All Stories

  1. Programming patchy particles to form three-dimensional dodecagonal quasicrystals

    Article • The Journal of Chemical Physics, May 2021, American Institute of Physics

    Jonathan Doye

  2. Programming patchy particles to form complex periodic structures

    Article • The Journal of Chemical Physics, December 2019, American Institute of Physics

    Jonathan Doye

  3. Incorporating particle flexibility in a density functional description of nematics and cholesterics

    Article • Molecular Physics, May 2018, Taylor & Francis

    Jonathan Doye

  4. Coarse-grained modelling of supercoiled RNA

    Article • The Journal of Chemical Physics, December 2015, American Institute of Physics

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, June 2015, American Institute of Physics

    Jonathan Doye

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

    Article • Nucleic Acids Research, June 2015, Oxford University Press (OUP)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, April 2015, American Institute of Physics

    Jonathan Doye

  8. Modelling Toehold-Mediated RNA Strand Displacement

    Article • Biophysical Journal, March 2015, Elsevier

    Jonathan Doye

  9. Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

    Article • Scientific Reports, January 2015, Nature

    Jonathan Doye

  10. CO oxidation catalysed by Pd-based bimetallic nanoalloys

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Jonathan Doye

  11. Ni-based nanoalloys: Towards thermally stable highly magnetic materials

    Article • The Journal of Chemical Physics, December 2014, American Institute of Physics

    Jonathan Doye

  12. The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation

    Article • The Journal of Physical Chemistry B, December 2014, American Chemical Society (ACS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, December 2014, American Institute of Physics

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, August 2014, American Institute of Physics

    Jonathan Doye

  15. A nucleotide-level coarse-grained model of RNA

    Article • The Journal of Chemical Physics, June 2014, American Institute of Physics

    Jonathan Doye

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

    Article • Nucleic Acids Research, September 2013, Oxford University Press (OUP)

    Jonathan Doye

  17. Note: Homogeneous TIP4P/2005 ice nucleation at low supercooling

    Article • The Journal of Chemical Physics, September 2013, American Institute of Physics

    Jonathan Doye

  18. Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

    Article • Natural Computing, August 2013, Springer Science + Business Media

    Jonathan Doye

  19. DNA hybridization kinetics: zippering, internal displacement and sequence dependence

    Article • Nucleic Acids Research, August 2013, Oxford University Press (OUP)

    Jonathan Doye

  20. Computing Phase Diagrams for a Quasicrystal-Forming Patchy-Particle System

    Article • Physical Review Letters, June 2013, American Physical Society (APS)

    Jonathan Doye

  21. Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

    Article • ACS Nano, March 2013, American Chemical Society (ACS)

    Jonathan Doye

  22. Coarse-grained simulations of DNA overstretching

    Article • The Journal of Chemical Physics, February 2013, American Institute of Physics

    Jonathan Doye

  23. Coarse-graining DNA for simulations of DNA nanotechnology

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, November 2012, American Institute of Physics

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, October 2012, American Institute of Physics

    Jonathan Doye

  26. DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

    Article • The Journal of Physical Chemistry B, September 2012, American Chemical Society (ACS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, June 2012, American Institute of Physics

    Jonathan Doye

  28. Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles

    Article • The Journal of Chemical Physics, February 2012, American Institute of Physics

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, February 2012, American Institute of Physics

    Jonathan Doye

  30. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

    Article • Nanoscale, January 2012, Royal Society of Chemistry

    Jonathan Doye

  31. Evolutionary dynamics in a simple model of self-assembly

    Article • Physical Review E, June 2011, American Physical Society (APS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, March 2011, American Institute of Physics

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, February 2011, American Institute of Physics

    Jonathan Doye

  34. Templated self-assembly of patchy particles

    Article • Soft Matter, January 2011, Royal Society of Chemistry

    Jonathan Doye

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

    Article • Journal of Theoretical Biology, November 2010, Elsevier

    Jonathan Doye

  36. Self-assembly, modularity, and physical complexity

    Article • Physical Review E, August 2010, American Physical Society (APS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, June 2010, American Institute of Physics

    Jonathan Doye

  38. DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

    Article • Physical Review Letters, April 2010, American Physical Society (APS)

    Jonathan Doye

  39. Extracting bulk properties of self-assembling systems from small simulations

    Article • Journal of Physics Condensed Matter, February 2010, Institute of Physics Publishing

    Jonathan Doye

  40. Modelling the self-assembly of virus capsids

    Article • Journal of Physics Condensed Matter, February 2010, Institute of Physics Publishing

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, November 2009, American Institute of Physics

    Jonathan Doye

  42. Self-assembly of monodisperse clusters: Dependence on target geometry

    Article • The Journal of Chemical Physics, November 2009, American Institute of Physics

    Jonathan Doye

  43. Self-Assembly and Evolution of Homomeric Protein Complexes

    Article • Physical Review Letters, March 2009, American Physical Society (APS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, February 2009, American Institute of Physics

    Jonathan Doye

  45. Comment on “Critical analysis of negative heat capacities in nanoclusters” by Michaelian K. and Santamaría-Holek I.

    Article • EPL (Europhysics Letters), May 2008, Institute of Physics Publishing

    Jonathan Doye

  46. Preferential attachment during the evolution of a potential energy landscape

    Article • The Journal of Chemical Physics, September 2007, American Institute of Physics

    Jonathan Doye

  47. Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

    Article • The Journal of Chemical Physics, August 2007, American Institute of Physics

    Jonathan Doye

  48. Exploring the origins of the power-law properties of energy landscapes: An egg-box model

    Article • Physica A Statistical Mechanics and its Applications, August 2007, Elsevier

    Jonathan Doye

  49. Phase diagram of model anisotropic particles with octahedral symmetry

    Article • The Journal of Chemical Physics, August 2007, American Institute of Physics

    Jonathan Doye

  50. Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour

    Article • Zeitschrift für Physik D, May 2007, Springer Science + Business Media

    Jonathan Doye

  51. A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network

    Article • Physica A Statistical Mechanics and its Applications, April 2007, Elsevier

    Jonathan Doye

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

    Article • Physical Review E, March 2007, American Physical Society (APS)

    Jonathan Doye

  53. Controlling crystallization and its absence: proteins, colloids and patchy models

    Article • Physical Chemistry Chemical Physics, January 2007, Royal Society of Chemistry

    Jonathan Doye

  54. Protein crystallization in vivo

    Article • Current Opinion in Colloid & Interface Science, April 2006, Elsevier

    Jonathan Doye

  55. Theoretical study of the melting of aluminum clusters

    Article • Physical Review B, March 2006, American Physical Society (APS)

    Jonathan Doye

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

    Article • The Journal of Chemical Physics, March 2006, American Institute of Physics

    Jonathan Doye

  57. Lead clusters: Different potentials, different structures

    Article • Computational Materials Science, March 2006, Elsevier

    Jonathan Doye

  58. ENERGY LANDSCAPES, SCALE-FREE NETWORKS AND APOLLONIAN PACKINGS

    Article • September 2005, World Scientific Pub Co Pte Lt

    Jonathan Doye

  59. Mapping the Magic Numbers in Binary Lennard-Jones Clusters

    Article • Physical Review Letters, August 2005, American Physical Society (APS)

    Jonathan Doye

  60. Identifying communities within energy landscapes

    Article • Physical Review E, April 2005, American Physical Society (APS)

    Jonathan Doye

  61. Characterizing the network topology of the energy landscapes of atomic clusters

    Article • The Journal of Chemical Physics, February 2005, American Institute of Physics

    Jonathan Doye

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

    Article • Physical Review E, January 2005, American Physical Society (APS)

    Jonathan Doye

  63. Global Optimization of Morse Clusters by Potential Energy Transformations

    Article • INFORMS Journal on Computing, November 2004, INFORMS

    Jonathan Doye

  64. Pressure effects on the structure of nanoclusters

    Article • Physical Review B, March 2004, American Physical Society (APS)

    Jonathan Doye

  65. Inhibition of protein crystallization by evolutionary negative design

    Article • Physical Biology, February 2004, Institute of Physics Publishing

    Jonathan Doye, Professor Michele Vendruscolo

  66. Stationary points and dynamics in high-dimensional systems

    Article • The Journal of Chemical Physics, December 2003, American Institute of Physics

    Jonathan Doye

  67. Comment on “Strontium clusters: Many-body potential, energetics, and structural transitions” [J. Chem. Phys. 115, 3640 (2001)]

    Article • The Journal of Chemical Physics, December 2003, American Institute of Physics

    Jonathan Doye

  68. Identifying structural patterns in disordered metal clusters

    Article • November 2003, American Physical Society (APS)

    Jonathan Doye

  69. A model metal potential exhibiting polytetrahedral clusters

    Article • The Journal of Chemical Physics, July 2003, American Institute of Physics

    Jonathan Doye

  70. Adsorption and diffusion on nanoclusters of C60 molecules

    Article • Surface Science, June 2003, Elsevier

    Jonathan Doye

  71. Comment on “Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids” [J. Chem. Phys. 116, 10297 (2002)]

    Article • The Journal of Chemical Physics, March 2003, American Institute of Physics

    Jonathan Doye, Dr Antonio Scala

  72. The favored cluster structures of model glass formers

    Article • The Journal of Chemical Physics, February 2003, American Institute of Physics

