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.
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ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
August 28–31, 2011
Washington, DC, USA
Conference Sponsors:
- Design Engineering Division and Computers and Information in Engineering Division
ISBN:
978-0-7918-5481-5
PROCEEDINGS PAPER
Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers Available to Purchase
Mohammad Poursina,
Mohammad Poursina
Rensselaer Polytechnic Institute, Troy, NY
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Jeremy Laflin,
Jeremy Laflin
Rensselaer Polytechnic Institute, Troy, NY
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Kurt S. Anderson
Kurt S. Anderson
Rensselaer Polytechnic Institute, Troy, NY
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Mohammad Poursina
Rensselaer Polytechnic Institute, Troy, NY
Jeremy Laflin
Rensselaer Polytechnic Institute, Troy, NY
Kurt S. Anderson
Rensselaer Polytechnic Institute, Troy, NY
Paper No:
DETC2011-48376, pp. 125-135; 11 pages
Published Online:
June 12, 2012
Citation
Poursina, M, Laflin, J, & Anderson, KS. "Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers." Proceedings of the ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. Volume 4: 8th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, Parts A and B. Washington, DC, USA. August 28–31, 2011. pp. 125-135. ASME. https://doi.org/10.1115/DETC2011-48376
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