Citations


  • Energy landscapes reviews
    Energy Landscapes by D.J. Wales
    Cambridge University Press (Cambridge) 2003
    Hardback edition: ISBN 0521814154
    D.J. Wales, Phil. Trans. Roy. Soc. A, 370, 2877-2899 (2012).
    D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010)
    Energy Landscapes: Some New Horizons
    K. Klenin, B. Strodel, D.J. Wales and W. Wenzel, Biochimica et Biophysica Acta, 1814, 977-1000 (2011)
    Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics
    D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006)
    Feature Article: Potential Energy and Free Energy Landscapes
    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: from Clusters to Biomolecules

  • Thermodynamics of finite systems
    F. Calvo, D.J. Wales, J.P.K. Doye, R.S. Berry, P. Labastie and M. Schmidt, Europhys. Lett., 82, 43003 (2008).
    Comment on "Critical analysis of negative heat capacities in nanoclusters"
    J.P.K. Doye and D.J. Wales, J. Chem. Phys., 102, 9673-9688, (1995)
    An order parameter approach to coexistence in atomic 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
    R.M. Lynden-Bell and D.J. Wales, J. Chem. Phys., 101, 1460-1476 (1994)
    Free Energy Barriers to Melting in Atomic Clusters
    D.J. Wales and R.S. Berry, Phys. Rev. Lett., 73, 2875-2878 (1994)
    Coexistence in Finite Systems
    D.J. Wales and J.P.K. Doye, J. Chem. Phys., 119, 12409-12416 (2003)
    Coexistence and phase separation in clusters: From the small to the not-so-small regime


  • Growth in the number of minima (and transition states) with system size
    F.H. Stillinger and T.A. Weber, Phys. Rev. A, 25, 978 (1982)
    Hidden Structure in Liquids
    F.H. Stillinger and T.A. Weber, Science, 225, 983-989 (1984)
    Packing Structures and Transitions in Liquids and Solids
  • D.J. Wales and J.P.K. Doye, J. Chem. Phys., 119, 12409-12416 (2003)
    Stationary Points and Dynamics in High-Dimensional Systems

  • Basin-hopping global optimization
    M.T. Oakley, R.L. Johnston and D.J. Wales, Phys. Chem. Chem. Phys., 15, 3965-3976 (2013).
    Symmetrisation Schemes for Global Optimisation of Atomic Clusters
    D.J. Wales and J.P.K. Doye, J. Phys. Chem. A, 101, 5111 (1997)
    Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
    Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 84, 6611 (1987).
    Z. Li and H. A. Scheraga, J. Mol. Struct., 179, 333 (1988).

  • Basin-sampling and the superposition approach to thermodynamics
    K. Mochizuki, C.S. Whittleston, S. Somani, H. Kusumaatmaja and D.J. Wales, Phys. Chem. Chem. Phys., 16, 2842-2853, 2014.
    A Conformational Factorisation Approach for Estimating the Binding Free Energies of Macromolecules
    D.J. Wales, Chem. Phys. Lett., 584, 1-9 (2013).
    Frontiers Article: Surveying a Complex Potential Energy Landscape: Overcoming Broken Ergodicity Using Basin-Sampling
    T.V. Bogdan, D.J. Wales and F. Calvo, J. Chem. Phys., 124, 044102 (2006).
    Equilibrium Thermodynamics from Basin-Sampling
    B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008).
    Frontiers Article: Free Energy Surfaces from an Extended Harmonic Superposition Approach and Kinetics for Alanine Dipeptide
    D. J. Wales, Mol. Phys., 78, 151-171 (1993)
    Coexistence in Small Inert Gas Clusters

  • Dijkstra-based missing connection algorithm for linking (possibly distant) minima
    J.M. Carr, S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 122, 234903 (2005).
    Finding Pathways Between Distant Local Minima

  • Multi-funnel landscapes
    F. Calvo, Phys. Rev. E, 82, 046703 (2010)
    Free-energy landscapes from adaptively biased methods: Application to quantum systems

    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

  • Disconnectivity graphs
    O.M. Becker and M. Karplus, J. Chem. Phys., 106, 1495 (1997)
    The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics
    D.J. Wales, M.A. Miller and T.R. Walsh, Nature, 394, 758-760 (1998)
    Archetypal Energy Landscapes

