Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

ABSTRACT: Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials

SUBMITTER: Savelyev A 

PROVIDER: S-EPMC2712212 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature