title: A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method.
abstract: We present a new class of coarse-grained (CG) force fields (FFs) for B-DNA with explicit ions suited for large-scale mesoscale simulations at microsecond-micrometer scale using a wide spectrum of particle simulation methods from molecular dynamics to dissipative particle dynamics. The effective solvent-mediated pairwise interactions making up the FFs are obtained by inverting radial distribution functions and other particle-particle distributions obtained from all-atom simulations of numbers of octadecamer DNA fragments from the Ascona B-DNA library. The inverse Monte Carlo (IMC) method, later known as Newton inversion (NI) (Lyubartsev, A. P.; Laaksonen, A. Phys. Rev. E, 1995, 52, 3730-3737), was used together with the iterative Boltzmann inversion (IBI) scheme to compute the effective CG potentials. We show that this systematic structure-based approach is capable of providing converged potentials that accurately reproduce the structural features of the underlying atomistic system within a few percents of relative difference. We also show that a simple one-site-per-nucleotide model with 10 intramolecular pair interaction potentials is able to reproduce key features of DNA, for example, the persistence length and its dependence on the ionic concentration, experimentally determined around 50 nm at physiological salt concentration.
authors.affiliation: Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur , 5000 Namur, Belgium.|Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.|Science for Life Laboratory, 17121 Solna, Sweden.
authors.forename: Aymeric
authors.initials: A
authors.lastname: Naômé
authors.affiliation: Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.|Science for Life Laboratory, 17121 Solna, Sweden.|Stellenbosch Institute of Advanced Studies (STIAS), Wallenberg Research Centre, Stellenbosch University , 7600 Stellenbosch, South Africa.
authors.forename: Aatto
authors.initials: A
authors.lastname: Laaksonen
authors.affiliation: Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, University of Namur , 5000 Namur, Belgium.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Vercauteren