Multi-resolution dimer models in heat baths with short-range and long-range interactions

On standardised moments of force distribution in simple liquids

The force distribution of a tagged atom in a Lennard-Jones fluid in the canonical ensemble is studied with a focus on its dependence on inherent physical parameters: number density (n) and temperature (T). Utilising structural information from molecular dynamics simulations of the Lennard-Jones fluid, explicit analytical expressions for the dependence of standardised force moments on n and T are derived. Leading order behaviour of standardised moments of the force distribution are obtained in the limiting cases of small density (n → 0) and low temperature (T → 0), while the variations in the standardised moments are probed for general n and T using molecular dynamics simulations. Clustering effects are seen in molecular dynamics simulations and their effect on these standardised moments is discussed.

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or multi-resolution methodologies address this difficulty by using molecular dynamics (MD) and coarse-grained models in different parts of the cell. Their applicability depends on the accuracy and properties of the coarse-grained model which approximates the detailed MD description. A family of stochastic coarse-grained (SCG) models, written as relatively low-dimensional systems of nonlinear stochastic differential equations, is presented. The nonlinear SCG model incorporates the non-Gaussian force distribution which is observed in MD simulations and which cannot be described by linear models. It is shown that the nonlinearities can be chosen in such a way that they do not complicate parametrization of the SCG description by detailed MD simulations. The solution of the SCG model is found in terms of gamma functions.

Multi-resolution simulations of intracellular processes

This is an introduction to the Thematic Issue of Interface Focus containing papers by speakers of the Theo Murphy International Scientific Meeting on ‘Multi-resolution simulations of intracellular processes’