498 citations · 3.5k across the 66 of their papers we have counts for
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The Interplay of Heterogeneity and Product Detachment in Templated Polymer Copying
Jeremy E. B. Guntoro, Benjamin J. Qureshi, Thomas E. Ouldridge
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known method…
Thermodynamic limits on general far-from-equilibrium molecular templating networks
Benjamin Qureshi, Jenny M. Poulton, Thomas E. Ouldridge
Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property…
The Role of Sequence Information in Minimal Models of Molecular Assembly
Jeremy Guntoro, Thomas Ouldridge
Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental buil…
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…