NYCCS/Computer Science Seminar
Carlos Simmerling, Tuesday, October 14, 2008
Carlos Simmerling, SBU - Functional Motions of Proteins Studied through Molecular Dynamics
Experimental methods have been highly successful in determining
3-dimensional biomolecular structures. However, most approaches
provide only time- and ensemble-averaged data, making it much more
difficult to study the dynamic and energetic aspects of biological
systems. Atomic-resolution simulations are highly complementary to
experiments, and can provide data with unparalleled resolution in time
and space. Increasingly powerful supercomputers have enabled atomistic
simulations to address many important questions. However, the current
hardware trend is toward massively parallel architectures, and
traditional "brute-force" molecular dynamics simulations are unable to
scale well to the tens of thousands of processors on these machines.
This seminar will present our recent work in biomolecular simulation
algorithms, including the coupling of multiple simulations that share
information to significantly improve efficiency as compared to
uncoupled simulations. Applications include the study of protein
structure and stability as well as the modeling of slow yet
functionally important dynamics that have been inaccessible to
traditional simulations.