498 citations · 3.5k across the 66 of their papers we have counts for
9 papers · 1 filter
Characterizing the bending and flexibility induced by bulges in DNA duplexes
John S. Schreck, Thomas E. Ouldridge, Flavio Romano +2
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used ex…
New Langevin and Gradient Thermostats for Rigid Body Dynamics
R. L. Davidchack, T. E. Ouldridge, M. V. Tretyakov
We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of an…
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 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…
DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
John S. Schreck, Thomas E. Ouldridge, Flavio Romano +4
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybrid…