Fast far-field potential evaluation in multibody-based simulations of biopolymers

Mohammad Poursina, Kurt S. Anderson

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A novel algorithm to approximate the long-range potential field in multiscale simulations of biopolymers is presented. These models contain various domains including single particles, as well as regions with coarse-grained clusters in which high frequency modes of motion are suppressed. Herein, coarse-grained regions are formed via treating groups of atoms as rigid and/or flexible bodies/clusters connected together via kinematic joints, and as such, multibody dynamic techniques are used to form and solve the equations of motion. In such simulations with n particles, the evaluation of the potential field with computational complexity of O(n2), if not performed wisely, may become a bottleneck. This paper presents the approximation of the potential field due to the interaction between a charged particle and a body containing charged particles. This approximation is expressed in terms of physical and geometrical properties of the bodies such as the entire charge of the cluster and a pseudo-inertia tensor. Further, a divide-and-conquer scheme is introduced to implement the presented far-field potential evaluations. In this scheme adjacent charged bodies are combined together to form new bodies. The mathematical framework to create these new assemblies is presented. Then the potential of the resulting bodies on the charged particles which are far from them are recursively calculated.

Original languageEnglish (US)
Title of host publication9th International Conference on Multibody Systems, Nonlinear Dynamics, and Control
PublisherAmerican Society of Mechanical Engineers
ISBN (Print)9780791855966
DOIs
StatePublished - Jan 1 2013
EventASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2013 - Portland, OR, United States
Duration: Aug 4 2013Aug 7 2013

Publication series

NameProceedings of the ASME Design Engineering Technical Conference
Volume7 A

Other

OtherASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2013
CountryUnited States
CityPortland, OR
Period8/4/138/7/13

ASJC Scopus subject areas

  • Modeling and Simulation
  • Mechanical Engineering
  • Computer Science Applications
  • Computer Graphics and Computer-Aided Design

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    Poursina, M., & Anderson, K. S. (2013). Fast far-field potential evaluation in multibody-based simulations of biopolymers. In 9th International Conference on Multibody Systems, Nonlinear Dynamics, and Control (Proceedings of the ASME Design Engineering Technical Conference; Vol. 7 A). American Society of Mechanical Engineers. https://doi.org/10.1115/DETC2013-13416