Publications

Chemical Physics

2006

• A. W. Wilber, J. P. K. Doye, A. A. Louis, E. G. Noya, M. A. Miller, P. Wong, submitted
  Reversible self-assembly of patchy particles into monodisperse clusters
• J.P.K. Doye and L. Meyer, submitted
  The structure of binary Lennard-Jones clusters: The effects of atomic size ratio
• E.G. Noya and J.P.K. Doye, J. Chem. Phys. 124, 104503 (2006)
  Structural transitions in the 309-atom magic number Lennard-Jones cluster
• C.P. Massen and J.P.K. Doye, submitted
  A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network
• J.P.K. Doye and W.C.K. Poon, Curr. Opin. Colloid In., 11, 40-46 (2006)
  Protein Crystallization in vivo
• E.G. Noya, J.P.K. Doye and F. Calvo, Phys. Rev. B 73, 125407 (2006)
  Melting of aluminium clusters
• C.P. Massen and J.P.K. Doye, submitted
  Power-law distributions for the areas of the basins of attraction on a potential energy landscape
• E.G. Noya, J.P.K. Doye, D.J. Wales and A. Aguado, submitted
  Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour
• J.P.K. Doye, Comp. Mater. Sci. 35, 227-231 (2006)
  Lead clusters: different potentials, different structures
• J.P.K. Doye, in `Global Optimization: Scientific and Engineering Case Studies' (Nonconvex Optimization and Its Applications Series: Vol. 85), ed. J.D. Pinter (Springer, 2006), pp. 103-139
  Physical perspectives on the global optimization of atomic clusters

2005

• J.P.K. Doye and L. Meyer, Phys. Rev. Lett. 95, 063401 (2005)
  Mapping the magic numbers in binary Lennard-Jones clusters
• J.P.K. Doye and C.P. Massen, in `Complexity, Metastability and Nonextensivity', ed. C. Beck, G. Benedek, A. Rapisarda and C. Tsallis (World Scientific, 2005), pp. 375-384
  Energy landscapes, scale-free networks and Apollonian packings
• C.P. Massen and J.P.K. Doye, Phys. Rev. E, 71, 046101 (2005)
  Identifying "communities" within energy landscapes
• J.P.K. Doye and C.P. Massen, J. Chem. Phys. 122, 084105 (2005)
  Characterizing the network topology of the energy landscapes of atomic clusters
• J.P.K. Doye and C.P. Massen, Phys. Rev. E 71, 016128 (2005)
  Space-filling disk packings as model spatial scale-free networks

2004

• J.P.K. Doye, A. A. Louis and M. Vendruscolo, Physical Biology 1, P9-P13 (2004)
  Inhibition of protein crystallization by evolutionary negative design
• F. Calvo and J.P.K. Doye, Phys. Rev. B 69, 125414 (2004)
  Pressure effects on the structure of nanoclusters
• J.P.K. Doye, R.H. Leary, M. Locatelli and F. Schoen, INFORMS J. Comput. 16, 371-379 (2004)
  Global optimization of Morse clusters by potential energy transformations

2003

• J.P.K. Doye and F. Calvo, J. Chem. Phys. 119, 12680-12681 (2003)
  Comment on "Strontium clusters: Many-body potential, energetics, and structural transitions"
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 119, 12409-12416 (2003)
  Stationary points and dynamics in high-dimensional systems
• J.P.K. Doye, Phys. Rev. B 68, 195418 (2003)
  Identifying structural patterns in 'disordered` metal clusters
• J.P.K. Doye, J. Chem. Phys., 119, 1136-1147 (2003)
  A model metal potential exhibiting polytetrahedral clusters
• F. Baletto, J.P.K. Doye, R. Ferrando and C. Mottet, Surf. Sci. 532-535, 898-904 (2003)
  Adsorption and diffusion on nanoclusters of C₆₀ molecules
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 118, 5263-5264 (2003)
  Comment on "Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids"
• J.P.K. Doye, D.J. Wales, F.H.M. Zetterling and M. Dzugutov, J. Chem. Phys. 118, 2792-2799 (2003)
  The favoured cluster structures of model glass formers
• J.P.K. Doye and S.C. Hendy, Eur. Phys. J. D 22, 99-107 (2003)
  On the structure of small lead clusters

