Lista de obras - Thomas E. Ouldridge - Dominio Público Uruguay

A nucleotide-level coarse-grained model of RNA ⬇️

artículo científico publicado en 2014

Biochemical Machines for the Interconversion of Mutual Information and Work ⬇️

artículo científico publicado en 2017

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

artículo científico publicado en 2015

Coarse-grained simulations of DNA overstretching.

artículo científico publicado en 2013

Coarse-graining DNA for simulations of DNA nanotechnology.

artículo científico publicado en 2013

DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

Extracting bulk properties of self-assembling systems from small simulations ⬇️

artículo científico publicado el 23 de febrero de 2010

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2017

Guiding the folding pathway of DNA origami

artículo científico publicado en 2015

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

Modelling DNA origami self-assembly at the domain level ⬇️

artículo científico publicado en 2015

Modelling toehold-mediated RNA strand displacement. ⬇️

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2017

New Langevin and gradient thermostats for rigid body dynamics. ⬇️

artículo científico publicado en 2015

Nonequilibrium correlations in minimal dynamical models of polymer copying

artículo científico publicado en 2019

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Programmable energy landscapes for kinetic control of DNA strand displacement.

artículo científico publicado en 2014

Sequence-dependent thermodynamics of a coarse-grained DNA model.

artículo científico publicado en 2012

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

artículo científico publicado el 28 de febrero de 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2009

Lista de obras de Thomas E. Ouldridge

A nucleotide-level coarse-grained model of RNA ⬇️

Biochemical Machines for the Interconversion of Mutual Information and Work ⬇️

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

Coarse-grained simulations of DNA overstretching.

Coarse-graining DNA for simulations of DNA nanotechnology.

DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism

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

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

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

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

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

Extracting bulk properties of self-assembling systems from small simulations ⬇️

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

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

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

Guiding the folding pathway of DNA origami

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

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

Modelling DNA origami self-assembly at the domain level ⬇️

Modelling toehold-mediated RNA strand displacement. ⬇️

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

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

New Langevin and gradient thermostats for rigid body dynamics. ⬇️

Nonequilibrium correlations in minimal dynamical models of polymer copying

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

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

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

Programmable energy landscapes for kinetic control of DNA strand displacement.

Sequence-dependent thermodynamics of a coarse-grained DNA model.

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

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

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

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

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

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