Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations.

ABSTRACT: An algorithm is described for the interaction of a hierarchy of objects that seeks to circumvent a fundamental problem in coarse-grained modelling which is the loss of fine detail when components become bundled together. A "currants-in-jelly" model is developed that provides a flexible approach in which the contribution of the soft high-level objects (jelly-like) are employed to protect the underlying atomic structure (currants), while still allowing them to interact. Idealised chains were used to establish the parameters to achieve this degree of interaction over a hierarchy spanning four levels and in a more realistic example, the distortion experienced by a protein domain structure during collision was measured and the parameters refined. This model of steric repulsion was then combined

SUBMITTER: Taylor WR 

PROVIDER: S-EPMC5272901 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature