A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
File(s)
Published version
Author(s)
Sengar, Aditya
Ouldridge, Thomas E
Henrich, Oliver
Rovigatti, Lorenzo
Sulc, Petr
Type
Journal Article
Abstract
The oxDNA model of DNA has been applied widely to systems in biology,
biophysics and nanotechnology. It is currently available via two independent
open source packages. Here we present a set of clearly-documented exemplar
simulations that simultaneously provide both an introduction to simulating the
model, and a review of the model's fundamental properties. We outline how
simulation results can be interpreted in terms of -- and feed into our
understanding of -- less detailed models that operate at larger length scales,
and provide guidance on whether simulating a system with oxDNA is worthwhile.
biophysics and nanotechnology. It is currently available via two independent
open source packages. Here we present a set of clearly-documented exemplar
simulations that simultaneously provide both an introduction to simulating the
model, and a review of the model's fundamental properties. We outline how
simulation results can be interpreted in terms of -- and feed into our
understanding of -- less detailed models that operate at larger length scales,
and provide guidance on whether simulating a system with oxDNA is worthwhile.
Date Issued
2021-06
Date Acceptance
2021-05-27
Citation
Frontiers in Molecular Biosciences, 2021, 8, pp.1-22
ISSN
2296-889X
Publisher
Frontiers Media
Start Page
1
End Page
22
Journal / Book Title
Frontiers in Molecular Biosciences
Volume
8
Copyright Statement
© 2021 Sengar, Ouldridge, Henrich, Rovigatti and Šulc. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
License URL
Sponsor
The Royal Society
Commission of the European Communities
Identifier
http://arxiv.org/abs/2104.11567v1
Grant Number
UF150067
851910
Subjects
q-bio.BM
q-bio.BM
cond-mat.soft
physics.bio-ph
Publication Status
Published
Article Number
693710
Date Publish Online
2021-06-17