Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics.
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. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.
FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
Adithya
A
Vijaykumar
Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
Thomas E
0000000181148602
TE
Ouldridge
FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
Pieter Rein
PR
Ten Wolde
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
Peter G
PG
Bolhuis
D000465:Algorithms; D016880:Anisotropy; D056004:Molecular Dynamics Simulation; D010316:Particle Size; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
D011506:Proteins