research opportunities. Breadth and
depth of exposure is a hallmark of the program, and one which we believe emphasizes the importance of multidisciplinary,
collaborative approaches to real-world
engineering problems in biology and medicine. Graduate training includes course
instruction, participation in seminar
courses, and extensive involvement in
selected projects emphasizing synthesis
and design skills. The graduate program is
based in the Health Sciences Center, adjacent to University Hospital, and in close
proximity to the Basic Sciences,
Engineering, and Business Schools.

E. Graduate Record Examination

(GRE) General Test scores;

Admission

Chiang, Fu-Pen, Ph.D., 1966, University of

Florida: Development and application of various
optical techniques such as moir, holographic,
interferometry, and speckle interferometry for
stress analysis; nondestructive evaluation and
metrology.

Students may matriculate directly into

either the M.S. or Ph.D. programs. For
admission to the Program in Biomedical
Engineering, the following are normally
required:
A. A four-year undergraduate degree
in engineering or related field such as
the physical sciences or mathematics;

F. Acceptance by both the Program

and the Graduate School.
Stipends and tuition scholarships
are available for selected students.
Distribution of these awards will be based
on GRE test scores, undergraduate performance, professional experience, and
research/career objectives as outlined in
a personal statement.

Faculty
Distinguished Professors
Chu, Benjamin, Ph.D., 1959, Cornell University:
Synthesis; characterization and processing
of biomaterials; molecular manipulation and
self-assembly in biomimetic mineralization;
DNA complexation for gene therapy.
Rafailovich, Miriam, Ph.D., 1980, University at Stony
Brook: Polymeric liquids; phase transitions; thin film
wetting phenomena; biopolymers.
Rubin, Clinton, T., Chair, Ph.D., 1983, Bristol
University: Tissue adaptation; biophysical treatment of musculoskeletal disorders.

Professors
Benveniste, Helene, Ph.D., 1991, University
of Copenhagen, Denmark: Understanding
diagnostic MR contrast parameters suitable to
visualize neuro-pathology in neurodegenerative
diseases.
Brink, Peter, Ph.D., 1976, University of Illinois:
Biophysical properties of gap junction properties.

Chon, Ki, Ph.D., 1993, USC Los Angeles:

Signal processing; development of novel
algorithms to understand dynamic processes.
Clark, Richard, M.D., 1971, University of
Rochester: Tissue engineering in wound repair.

B. An official transcript of undergraduate record and of any work completed at

the graduate level;

Cohen, Ira, M.D., Ph.D., 1974, New York

University: Electrophysiology of the heart.

C. Letters of recommendation from

three previous or current instructors/
employers;

Fowler, Joanna, Ph.D., 1967, University of

Colorado: Radiotracer synthesis with
positron emitters.

D. Submission of a personal statement

outlining your background, interests,
and career goals in the field of
biomedical engineering;

Grine, Fred, Ph.D., 1984, University of the

Witwatersrand, Johannesburg, South Africa:
Tooth enamel thickness and structure and the
stresses experienced by tooth enamel during
masticatory loading in primates.

Djuric, Petar, Ph.D., 1990, University of Rhode

Island: Acoustic signal processing.

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Hannon, Gregory, Ph.D., 1992, Case Western

Reserve University: Explores the mechanisms
and regulation of RNA interference as well as
its applications to cancer research.
Harrington, Donald, M.D., Ph.D., 1966,
Marquette University: Magnetic Resonance
Imaging in medicine.
Hsiao, Benjamin, Ph.D., 1987, Institute of
Materials Science at University of Connecticut:
Structural and morphological development of
complex polymer systems during preparation
and processing in real time.
Hurst, Lawrence C., M.D., 1973, University of
Vermont: Etiology of carpal tunnel syndrome;
etiology of Dupuytrens contracture.
Jacobsen, Chris, Ph.D., 1988, Stony Brook
University: X-ray microscopy and holography.
Jesty, Jolyon, Ph.D., 1975, Yale University:
Control mechanisms of coagulation, experimental and theoretical analyses.
Kaufman, Arie E., Ph.D., 1977, Ben-Gurion
University: Computer graphics; visualization;
interactive systems; 3-D virtual colonoscopy;
computer architecture.
Krukenkamp, Irwin B., M.D., 1982, University
of Maryland: Systolic and diastolic mechanics
and myocardial oxygen consumption.
Liang, Jerome, Ph.D., 1987, City University of
New York: Development of medical imaging
hardware for single photon detection.
Mathias, Richard, Ph.D., 1975, UCLA:
Research in biophysics seeks physical
insights into how cells and tissues function.
Moore, Leon, Ph.D., 1976, University of
Southern California: Renal physiology.
Qin, Yi-Xian, Ph.D., 1997, Stony Brook
University: Physical mechanisms involved in
the control of tissue growth, healing, and
homeostasis, especially bone adaptation
influenced by mechanical environment.
Reichek, Nathaniel, M.D., 1965, Columbia
University: Cardiac Magnetic Resonance Imaging;
myocardial mechanics, perfusion, viability.
Stein, Lincoln, Ph.D., 1989, Harvard
University: Genome informatics; developing
databases, data-analysis tools, and user
interfaces to organize, manage, and visualize
that vast body of information.

