498 citations · 3.5k across the 66 of their papers we have counts for
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Design of DNA Strand Displacement Reactions
Križan Jurinović, Merry Mitra, Rakesh Mukherjee +1
DNA strand displacement (SD) reactions are central to the operation of many synthetic nucleic acid systems, including molecular circuits, sensors, and machines. Over the years, a b…
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 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…
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…