The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology,
biophysics and nanotechnology. It is currently available via two independent open source …

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-
grained model of DNA similar to that recently introduced in a study of DNA nanotweezers …

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …

originally designed to reproduce the properties of DNA molecules with average sequences.
The new parametrization introduces sequence-dependent stacking and base-pairing …

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model
includes anisotropic potentials between bases involved in base stacking and base pair …

DNA origami is a robust assembly technique that folds a single-stranded DNA template into
a target structure by annealing it with hundreds of short 'staple'strands,,,. Its guiding design …

To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …

Improved understanding of molecular systems has only emphasised the sophistication of
networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a …

We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic
thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin …

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 …