Recent Publications Archive


  • A.M. Belenguer, G.I. Lampronti, D.J. Wales, J.K.M. Sanders, J. Am. Chem. Soc., 136, 16156-16166 (2014).
    Direct Observation of Intermediates in a Thermodynamically Controlled Solid-State Dynamic Covalent Reaction
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  • A.J. Ballard and D.J. Wales, J. Chem. Theor. Comput., 10, 5599-5605 (2014).
    Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations

  • J. Hernandez-Rojas and D.J. Wales, Chem. Phys., 444, 23-29 (2014).
    The Effect of Dispersion Damping Functions on the Structure of Water Clusters
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  • G. Lever, D.J. Cole, R. Lonsdale, K.E. Ranaghan, D.J. Wales, A.J. Mulholland, C.-K. Skylaris, and M.C. Payne, J. Phys. Chem. Lett., 5, 3614-3619 (2014).
    Large-Scale Density Functional Theory Transition State Searching in Enzymes
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  • D. Mehta, T. Chen, J.D. Hauenstein and D.J. Wales, J. Chem. Phys. Communications, 141, 121104 (2014).
    Newton Homotopies for Sampling Stationary Points of Potential Energy Landscapes
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  • D. Schebarchov and D.J. Wales, Phys. Rev. Lett. 113, 156102 (2014).
    Structure Prediction for Multicomponent Materials Using Biminima
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  • C. Shang and D.J. Wales, J. Chem. Phys. Communications, 141, 071101 (2014).
    Optimal Parameters for Basin-Hopping Global Optimization Based on Tsallis Statistics
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  • Q. Lu, J. Kim, J. D. Farrell, D.J. Wales and J.E. Straub, J. Chem. Phys., 141, 18C525 (2014).
    Investigating the Solid-Liquid Phase Transition of Water Nanofilms Using the Generalized Replica Exchange Method

  • J.D. Stevenson and D.J. Wales, J. Chem. Phys. Communications, 141, 041104 (2014).
    Analysing Kinetic Transition Networks for Rare Events
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  • J.W.R. Morgan and D.J. Wales, Nanoscale, 6, 10717-10726 (2014).
    Energy Landscapes of Planar Colloidal Clusters
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  • S. Martiniani, J.D. Stevenson, D.J. Wales and D. Frenkel, Phys. Rev. X, 4, 031034 (2014).
    Superposition Enhanced Nested Sampling
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  • A. Arcella, G. Portella, R. Collepardo-Guevara, D. Chakraborty, D.J. Wales and M. Orozco, J. Phys. Chem. A, 118, 8540-8548 (2014).
    The Structure and Properties of DNA in Apolar Solvents
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  • D. Mehta, C. Hughes, M. Kastner and D.J. Wales, J. Chem. Phys., 140, 224503 (2014).
    Potential Energy Landscape of the Two-Dimensional XY Model: Higher-Index Stationary Points
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  • D. Mehta, J.D. Hauenstein and D.J. Wales, J. Chem. Phys., 140, 224114 (2014).
    Certification and the Potential Energy Landscape
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  • S.N. Fejer, D. Chakrabarti, H. Kusumaatmaja and D.J. Wales, Nanoscale, 6, 9448-9456 (2014).
    Design Principles for Bernal Spirals and Helices with Tunable Pitch

  • C. Hughes, D. Mehta and D.J. Wales, J. Chem. Phys., 140, 194104 (2014).
    An Inversion-Relaxation Approach for Sampling Stationary Points of Spin Model Hamiltonians
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  • D.J. Wales, ACS Nano, 8, 1081-1085, (2014).
    Perspective: Chemistry, Geometry and Defects in Two Dimensions

  • J.D. Farrell and D.J. Wales, J. Phys. Chem. A, DOI: 10.1021/jp4119666. Published Online: Feb 28, 2014.
    Clusters of Coarse-Grained Water Molecules
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  • B. Barz, D.J. Wales and B. Strodel, J. Phys. Chem. B, 118, 1003-1011 (2014).
    A Kinetic Approach to the Sequence-Aggregation Relationship in Disease-Related Protein Assembly
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  • O. Ivchenko, C.S. Whittleston, J.M. Carr, P. Imhof, S. Goerke and D.J. Wales, J. Phys. Chem. B, 118, 1969-1975 (2014).
    Proton Transfer Pathways, Energy Landscape, and Kinetics in Creatine-Water Systems
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  • D. Schebarchov and D.J. Wales, J. Chem. Phys. Communications, 139, 221101 (2013).
    A New Paradigm for Structure Prediction in Multicomponent Systems
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  • D.J. Wales and P. Salamon, Proc. Natl. Acad. Sci. USA, 111, 617-622, 2014.
    Observation Time Scale, Free Energy Landscapes, and Molecular Symmetry
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  • D. Mehta, C. Hughes, M. Schroeck and D.J. Wales, J. Chem. Phys., 139, 194503, 2013.
    Potential Energy Landscapes for the 2D XY Model: Minima, Transition States and Pathways
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  • 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
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  • F.Y. Naumkin and D.J. Wales, Advances in Quantum Methods and Applications in Chemistry, Physics, and Biology, Progress in Theoretical Chemistry and Physics, 27, 211-220, 2013.
    Hydrogen in Light-Metal Cage Assemblies: Towards a Nanofoam Storage

  • D. Chakrabarti, H. Kusumaatmaja, V. Rühle and D.J. Wales, Phys. Chem. Chem. Phys., 16, 5014-5025 (2014).
    Perspectives Article: Exploring Energy Landscapes: From Molecular to Mesoscopic Systems

  • 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

  • F. Calvo, A. Fortunelli, F. Negreiros and D.J. Wales, J. Chem. Phys. Communication, 139, 111102 (2013).
    Kinetics of Chemical Ordering in Ag-Au and Ag-Ni Nanoalloys

  • S. Somani and D.J. Wales, J. Chem. Phys., 139, 121909 (2013).
    Energy Landscapes and Global Thermodynamics for Alanine Peptides

  • D.J. Wales, Chem. Phys. Lett., 584, 1-9 (2013).
    Frontiers Article: Surveying a Complex Potential Energy Landscape: Overcoming Broken Ergodicity Using Basin-Sampling

  • C.J. Forman, S.N. Fejer, D. Chakrabarti, P.D. Barker and D.J. Wales, J. Phys. Chem. B, 117, 7918-7928 (2013).
    Local Frustration Determines Molecular and Macroscopic Helix Structures

  • S.W.Olesen, S.N. Fejer, D. Chakrabarti and D.J. Wales, RSC Advances, 3, 12905-12908 (2013).
    A Left-Handed Building Block Self-Assembles Into Right- and Left-Handed Helices

  • J.D. Farrell, C. Lines, J.J. Shepherd, D. Chakrabarti, M.A. Miller and D.J. Wales, Soft Matter, Soft Matter, 9, 5407-5416, (2013).
    Energy Landscapes and Rearrangement Mechanisms of Dipolar Particles
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  • D. Asenjo, J.D. Stevenson, D.J. Wales and D. Frenkel, J. Phys. Chem. A, 117, 12717-12723 (2013).
    Visualizing Basins of Attraction for Different Minimization Algorithms

  • D. Mehta, J.D. Hauenstein and D.J. Wales, J. Chem. Phys. Communication, 138, 171101 (2013).
    Certifying the Potential Energy Landscape
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  • H. Kusumaatmaja and D.J. Wales, Phys. Rev. Lett., 110, 165502, (2013).
    Defect Motifs for Constant Mean Curvature Surfaces

  • J.W.R. Morgan, D. Chakrabarti, N. Dorsaz and D.J. Wales, ACS Nano, 7, 1246-1256 (2013).
    Designing a Bernal Spiral from Patchy Colloids

  • 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

  • M.Sacchi, D.J. Wales and S.J. Jenkins, Phys. Chem. Chem. Phys., 14, 15879-15887 (2012).
    Mode-Specificity and Orientation-Specific Energy Redistribution in the Chemisorption of CH4 on Ni{100}

  • J.O. Richardson, D.J. Wales, S.C. Althorpe, R.P. McLaughlin, M. Viant, O. Shih, and R.J. Saykally, J. Phys. Chem. A, 117, 6960-6966 (2013).
    Investigation of Terahertz Vibration-Rotation Tunneling Spectra for the Water Octamer
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  • 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

  • F. Calvo, F.Y. Naumkin and D.J. Wales, Chem. Phys. Lett., 551, 38-41 (2012).
    Nuclear Quantum Effects on the Stability of Cationic Neon Clusters
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  • 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

  • D.J. Wales, in `From Computational Biophysics to Systems Biology (CBSB11) - Celebrating Harold Scheraga's 90th Birthday', Proceedings, 20-22 July 2011, Julich, Germany, edited by P. Carloni, U.H.E. Hansmann, T. Lippert, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann, Forschungszentrum Julich GmbH, Institute for Advanced Simulation, Julich Supercomputing Centre; IAS Series, Vol. 8, ISBN 978-3-89336-748-1, pp. 217-230, 2012.
    Exploring Energy Landscapes: From Molecules to Nanodevices

