Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial

Matthew Sample; Michael Matthies; Petr \v{S}ulc

REVIEW

Not yet reviewed by Pith; the record is open.

Re-run · record.json Download PDF Read on arXiv ↗

This paper has not been read by Pith yet. Machine review is queued; the pith claim, tier, and objections will appear here once it completes.

SPECIMEN: schema-true, not a live event

T0 review · schema-true

One-sentence machine reading of the paper's core claim.

pith:XXXXXXXX · record.json · timestamp

arxiv 2308.01455 v1 pith:GV56WQMR submitted 2023-08-02 physics.bio-ph physics.comp-phphysics.ed-ph

Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial

Michael Matthies , Matthew Sample , Petr \v{S}ulc This is my paper

classification physics.bio-ph physics.comp-phphysics.ed-ph

keywords modeltutorialoxdnacoarse-grainednanotechnologysimulationssystemsuser

verification ladder T0 review T1 audit T2 compute T3 formal T4 reserved

0 comments

read the original 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.

Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial

discussion (0)