Associate Professors
Bluestein, Daniel, Ph.D., 1992, Tel Aviv
University, Israel: Dynamics of fluid flow and
cellular transport through vessels.
Button, Terry, Ph.D., 1989, University at
Buffalo: High-resolution computer-aided
tomography.
Chen, Weiliam, Ph.D., 1993, University of
Michigan: Controlled release biodegradable
DNA delivery vehicles for gene therapy; innovative drug delivery systems.
Dilmanian, F. Avraham, Ph.D., 1980,
Massachusetts Institute of Technology:
Computed tomography; radiation therapy.

94

Entcheva, Emilia, Ph.D., 1998, University of

Memphis: Cardiac bioelectricity, electrical
stimulation of cardiac tissue, mechanisms of
cardiac arrhythmias, defibrillation and modulation of cell function through gene transfer.
Frame, Molly, Ph.D., 1990, University of
Missouri: Microvascular flow control at the
fluid dynamic and molecular levels.
Gindi, Gene, Ph.D., 1982, University of Arizona:
Algorithm development for medical imaging.
Hadjiargyrou, Michael, Ph.D., 1992, City
University of New York: Molecular mechanisms
of bone development and regeneration.
Judex, Stefan, Ph.D., 1999, University of
Calgary, Canada: Molecular bioengineering;
mechanical, molecular, and genetic influences
on the adaptation of bone and connective
tissues to physiologic stimuli.
McCombie, Richard, Ph.D., 1982, University
of Michigan: Structure and function in
complex genomes.
Pan, Yingtian, Ph.D., 1992, National Laser
Technology Laboratories, China: Optical/NIR
spectroscopy and imaging methods and
applying these techniques to provide clinical
diagnostic information.

University: cDNA microarrays, functional

genomics technologies; translational research.
Goldstein, Rita, Ph.D., 1999, University of
Miami: Multidisciplinary approach to measure
brain function such as functional (fMRI),
(PET), (ERP) recordings, and neuropsychology.
Miura, Michiko, Ph.D., 1984, University of
California, Davis: Drug delivery methods;
developing new boron-carriers for BNCT.
Mujica-Parodi, Lilianne, Ph.D., 1998, Columbia
University: Relationships between four simultaneously or near-simultaneously interacting
systems: neural, cardiac, endocrine, and
cognitive, to better understand the neurobiology
of arousal, fear, and stress.
Neuwald, Andrew, Ph.D., 1987, University of
Iowa: Statistical and algorithmic methods with
their application to the classification and
modeling of protein domains.
Rizzo, Robert, Ph.D., 2001, Yale University:
Application of computational techniques to
drug discovery.
Schlyer, David, Ph.D., 1976, University of
California, San Diego: Cyclotron targetry development; nuclear cross-section measurement;
biomedical imaging technology.

Powers, Scott, Ph.D., 1983, Columbia

University: Cancer gene discovery; cancer
diagnostics and therapeutics; cancer biology.

Sitharaman, Balaji, Ph.D., 2005, Rice University:

Research related to related to the diagnosis/
treatment of disease and tissue regeneration.

Mueller, Klaus, Ph.D., 1998, Ohio State

University: Computer graphics, data
visualization, medical imaging.

Strey, Helmut, Graduate Program Director, Ph.D.,

1993, Technical University, Munich:
Nanostructured materials for applications in
bioseparation, drug delivery and biosensors.

Rastegar, Jahangir, Ph.D., 1976, Stanford

University: Robotics; biomechanics.
Reinitz, John, Ph.D., 1988, Yale University:
Generation of body form, specifically the
determination of morphogenetic fields.
Skiena, Steven, Ph.D., 1988, University of
Illinois: Computational geometry; biologic
algorithms.
Solomon, Irene, Ph.D., 1994, University of
California at Davis: Reflex and central neural
control of cardiovascular and respiratory function.
Simmerling, Carlos, Ph.D., 1994, University of
Illinois, Chicago: Simulate known properties of
molecules, assist in the refinement and
interpretation of experimental data.
Stein, Lincoln, M.D., Ph.D., 1989, Harvard
Medical School and University: Proactive
approach to the genome information explosion
by developing databases, data-analysis tools,
and user interfaces to organize, manage, and
visualize that vast body of information.
Zhang, Michael, Ph.D., 1987, Rutgers
University: Identifying functional elements in
eukaryotic genomes using mathematical and
statistical methods.
Zhu, Wei, Ph.D., 1996, University of California,
Los Angeles: Brain image analysis, design and
analysis of clinical trials and other biomedical
studies, and genetics modeling.