  • F.Y. Naumkin and D.J. Wales, Chem. Phys. Lett., 545, 44-49 (2012).
    Hydrogen Trapped in Ben Cluster Cages: The Atomic Encapsulation Option

  • F.Y. Naumkin and D.J. Wales, Int. J. Quant. Chem., 112, 3068-3075 (2012).
    Beryllium Cluster Cages Endohedrally Doped by Hydrogen: H2@Ben (8 ≤ n ≤ 14)

  • E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer, J. M. Carr and D.J. Wales, J. Comp. Chem., 33, 2209 (2012).
    Erratum to: Symmetrisation of the AMBER and CHARMM Force Fields, J. Comp. Chem., 31, 1402-1409 (2010)

  • R.J. Saykally and D.J. Wales, Science, 336, 814-815, (2012).
    Pinning Down the Water Hexamer

  • J.R. Green T.S. Hofer, D.J. Wales and R.S. Berry, Mol. Phys., 110, 1839-1848 (2012).
    Chaotic Dynamics Near Steep Transition States

  • M.T. Oakley, R.L. Johnston and D.J. Wales, J. At. Mol. Opt. Phys., 2012, 192613, (2012).
    The Effect of Nonnative Interactions on the Energy Landscapes of Frustrated Model Proteins

  • S. Lukman, R. Robinson, D.J. Wales and C. Verma, PROTEINS: Structure, Function, and Bioinformatics, 80, 1066-1077 (2012).
    Conformational Dynamics of Capping Protein and Interaction Partners: Simulation Studies
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  • D.J. Wales and T. Head-Gordon, J. Phys. Chem. B, 136, 8394-8411 (2012).
    Evolution of the Potential Energy Landscape with Static Pulling Force for Two Model Proteins

  • F. Calvo, E. Yurtsever and D.J. Wales, J. Chem. Phys., 136, 024393 (2012).
    Energy Landscapes of Ion Clusters in Isotropic Quadrupolar and Octupolar Traps
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  • J.R. Green T.S. Hofer, R.S. Berry and D.J. Wales, J. Chem. Phys., 184307 (2011).
    Characterizing Molecular Motion in H2O and H3O+ With Dynamical Instability Statistics

  • M.Sacchi, D.J. Wales and S.J. Jenkins, Computational and Theoretical Chemistry, 990, 144-151 (2012).
    Bond-Selective Energy Redistribution in the Chemisorption of CH3D and CD3H on Pt{110}(1x2): a First-Principles Molecular Dynamics Study

  • F.Y. Naumkin and D.J. Wales, J. Phys. Chem. A, 115, 12105-12110 (2011).
    H2 Molecules Encapsulated in Extended Ben Cluster Cages: Towards Light-Metal Nanofoams for Hydrogen Storage

  • D. Chakrabarti, T.S. Totton, M. Kraft and D.J. Wales, Phys. Chem. Chem. Phys., 13, 21362-21366 (2011).
    A survey of the potential energy surface for the (benzene)13 cluster

  • M.T. Oakley, R.L. Johnston and D.J. Wales, J. Phys. Chem. B, 115, 11525-11529 (2011).
    Energy Landscape and Global Optimisation for a Frustrated Model Protein
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  • M. Sacchi, D.J. Wales and S.J. Jenkins, J. Phys. Chem. C, 115, 21832�21842 (2011).
    Mode-Specific Chemisorption of CH4 on Pt{110}(1x2) Explored by First-Principles Molecular Dynamics
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  • S. Acosta-Gutierrez, J. Hernandez-Rojas, J. Breton, J. M. Gomez Llorente and D.J. Wales, J. Chem. Phys., 135, 124308 (2011).
    Physical Properties of Small Water Clusters in Low and Moderate Electric Fields
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  • F. Calvo, F.Y. Naumkin and D.J. Wales, J. Chem. Phys., 135, 124308 (2011).
    Interplay Between Charge and Vibrational Delocalisation in Cationic Helium Clusters
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  • F. Calvo, J.P.K. Doye D.J. Wales, Nanoscale, 4, 1085-1100 (2012).
    Energy Landscapes of Colloidal Clusters: Thermodynamics and Rearrangement Mechanisms

