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Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications

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Title: Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications
Authors: Henrich, O
Gutiérrez Fosado, YA
Curk, T
Ouldridge, TE
Item Type: Journal Article
Abstract: During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
Issue Date: 10-May-2018
Date of Acceptance: 19-Apr-2018
URI: http://hdl.handle.net/10044/1/59745
DOI: https://dx.doi.org/10.1140/epje/i2018-11669-8
ISSN: 1292-8941
Publisher: EDP Sciences
Start Page: 57
End Page: 57
Journal / Book Title: European Physical Journal E. Soft Matter
Volume: 41
Issue: 5
Copyright Statement: © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: The Royal Society
Funder's Grant Number: UF150067
Keywords: Topical issue: Advances in Computational Methods for Soft Matter Systems
cond-mat.soft
physics.bio-ph
physics.comp-ph
q-bio.BM
01 Mathematical Sciences
02 Physical Sciences
Fluids & Plasmas
Publication Status: Published online
Conference Place: France
Appears in Collections:Faculty of Engineering
Bioengineering



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