Assistant Professors
Dhundale, Anil, Ph.D., 1987, Stony Brook

Wagshul, Mark, Ph.D., 1992, Harvard University:

Utilizing MRI techniques for better understanding,
diagnosing, and treating disease.
Zhao, Wei, Ph.D., 1997, University of Toronto,
Canada: Development of novel detector concept
and new clinical applications for early detection
of cancer.
Zhong, Zhong, Ph.D., 1996, Stony Brook
University: Medical imaging and diagnosis
using monochromatic X-rays, X-ray phase
contrast, and X-ray optics.

Research Faculty
Ding, Yu-Shin, Ph.D., 1987, Stony Brook
University: Investigation of biochemical transformations and drug mechanisms in primates
and humans.
Gatley, John, Ph.D., 1975, University of
Newcastle-upon-Tyme, England: Medical
radionuclide imaging.
Goldfarb, James, Ph.D., 2000, Catholic
University of Nijmegen: Application of
magnetic resonance imaging (MRI) to the
cardiovascular system, particularly in the areas
of myocardial function and blood vessels.
Hainfeld, James, Ph.D., University of TexasAustin: Development of organometallic cluster
compounds to be used as high resolution
molecular labels.
Kolsky, Kathryn, Ph.D., 1989, Carnegie Mellon
University: Development and production of

BIOMEDICAL ENGINEERING

radioisotopes using the BLIP facility, a highenergy charged particle accelerator.

Logan, Jean, Ph.D., 1976, Louisiana State
University: Kinetic modeling of data from PET
experiments.
Miller, Lisa, Ph.D., 1995, Albert Einstein
College of Medicine: Chemical makeup of
tissue in disease using high-resolution infrared
and X-ray imaging.
Pena, Louis, Ph.D., 1991, University of
California, Los Angeles: PET probes to detect
the upregulation of cytokine receptors.
Thanos, Peter, Ph.D.: Gene therapy and
dopaminergic mechanisms of alcohol and
drug abuse.
Tracey, Kevin, M.D., 1983, Boston University:
Research focuses on the roles of individual
mediators of systemic inflammation, and their
regulation by interactions between the brain
and the innate immune system.
Vaska, Paul, Ph.D., 1997, Stony BrookUniversity:
Instrumentation for positron emission tomography.
Vazquez, Marcelo, M.D., Ph.D., 1990,
National University of La Plata, Argentina:
Study of the mechanisms of central nervous
system damage induced by space radiation
using in vitro (neural stem cells and neurons)
and in vivo models.
Wang, Yi, ScD., 1999, Washington University,
St. Louis: Noninvasive in vivo cardiovascular
imaging for the heart functional and morphological assessment using magnetic resonance
imaging and image processing techniques.

Degree Requirements
Requirements for the M.S. Degree
A minimum of 31 graduate credits are
required to earn the Master of Science
in BME (non-thesis option) or 37 credits
for the M.S. degree (thesis option).
The program of study can be chosen from
any of the following approved tracks/
specializations: Biomechanics, Biosignals,
General, Medical Physics, or Molecular
Bioengineering. The General program of
study can be custom tailored in consultation with a students faculty advisor/mentor to accommodate almost any BME
area of interest. The following courses
must be taken by all first-year graduate
students:
BME 501 Molecular Principles in Cell
Biology;
BME 502 Advanced Numerical and
Computation Analysis to Biological
Systems;
BME 505 Principles and Practice of
BME;
BME 520 Laboratory Rotation I; and
BME 521 Laboratory Rotation II.

All students (except those pursuing the

Medical Physics Track) must also fulfill a
business/management course requirement, which can be met by taking BME
509 Fundamentals of the Bioscience
Industry, or any MBA class (MBA 501 to
507, 511, or 589) from the School of
Business. A given track/specialization
will have additional requirements, which
includes a minimum of six technical
elective courses (three or which have to
be BME).
Thesis or Non-Thesis Options
The student has the option of earning
the Master of Science Degree in BME
on either a thesis or non-thesis track. If
non-thesis, the student undertakes elective graduate coursework to complete
the 31 credits. In the thesis option, the
student must additionally complete six
credits of BME 599 Thesis Research and
submit and defend a written thesis. A
grade point average of B or better must
be attained for the core BME courses
taken, and an overall grade point average of 3.0 out of 4.0 must be maintained.
For the non-thesis option, most students
can complete this program within three
academic semesters, and most students
complete the thesis option in four academic semesters. The non-thesis option
is recommended for students who wish
to pursue a career in industry that does
not involve research and development.
Students pursing the non-thesis option
cannot use BME 599 to fulfill any
requirements (i.e., it is not a technical
elective nor core course). The thesis
option is recommended for students who
will be continuing on for their doctoral
degree and for students who wish to
pursue an industrial career with an
R&D focus. All BME students must also
take GRD 500.

Requirements for the Ph.D. Degree

A. Completion of the M.S. degree in
Biomedical Engineering or equivalent
graduate program
B. Satisfactory completion of the BME
qualifying exam
C. Plan of Study
Students matriculating into the doctoral
(Ph.D.) degree program must complete
all the requirements for the M.S. degree
in BME at Stony Brook or enter the
program with a relevant M.S. degree.
This latter option is termed admission
with Advanced Standing. After completion of the M.S. degree or admission

with Advanced Standing, there are no

course requirements per se, though certain courses may be required to fill any
gaps in the students knowledge.
Following completion of a qualifying
exam, an independent basic research program will be undertaken. Subsequently,
the student will present and defend his or
her dissertation proposal. Successful
completion of this stage will enable the
student to Advance to Candidacy. One
semester of teaching practicum must be
satisfactorily performed. Completion of
the research program will culminate in
the submission and oral defense of a
doctoral dissertation. The University
requires at least two consecutive
semesters of full-time graduate study.
D. Teaching Requirements
The BME teaching requirement for
the Ph.D. degree can be fulfilled in any
of the following three manners:
1. Deliver four lectures in a BME
undergraduate or graduate course and
present a seminar that covers the stateof-the-art in your field of research.
2. Teach a BME course, either as the
instructor of record (if you have G5
student status) or as the principal
instructor (for G4 student status).
3. Petition for something else that is
equivalent to the above.
E. Thesis Proposal Examination
After successful completion of the qualifying examination, the student selects a
thesis advisor and writes a proposal for
thesis research. After approval by the
thesis advisor, the proposal is orally
defended before a thesis committee.
F. Advancement to Candidacy
After successful completion of all
required and elective courses, the qualifying examination, and the thesis proposal examination, the student will be
recommended to the Graduate School
for advancement to candidacy.
G. Dissertation
The research for the Ph.D. dissertation
is conducted under the supervision of the
thesis committee. The dissertation must
represent a significant contribution to the
scientific and/or engineering literature.
Upon approval of the completed dissertation by the thesis committee, a formal
public oral defense of the dissertation is
scheduled at which the student presents
his or her findings and is questioned by
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BIOMEDICAL ENGINEERING

members of the examining committee and

by other members of the audience. On
acceptance of the dissertation by the thesis
committee, all requirements for the
degree will have been satisfied.
H. Time Limit/Residency Requirements
All requirements for the Ph.D. degree
must be completed within seven years
after completing 24 credits of graduate
study. The University requires at least
two consecutive semesters of full-time
graduate study.

Courses
The goal of the Program in Biomedical
Engineering is to promote actively the
development of a versatile engineering
graduate. This requires that the engineering student understand biological
concepts as well as engineering concepts
outside of his or her defined major. The
core set of biomedical engineering courses
will expose the biomedical engineering
student to the principles of cell, tissue,
and organ biology, as well as ensure that
the students attain a credible level of
sophistication in the engineering and
basic science concepts that lie outside of
their major, and which traverse multiple
areas of biomedical engineering.
BME 501 Engineering Principles in Cell,
Tissue, and Organ Systems
Course content is directed toward describing
the microscopic physical interactions between
cells and their environment as electromechano-chemical processes occurring at surfaces. This is provided in the context of basic
molecular biology and cell physiology concepts.
Emphasis is placed on developing of the critical
role of non-linear dynamics, physical chemistry
of adsorption and desorption processes, self
assembly in cellular automata, and how complexity arises within simple physical systems.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 502 Advanced Numerical and

Computation Analysis Applied to Biological
Systems
Numerical analyses of biological data. A
unified mathematical/time series framework
for modeling and mining biological data.
Applications range from cardio-respiratory,
renal blood pressure/flow and sequence
(DNA, RNA, proteins) to gene expression
data. Tools of data analysis include linear
algebra, interpolation and extrapolation,
parametric and nonparametric spectral estimation with the FFT and singular value
decomposition, statistical description of data
and integration of ordinary differential equations. Special focus will be placed on the use
of linear and nonlinear numerical methods for
the identification of physiological system
dynamics and the development of computer
simulation techniques to study dynamic

96

response of physiological systems.

