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 publicationProceedings of the ASME Design Engineering Technical Conference
PublisherAmerican Society of Mechanical Engineers
Volume7 A
ISBN (Print)9780791855966
DOIs
StatePublished - 2013
Externally publishedYes
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

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

Fingerprint

Biopolymers
Charged particles
Far Field
Potential Field
Evaluation
Simulation
Equations of motion
Tensors
Computational complexity
Kinematics
Multiscale Simulation
Multibody Dynamics
Divide and conquer
Atoms
Approximation
Inertia
Equations of Motion
Computational Complexity
Tensor
Adjacent

ASJC Scopus subject areas

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

Cite this

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

Fast far-field potential evaluation in multibody-based simulations of biopolymers. / Poursina, Mohammad; Anderson, Kurt S.

Proceedings of the ASME Design Engineering Technical Conference. Vol. 7 A American Society of Mechanical Engineers, 2013.

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

Poursina, M & Anderson, KS 2013, Fast far-field potential evaluation in multibody-based simulations of biopolymers. in Proceedings of the ASME Design Engineering Technical Conference. vol. 7 A, American Society of Mechanical Engineers, ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2013, Portland, OR, United States, 8/4/13. https://doi.org/10.1115/DETC2013-13416
Poursina M, Anderson KS. Fast far-field potential evaluation in multibody-based simulations of biopolymers. In Proceedings of the ASME Design Engineering Technical Conference. Vol. 7 A. American Society of Mechanical Engineers. 2013 https://doi.org/10.1115/DETC2013-13416
Poursina, Mohammad ; Anderson, Kurt S. / Fast far-field potential evaluation in multibody-based simulations of biopolymers. Proceedings of the ASME Design Engineering Technical Conference. Vol. 7 A American Society of Mechanical Engineers, 2013.
@inproceedings{57826976337645f8a60105e8f61e9fd5,
title = "Fast far-field potential evaluation in multibody-based simulations of biopolymers",
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.",
author = "Mohammad Poursina and Anderson, {Kurt S.}",
year = "2013",
doi = "10.1115/DETC2013-13416",
language = "English (US)",
isbn = "9780791855966",
volume = "7 A",
booktitle = "Proceedings of the ASME Design Engineering Technical Conference",
publisher = "American Society of Mechanical Engineers",

}

TY - GEN

T1 - Fast far-field potential evaluation in multibody-based simulations of biopolymers

AU - Poursina, Mohammad

AU - Anderson, Kurt S.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84896939598&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84896939598&partnerID=8YFLogxK

U2 - 10.1115/DETC2013-13416

DO - 10.1115/DETC2013-13416

M3 - Conference contribution

AN - SCOPUS:84896939598

SN - 9780791855966

VL - 7 A

BT - Proceedings of the ASME Design Engineering Technical Conference

PB - American Society of Mechanical Engineers

ER -