[bioundgrd] Fwd: D.E. Shaw Research Tech Talk

[Joyce Roberge]

D. E. Shaw Research Talk

Date:           Thursday, Sep 22, 2011
Time:           5:00 PM - 7:00 PM
Location:     Building 56 (56-614)

Refreshments will be served!

About The Talk

D. E. Shaw Research is an independent research laboratory that conducts basic scientific research in the field of computational biochemistry under the direct scientific leadership of Dr. David E. Shaw.  Our group is currently focusing on molecular simulations involving proteins and other biological macromolecules of potential interest from both a scientific and a pharmaceutical perspective.  Members of the lab include computational chemists and biologists, computer scientists and applied mathematicians, and computer architects and engineers, all working collaboratively within a tightly coupled interdisciplinary research environment.

Our lab has designed and constructed a massively parallel supercomputer called Anton specifically for the execution of molecular dynamics (MD) simulations.  Each Anton computer can simulate a single MD trajectory as much as a millisecond or so in duration -- a timescale at which biologically significant phenomena occur.  Anton has already generated the world’s longest MD trajectory.

Join us for an overview of our work on parallel algorithms and machine architectures for high-speed MD simulations and a description of the simulations that have helped elucidate the dynamics and functional mechanisms of biologically important proteins.

About The Speakers

Paul Maragakis

Paul Maragakis performs molecular dynamics simulations of biomolecular systems, with a recent focus on validating the methodology of simulations through comparison with experimental data. Paul performed the research leading to his Ph.D. in physics at the Max Planck Institute of Quantum Optics. He earned a B.Sc. in physics at the Aristotle University of Thessaloniki. Prior to joining DESRES, he held a Marie Curie Fellowship while working with Martin Karplus jointly in the Departments of Chemistry of the University of Strasbourg and Harvard, where he studied the behavior of floppy, sticky, fluctuating, ever-changing proteins. His earlier work includes a postdoctoral fellowship in physics at Harvard, where he studied the electronic properties of DNA.

Thomas Mildorf

Thomas Mildorf focuses on analysis of molecular dynamics simulations and associated numerical and statistical issues. Thomas graduated from MIT with dual S.B. degrees in mathematics and biology.  In 2006, he was a William Lowell Putnam prize winner.



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