Fast electrostatic force and moment calculations in multibody-based simulations of coarse-grained biopolymers

Mohammad Poursina, Jeremy Laflin, Kurt S. Anderson

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

3 Scopus citations

Abstract

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

Original languageEnglish (US)
Title of host publicationASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011
Pages125-135
Number of pages11
EditionPARTS A AND B
DOIs
StatePublished - Dec 1 2011
EventASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011 - Washington, DC, United States
Duration: Aug 28 2011Aug 31 2011

Publication series

NameProceedings of the ASME Design Engineering Technical Conference
NumberPARTS A AND B
Volume4

Other

OtherASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011
CountryUnited States
CityWashington, DC
Period8/28/118/31/11

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ASJC Scopus subject areas

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

Cite this

Poursina, M., Laflin, J., & Anderson, K. S. (2011). Fast electrostatic force and moment calculations in multibody-based simulations of coarse-grained biopolymers. In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011 (PARTS A AND B ed., pp. 125-135). (Proceedings of the ASME Design Engineering Technical Conference; Vol. 4, No. PARTS A AND B). https://doi.org/10.1115/DETC2011-48376