Coarse-Grained Simulations Of Dna And Rna Systems With Oxdna And Oxrna Models: Tutorial
- Resource Type
- Conference
- Authors
- Sample, Matthew L.; Matthies, Michael; Sulc, Petr
- Source
- 2023 Winter Simulation Conference (WSC) Simulation Conference (WSC), 2023 Winter. :91-105 Dec, 2023
- Subject
- Engineering Profession
General Topics for Engineers
Transportation
Biological system modeling
RNA
DNA
Tutorials
Nanotechnology
- Language
- ISSN
- 1558-4305
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.