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List of works by Thomas E. Ouldridge

A nucleotide-level coarse-grained model of RNA

scientific article published on 01 June 2014

Biochemical Machines for the Interconversion of Mutual Information and Work

scientific article published on 10 January 2017

Characterizing the bending and flexibility induced by bulges in DNA duplexes.

scientific article published in April 2015

Coarse-grained simulations of DNA overstretching.

scientific article published in February 2013

Coarse-graining DNA for simulations of DNA nanotechnology.

scientific article published on 11 October 2013

DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism

scientific article published on 17 September 2012

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.

scientific article published on 8 June 2015

DNA nanotweezers studied with a coarse-grained model of DNA.

scientific article published on 26 April 2010

Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

scientific article published on 22 May 2020

Designing the optimal bit: balancing energetic cost, speed and reliability.

scientific article

Direct Simulation of the Self-Assembly of a Small DNA Origami.

scientific article published on 14 January 2016

Extracting bulk properties of self-assembling systems from small simulations

scientific article published on February 23, 2010

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.

scientific article published on 17 November 2015

Fundamental Costs in the Production and Destruction of Persistent Polymer Copies.

scientific article published on 11 April 2017

Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions.

scientific article published in December 2017

Guiding the folding pathway of DNA origami

scientific article published in Nature

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

scientific article published on October 14, 2012

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.

scientific article published on June 2015

Modelling DNA origami self-assembly at the domain level

scientific article published in October 2015

Modelling toehold-mediated RNA strand displacement.

scientific article

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly.

scientific article published in April 2018

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

scientific article published in March 2017

New Langevin and gradient thermostats for rigid body dynamics.

scientific article published in April 2015

Nonequilibrium correlations in minimal dynamical models of polymer copying

scientific article published on 18 January 2019

On the biophysics and kinetics of toehold-mediated DNA strand displacement

scientific article published on 09 September 2013

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.

scientific article published on 5 March 2013

Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.

scientific article

Programmable energy landscapes for kinetic control of DNA strand displacement.

scientific article published on 10 November 2014

Sequence-dependent thermodynamics of a coarse-grained DNA model

scientific article published on October 7, 2012

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

scientific article published on February 28, 2011

The effect of topology on the structure and free energy landscape of DNA kissing complexes.

scientific article

The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics.

scientific article published on 21 November 2017

The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway.

scientific article published in November 2014

The role of loop stacking in the dynamics of DNA hairpin formation.

scientific article published on 2 December 2014

The self-assembly of DNA Holliday junctions studied with a minimal model

scientific article published on 01 February 2009