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Coarse-grained modelling of strong DNA bending II: Cyclization
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuati…
Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge +2
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than i…
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…
Force-induced rupture of a DNA duplex
Majid Mosayebi, Ard A. Louis, Jonathan P. K. Doye +1
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a sy…
CO Oxidation Catalysed by Pd-based Bimetallic Nanoalloys
Dennis Palagin, Jonathan P. K. Doye
Density functional theory based global geometry optimization has been used to demonstrate the crucial influence of the geometry of the catalytic cluster on the energy barriers for…