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 multiple generations of 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

Ken Mackenzie

Ken develops software, and works on architectural simulation and design, for Anton. He came to DESRES from Reservoir Labs, where he worked on simulators, compilers, and runtime systems for embedded multiprocessors. Prior to that, he was as an Assistant Professor in the College of Computing at the Georgia Institute of Technology. Ken obtained a Ph.D. and S.M., both in electrical engineering and computer science, as well as an S.B. in electrical engineering, from MIT.

Timothy Palpant

Timothy is involved with simulation studies of biological systems. Timothy earned a B.S. in biology and applied mathematics from the University of North Carolina, Chapel Hill. As an undergraduate, he studied nucleosome positioning and its role in transcriptional regulation.