Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial

Matthew L. Sample; Michael Matthies; Petr Šulc

doi:10.1109/WSC60868.2023.10407580

Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial

Matthew L. Sample, Michael Matthies, Petr Šulc

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and nanotechnology settings. The tutorial is aimed at new users asking "Where should I start if I want to use oxDNA". We assume no prior background in using the model. This tutorial shows basic examples that can get a novice user started with the model, and points the prospective user towards additional reading and online resources depending on which aspect of the model they are interested in pursuing.

Original language	English (US)
Title of host publication	2023 Winter Simulation Conference, WSC 2023
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	91-105
Number of pages	15
ISBN (Electronic)	9798350369663
DOIs	https://doi.org/10.1109/WSC60868.2023.10407580
State	Published - 2023
Externally published	Yes
Event	2023 Winter Simulation Conference, WSC 2023 - San Antonio, United States Duration: Dec 10 2023 → Dec 13 2023

Publication series

Name	Proceedings - Winter Simulation Conference
ISSN (Print)	0891-7736

Conference

Conference	2023 Winter Simulation Conference, WSC 2023
Country/Territory	United States
City	San Antonio
Period	12/10/23 → 12/13/23

ASJC Scopus subject areas

Software
Modeling and Simulation
Computer Science Applications

Access to Document

10.1109/WSC60868.2023.10407580

Cite this

Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial. / Sample, Matthew L.; Matthies, Michael; Šulc, Petr.
2023 Winter Simulation Conference, WSC 2023. Institute of Electrical and Electronics Engineers Inc., 2023. p. 91-105 (Proceedings - Winter Simulation Conference).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Sample, ML, Matthies, M & Šulc, P 2023, Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial. in 2023 Winter Simulation Conference, WSC 2023. Proceedings - Winter Simulation Conference, Institute of Electrical and Electronics Engineers Inc., pp. 91-105, 2023 Winter Simulation Conference, WSC 2023, San Antonio, United States, 12/10/23. https://doi.org/10.1109/WSC60868.2023.10407580

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abstract = "We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and nanotechnology settings. The tutorial is aimed at new users asking {"}Where should I start if I want to use oxDNA{"}. We assume no prior background in using the model. This tutorial shows basic examples that can get a novice user started with the model, and points the prospective user towards additional reading and online resources depending on which aspect of the model they are interested in pursuing.",

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Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial

Abstract

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Conference

ASJC Scopus subject areas

Access to Document

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