### 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 language | English (US) |
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Title of host publication | Proceedings of the ASME Design Engineering Technical Conference |

Pages | 125-135 |

Number of pages | 11 |

Volume | 4 |

Edition | PARTS A AND B |

DOIs | |

State | Published - 2011 |

Externally published | Yes |

Event | ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011 - Washington, DC, United States Duration: Aug 28 2011 → Aug 31 2011 |

### Other

Other | ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011 |
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Country | United States |

City | Washington, DC |

Period | 8/28/11 → 8/31/11 |

### Fingerprint

### ASJC Scopus subject areas

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

### Cite this

*Proceedings of the ASME Design Engineering Technical Conference*(PARTS A AND B ed., Vol. 4, pp. 125-135) https://doi.org/10.1115/DETC2011-48376

**Fast electrostatic force and moment calculations in multibody-based simulations of coarse-grained biopolymers.** / Poursina, Mohammad; Laflin, Jeremy; Anderson, Kurt S.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*Proceedings of the ASME Design Engineering Technical Conference.*PARTS A AND B edn, vol. 4, pp. 125-135, ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011, Washington, DC, United States, 8/28/11. https://doi.org/10.1115/DETC2011-48376

}

TY - GEN

T1 - Fast electrostatic force and moment calculations in multibody-based simulations of coarse-grained biopolymers

AU - Poursina, Mohammad

AU - Laflin, Jeremy

AU - Anderson, Kurt S.

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84863605745&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863605745&partnerID=8YFLogxK

U2 - 10.1115/DETC2011-48376

DO - 10.1115/DETC2011-48376

M3 - Conference contribution

AN - SCOPUS:84863605745

SN - 9780791854815

VL - 4

SP - 125

EP - 135

BT - Proceedings of the ASME Design Engineering Technical Conference

ER -