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Efficient Coarse-Grained Molecular Simulations in the Multibody Dynamics Scheme

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Multibody Dynamics

Part of the book series: Computational Methods in Applied Sciences ((COMPUTMETHODS,volume 28))

Abstract

The numerical simulation of highly complex biomolecular systems such as DNAs, RNAs, and proteins become intractable as the size and fidelity of these systems increase. Herein, efficient techniques to accelerate multibody-based coarse-grained simulations of such systems are presented. First, an adaptive coarse-graining framework is explained which is capable of determining when and where the system model needs to change to achieve an optimal combination of speed and accuracy. The metrics to guide these on-the-fly instantaneous model adjustments and the issues associated with post-transition system’s states are addressed in this book chapter. Due to its highly modular and parallel nature, the Generalized Divide-and-Conquer Algorithm (GDCA) forms the bases for a suite of dynamics simulation tools used in this work. For completeness, the fundamental aspects of the GDCA are presented herein. Finally, a novel method for the efficient and accurate approximation of far-field force and moment terms are developed. This aspect is key to the success of any large molecular simulation since more than 90 % of the computational load in such simulations is associated with pairwise force calculations. The presented approximations are efficient, accurate, and highly compatible with multibody-based coarse-grained models.

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Acknowledgements

Support for this work received under National Science Foundation through award No. 0757936 is gratefully acknowledged. The author would like to thank Professor Alain Laederach from the University of North Carolina, Mr. Michael Sherman from Simbios: NIH Center for Biomedical Computation at Stanford University, and Dr. Kishor Bhalerao from the University of Melbourne for several useful discussions. They also would like to thank Jeremy Laflin who independently validated some of the simulation results.

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  1. Computational Dynamics Laboratory (CDL), Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute (RPI), Troy, NY, 12180, USA

    Mohammad Poursina & Kurt S. Anderson

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  1. Mohammad Poursina
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Correspondence to Mohammad Poursina .

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  1. Institute for Mechanics, Materials and Civil Engineering, Universite catholique de Louvain (UCL), Place du Levant 2, Louvain-la-Neuve, 1348, Belgium

    Jean-Claude Samin

  2. Institute for Mechanics, Materials and Civil Engineering, Universite catholique de Louvain (UCL), Place du Levant 2, Louvain-la-Neuve, 1348, Belgium

    Paul Fisette

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Poursina, M., Anderson, K.S. (2013). Efficient Coarse-Grained Molecular Simulations in the Multibody Dynamics Scheme. In: Samin, JC., Fisette, P. (eds) Multibody Dynamics. Computational Methods in Applied Sciences, vol 28. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5404-1_7

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