ITR: Reduced Basis Methodologies for Computation, Analysis and Visualization of Bio-Molecular Simulations

William Marsh Rice University, Houston TX

Investigators

Abstract

`The PIs will investigate and develop software and computational methods to address one of the most challenging current problems in molecular dynamics (MD) simulations - large proteins, consisting of tens of thousands of atoms in solution over the physiological range of at least a microsecond of folding time. This will be accomplished using a reduced basis approach based on singular value decomposition (SVD) of the MD trajectory. The work will entail: - developing a block SVD updating scheme that will enable new trajectory information to be adjoined to a current truncated SVD approximation to a prior trajectory and avoid having to store the entire trajectory - developing, analyzing, and implementing a reduced basis integrator that will work in concert with the SVD updating scheme to compute the reduced basis simulation more rapidly - adapting the fast marching algorithms developed for latent semantic indexing to develop the rapid graphical query tools to locate sites that potentially match local structures of interest - developing the I/O support and visualization capabilities to handle the extremely large data manipulation and representation problems that will be generated The result of the research will be an efficient time integration scheme that can drastically limit storage and yet resolve detail on multiple scales. It will be demonstrated on a fully solvated protein molecule over a time scale of a microsecond, and the high order, low frequency motions will be visualized.