423 citations · 2.3k across the 33 of their papers we have counts for
6 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…
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…
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…
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…
A comparison between parallelization approaches in molecular dynamics simulations on GPUs
Lorenzo Rovigatti, Petr Šulc, István Z. Reguly +1
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where…