2008-2009 Bulletin – PDF - SEAS Bulletin - Columbia University

ehind the development of cell-based tissue substitutes.
Topics include biocompatibility, biological
grafts, gene therapy-transfer, and bioreactors.
BMEN E4540y Bioelectrochemistry
Lect: 3. 3 pts. Professor Pilla.
Prerequisite: elementary physical and organic
chemistry. Application of electrochemical kinetics
to interfacial processes occurring in biomedical
systems. Basics of electrochemistry, electrochemical
instrumentation, and relevant cell and electrophysiology
reviewed. Applications to interpretation
of excitable and nonexcitable membrane phenomena,
with emphasis on heterogeneous mechanistic
steps. Examples of therapeutic devices created
as a result of bioelectrochemical studies.
BMEN E4560y Dynamics of biological
membranes
Lect: 3. 3 pts. Not given in 2008–2009.
Prerequisite: Undergraduate cell biology or BMEN
E4001. The structure and dynamics of biological
(cellular) membranes are discussed, with an
emphasis on biophysical properties. Topics will
include membrane composition, fluidity, lipid
asymmetry, lipid-protein interactions, membrane
turnover, membrane fusion, transport, lipid phase
behavior. In the second half of the semester, students
will lead discussions of recent journal articles.
BMEN E4570x Science and engineering of
body fluids
Lect: 3. 3 pts. Professor Matsuoka.
Prerequisites: General chemistry, organic chemistry,
and basic calculus. Body fluids as a dilute
solution of polyelectrolyte molecules in water.
Study of physical behavior as affected by the
presence of ions in surrounding environments.
The physics of covalent, ionic, and hydrogen
bonds are reviewed, in relation to the structure/
properties of the body fluid. Selected physiological
processes are examined in physical-chemical
terms for polymers.
BMEN E4601y Cellular electricity
Lect: 2 Lab: 3. 3 pts. Not given in 2008–2009.
Bioelectricity of the cell membrane. Basis of cell
resting voltage, voltage changes that lead to the
action potential and electrical oscillations used
in sensing systems. Laboratory includes building
electronic circuits to measure capacitance of artificial
membranes and ion pumping in frog skin.
MEBM E4702x Advanced musculoskeletal
biomechanics
Lect: 2.5. Lab: 0.5. 3 pts. Not given in 2008–2009.
Advanced analysis and modeling of the musculoskeletal
system. Topics include advanced concepts
of 3-D segmental kinematics, musculoskeletal
dynamics, experimental measurements of joint
kinematics and anatomy, modeling of muscles
and locomotion, multibody joint modeling, introduction
to musculoskeletal surgicalsimulations.
BMEN E4737x Computer control of medical
instrumentation
Lect: 2. Lab: 1. 3 pts. Not given in 2008–2009.
Prerequisite: basic knowledge of the C programming
language. Acquisition and presentation of
data for medical interpretation. Operating principles
of medical devices: technology of medical
sensors, algorithms for signal analysis, computer
interfacing and programming, interface design.
Laboratory assignments cover basic measurement
technology, interfacing techniques, use of
Labview software instrument interrogation and
control, automated ECG analysis, ultrasonic
measurements, image processing applied to
x-ray images and CAT scans.
BMEN E4738y Transduction and acquisition
of biomedical data
Lect: 2. Lab: 1. 3 pts. Not given in 2008–2009.
Data transduction and acquisition systems used
in biomedicine. Assembly of bio-transducers and
the analog/digital circuitry for acquiring electrocardiogram,
electromyogram, and blood pressure
signals. Each small group will develop and construct
a working data acquisition board, which will
be interfaced with a signal generator to elucidate
the dynamics of timing constraints during retrieval
of bio-data.
BMEN E4750y Sound and hearing
Lect: 3. 3 pts. Professor Olson.
Prerequisites: general physics sequence and two
semesters of calculus. Introductory acoustics,
basics of waves and discrete mechanical systems.
The mechanics of hearing—how sound is transmitted
through the external and middle ear to the
inner ear, and the mechanical processing of sound
within the inner ear.
CBMF W4761y Computational genomics
Lect: 3. 3 pts. Professor Leslie.
Prerequisites: Working knowledge of at least one
programming language, and some background
in probability and statistics. Computational techniques
for analyzing and understanding genomic
data, including DNA, RNA, protein, and gene
expression data. Basic concepts in molecular
biology relevant to these analyses. Emphasis on
techniques from artificial intelligence and machine
learning. String-matching algorithms, dynamic
programming, hidden Markov models, expectation-maximization,
neural networks, clustering
algorithms, support vector machines. Students
with life sciences backgrounds who satisfy the
prerequisites are encouraged to enroll.
BMEN E4810y Artificial organs
Lect: 3. 3 pts. Not given in 2008–2009.
Analysis and design of replacements for the
heart, kidneys, and lungs. Specification and realization
of structures for artificial organ systems.
BMEN E4894x Biomedical imaging
Lect: 3. 3 pts. Professor Hielscher.
This course covers image formation, methods of
analysis, and representation of digital images.
Measures of qualitative performance in the context
of clinical imaging. Algorithms fundamental to the
construction of medical images via methods of
computed tomography, magnetic resonance,
and ultrasound. Algorithms and methods for the
enhancement and quantification of specific features
of clinical importance in each of these modalities.
BMEN E4898y Biophotonics
Lect: 3. 3 pts. Not given in 2008–2009.
Prerequisite: BMEN E4894, PHYS C1403, or the
instructor’s permission. This course provides a
broad-based introduction into the field of biophotonics.
Fundamental concepts of optical, thermal,
and chemical aspects of the light-tissue interactions
are presented. The application of these concepts
for medical therapy and diagnostics is discussed.
The course includes theoretical modeling
of light-tissue interactions as well as optical medical
instrument design and methods of clinical
data interpretation.
BMEN E6003x: Computational modeling of
physiological systems
Lect: 3. 3pts. Professor Morrison.
Prerequisites: BMEN E4001-E4002 and APMA
E4200 or the equivalent. Advanced modeling and
quantitative analysis of selected molecular, cellular,
or organ systems. Four systems are analyzed,
with emphasis on biologic systems. Systems may
include muscle contraction, respiratory physiology,
nerve transmission, pharmacokinetics, circulatory
control, auditory signal processing, cell signaling,
molecular transport, excitable membranes, and
statistical data analysis.
EEBM E6020y Methods of computational
neuroscience
Lecture: 3. 4.5 pts. Instructor to be announced.
Prerequisite: BMEB W4011 or the instructor’s permission.
Formal methods in computational neuroscience,
including methods of signal processing,
communications theory, information theory, systems
and control, system identification and
machine learning. Molecular models of transduction
pathways. Robust adaptation and integral
feedback. Stimulus representation and groups.
Stochastic and dynamical systems models of
spike generation. Neural diversity and ensemble
encoding. Time encoding machines and neural
codes. Stimulus recovery with time decoding
machines. MIMO models of neural computation.
Synaptic plasticity and learning algorithms. Major
project(s) in Matlab.
BMEE E6030y Neural modeling and
neuroengineering
Lect: 3. 3 pts. Not given in 2008–2009.
Prerequisites: APMA E3101, ELEN 3202, and
ELEN-BMEN E4011, or the equivalent, or the
instructor’s permission. Engineering perspective
on the study of multiple levels of brain organization,
from single neurons to cortical modules and
systems. Mathematical models of spiking neu-
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SEAS 2008–2009