423 citations · 557 across the 6 of their papers we have counts for
5 papers
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…
DNA nanotechnology: understanding and optimisation through simulation
Thomas E. Ouldridge
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures.…
The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway
Thomas E. Ouldridge, Pieter Rein ten Wolde
Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation si…
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
Christian Matek, Thomas E. Ouldridge, Jonathan P. K. Doye +1
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can inf…
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…