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A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Namur, Belgium.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Stellenbosch University, South Africa.
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, 3541-3549 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2014. Vol. 10, no 8, 3541-3549 p.
National Category
Physical Sciences Chemical Sciences
Identifiers
URN: urn:nbn:se:su:diva-107434DOI: 10.1021/ct500222sISI: 000340351200064OAI: oai:DiVA.org:su-107434DiVA: diva2:747856
Note

AuthorCount:3;

Available from: 2014-09-17 Created: 2014-09-15 Last updated: 2017-12-05Bibliographically approved

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Naomé, AymericLaaksonen, Aatto
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