Spring, 3 credits, ABCF grading
May be repeated once for credit

BME 503 Cell and Molecular Imaging

This course will cover basics of optics,
microscopy, spectroscopy, and fluorescence in
the context of imaging at the cellular and
molecular level. Recently developed advanced
imaging techniques for probing protein
interactions and live cell functions are also
discussed. The course is organized into three
modules: optics and spectroscopy (e.g., properties of light, polarization, diffraction, spectra);
fundamentals of fluorescence and applications
to molecular and cellular measurements (e.g.,
Jablonsky diagram, Stokes shift, emission,
excitation spectra, fluorescence anisotropy);
and signal processing, image analysis techniques, and scientific visualization (e.g.,
temporal and spatial filters, 1D and 2D Fast
Fourier transform, spectral analysis, crosscorrelation). Theory will be complemented
by extensive use of Matlab and its Image
Processing Toolbox.
Fall, 3 credits, ABCF grading

BME 504 Biomaterials Science and Analysis

Course content is directed toward providing an
introductory treatment of the engineering
issues implicit in understanding living
tissue interactions with processed materials.
Emphasis on identifying and eliminating surface contamination, corrosion, and optimizing
material surface properties and compatibility.
Spring, 3 credits, ABCF grading

BME 505 Principles and Practice of

Biomedical Engineering
Introduces first-year students to the basic
and clinical research at the cutting edge of
biomedical engineering. The course has two
key components. The first is a seminar
series presented by internationally renowned
bioengineers. An interactive discussion of
topic-specific scientific literature precedes the
formal presentation. The second component of
the course is teaming up with a physician in
rounds, the operating theater, clinics, etc., to
get exposure to the real-life problems that
face the medical community. It is hoped that
the mix of science and clinic will move students toward determining how they can make
contributions to health and society.
2 credits, ABCF grading

BME 506 Principles and Practice of BME

The goal of this course is to expose students
to the cutting edge of biomedical engineering,
including the clinical challenges that arise in
this discipline. The course has two key components. The first is a seminar series presented
by internationally renowned bioengineers,
including Stony Brook faculty, which cover
areas such as biomechanics, medical imaging,
biomaterials, tissue engineering, drug/medical device development, bioinformatics, and
functional genomics. Topics related to the
impact of technology on medicine are also
addressed, including ethics. An interactive
discussion of topic-specific scientific literature
precedes the formal presentation. The second
component of the course is teaming up with a
physician in rounds, the operating theatre,
clinics, etc., to get exposure to the real-life

problems which face the medical community.

It is hoped that the mix of science and clinic
will move students toward determining how
they can make contributions to health and
society. Required course for BME M.S. and
Ph.D. students.
Fall and spring, 1 credit, ABCF grading

BME 507 Fundamentals of Biomedical

Engineering Management
This course exposes the engineering student to
the responsibilities that focus on the management issues in biomedical engineering.
Management functions are explored and the
students learn how to integrate these functions
with engineering responsibilities.
Fall, 3 credits, ABCF grading

BME 508 Molecular and Cellular

Biomechanics
Course content revolves around the effects and
interactions of mechanical forces at the cellular
and molecular level. The topics will range from
describing the molecular and cellular basis of
the adaptation of tissues to physical signals, to
prescribing specific mechanical environments
for improved tissue engineering, to delineating
relevant molecular, cellular, and biomechanical
techniques, all the way to issues involved in the
development and approval of diagnostics and
therapeutics in molecular engineering. For
a deeper understanding of the course material
as well as to allow students to apply their
newly gained knowledge, this course will
contain a module on the design and analysis
of experiments (i.e., applied biostatistics)
and incorporate practical exercises in both
laboratory (e.g., a real-time PCR experiment)
or simulated computer settings (e.g., modeling
of cell behavior).
Prerequisite: BME 501 or permission of
instructor
Fall and spring, 3 credits, ABCF grading
May be repeated once for credit

BME 509 Fundamentals of the Bioscience

Industry
A four-module course set up to provide students with a comprehensive introduction to
the complexities of the bioscience business
environment.
Prerequisite: Must be either a BME or M.B.A.
graduate student (West Campus). All other
students must obtain permission from the
instructor
Spring, 3 credits, ABCF grading

BME 510 Biomechanics

This course emphasizes the application of
continuum mechanics to living tissues and
organs to describe the material properties
and their behavior under loading and stress.
The interrelationship between biomechanics
and physiology is examined in normal function
and in disease processes. This course focuses
on the physiology of tissue and organ systems
in the context of mechanics, stress, strain,
viscoelasticity, and material behavior, and the
constitutive equations and the field equations
governing fluids and fluid flow, with an
emphasis on the cardiovascular and musculoskeletal systems. Emphasis is placed on
the utilization of engineering principles to
analyze processes at the tissue and organ

BIOMEDICAL ENGINEERING

levels, covering soft and hard tissues and

organs (blood, cardiovascular system, bone,
cartilage, etc.), and to understand how these
principles could be applied towards the design
and development of prosthetic devices.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 517 Radiation Physics

This graduate offering provides an initial
physical background required for the study of
medical physics. Sources of ionizing radiation
including radioactivity (natural and manmade)
and X-ray producing devices are studied as
well as sources of nonionizing radiation such as
radiofrequency and ultrasound. The physical
aspects of these radiations are characterized
by their interaction with matter and methods
for their detection. Each student will select
and present a proposal for solving a clinical
medical physics problem.
Prerequisites: Modern physics or equivalent
Fall, 3 credits, ABCF grading

BME 518 Radiobiology

The biological consequences of irradiation
(ionizing, ultrasound, laser, RF, etc.) will be
examined. Interaction mechanisms will first be
examined followed by examination of the radiation impact at the molecular and cellular level.
The use of radiation for therapeutic gain will be
considered. As well, models will be developed
for risk estimates. Topics to be covered will
include target theory, biological response,
NSD, and risk estimates.
Spring, 3 credits, ABCF grading

BME 519 Medical Health Physics

This course discusses the health physics and
safety issues associated with radiological
devices, facilities, and procedures.
Prerequisite: BME 517
Spring, 3 credits, ABCF grading
May be repeated once for credit

BME 520 Lab Rotation I

1-3 credits, S/U grading

BME 521 Lab Rotation II

1-3 credits, S/U grading

BME 525 Tissue Engineering

Course deals with basics of biomaterial formulation that are relevant to tissue engineering,
leading to the principles and practice of
designing an engineered tissue, which will be
facilitated by a design project.
Spring, 3 credits, ABCF grading
May be repeated once for credit

BME 526 Biological Systems Engineering

This course is a hands-on study of systems
engineering in biology, using computer modeling to conceptualize and simulate a wide
variety of applications. Computer wizardry
not required; all skills taught in class.
Appropriate and applicable to all BME tracks.
Fall, 3 credits, ABCF grading
May be repeated once for credit

hardware, and performance characteristics

are considered.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 531 Biosensing and Bioimaging

Basic concepts of biosensing and bioimaging,
which include the elements of biological systems and bioimmobilizers, traditional electrode
and novel optical transducers, and advanced
biomedical optical imaging systems.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 532 Time Series Modeling of Biological

Systems
A unified mathematical/time series framework
for modeling and mining biological data.
Applications range from cardio-respiratory,
renal blood pressure/flow and sequence (DNA,
RNA, proteins) to gene expression data. Tools
of data analysis include neural networks, timeinvariant and time-varying spectral methods,
fractal and nonlinear dynamics techniques, hidden markov model, clustering analysis, and
various system identification techniques.
Spring, 3 credits, ABCF grading

BME 534 Functional Genomics

Course provides foundation in concepts of
functional genomics and proteomics. Topics
include organization and complexity of the
mammalian genome and mechanisms of
expression of genes, gene expression analysis
technologies with a strong focus on construction and utilization of DNA microarrays, and
tools for determining gene function by perturbation of gene expression.
Spring, 3 credits, ABCF grading
May be repeated once for credit

BME 540 Radiation Oncology Physics

This course provides a background in therapeutic instrumentation, dosimetry, and treatment planning.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 546 Statistical Analysis of

Physiological Data
Statistical methods useful in analyzing common types of physiological data. Topics include
probability, data distributions, hypothesis
testing, with parametric and non-parametric
methods, ANOVA, regression and correlation,
and power analysis. Emphasis is on experimental design and appropriate and efficient
use of statistical software.
Prerequisite: Permission is required
1 credit, ABCF grading

BME 547 Model-Based Analysis of

Physiological Data
The analysis of common biochemical and
physiological data by non-linear regression of
data models and biophysical models of physiological and biochemical processes. Examples
include binding kinetics, compartmental mass
transfer, and spectral analysis.
Prerequisite: Permission is required
1 credit, ABCF grading

BME 530 Medical Image Formation

This course covers the physical aspects of medical image formation. Image receptor design/
optimization, reconstruction techniques, device

BME 548 Measurement and Analysis in

Physiological Research
The acquisition and analysis of data-arising

from common biochemical and physiological

measurements. Topics include computer-based
data acquisition and processing, densitometry,
microscopy, and image analysis and processing.
Emphasis is on experimental design and
strategies for optimizing signal to noise ratio of
measurements.
1 credit, ABCF grading

BME 549 Experimental Techniques in

Systems Physiology
A series of lectures and laboratory exercises
designed to introduce students to in vitro
experimental techniques used in systems physiology. Emphasis will be placed on the ethical
use of rodents in biomedical research and the
measurement of physiological variables. Data
acquisition and analysis procedures used in
cardiovascular, respiratory, and neural and
renal physiology will also be covered.
Prerequisite: permission is required
1 credit, ABCF grading

BME 550 Mathematical Models of

Physiologic and Biophysical Systems
An introduction to mathematical modeling of
cell and tissue function. Topics include the
derivation and numerical solution of models of
cell homeostasis, membrane transport and
excitability, and cell signaling and metabolism.
Grading is based on problems, student presentation, and completion of a modeling project.
Prerequisite: Permission is required
3 credits, ABCF grading

BME 571 Microfluids in Biological Systems

This course will outline theory and applications
of special fluid handling conditions associated
with living systems.
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 572 Biomolecular Analysis

This interdisciplinary course is intended for
graduate students and advanced undergraduates in departments such as Biomedical
Engineering, Chemistry, Physics, Biology, and
Chemical Engineering. This course will give an
introduction to single molecule experiments
using fluorescence, optical traps, AFM cantilevers, microneedles, and magnetic microbeads as well as micro and nanofluidic devices.
Prerequisite: BME 501 and 502, or instructor
approval
Fall, 3 credits, ABCF grading
May be repeated once for credit

BME 599 Biomedical Engineering Research

Research to be supported by a faculty member
of the Department of Biomedical Engineering.
Students must have permission of instructor
and enroll in appropriate section. Faculty to be
identified by the student.
Fall and spring, 1-9 credits, S/U grading
May be repeated for credit

BME 601 Cardiovascular Fluid Mechanics

The course will cover the application of fluid
mechanics principles to the analysis of blood
flow in the cardiovascular system under
normal and pathological conditions. It will
follow an historical time line by beginning with
the most basic models of arterial blood flow,
and proceed to the most advanced theories

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related to physiology and pathology flow

phenomena, including an examination of the
most up-to-date research in the area and the
development of devices and implants.
Spring, alternate years, 3 credits, ABCF grading

BME 602 Topics in Biomedical Applications

of Neural Networks
This is a project-based course that includes
weekly seminars discussing advanced topics in
fuzzy logic and neural networks and their
applications in biomedical devices. Applications
include drug delivery, diagnostics, and management information handling. Students utilize
simulation software to develop algorithms to
deal successfully with training data sets of
their own choosing.
Fall, alternate years, 3 credits, ABCF grading

BME 604 Finite Element Modeling in Biology

and Medicine
Both finite difference and FEM are applied to
solve the equations of incompressible and compressible fluid flow in porous media with
emphasis on flows in skeletal tissues, i.e., bone
and cartilage. Steady-state, transient flow, permeability, and surface boundary conditions are
discussed. Practical and recent studies in the
field are also discussed. Programming using
FORTRAN or C languages will be required.
The student is also introduced to commercially
available software packages.
Spring, alternate years, 3 credits,
ABCF grading

BME 605 Biomechanics of Tactile Sensory

Systems
Detailed study of the biomechanics of tactile
neurophysiology for engineers entering the
field of haptics and robotics manipulations.
Anatomy and electrophysiology of transducer
cells and neurons starting at the fingertips
and extending to the somatosensory cortex.
Characteristics of the external stimulus and
its peripheral transformation. Relations of
these topics to perceptual and/or behavioral
responses.
Spring, alternate years, 3 credits,
ABCF grading

BME 606 Drug Gene Delivery

Applications of biodegradable and biocompatible polymers in the design of drug and
gene delivery systems for site-specific
applications. A broad overview on the origin
and development of controlled release therapeutic devices will be provided. Existing and
proven commercial products will be examined.
The second half of the course will be devoted
to the use of DNA as a therapeutic entity and
issues relevant to DNA delivery will be
explored. An assessment of the most up-to-date
DNA delivery technologies will be presented.
Students are required to write a term paper on
a drug or gene delivery topics of their choice.
Students are also expected to give presentations on drug delivery and gene therapy
related topics during the course.
Fall, alternate years, 3 credits, ABCF grading
May be repeated for credit

BME 610 Magnetic Resonance

This course provides a comprehensive study of
magnetic resonance and its applications in
medical imaging. An introduction of NMR is

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followed with development of the hardware

and processing aspects required for MR image
formation. An overview of basic and advanced
MR imaging techniques is provided. Each
student will select a topic in MR imaging for
presentation at the conclusion of the course.
Fall, 3 credits, ABCF grading
May be repeated for credit

BME 612 Biomedical Engineering Aspects for

the Use of Radiation in Medicine
This course provides a comprehensive study of
the use of radiation in medicine. Physical
aspects of the interaction of radiation with
matter and for the radiation production are
initially considered. The underlying principles
of current radiation-based medical imaging is
considered next. Topics include radiography,
fluoroscopy, radionuclide imaging, and computed tomography. The use of radiation for the
treatment of malignancy is considered with the
focus on required technology. Finally, advanced
applications of radiation are considered with
focus on imaging and treatment. Each student
will select a topic examining the engineering or
technical application of radiation in medicine
for presentation at the conclusion of the course.
Spring, 3 credits, ABCF grading

