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

A. Sengar; T. E. Ouldridge; O. Henrich; L. Rovigatti; P. Šulc

doi:10.3389/fmolb.2021.693710

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

A. Sengar, T. E. Ouldridge, O. Henrich, L. Rovigatti, P. Šulc

Molecular Sciences, School of (SMS)

Research output: Contribution to journal › Review article › peer-review

28 Scopus citations

Abstract

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.

Original language	English (US)
Article number	693710
Journal	Frontiers in Molecular Biosciences
Volume	8
DOIs	https://doi.org/10.3389/fmolb.2021.693710
State	Published - Jun 17 2021

Keywords

biophysics
coarse-grained modelling
deoxyribonucleic acid
molecular simulation (molecular modeling)
nanotechnology

ASJC Scopus subject areas

Biochemistry
Biochemistry, Genetics and Molecular Biology (miscellaneous)
Molecular Biology

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10.3389/fmolb.2021.693710

Cite this

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

abstract = "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{\textquoteright}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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AU - Ouldridge, T. E.

AU - Henrich, O.

AU - Rovigatti, L.

AU - Šulc, P.

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AB - 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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KW - molecular simulation (molecular modeling)

KW - nanotechnology

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

Abstract

Keywords

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