From Molecular Dynamics to Brownian Dynamics

Three coarse-grained molecular dynamics (MD) models are investigated with the
aim of developing and analyzing multiscale methods which use MD simulations in
parts of the computational domain and (less detailed) Brownian dynamics (BD)
simulations in the remainder of the domain. The first MD model is formulated in
one spatial dimension. It is based on elastic collisions of heavy molecules
(e.g. proteins) with light point particles (e.g. water molecules). Two
three-dimensional MD models are then investigated. The obtained results are
applied to a simplified model of protein binding to receptors on the cellular
membrane. It is shown that modern BD simulators of intracellular processes can
be used in the bulk and accurately coupled with a (more detailed) MD model of
protein binding which is used close to the membrane.