Work

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

Year: 2021

Type: review

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.

Source: Frontiers in Molecular Biosciences

DOI: 10.3389/fmolb.2021.693710

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

Institutions: Imperial College London, University of Strathclyde, Institute for Complex Systems, Sapienza University of Rome, Arizona State University

Language: English

Topic: Advanced biosensing and bioanalysis techniques

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,950

Funders: National Science Foundation, European Commission, Engineering and Physical Sciences Research Council, European Research Council