Advanced Coarse-Graining of Molecular Dynamics: Stochastic Models Beyond Gaussian Forces

Abstract

Integrating atomistic and molecular data into models of cellular activity is difficult due to the significant disparity in spatial and temporal scales between atomic and cellular activities. Multiscale or multiresolution techniques mitigate this challenge by using molecular dynamics (MD) and coarse-grained models in various regions of the cell. Their application relies on the precision and characteristics of the coarse-grained model that approximates the comprehensive molecular dynamics description. A series of stochastic coarse-grained (SCG) models is introduced, formulated as low-dimensional systems 
of nonlinear stochastic differential equations. The nonlinear SCG model integrates the non Gaussian force distribution shown in MD simulations, which linear models cannot adequately represent. The nonlinearities may be selected to ensure they do not impede the parametrisation of the SCG description via extensive MD simulations. The resolution of the SCG model is expressed in terms of gamma functions.