    Jonathan Doye

  73. On the structure of small lead clusters

    Article • Zeitschrift für Physik D, January 2003, Springer Science + Business Media

    Jonathan Doye

  74. Surface-reconstructed icosahedral structures for lead clusters

    Article • December 2002, American Physical Society (APS)

    Jonathan Doye

  75. Equilibrium properties of clusters in the harmonic superposition approximation

    Article • Chemical Physics Letters, November 2002, Elsevier

    Jonathan Doye

  76. Network Topology of a Potential Energy Landscape: A Static Scale-Free Network

    Article • Physical Review Letters, May 2002, American Physical Society (APS)

    Jonathan Doye

  77. Entropic effects on the structure of Lennard-Jones clusters

    Article • The Journal of Chemical Physics, May 2002, American Institute of Physics

    Jonathan Doye

  78. Saddle points and dynamics of Lennard-Jones clusters, solids, and supercooled liquids

    Article • The Journal of Chemical Physics, March 2002, American Institute of Physics

    Jonathan Doye

  79. Collapse of Lennard-Jones homopolymers: Size effects and energy landscapes

    Article • The Journal of Chemical Physics, February 2002, American Institute of Physics

    Jonathan Doye

  80. Evidence of Kinetic Trapping in Clusters of C 60 Molecules

    Article • Physical Review Letters, January 2002, American Physical Society (APS)

    Jonathan Doye

  81. Characterization of anharmonicities on complex potential energy surfaces: Perturbation theory and simulation

    Article • The Journal of Chemical Physics, December 2001, American Institute of Physics

    Jonathan Doye

  82. Modeling the structure of clusters ofC60molecules

    Article • November 2001, American Physical Society (APS)

    Jonathan Doye

  83. Comment on “Effect of Potential Energy Distribution on the Melting of Clusters”

    Article • Physical Review Letters, August 2001, American Physical Society (APS)

    Jonathan Doye

  84. Polytetrahedral Clusters

    Article • Physical Review Letters, June 2001, American Physical Society (APS)

    Jonathan Doye

  85. Dynamics and thermodynamics of supercooled liquids and glasses from a model energy landscape

    Article • May 2001, American Physical Society (APS)

    Jonathan Doye

  86. Entropic Effects on the Size Dependence of Cluster Structure

    Article • Physical Review Letters, April 2001, American Physical Society (APS)

    Jonathan Doye

  87. Global optimization and the energy landscapes of Dzugutov clusters

    Article • Faraday Discussions, January 2001, Royal Society of Chemistry

    Jonathan Doye

  88. Entropic tempering: A method for overcoming quasiergodicity in simulation

    Article • December 2000, American Physical Society (APS)

    Jonathan Doye

  89. Effect of compression on the global optimization of atomic clusters

    Article • December 2000, American Physical Society (APS)

    Jonathan Doye

  90. Computer simulations of the mechanism of thickness selection in polymer crystals

    Article • Polymer, December 2000, Elsevier

    Jonathan Doye

  91. The effect of temperature jumps during polymer crystallization

    Article • Polymer, February 2000, Elsevier

    Jonathan Doye

  92. Energy Landscapes: From Clusters to Biomolecules

    Article • January 2000, Wiley

    Jonathan Doye

  93. The dynamics of structural transitions in sodium chloride clusters

    Article • The Journal of Chemical Physics, December 1999, American Institute of Physics

    Jonathan Doye

  94. Tetrahedral global minimum for the 98-atom Lennard-Jones cluster

    Article • December 1999, American Physical Society (APS)

    Jonathan Doye

  95. Evolution of the potential energy surface with size for Lennard-Jones clusters

    Article • The Journal of Chemical Physics, November 1999, American Institute of Physics

    Jonathan Doye

  96. Structural relaxation in atomic clusters: Master equation dynamics

    Article • October 1999, American Physical Society (APS)

    Jonathan Doye

  97. The double-funnel energy landscape of the 38-atom Lennard-Jones cluster

    Article • The Journal of Chemical Physics, April 1999, American Institute of Physics

    Jonathan Doye

  98. The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization

    Article • The Journal of Chemical Physics, April 1999, American Institute of Physics

    Jonathan Doye

  99. Kinetic Monte Carlo simulations of the growth of polymer crystals

    Article • The Journal of Chemical Physics, February 1999, American Institute of Physics

    Jonathan Doye

  100. Structural transitions and global minima of sodium chloride clusters

    Article • January 1999, American Physical Society (APS)

    Jonathan Doye

  101. Structural relaxation in Morse clusters: Energy landscapes

    Article • The Journal of Chemical Physics, January 1999, American Institute of Physics

    Jonathan Doye

  102. Crystallization of a polymer on a surface

    Article • The Journal of Chemical Physics, December 1998, American Institute of Physics

    Jonathan Doye

  103. Thermodynamics and the global optimization of Lennard-Jones clusters

    Article • The Journal of Chemical Physics, November 1998, American Institute of Physics

    Jonathan Doye

  104. Mechanism of Thickness Determination in Polymer Crystals

    Article • Physical Review Letters, September 1998, American Physical Society (APS)

    Jonathan Doye

  105. Thermodynamics of Global Optimization

    Article • Physical Review Letters, February 1998, American Physical Society (APS)

    Jonathan Doye

  106. The effect of chain stiffness on the phase behaviour of isolated homopolymers

    Article • The Journal of Chemical Physics, February 1998, American Institute of Physics

    Jonathan Doye

  107. Global minima for transition metal clusters described by Sutton–Chen potentials

    Article • New Journal of Chemistry, January 1998, Royal Society of Chemistry

    Jonathan Doye

  108. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

    Article • The Journal of Physical Chemistry A, July 1997, American Chemical Society (ACS)

    Jonathan Doye

  109. Structural predictions for (C60)N clusters with an all-atom potential

    Article • Chemical Physics Letters, May 1997, Elsevier

    Jonathan Doye

  110. Comment on “Relaxation of collective excitations in LJ-13 cluster” [J. Chem. Phys. 105, 3679 (1996)]

    Article • The Journal of Chemical Physics, March 1997, American Institute of Physics

    Jonathan Doye

  111. Thermally-induced surface reconstructions of Mackay icosahedra

    Article • Zeitschrift für Physik D, March 1997, Springer Science + Business Media

    Jonathan Doye

  112. Surveying a potential energy surface by eigenvector-following

    Article • Zeitschrift für Physik D, March 1997, Springer Science + Business Media

    Jonathan Doye

  113. Structural consequences of the range of the interatomic potential A menagerie of clusters

    Article • Journal of the Chemical Society Faraday Transactions, January 1997, Royal Society of Chemistry

    Jonathan Doye

  114. Surveying a potential energy surface by eigenvector-following

    Article • January 1997, Springer Science + Business Media

    Jonathan Doye

  115. Thermally-induced surface reconstructions of Mackay icosahedra

    Article • January 1997, Springer Science + Business Media

    Jonathan Doye

  116. The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to

    Article • Journal of Physics B Atomic Molecular and Optical Physics, November 1996, Institute of Physics Publishing

    Jonathan Doye

  117. On potential energy surfaces and relaxation to the global minimum

    Article • The Journal of Chemical Physics, November 1996, American Institute of Physics

    Jonathan Doye

  118. The structure of (C60)N clusters

    Article • Chemical Physics Letters, November 1996, Elsevier

    Jonathan Doye

  119. The Structure and Stability of Atomic Liquids: From Clusters to Bulk

    Article • Science, January 1996, American Association for the Advancement of Science

    Jonathan Doye

  120. Theoretical Predictions of Structure and Thermodynamics in the Large Cluster Regime

    Article • January 1996, Springer Science + Business Media

    Jonathan Doye

  121. What can calculations employing empirical potentials teach us about bare transition-metal clusters?

    Article • Journal of the Chemical Society Dalton Transactions, January 1996, Royal Society of Chemistry

    Jonathan Doye

  122. Magic numbers and growth sequences of small face-centred-cubic and decahedral clusters

    Article • Chemical Physics Letters, December 1995, Elsevier

    Jonathan Doye

  123. Magic numbers and growth sequences of small face-centered-cubic and decahedral clusters

    Article • Chemical Physics Letters, December 1995, Elsevier

    Jonathan Doye

  124. The effect of the range of the potential on the structures of clusters

    Article • The Journal of Chemical Physics, September 1995, American Institute of Physics

    Jonathan Doye

  125. Coexistence and phase separation in clusters: From the small to the not-so-small regime

    Article • The Journal of Chemical Physics, August 1995, American Institute of Physics

    Jonathan Doye

  126. An order parameter approach to coexistence in atomic clusters

    Article • The Journal of Chemical Physics, June 1995, American Institute of Physics

    Jonathan Doye

  127. Calculation of thermodynamic properties of small Lennard-Jones clusters incorporating anharmonicity

    Article • The Journal of Chemical Physics, June 1995, American Institute of Physics

    Jonathan Doye

  128. Systematic investigation of the structures and rearrangements of six-atom clusters bound by a model anisotropic potential

    Article • Journal of the Chemical Society Faraday Transactions, January 1992, Royal Society of Chemistry

    Jonathan Doye

  129. Physical Perspectives on the Global Optimization of Atomic Clusters

    Article • Springer Science + Business Media

    Jonathan Doye