Zuckerman and Faeder Receive R01 Grant

Abstract:
There is a “silicon ceiling” that ultimately limits many, if not most, types of dynamical biological simulations. That is, even the world’s most powerful computers cannot generate sufficiently long simulations, whether for atomistic models of proteins or for realistic models of cell behavior.  In many cases, the key events may occur beyond simulation timescales – such as protein folding, conformational transitions of proteins, assembly of protein complexes, or transitions of cell behavior from healthy to pathological states.  We therefore propose a response to PA-14-156, “Extended Development, Hardening and Dissemination of Technologies in Biomedical Computing, Informatics and Big Data Science (RO1),”in which we will continue to enhance the “WESTPA” software package.  WESTPA is a tool for controlling other software tools: it orchestrates up to thousands of trajectories run natively by other software at any scale (e.g., Gromacs, Amber, BioNetGen, MCell) using a “weighted ensemble” strategy.  Not only does WESTPA parallelize the use of dynamics engines – but because of the statistical process by which trajectories are added and removed, WESTPA can obtain estimates of key kinetic as well as equilibrium observables in significantly less computing time than would be required in ordinary parallelization.  The aims of the proposal are to improve the ease of use and interoperability of WESTPA; to improve its performance and reliability; to demonstrate the effectiveness of WESTPA through a series of “showcase” examples from molecular to cellular scale using a variety of dynamics engines; and to improve instructional materials based on the showcase examples.

See more about WESTPA.

See the grant description on the NIH website.

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