498 citations · 3.5k across the 66 of their papers we have counts for
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Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Petr Šulc, Thomas E. Ouldridge, Flavio Romano +2
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consi…
Coarse-grained simulations of DNA overstretching
Flavio Romano, Debayan Chakraborty, Jonathan P. K. Doye +2
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the expe…
Sequence-dependent thermodynamics of a coarse-grained DNA model
Petr Šulc, Flavio Romano, Thomas E. Ouldridge +3
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally des…
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Christian Matek, Thomas E. Ouldridge, Adam Levy +2
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained…
Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble
Thomas E. Ouldridge
In this paper we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter {\bf 22}, 104102 (2010)] for dealing with the inference of bul…
The effect of topology on the structure and free energy landscape of DNA kissing complexes
Flavio Romano, Alex Hudson, Jonathan P. K. Doye +2
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologicall…