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List of works by Jonathan Doye

A nucleotide-level coarse-grained model of RNA

scientific article published on 01 June 2014

CO oxidation catalysed by Pd-based bimetallic nanoalloys

scientific article published on 30 March 2015

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.

scientific article

Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model.

scientific article published on 30 October 2017

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

scientific article published in April 2015

Characterizing the network topology of the energy landscapes of atomic clusters

scientific article published on 01 February 2005

Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis

scientific article published on 29 July 2020

Coarse-grained modelling of supercoiled RNA.

scientific article published on December 2015

Coarse-grained modelling of the structural properties of DNA origami

scientific article published on 01 February 2019

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

Computing phase diagrams for a quasicrystal-forming patchy-particle system

scientific article published on 20 June 2013

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

scientific article published on 09 November 2020

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.

scientific article published on 27 December 2017

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

DNA-stabilized Ag-Au bimetallic clusters: the effects of alloying and embedding on optical properties

scientific article published on 01 August 2016

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

scientific article published on 01 December 2019

Design principles for rapid folding of knotted DNA nanostructures

scientific article published on 18 February 2016

Designer protein assemblies with tunable phase diagrams in living cells

scientific article published on 13 July 2020

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

scientific article published on 14 January 2016

Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model

scientific article published on 01 August 2014

Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

scientific article published on 06 October 2011

Entropic effects on the size dependence of cluster structure

scientific article published on 01 April 2001

Evidence of kinetic trapping in clusters of C60 molecules

scientific article published on 31 January 2002

Evolutionary dynamics in a simple model of self-assembly.

scientific article published on 13 June 2011

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

Force-Induced Unravelling of DNA Origami

scientific article published on 31 May 2018

Free energy landscapes for homogeneous nucleation of ice for a monatomic water model

scientific article published on 01 February 2012

Global optimization and the energy landscapes of Dzugutov clusters

scientific article published on 01 January 2001

Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics.

scientific article

Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model

scientific article published on 22 July 2019

Identifying communities within energy landscapes.

scientific article published in April 2005

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

scientific article published on June 2015

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

scientific article published in November 2012

Mapping the magic numbers in binary Lennard-Jones clusters

scientific article published on 02 August 2005

Measuring Internal Forces in Single-Stranded DNA: Application to a DNA Force Clamp

scientific article published on 04 November 2020

Modelling the self-assembly of virus capsids.

scientific article published on 23 February 2010

Modelling toehold-mediated RNA strand displacement.

scientific article

Monodisperse self-assembly in a model with protein-like interactions

scientific article published on 01 November 2009

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

scientific article published in April 2018

Network topology of a potential energy landscape: a static scale-free network

scientific article published on 20 May 2002

Ni-based nanoalloys: towards thermally stable highly magnetic materials

scientific article

Note: Heterogeneous ice nucleation on silver-iodide-like surfaces

scientific article published on 01 December 2014

Note: Homogeneous TIP4P/2005 ice nucleation at low supercooling

scientific article published on 01 September 2013

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

Phase diagram of model anisotropic particles with octahedral symmetry

scientific article published on 01 August 2007

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

scientific article

Polytetrahedral clusters

scientific article published on 01 June 2001

Power-law distributions for the areas of the basins of attraction on a potential energy landscape

scientific article published on 19 March 2007

Preferential attachment during the evolution of a potential energy landscape

scientific article published on 01 September 2007

Programming patchy particles to form complex periodic structures

scientific article published on 01 December 2019

Publisher's Note: "Perturbative density functional methods for cholesteric liquid crystals" [J. Chem. Phys. 146, 184504 (2017)].

scientific article published in May 2017

Re-entrant phase behavior for systems with competition between phase separation and self-assembly

article

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

scientific article published on 01 August 2007

Rolling circle amplification shows a sinusoidal template length-dependent amplification bias.

scientific article published on 9 December 2017

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

scientific article published on 24 November 2020

Self-assembly and evolution of homomeric protein complexes.

scientific article published on 18 March 2009

Self-assembly of monodisperse clusters: Dependence on target geometry

scientific article published on 01 November 2009

Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal

scientific article published on 10 November 2016

Self-assembly, modularity, and physical complexity

scientific article published on 27 August 2010

Self-similar disk packings as model spatial scale-free networks

scientific article published on 21 January 2005

Sequence-dependent thermodynamics of a coarse-grained DNA model

scientific article published on October 7, 2012

Structural relaxation in atomic clusters: master equation dynamics.

scientific article published in October 1999

Structural transitions in the 309-atom magic number Lennard-Jones cluster

scientific article published on 01 March 2006

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

scientific article published on February 28, 2011

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

scientific article published on 01 November 2019

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

scientific article published on 07 August 2010

The effect of temperature jumps during polymer crystallization

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

scientific article

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

The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry.

scientific article published on June 2010