423 citations · 769 across the 4 of their papers we have counts for
4 papers
The oxDNA coarse-grained model as a tool to simulate DNA origami
Jonathan P. K. Doye, Hannah Fowler, Domen Prešern +12
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
Coarse-grained modelling of the structural properties of DNA origami
Benedict E. K. Snodin, John S. Schreck, Flavio Romano +2
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. T…
Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA
Benedict E. K. Snodin, Ferdinando Randisi, Majid Mosayebi +8
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded…
Coarse-graining DNA for simulations of DNA nanotechnology
Jonathan P. K. Doye, Thomas E. Ouldridge, Ard A. Louis +8
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 coar…