Publications

Chemical Physics

2012

F. Romano, A. Hudson, J.P.K. Doye, T.E. Ouldridge and A.A. Louis, J. Chem. Phys. 136, in press (2012)
The effect of topology on the structure and free energy landscapes of DNA kissing complexes
M. N. van der Linden, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 136, 054904 (2012)
Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles
A. Reinhardt and J.P.K. Doye, J. Chem. Phys. 136, 054501 (2012).
Free energy landscapes for homogeneous nucleation of ice for a monatomic model of water
F. Calvo, J.P.K. Doye and D. J. Wales, Nanoscale, 4, 1085-1100 (2012)
Energy landscapes of colloidal clusters: Thermodynamics and rearrangement mechanisms

2011

I.G. Johnston, S.E. Ahnert, A.A. Louis and J.P.K. Doye, Phys. Rev. E 83, 066105 (2011)
Evolutionary dynamics in a simple model of self-assembly
A. Reinhardt, A.J. Williamson, J.P.K. Doye, J. Carrete, L.M. Varela and A.A. Louis, J. Chem. Phys. 134, 104905 (2011)
Reentrant phase behaviour for systems with competition between phase separation and self-assembly
T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Chem. Phys, 134, 085101 (2011)
Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
A.J. Williamson, A.W. Wilber, J.P.K. Doye and A.A. Louis, Soft Matter, 7, 3423-3431 (2011)
Templated self-assembly of patchy particles

2010

S.E. Ahnert, I.G. Johnston, T.M.A. Fink, J.P.K. Doye and A.A. Louis, Phys. Rev. E 82, 026117 (2010)
Self-assembly, modularity and physical complexity
S. F. Greenbury, I.G. Johnston, M. A. Smith, J.P.K. Doye and A.A. Louis, J. Theor. Biol. 267, 48-61 (2010)
The effects of topology on robustness and evolvability in genetic regulatory networks
E.G. Noya, C. Vega, J.P.K. Doye and A. A. Louis, J. Chem. Phys. 132, 234511 (2010)
The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry
T.E. Ouldridge, A.A. Louis and J.P.K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
DNA nanotweezers studied with a coarse-grained model of DNA
I.G. Johnston, A.A. Louis and J.P.K. Doye, J. Phys.: Condens. Matter 22, 104101 (2010)
Modelling the self-assembly of virus capsids
T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)
Extracting bulk properties of self-assembling systems from small simulations

2009

A.W. Wilber, J.P.K. Doye, A.A. Louis and A.C.F. Lewis, J. Chem. Phys. 131, 175102 (2009)
Monodisperse self-assembly in a model with protein-like interactions
A.W. Wilber, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 131, 175101 (2009)
Self-assembly of monodisperse clusters: Dependence on target geometry
G. Villar, A.W. Wilber, A.J. Williamson, P. Thiara, J.P.K. Doye, A.A. Louis, M.N. Jochum, A.C.F. Lewis and E.D. Levy, Phys. Rev. Lett. 102, 118106 (2009)
The self-assembly and evolution of homomeric protein complexes
T.E. Ouldridge, I.G. Johnston, A.A. Louis and J.P.K. Doye, J. Chem. Phys. 130, 065101 (2009)
The self-assembly of DNA Holliday junctions studied with a minimal model

2008

F. Calvo, D. J. Wales, J.P.K. Doye, R.S. Berry, P. Labastie and M. Schmidt, EPL 82, 43003 (2008)
Comment on `Critical analysis of negative heat capacities in nanoclusters'

2007

C.P. Massen and J.P.K. Doye, J. Chem. Phys. 127, 114306 (2007)
Preferential attachment during the evolution of a potential energy landscape
A.W. Wilber, J.P.K. Doye, A.A. Louis, E.G. Noya, M.A. Miller, P. Wong, J. Chem. Phys. 127, 085106 (2007)
Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
E.G. Noya, C. Vega, J.P.K. Doye and A. A. Louis, J. Chem. Phys. 127, 054501 (2007)
Phase diagram of model anisotropic particles with octahedral symmetry
C.P. Massen, J.P.K. Doye and R.W. Nash, Physica A 382, 683-692 (2007)
Exploring the origins of the power-law properties of energy landscapes: An egg-box model
E.G. Noya, J.P.K. Doye, D.J. Wales and A. Aguado, Eur. Phys. J. D 43, 57-60 (2007)
Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour
J.P.K. Doye, A.A. Louis, I-C. Lin, L.R. Allen, E.G. Noya, A.W. Wilber, H.C. Kok, R. Lyus, Phys. Chem. Chem. Phys. 9, 2197-2205 (2007)
Controlling crystallization and its absence: Proteins, colloids and patchy models
C.P. Massen and J.P.K. Doye, Phys. Rev. E 75, 037101 (2007)
Power-law distributions for the areas of the basins of attraction on a potential energy landscape
C.P. Massen and J.P.K. Doye, Physica A 377, 351-362 (2007)
A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network

2006

C.P. Massen and J.P.K. Doye, cond-mat/0610077
Thermodynamics of community structure
J.P.K. Doye and L. Meyer, cond-mat/0604250
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
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)
Theoretical study of the melting of aluminum clusters
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)
Surveying a 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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