  We present a new, nucleotide-level model for RNA, oxRNA, based on the
coarse-graining methodology recently developed for the oxDNA model of DNA. The
model is designed to reproduce structural, mechanical and thermodynamic
properties of RNA, and the coarse-graining level aims to retain the relevant
physics for RNA hybridization and the structure of single- and double-stranded
RNA. In order to explore its strengths and weaknesses, we test the model in a
range of nanotechnological and biological settings. Applications explored
include the folding thermodynamics of a pseudoknot, the formation of a kissing
loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a
hairpin motif. We argue that the model can be used for efficient simulations of
the structure of systems with thousands of base pairs, and for the assembly of
systems of up to hundreds of base pairs. The source code implementing the model
is released for public use.
