[BNC-all] reminder - Seminar on DNA Mechanics by Noel Perkins on 10/12 at 4:30

[Deborah Starewich]

All,
 
Please send the following reminder to your faculty.  Thanks
 
Mechanical Engineering Graduate Seminar
Thursday, October 12, 2006                                         4:30 p.m.
Mechanical Engineering Building, Room 161
 
LONG-LENGTH SCALE MECHANICS OF DNA USING COMPUTATIONAL ROD THEORY
 
Dr. Noel Perkins 
University of Michigan
 
Abstract 
       DNA is a long-chain biopolymer whose structure greatly influences its
function. Here, structure may refer to the geometry and stress of the
molecule and function may refer to many biological processes including
replication, gene transcription and gene repair.  For example, the
protein-induced ³looping² of certain DNA strands is a well-known mechanism
for gene regulation. In cases such as illustrated below, the structural loop
serves as a biological ³switch² that prevents transcription.  This talk will
consider DNA structures that form on scales ranging from tens of nanometers
through several microns or longer (hundreds to many thousands of base
pairs). Such ³long-length scale² structures include DNA loops and supercoils
which are simply too large to resolve using the all-atom descriptions of
molecular dynamics. Instead, we¹ll describe these structures using a
continuum model for DNA in the form of a nonlinear computational rod theory.
The formulation accounts for the elasticity of the DNA strand and its
intrinsic curvature and chiral construction (which are also
sequence-dependent). Example results will illustrate the formation of
supercoils (plectonemes) and the expected DNA loops for wild-type and
mutated forms of the Lac-repressor DNA/protein complex.
Brief Biosketch 
        Noel Perkins received his education at U. C. Berkeley where he was
awarded his B.S. (1982), M.S. (1984), and Ph.D. (1986) degrees in Mechanical
Engineering. Following a postdoctoral appointment at the Institute for Sound
and Vibration Research (Southampton, England), he joined The University of
Michigan in 1987 where he is presently an Arthur F. Thurnau Professor in
Mechanical Engineering.
       Professor Perkins' research interests include vibration analysis,
nonlinear dynamics, fluid/structure interaction, and electronic
instrumentation, topics on which he has published more than 100 technical
papers. His current research projects include the dynamics of flexible
cables, the modeling of DNA and DNA-protein complexes, the physics of fly
casting and golf, and instrumentation for sports training. Past projects
include the dynamics of engine power train systems, belt drive systems,
paper forming machinery, and tracked vehicles.
       He has served as an Associate Editor for the ASME Journal of Applied
Mechanics and is a Member of the Editorial Boards for the Journal of
Vibration and Control and for Vibroengineering.  He is a Fellow of the
American Society of Mechanical Engineers.  His contributions as a
researcher, inventor and educator have been recognized through the Academic
Challenge Award from the Technical University of Munich and ISPO, The Arthur
F. Thurnau Professorship from the University of Michigan,  The Office of
Naval Research Young Investigator Award, The SAE Ralph R. Teetor Award, The
University of Michigan Faculty Recognition Award, The General Motors
Outstanding Distance Learning Faculty Award, and the University of Michigan
Amoco Undergraduate Teaching Award.  He is also the co-founder and co-owner
of CastAnalysis, LLC which produces novel products for the sport of fly
fishing.
 
Refreshments will be served at 4:00 p.m. in room ME 254
 
 
Donna Cackley
Area Secretary
School of Mechanical Engineering
Purdue University
Ph: (765) 494-5737
 <mailto:cackley at purdue.edu>
 


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