BME 615 Clinical Nuclear Imaging

This course is designed to prepare the Medical
Physics graduate student in the area of clinical
medical imaging. In this clinical rotation, medical physics methods for planar film, DR, CR,
mamography, fluoroscopy, CT, ultrasound, and
MRI performance evaluations will be introduced. In addition, basic medical ethics, radiographic anatomy, and radiation safety will be
covered. A total of 200 clinical hours will be
completed in this program.
Prerequisites: BME 517; BME 518; BME
519; BME 530 or BME 540
Fall, every year, 4 credits, S/U grading
May be repeated once for credit

BME 616 Clinical Nuclear Medicine Imaging

This course is designed to prepare the
Medical Physics graduate student in the area
of clinical nuclear medicine imaging. In this
clinical rotation, the students will be exposed to
radionuclide processes, radiopharmaceuticlas
including radioactive gases and aerosolsprepartio, characteristics and radiation
dosimetry, in vitro and in vivo radiation
detection systems, and imaging systems and
their performance evaluations. In addition,
basic medical ethics, clinical interpretations,
and radiation safety will be covered. A total
of 150 clinical hours will be completed in this
program.
Fall, every year, 4 credits, S/U grading
May be repeated once for credit

BME 617 Clinical Radiation Oncology Physics

This course is designed to prepare the Medical
Physics graduate student in the area of clinical
radiation oncology physics. In this clinical
rotation, the student will learn by observation
and participation some of a selection of the
following medical physics procedures: LINAC
Beam Dosimetry (ion chamber measurement
techniques), film dosimetry (radiographic and
radiochromic), diode dosimetry, TLD dosimetry, water phantom scanning, implementation
of photon and electron beam calibration

protocols (AAPM TG51), LINAC beam data

measurement and tabulation, commissioning
a TPS system, LINAC, acceptance testing,
LINAC monthly QA, HDR QA and planning,
and IMRT inverse planning and IMRT clinical
QA. A total of 120 clinical hours will be
completed in this program.
Prerequisite: BME 517 and BME 540 with a
B+ or better
Spring, every year, 4 credits, S/U grading

BME 620 Space Radiation Biology

An extensive series of lectures, training
sessions, and laboratory activities sponsored
by NASAs Radiation Health Program in
collaboration with BNL. The material is
oriented to cover basic and state-of-the-art
concepts in space radiation environment,
physics, and radiobiology. Content includes
basic concepts in physics, dosimetry, radiobiology, space radiation problems, and accelerator
operations. Concurrent sessions are provided
to complete specific BNL training and plan
and prepare experiments for low- and highLET radiation exposures. Students are
trained in NSRL operations and are able to
run control experiments using gamma rays in
preparation for NSRL runs, and subsequently,
experiments at the NSRL using heavy ions.
Data obtained from different endpoints are
discussed and analyzed with the instructors.
Homework is used to test the students level
of comprehension of the lectures and laboratory activities. The write-up of a full BNL
beam time request proposal is required of
each student.
4 credits, ABCF grading

BME 690 Biomedical Engineering Research

Biomedical engineering research for doctoral
students who have already received their
M.S. degree, but have not yet advanced to
candidacy.
Fall and spring, 1-9 credits, ABCF grading
May be repeated for credit

BME 698 Practicum in Teaching

Undergraduate teaching to be supervised by a
faculty member of the program in Biomedical
Engineering. Course to be identified by the
student and graduate studies director.
Fall and spring, 1-3 credits, S/U grading
May be repeated for credit

BME 699 Dissertation Research On Campus

Prerequisite: Students must be advanced to
candidacy (G5); permission of instructor and
enroll in appropriate section; major portion
of research must take place on SB campus, at
Cold Spring Harbor, or at Brookhaven
National Lab
Fall, spring, and summer, 1-9 credits,
ABCF grading
May be repeated for credit

BME 700 Dissertation Research Off

CampusDomestic
Prerequisite: Must be advanced to candidacy
(G5); major portion of research will take
place off campus, but in the U.S. and/or
U.S. provinces (Brookhaven National Lab
and Cold Spring Harbor Lab are considered
on campus); all international students

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must enroll in one of the graduate student

insurance plans and should be advised
by an International Advisor
Fall, spring, summer, 1-9 credits,
S/U grading
May be repeated for credit

BME 701 Dissertation Research Off

CampusInternational
Prerequisite: Must be advanced to candidacy
(G5); major portion of research will take
place outside of the U.S. and/or U.S.
provinces; domestic students have the option
of the health plan and may also enroll in
MEDEX; international students who are in
their home country are not covered by
mandatory health plan and must contact the
Insurance Office for the insurance charge to
be removed; international students who are
not in their home country are charged for the
mandatory health insurance (if they are to be
covered by another insurance plan, they must
file a waiver by the second week of classes;
the charge will only be removed if the other
plan is deemed comparable); all international
students must receive clearance from an
International Advisor
Fall, spring, summer, 1-9 credits, S/U grading
May be repeated for credit

BME 800 BME Research

O credit, S/U grading
May be repeated

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