498 citations · 7.6k across the 97 of their papers we have counts for
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Modelling toehold-mediated RNA strand displacement
Petr Šulc, Thomas E. Ouldridge, Flavio Romano +2
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during…
The role of loop stacking in the dynamics of DNA hairpin formation
Majid Mosayebi, Flavio Romano, Thomas E. Ouldridge +2
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions…
A nucleotide-level coarse-grained model of RNA
Petr Šulc, Flavio Romano, Thomas E. Ouldridge +2
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce…
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…
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…