An efficient multi-scale Green's Functions Reaction Dynamics scheme

Abstract

Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles in a low-density region are just diffusing and not interacting. In this case one can avoid the costly integration of microscopic equations of motion, such as molecular dynamics (MD), and instead turn to an event-based scheme in which the times to the next particle interaction and the new particle positions at that time can be sampled. At high (local) concentrations, however, e.g. when particles are interacting in a nontrivial way, particle positions must still be updated with small time steps of the microscopic dynamical equations. The efficiency of a multi-scale simulation that uses these two schemes largely depends on the coupling between them and the decisions when to switch between the two scales. Here we present an efficient scheme for multi-scale MD-GFRD simulations. It has been shown that MD-GFRD schemes are more efficient than brute-force molecular dynamics simulations up to a molar concentration of $10^2\mu M$. In this paper, we show that the choice of the propagation domains has a relevant impact on the computational performance. Domains are constructed using a local optimization of their sizes and a minimal domain size is proposed. The algorithm is shown to be more efficient than brute-force Brownian dynamics simulations up to a molar concentration of $10^3\mu M$ and is up to an order of magnitude more efficient compared with previous MD-GFRD schemes.

References in corpus (7)

• Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
• Spatio-temporal correlations can drastically change the response of a MAPK pathway
• First-Passage Kinetic Monte Carlo method
• A First-Passage Kinetic Monte Carlo Algorithm for Complex Diffusion-Reaction Systems
• Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
• Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics
• Role of anisotropy for protein-protein encounter

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• On the formalization of Asynchronous First Passage Algorithms