Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

Adithya Vijaykumar; Thomas E. Ouldridge; Pieter Rein ten Wolde; Peter G. Bolhuis

doi:10.1063/1.4977515

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arXiv · 1611.09239

Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

Adithya Vijaykumar·Thomas E. Ouldridge·Pieter Rein ten Wolde·Peter G. Bolhuis

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Abstract

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.

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Adithya Vijaykumar, Thomas E. Ouldridge, Pieter Rein ten Wolde, Peter G. Bolhuis. 2016-11-28. Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics. https://doi.org/10.1063/1.4977515

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