2023/08/02 by Michael Matthies, Matthies, Michael, Matthew Sample +3
Biochemistry, Genetics and Molecular Biology · #Advanced biosensing and bioanalysis techniques #Biological Physics (physics.bio-ph) #Computational Physics (physics.comp-ph) #DNA and Nucleic Acid Chemistry #FOS: Physical sciences #Physics Education (physics.ed-ph) #RNA and protein synthesis mechanisms
paper · pdf · doi:10.48550/arxiv.2308.01455
openalex publication_date 2023/08/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.