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Thursday, October 03

Efficient Algorithms for Computer Simulation of Molecular Dynamics in Polymers and Biopolymers

Shawn Duan, South Dakota State University, Brookings
JICS Seminar
1:00 PM — 2:30 PM, Joint Institute for Computational Sciences (Building 5100), Boardroom (262)
Contact: Angie Chance (, 865.241.0643


Abstract In computer simulation of motion behaviors associated with molecular structures in polymer and biopolymer materials, the number of atoms involved could potentially be in millions while on the temporal scale. The desired simulation runs can amount to order of 1015 time steps that may overwhelm computing efficiency of the most powerful super computer. Thus efficient algorithms are indispensible in such simulation applications. Two efficient algorithms have been developed for computer simulation of dynamics of molecular structures in polymers. The algorithms are based on placing hard constraints on the lightly-excited degrees of freedom (DOF) of an atom with high frequencies, such as inter-atomic oscillations and rotation about double bonds, so that a reduced molecular structure with rigid subsets and joints is formed. Then Kane's dynamical equations and internal coordinate method are applied to the reduced model for formation and solution of equations of motion. The first algorithm has an O(N) computational efficiency for sequential computing. The second algorithm will provide an O(log2N) computing efficiency for parallel implementation (N: total number of subsets).