2002

• S.C. Hendy and J.P.K. Doye, Phys. Rev. B 66, 235402 (2002)
  Surface-reconstructed icosahedral structures for lead clusters
• F. Calvo, J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 366, 176-183 (2002)
  Equilibrium properties of clusters in the harmonic superposition approximation
• J.P.K. Doye, Phys. Rev. Lett. 88, 238701 (2002)
  The network topology of a potential energy landscape: A static scale-free network
• J.P.K. Doye and F. Calvo, J. Chem. Phys. 116, 8307-8317 (2002)
  Entropic effects on the structure of Lennard-Jones clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 116, 3777-3788 (2002)
  Saddle points and dynamics of Lennard-Jones clusters, solids and supercooled liquids
• F. Baletto, J.P.K. Doye and R. Ferrando, Phys. Rev. Lett. 88, 075503 (2002)
  Evidence of kinetic trapping in clusters of C₆₀ molecules
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 116, 2642-2649 (2002)
  Collapse of Lennard-Jones homopolymers: size effects and energy landscapes

2001

• J.P.K. Doye, D.J. Wales, W. Branz and F. Calvo, Phys Rev. B 64, 235409 (2001)
  Modelling the structure of clusters of C₆₀ molecules
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 115, 9627-9636 (2001)
  Characterization of anharmonicities on complex potential energy surfaces: Perturbation theory and simulation
• F. Calvo, J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 87, 119301 (2001)
  Comment on ``Effect of Potential Energy Distribution on the Melting of Clusters''
• J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 86, 5719-5722 (2001)
  Polytetrahedral clusters
• J.P.K. Doye, D.J. Wales and S.I. Simdyankin, Faraday Discuss. 118, 159-170 (2001)
  Global optimization and the energy landscapes of Dzugutov clusters
• D.J. Wales and J.P.K. Doye, Phys. Rev. B 63, 214204 (2001)
  Dynamics and thermodynamics of supercooled liquids and glasses from a model energy landscape
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 114, 7312-7329 (2001)
  Quantum partition functions from classical distributions. Application to rare-gas clusters
• J.P.K. Doye and F. Calvo, Phys. Rev. Lett. 86, 3570-3573 (2001)
  Entropic effects on the size dependence of cluster structure
• F. Calvo and J.P.K. Doye, Phys. Rev. E 63, 010902(R) (2001)
  Entropic tempering: A method for overcoming quasi-ergodicity

2000

• J.P.K. Doye, Phys. Rev. E 62, 8753-8761 (2000)
  The effect of compression on the global optimization of atomic clusters
• D.J. Wales, J.P.K. Doye, M.A. Miller, P.N. Mortenson and T.R. Walsh, Adv. Chem. Phys. 115, 1-111 (2000)
  Energy Landscapes of Clusters, Biomolecules and Solids
• J.P.K. Doye, Polymer 41, 8857-8867 (2000)
  Computer simulations of the mechanism of thickness selection in polymer crystals
• J.P.K. Doye and D. Frenkel, Polymer 41, 1519-1528 (2000) 
  The effect of temperature jumps during polymer crystallization

1999

• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 111, 11070-11079 (1999)
  The dynamics of structural transitions in sodium chloride clusters
• R. H. Leary and J.P.K. Doye, Phys. Rev. E 60, R6320-R6322 (1999)
  Tetrahedral global minimum for the 98-atom Lennard-Jones cluster
• J.P.K. Doye, M.A. Miller and D.J. Wales, J. Chem. Phys. 111, 8417-8428 (1999)
  Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters
• M.A. Miller, J.P.K. Doye and D.J. Wales, Phys. Rev. E 60, 3701-3718 (1999)
  Structural relaxation in atomic clusters: Master equation dynamics
• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 110, 7073-7086 (1999)
  The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization
• J.P.K. Doye, M.A. Miller and D.J. Wales, J. Chem. Phys. 110, 6896-6906 (1999)
  The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 110, 2692-2702 (1999)
  Kinetic Monte Carlo simulations of the growth of polymer crystals
• J.P.K. Doye and D.J. Wales, Phys. Rev. B 59, 2292-2300 (1999)
  Structural transitions and global minima of Sodium Chloride Clusters
• M.A. Miller, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 110, 328-334 (1999)
  Structural relaxation in Morse clusters: Energy landscapes

