794 citations · 3.6k across the 30 of their papers we have counts for
5 papers · 1 filter
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
Aditya Sengar, Thomas E. Ouldridge, Oliver Henrich +2
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we pre…
Coarse-Grained Nucleic Acid-Protein Model for Hybrid Nanotechnology
Jonah Procyk, Erik Poppleton, Petr Šulc
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatil…
Coarse-grained modelling of supercoiled RNA
Christian Matek, Petr Šulc, Ferdinando Randisi +2
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the m…
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…