Lista de obras - J Doye - Dominio Público Uruguay

A nucleotide-level coarse-grained model of RNA ⬇️

artículo científico publicado en 2014

CO oxidation catalysed by Pd-based bimetallic nanoalloys ⬇️

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

Characterizing the network topology of the energy landscapes of atomic clusters

artículo científico publicado en 2005

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

artículo científico publicado en 2020

Coarse-grained modelling of supercoiled RNA. ⬇️

artículo científico publicado en 2015

Coarse-grained modelling of the structural properties of DNA origami

artículo científico publicado en 2019

Coarse-grained simulations of DNA overstretching.

artículo científico publicado en 2013

Coarse-graining DNA for simulations of DNA nanotechnology.

artículo científico publicado en 2013

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

artículo científico publicado en 2013

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

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

artículo científico publicado en 2016

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

artículo científico publicado en 2019

Design principles for rapid folding of knotted DNA nanostructures

artículo científico publicado en 2016

Designer protein assemblies with tunable phase diagrams in living cells

artículo científico publicado en 2020

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

artículo científico publicado en 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

artículo científico publicado en 2002

Evolutionary dynamics in a simple model of self-assembly.

artículo científico publicado en 2011

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

Force-Induced Unravelling of DNA Origami

artículo científico publicado en 2018

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

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2019

Identifying communities within energy landscapes.

artículo científico publicado en 2005

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

artículo científico publicado en 2015

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

artículo científico publicado en 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.

artículo científico publicado en 2010

Modelling toehold-mediated RNA strand displacement. ⬇️

artículo científico publicado en 2015

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

artículo científico publicado en 2009

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

artículo científico publicado en 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 ⬇️

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

Phase diagram of model anisotropic particles with octahedral symmetry

artículo científico publicado en 2007

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

artículo científico publicado en 2015

Polytetrahedral clusters

artículo científico publicado en 2001

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

artículo científico publicado en 2007

Preferential attachment during the evolution of a potential energy landscape

artículo científico publicado en 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)].

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2017

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

artículo científico publicado en 2020

Self-assembly and evolution of homomeric protein complexes.

artículo científico publicado en 2009

Self-assembly of monodisperse clusters: Dependence on target geometry

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2005

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

artículo científico publicado el 7 de octubre de 2012

Structural relaxation in atomic clusters: master equation dynamics.

artículo científico publicado en 1999

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

artículo científico publicado en 2006

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

artículo científico publicado el 28 de febrero de 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.

artículo científico publicado en 2012

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

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

artículo científico publicado en 2010

Lista de obras de J Doye

A nucleotide-level coarse-grained model of RNA ⬇️

CO oxidation catalysed by Pd-based bimetallic nanoalloys ⬇️

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

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

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

Characterizing the network topology of the energy landscapes of atomic clusters

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

Coarse-grained modelling of supercoiled RNA. ⬇️

Coarse-grained modelling of the structural properties of DNA origami

Coarse-grained simulations of DNA overstretching.

Coarse-graining DNA for simulations of DNA nanotechnology.

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

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

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

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.

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

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

Design principles for rapid folding of knotted DNA nanostructures

Designer protein assemblies with tunable phase diagrams in living cells

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

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

Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

Entropic effects on the size dependence of cluster structure

Evidence of kinetic trapping in clusters of C60 molecules

Evolutionary dynamics in a simple model of self-assembly.

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

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

Force-Induced Unravelling of DNA Origami

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

Global optimization and the energy landscapes of Dzugutov clusters

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

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

Identifying communities within energy landscapes.

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

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

Mapping the magic numbers in binary Lennard-Jones clusters

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

Modelling the self-assembly of virus capsids.

Modelling toehold-mediated RNA strand displacement. ⬇️

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

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

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

Ni-based nanoalloys: towards thermally stable highly magnetic materials ⬇️

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

Note: Homogeneous TIP4P/2005 ice nucleation at low supercooling

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

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

Phase diagram of model anisotropic particles with octahedral symmetry

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

Polytetrahedral clusters

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

Preferential attachment during the evolution of a potential energy landscape

Programming patchy particles to form complex periodic structures

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

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

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

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

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Self-assembly and evolution of homomeric protein complexes.

Self-assembly of monodisperse clusters: Dependence on target geometry

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

Self-assembly, modularity, and physical complexity

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

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

Structural relaxation in atomic clusters: master equation dynamics.

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

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

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

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

The effect of temperature jumps during polymer crystallization

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

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

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

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