1998

• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 109, 10033-10041 (1998)
  Crystallization of a polymer on a surface
• J.P.K. Doye, D.J. Wales and M.A. Miller, J. Chem. Phys. 109, 8143-8153 (1998)
  Thermodynamics and the global optimization of Lennard-Jones clusters
• J.P.K. Doye and D. Frenkel, Phys. Rev. Lett. 81, 2160-2163 (1998)
  Mechanism of thickness determination in polymer crystals
• J.P.K. Doye and D.J. Wales, New J. Chem. 22, 733-744 (1998)
  Global minima for transition metal clusters described by Sutton-Chen potentials
• J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 80, 1357-1360 (1998)
  Thermodynamics of global optimization
• J.P.K. Doye, R.P. Sear and D. Frenkel, J. Chem. Phys. 108, 2134-2142 (1998)
  The effect of chain stiffness on the phase behaviour of isolated homopolymers

1997

• J.P.K. Doye and D.J. Wales, J. Chem. Soc., Faraday Trans. 93, 4233-4244 (1997) 
  Structural consequences of the range of the interatomic potential: a menagerie of clusters
• D.J. Wales and J.P.K. Doye, J. Phys. Chem. A, 101, 5111-5116 (1997)
  Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 Atoms
• J.P.K. Doye, A. Dullweber and D.J. Wales, Chem. Phys. Lett. 269, 408-412 (1997) 
  Structural predictions for (C₆₀ )_N clusters with an all-atom potential
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 106, 5296 (1997)
  Comment on ``Relaxation of collective excitations in LJ-13 cluster'' [J. Chem. Phys. 105, 3679 (1996)] 
• J.P.K. Doye and D.J. Wales, Z. Phys. D, 40, 466-468 (1997)
  Thermally-induced surface reconstructions of Mackay icosahedra
• J.P.K. Doye and D.J. Wales, Z. Phys. D, 40, 194-197 (1997)
  Traversing the potential energy surface by eigenvector-following: applications to global optimisation and the structural transformations of clusters

1996

• J.P.K. Doye, PhD Thesis (University of Cambridge, 1996)
  The structure, thermodynamics and dynamics of atomic clusters (html or postscript)
• J.P.K. Doye and D.J. Wales, J. Phys. B 29, 4859-4894 (1996)
  The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to C₆₀
• J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 262, 167-174 (1996)
  The structure of (C₆₀ )_N clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 105, 8428-8445 (1996)
  On potential energy surfaces and relaxation to the global minimum 
• D.J. Wales, L.J. Munro and J.P.K. Doye, J. Chem. Soc., Dalton Trans. 611-623 (1996)
  What can calculations employing empirical potentials teach us about bare transition metal clusters?
• J.P.K. Doye and D.J. Wales, Science 271, 484-487 (1996)
  The structure and stability of atomic liquids: from clusters to bulk
• D.J. Wales and J.P.K. Doye, in `Large Clusters of Atoms and Molecules' (NATO ASI Series E: Vol. 313), ed. T.P. Martin (Kluwer Academic, Dordrecht, 1996), pp. 241-279
  Theoretical predictions of structure and thermodynamics in the large cluster regime 

1995

• J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 247, 339-347 (1995)
  Magic numbers and growth sequences of small face-centred-cubic and decahedral clusters
• J.P.K. Doye, D.J. Wales and R.S. Berry, J. Chem. Phys. 103, 4234-4249 (1995)
  The effect of the range of the potential on the structures of clusters
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 103, 3061-3070 (1995)
  Coexistence and phase separation in clusters: From the small to the not-so-small regime
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 102, 9673-9688, (1995)
  An order parameter approach to coexistence in atomic clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 102, 9659-9672 (1995)
  Calculation of thermodynamic properties of small Lennard-Jones clusters incorporating anharmonicity

1992

• J.P.K. Doye and D.J. Wales, J. Chem. Soc., Far. Trans. 88, 3295-3304 (1992)
  Systematic investigation of the structures and rearrangements of six-atom clusters bound by a model anisotropic potential

Other

• J.P.K. Doye, I.M.Goldby, C.M. Line, S.J. Lloyd, E.P.S. Shellard and D. Tricker, Science & Christian Belief, 7, 117-139 (1995)
  Contemporary perspectives on chance, providence and free will: A critique of some modern authors 

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