  • Free energy disconnectivity graphs
    D.A. Evans and D.J. Wales, J. Chem. Phys., 118, 3891-3897 (2003)
    Free Energy Landscapes of Model Peptides and Proteins
    S.V. Krivov and M.Karplus, J. Chem. Phys., 117, 10894 (2002).
    Hidden complexity of free energy surfaces for peptide (protein) folding

  • Discrete path sampling
    D.J. Wales, Mol. Phys., 102, 891-908 (2004)
    Some Further Applications of Discrete Path Sampling to Cluster Isomerization
    D.J. Wales, Mol. Phys., 100, 3285-3306 (2002)
    Discrete Path Sampling

    DIJPAIR
    B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
    Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

    FREEPAIRS
    J.M. Carr and D.J. Wales, J. Phys. Chem. B, 112, 8760-8769 (2008).
    Folding Pathways and Rates for the Three-Stranded beta-sheet Peptide Beta3s Using Discrete Path Sampling

    SHORTCUT
    J.M. Carr and D.J. Wales, J. Chem. Phys., 123, 234901 (2005).
    Global Optimization and Folding Pathways of Selected alpha-Helical Proteins
    B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
    Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

    SHORTCUT BARRIER
    B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
    Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

    UNTRAP
    B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
    Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

  • Doubly-nudged elastic band algorithm
    S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 120, 2082-2094 (2004)
    A Doubly Nudged Elastic Band Method for Finding Transition States
    S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 120, 7820-7820, (2004)
    Erratum: A Doubly Nudged Elastic Band Method for Finding Transition States [J. Chem. Phys. 120, 2082 (2004)]
    D. Sheppard, R. Terrell and G. Henkelman, J. Chem. Phys., 128, 134106, (2008)
    Optimization methods for finding minimum energy paths

    Nudged elastic band algorithm
    G. Mills and H. Jonsson, Phys. Rev. Lett., 72, 1124 (1994).
    G. Mills, H. Jonsson and G. K. Schenter, Surf. Sci., 324, 305 (1995).
    H. Jonsson, G. Mills, and K. W. Jacobsen, Nudged elastic band method for finding minimum energy paths of transitions, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker, World Scientific, Singapore, (1998) p. 385.
    G. Henkelman, B. P. Uberuaga and H. Jonsson, J. Chem. Phys., 113, 9901 (2000).
    G. Henkelman and H. Jonsson, J. Chem. Phys., 113 , 9978 (2000).

  • Fastest-path analysis using Dijkstra's shortest path algorithm
    D.A. Evans and D.J. Wales, J. Chem. Phys., 121, 1080-1090 (2004)
    Folding of the GB1 Hairpin Peptide from Discrete Path Sampling
    E.W. Dijkstra, Numerische Math. 1, 269 (1959).
    A Note on Two Problems in Connexion with Graphs

  • Hybrid eigenvector-following
    L.J. Munro and D. J. Wales, Phys. Rev. B, 59, 3969-3980 (1999).
    Defect Migration in Crystalline Silicon
    Y. Zeng, P. Xiao and G. Henkelman, J. Chem. Phys., 140, 044115, (2014)
    Unification of algorithms for minimum mode optimization.

  • k-shortest paths analysis (recursive enumeration algorithm)
    J.M. Carr and D.J. Wales, Latest Advances in Atomic Cluster Collisions: Structure and Dynamics from the Nuclear to the Biological Scale, edited by J.-P. Connerade and A. Solov'yov, Imperial College Press, London, 321-330 (2008).
    The Energy Landscape as a Computational Tool
    V.M. Jimenez and A.Marzal, in Algorithm Engineering: 3rd International Workshop, WAE'99, London, UK, July 1999., edited by J.S. Vitter and C.D. Zaroliagis, vol. 1668, pp. 15--29. Springer Berlin, Heidelberg (1999).

  • L-BFGS minimization
    J.Nocedal, Math. Comput., 35, 773 (1980)
    Updating quasi-Newton matrices with limited storage
    D.Liu and J.Nocedal, Mathematical Programming B, 45, 503 (1989)
    On the Limited Memory Method for Large Scale Optimization

  • Local rigidification
    V. Rühle, H. Kusumaatmaja, D. Chakrabarti and D.J. Wales, J. Chem. Theory Comput., 9, 4026-4034 (2013).
    Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules
    H. Kusumaatmaja, C.S. Whittleston and D.J. Wales, J. Chem. Theory Comput., 8, 5159-5165 (2012).
    A Local Rigid Body Framework for Global Optimization of Biomolecules

  • NGT (new graph transformation) algorithm for calculation of phenomenological rate constants
    D.J. Wales, J. Chem. Phys., 130, 204111 (2009).
    Calculating Rate Constants and Committor Probabilities for Transition Networks by Graph Transformation

    GT (graph transformation) algorithm for calculation of phenomenological rate constants
    D.J. Wales, J. Chem. Phys., 130, 204111 (2009).
    Calculating Rate Constants and Committor Probabilities for Transition Networks by Graph Transformation
    S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 124, 234110 (2006)
    Graph Transformation Method for Calculating Waiting Times in Markov Chains
    S.A. Trygubenko and D.J. Wales, Mol. Phys., 104, 1497-1507 (2006)
    Kinetic Analysis of Discrete Path Sampling Stationary Point Databases

  • Optimal alignment of two structures with respect to overall translation, rotation and permutational isomerisation via the shortest augmenting path algorithm: PERMDIST
    D.J. Wales and J.M. Carr, J. Chem. Theory Comput., 8, 5020-5034 (2012).
    A Quasi-Continuous Interpolation Scheme for Pathways Between Distant Configurations

  • Quasi-continuous interpolation scheme
    D.J. Wales and J.M. Carr, J. Chem. Theory Comput., 8, 5020-5034 (2012).
    A Quasi-Continuous Interpolation Scheme for Pathways Between Distant Configurations

  • Self-consistent (re)grouping of stationary points on the PES into free energy minima and transition states
    J.M. Carr and D.J. Wales, J. Phys. Chem. B, 112, 8760-8769 (2008).
    Folding Pathways and Rates for the Three-Stranded beta-sheet Peptide Beta3s Using Discrete Path Sampling

  • Stone-Wales rearrangement
    Y. Kumeda, D.J. Wales and L.J. Munro, Chem. Phys. Lett., 341, 185-194 (2001)
    Transition States and Rearrangement Mechanisms from Hybrid Eigenvector-Following and Density Functional Theory. Application to C10H10 and Defect Migration in Crystalline Silicon
    A.J. Stone and D.J. Wales, Chem. Phys. Lett., 128, 501-503 (1986)
    Theoretical Studies of Icosahedral C60 and Some Related Structures


  • Catastrophe theory
  • T.V. Bogdan and D.J. Wales, J. Chem. Phys., 120, 11090-11099, (2004)
    New Results for Phase Transitions From Catastrophe Theory
  • D.J. Wales, Science, 293, 2067-2070 (2001)
    A Microscopic Basis for the Global Appearance of Energy Landscapes
    Abstract Full text
    Perspectives article: R.H. Leary, Science 293, 2013-2014 (2001)
    Flirting with Catastrophe
    NCSA press: http://www.npaci.edu/online/v5.19/leary.html

  • Range of the potential
  • F. Calvo, J.P.K. Doye and D.J. Wales, Nanoscale, 4, 1085-1100 (2012).
    Energy Landscapes of Colloidal Clusters: Thermodynamics and Rearrangement Mechanisms
  • D.J. Wales, ChemPhysChem, 11, 2491-2494 (2010)
    Highlights: Energy Landscapes of Clusters Bound by Short-Ranged Potentials
  • J.P.K. Doye and D.J. Wales, J. Chem. Soc., Faraday Trans., 93, 4233-4243 (1997)
    Structural Consequences of the Range of the Interatomic Potential. A Menagerie of 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
  • 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, 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
  • P.A. Braier, R.S. Berry and D.J. Wales, J. Chem. Phys., 93, 8745-8756 (1990)
    How the Range of Pair Interactions Governs Features of Multidimensional Potentials