  • J.O. Richardson, S.C. Althorpe and D.J. Wales, J. Chem. Phys., 135, 124109 (2011).
    Instanton Calculations of Tunnelling Splittings for Water Dimer and Trimer
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  • D.J. Wales, Phil. Trans. Roy. Soc. A, 370, 2877-2899 (2012).
    Decoding the Energy Landscape: Extracting Structure, Dynamics and Thermodynamics

  • H.L. McKay, S.J. Jenkins and D.J. Wales, J. Phys. Chem. C, 115, 17812-17828 (2011).
    Dissociative Chemisorption of Hydrazine on an Fe{211} Surface

  • D. Chakrabarti and D.J. Wales, Soft Matter, 7, 2325-2328 (2011).
    Hot Article: Coupled linear and rotary motion in supramolecular helix handedness inversion
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  • D. Frenkel and D.J. Wales, Nature Materials, 10, 410-411 (2011).
    Colloidal Self-Assembly: Designed to Yield

  • S.N. Fejer, D. Chakrabarti and D.J. Wales, Soft Matter, 7, 3553-3564 (2011).
    Self-Assembly of Anisotropic Particles

  • D. Chakrabarti, S.N. Fejer and D.J. Wales, in "Computational Nanoscience", edited by E. Bichoutskaia, Royal Society of Chemistry, 58-81 (2011).
    Self-Assembly of Nanoclusters: An Energy Landscape Perspective
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  • D.J. Wales, ChemPhysChem, 11, 2491-2494 (2010)
    Energy Landscapes of Clusters Bound by Short-Ranged Potentials

  • S. Chutinimitkul, S. Herfst, J. Steel, A.C. Lowen, J. Ye, D. van Riel, E.J.A. Schrauwen, T.M. Bestebroer, B. Koel, D.F. Burke, K.H. Sutherland-Cash, C.S. Whittleston, C.A. Russell, D.J. Wales, D.J. Smith, M. Jonges, A. Meijer, M. Koopmans, G.F. Rimmelzwaan, T. Kuiken, A.D.M.E. Osterhaus, A. Garcia-Sastre, D.R. Perez and R.A.M. Fouchier, J. Virology, 84, 11802-11813, (2010)
    Virulence-Associated Substitution D222G in Hemagglutinin of 2009 Pandemic Influenza A(H1N1) Virus Affects Receptor Binding,

  • B. Strodel, J.W.L. Lee, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 132, 13300-13312 (2010)
    Transmembrane Structures for Alzheimer's Abeta1-42 Oligomers

  • 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

  • M.C. Prentiss, D.J. Wales and P.G. Wolynes, PLoS Comput. Biol., 6, e1000835, (2010)
    The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

  • T.S. Totton, D. Chakrabarti, A.J. Misquitta, M. Sander, D.J. Wales and M. Kraft, Combustion and Flame, 157, 909-914 (2009)
    Modelling the Internal Structure of Nascent Soot Particles

  • H. McKay, D.J. Wales, S.J. Jenkins, J.A. Verges and P.L. de Andres, Phys. Rev. B, 81, 075425 (2010)
    Hydrogen on Graphene Under Stress: Molecular Dissociation and Gap Opening

  • D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010)
    Energy Landscapes: Some New Horizons

  • S.N. Fejer, D. Chakrabarti and D.J. Wales, ACS Nano, 4, 219-228 (2010).
    Emergent Complexity from Simple Anisotropic Building Blocks: Shells, Tubes and Spirals
    Featured in ACS Nano Podcast Episode 30.

  • M.S. Bauer, B. Strodel, S.N. Fejer, E.F. Koslover and D.J. Wales, J. Chem. Phys., 132, 054101 (2010).
    Interpolation Schemes for Peptide Rearrangements

  • D.J. Wales, in "Crystal Structure Prediction", edited by A. Oganov, Wiley-VCH, Weinheim, 29-54 (2010).
    Energy Landscapes and Structure Prediction Using Basin-Hopping

  • D. Chakrabarti, S.N. Fejer and D.J. Wales, Proc. Natl. Acad. Sci. USA, 106, 20164-20167 (2009).
    Rational Design of Helical Architectures

  • E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer and D.J. Wales, J. Comp. Chem., 131, 1402-1409 (2010).
    Symmetrisation of the AMBER and CHARMM Force Fields

  • F. Calvo and D.J. Wales, J. Chem. Phys., 131, 134504 (2009).
    Stepwise Melting of a Model Glass Former Under Confinement

  • M. Blanco-Rey, S.J. Jenkins and D.J. Wales, J. Phys. Chem. C, 113, 16757-16765 (2009).
    Mechanisms for H2 reduction on the PdO{101} surface and the Pd{100}-sqrt(5) x sqrt(5)R27o-O surface oxide

