A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

The oxDNA model of Deoxyribonucleic acid 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...

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Autores principales: Sengar, A., Ouldridge, T. E., Henrich, O., Rovigatti, L., Šulc, P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Molecular Biosciences
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256390/
https://www.ncbi.nlm.nih.gov/pubmed/34235181
http://dx.doi.org/10.3389/fmolb.2021.693710
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author Sengar, A.
Ouldridge, T. E.
Henrich, O.
Rovigatti, L.
Šulc, P.
author_facet Sengar, A.
Ouldridge, T. E.
Henrich, O.
Rovigatti, L.
Šulc, P.
author_sort Sengar, A.
collection PubMed
description The oxDNA model of Deoxyribonucleic acid 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.
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spelling pubmed-82563902021-07-06 A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results Sengar, A. Ouldridge, T. E. Henrich, O. Rovigatti, L. Šulc, P. Front Mol Biosci Molecular Biosciences The oxDNA model of Deoxyribonucleic acid 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. Frontiers Media S.A. 2021-06-17 /pmc/articles/PMC8256390/ /pubmed/34235181 http://dx.doi.org/10.3389/fmolb.2021.693710 Text en Copyright © 2021 Sengar, Ouldridge, Henrich, Rovigatti and Šulc. https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Molecular Biosciences
Sengar, A.
Ouldridge, T. E.
Henrich, O.
Rovigatti, L.
Šulc, P.
A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title_full A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title_fullStr A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title_full_unstemmed A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title_short A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results
title_sort primer on the oxdna model of dna: when to use it, how to simulate it and how to interpret the results
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256390/
https://www.ncbi.nlm.nih.gov/pubmed/34235181
http://dx.doi.org/10.3389/fmolb.2021.693710
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