Multi-particle collision dynamics for a coarse-grained model of soft colloids

A Coarse-Grained DNA Model for Bubble Formation and Dynamics

A coarse-grained molecular dynamics model for crystalline solids

A general mathematical framework for coarse-graining molecular dynamics (MD) model for solid system is presented. The formulation is based directly on the full MD model. The reduction of the atomic degrees of freedom is accomplished using the Mori–Zwanzig projection method. We also demonstrate how to simplify the model under this framework to make the numerical implementation much easier. Copyr...

Coarse Grained Molecular Dynamics

Coarse - graining polymers as soft colloids

We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed...

Allostery in a coarse-grained model of protein dynamics.

We propose a criterion for optimal parameter selection in coarse-grained models of proteins and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM disagrees with the bimodal distribution obtained from an all-atom model; however, the bimodal distribution is recovered by strengthening interactions between atoms t...