  • J.A. Elliott, Y. Shibuta and D.J. Wales, Phil. Mag, 89}, 3311-3332 (2009).
    Global Minima of Transition Metal Clusters Described by Finnis--Sinclair Potentials: a Comparison with Semi-Empirical Molecular Orbital Theory

  • D.J. Wales, H. McKay and E.L. Altschuler, Phys. Rev. B, 79, 224115 (2009).
    Defect Motifs for Spherical Topologies

  • H. McKay, S.J. Jenkins and D.J. Wales, J. Phys. Chem. C, 113, 15274-15287 (2009).
    Theory of NHx+/-H Reactions on Fe{211}

  • V.K. de Souza and D.J. Wales, J. Chem. Phys., 130, 194508 (2009).
    Connectivity in the Potential Energy Landscape for Binary Lennard-Jones Systems

  • D.J. Wales, J. Chem. Phys., 130, 204111 (2009).
    Calculating Rate Constants and Committor Probabilities for Transition Networks by Graph Transformation
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  • M. Khalili and D.J. Wales, J. Chem. Theor. Comput, 5, 1380–1392 (2009).
    Computer simulations of peptides from the P53 DNA binding domain

  • J.M. Carr and D.J. Wales, Phys. Chem. Chem. Phys., 11, 3341-3354 (2009).
    Refined kinetic transition networks for the GB1 hairpin peptide

  • S.N. Fejer, T. James, J. Hernandez-Rojas and D.J. Wales, Phys. Chem. Chem. Phys., 11, 2098-2014 (2009).
    Energy Landscapes for Shells Assembled from Pentagonal and Hexagonal Pyramids

  • D. Chakrabarti and D.J. Wales, Phys. Chem. Chem. Phys., 11, 1970-1976, (2009).
    Simulations of Rigid Bodies in an Angle-Axis Framework

  • N. Ning, F. Calvo, A.C.T. van Duin, D.J. Wales, and H. Vach, J. Phys. Chem. C, 113, 518-523 (2009).
    Spontaneous Self-Assembly of Silica Nanocages into Inorganic Framework Materials

  • 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

  • V.K. de Souza and D.J. Wales, J. Chem. Phys., 129, 164507 (2008)
    Energy Landscapes for Diffusion: Analysis of Cage-Breaking Processes

  • M.A. Miller, J.J. Shepherd and D.J. Wales, Mol. Phys., 106, 1655-1664 (2008).
    Structural Trends in Clusters of Quadrupolar Spheres

  • D.J. Wales, J.M. Carr, M. Khalili, V.K. de Souza, B. Strodel, and C.S. Whittleston, in "Energy Flow in Proteins", edited by D. Leitner and J. Straub, Taylor and Francis/CRC Press, 315-340, 2008.
    Pathways and Rates for Structural Transformations of Peptides and Proteins

  • 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

  • B. Strodel, A. Fitzpatrick, M. Vendruscolo, C.M. Dobson and D.J. Wales, J. Phys. Chem. B, 112, 9998-10004 (2008).
    Characterising the First Steps of Amyloid Formation for the ccbeta Peptide

  • D. Chakrabarti and D.J. Wales, Phys. Rev. E, 77, 051709 (2008).
    Energy Landscape of a Model Discotic Liquid Crystal

  • M.C. Prentiss, D.J. Wales and P.G. Wolynes, J. Chem. Phys., 128, 225106 (2008).
    Protein Structure Prediction Using Basin-Hopping

  • F. Calvo and D.J. Wales, J. Chem. Phys., 128, 154501 (2008).
    Relaxation of Caloric Curves on Complex Potential Energy Surfaces

  • 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"

  • D. Chakrabarti and D.J. Wales, Phys. Rev. Lett., 100, 127801 (2008).
    Tilted and Helical Columnar Phases for an Axially Symmetric Discoidal System

  • B. Strodel and D.J. Wales, J. Chem. Theor. Comput., 4, 657-672 (2008).
    Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide

  • M. Khalili and D.J. Wales, J. Phys. Chem. B, 112, 2456-2465 (2007).
    Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling

  • 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

  • E.F. Koslover and D.J. Wales, J. Chem. Phys., 127, 234105 (2007).
    Geometry Optimisation for Peptides and Proteins: Comparison of Cartesian and Internal Coordinates

  • S.N. Fejer and D.J. Wales, Phys. Rev. Lett., 99, 086106 (2007).
    Helix Self-Assembly from Anisotropic Molecules

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