[Colloquium] Guest Speaker Announcement

[Ponda Barnes]

REMINDER!!
 
 
TTI-C Guest Speaker
 
Presented by: Toyota Technological Institute at Chicago
 
Speaker: Ron Dror
Speaker's home page: http://people.csail.mit.edu/rondror
 
 
Date: Tuesday, October 9, 2007
Time: 12:00
Location:  TTI-C Conference room, 2nd floor
 
Title: Elucidating Protein Function via Fast, Scalable Molecular Dynamics
Simulations Ron Dror, D. E. Shaw Research
 
Abstract: 
 
Although molecular dynamics (MD) simulations of biomolecular systems often
run for days to months, many events of great scientific interest and
pharmaceutical relevance occur on long time scales that remain beyond reach.
Such events include functionally important changes in protein structures,
folding of proteins to their native three-dimensional structures, and
interactions between proteins or between proteins and candidate drug
molecules.  We present several new algorithms that significantly accelerate
parallel MD simulations compared with current state-of-the-art codes.  These
methods are embodied in a newly developed MD code called Desmond that
achieves unprecedented simulation throughput and parallel scalability on
commodity clusters.  For example, on a standard benchmark, Desmond's
performance on a conventional Opteron cluster with 2K processors slightly
exceeded the reported performance of IBM's Blue Gene/L machine with 32K
processors running its Blue Matter MD code.  The ability to perform long MD
simulations quickly has allowed us to provide an atomically detailed
explanation for the mechanisms of several proteins, including the
sodium-proton antiporter NhaA.
 
This is joint work with Kevin Bowers, Edmond Chow, Huafeng Xu, Shy Arkin,
Michael Eastwood, Brent Gregersen, Morten Jensen, John Klepeis, Istvan
Kolossvary, Mark Moraes, Federico Sacerdoti, John Salmon, Yibing Shan, and
David Shaw
 
If you have any questions or would like to meet the speaker, please contact
Ponda Barnes at pondabarnes at tti-c.org.
For future TTI-C events please visit http://ttic.uchicago.edu/cal/month.php.
(TTI-C 1427 E. 60th Street, Chicago, IL).
 
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