Wales group home page

[Address and Contact], [Publications], [Common Citations], [Software Downloads], [The OptBench Test Suite], [Transition State Benchmarks for two Peptides], [PhD and Post-Doc Opportunities], [Group Wiki, People], [Cambridge Landscape Database Including the Cambridge Cluster Database of Global Minima], [Self-Assembly Programme Grant] [Telluride Energy Landscapes Workshops] [Tutorials Wiki (world-readable)] [Python Energy Landscape Explorer (PELE)]




buy "Energy Landscapes": USA, UK


Some Journal Covers


Recent Publications


  • J.M. Carr, C.S. Whittleston, D.C. Wade and D.J. Wales, Phys. Chem. Chem. Phys., in press (2015).
    Energy Landscapes of a Hairpin Peptide Including NMR Chemical Shift Restraints

  • B. Fackovec, E. Vanden-Eijnden, and D.J. Wales, J. Chem. Phys. 143, 044119 (2015).
    Markov State Modeling and Dynamical Coarse-Graining via Discrete Relaxation Path Sampling

  • W.Y. Chow, D. Bihan, C.J. Forman, D.A. Slatter, D.G. Reid, D.J. Wales, R.W. Farndale and M.J. Duer, Sci. Rep., in press (2015).
    Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

  • S.N. Fejer and D.J. Wales, Soft Matter, in press (2015).
    Assembly of Soft Anisotropic Particles Into a Kagome lattice

  • D. Schebarchov and D.J. Wales, Phys. Chem. Chem. Phys., in press (2015).
    Quasi-combinatorial energy landscapes for nanoalloy structure optimisation

  • Y. Chebaro, A.J. Ballard, D. Chakraborty and D.J. Wales, Sci. Rep. 5 10386 (2015).
    Intrinsically Disordered Energy Landscapes

  • D. Mehta, T. Chen, J.W.R. Morgan and D.J. Wales, J. Chem. Phys., in press (2015).
    Exploring the Potential Energy Landscape of the Thomson Problem via Newton Homotopies

  • L.C. Smeeton, J.D. Farrell, M.T. Oakley, D.J. Wales and R.L. Johnston, J. Chem. Theor. Comput., in press (2015).
    Structures and Energy Landscapes of Hydrated Sulfate Clusters

  • S. Somani, Y. Okamoto, A.J. Ballard and D.J. Wales, J. Phys. Chem. B, 119, 6155-6169 (2015).
    Equilibrium Molecular Thermodynamics from Kirkwood Sampling

  • Z. Cournia, T. Allen, I. Andricioaei, B. Antonny, D. Baum, G. Brannigan, N.-V. Buchete, J.T. Deckman, L. Delemotte, C. del Val, R. Friedman, P. Keka1, H.-C. Hege, J. Henin, M. Kasimova, A. Kolocouris, M.L. Klein, S. Khalid, J. Lemieux, N. Lindow, M. Roy, J. Selent, M. Tarek, F. Tofoleanu, S. Vanni, S. Urban, D.J. Wales, J.C. Smith and A.-N. Bondar, J. Membrane Biology, in press (2015).
    Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory

  • C. Shang, C.S. Whittleston, K.H. Sutherland-Cash and D.J. Wales, J. Chem. Theor. Comput., in press (2015).
    Analysis of the Contrasting Pathogenicities Induced by the D222G Mutation in 1918 and 2009 Pandemic Influenza A Viruses

  • K.H. Sutherland-Cash, D. Chakrabarti and D.J. Wales, Chem. Phys. Lett., in press (2015).
    Free Energy Basin-Hopping

  • D.J. Wales, J. Chem. Phys., 142, 130901 (2015).
    Perspective: Insight Into Reaction Coordinates and Dynamics From the Potential Energy Landscape JCP Podcast audio (mp3)

  • A.J. Ballard, S. Martiniani, J.D. Stevenson, S. Somani and D.J. Wales, Wiley Interdisciplinary Reviews: Computational Molecular Science., in press (2015).
    Exploiting the Potential Energy Landscape to Sample Free Energy

  • F. Calvo and D.J. Wales, Chem. Phys. Lett., in press (2015).
    Harmonic Superposition Method for Grand-Canonical Ensembles

  • D. Chakraborty, R. Collepardo-Guevara and D.J. Wales, J. Am. Chem. Soc., 136, 18052-18061 (2014).
    Energy Landscapes, Folding Mechanisms and Kinetics of RNA Tetraloop Hairpins

  • S.T. Chill, J. Stevenson, V. Ruehle, C. Shang, P. Xiao, J.D. Farrell, D.J. Wales, G. Henkelman, J. Chem. Theor. Comput., 10, 5476-5482 (2014).
    Benchmarks for Characterisation of Minima, Transition States and Pathways in Atomic, Molecular, and Condensed Matter Systems

  • 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

  • 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

  • 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

  • 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

  • D. Schebarchov and D.J. Wales, Phys. Rev. Lett. 113, 156102 (2014).
    Structure Prediction for Multicomponent Materials Using Biminima

  • C. Shang and D.J. Wales, J. Chem. Phys. Communications, 141, 071101 (2014).
    Optimal Parameters for Basin-Hopping Global Optimization Based on Tsallis Statistics

  • 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

  • J.W.R. Morgan and D.J. Wales, Nanoscale, 6, 10717-10726 (2014).
    Energy Landscapes of Planar Colloidal Clusters

  • S. Martiniani, J.D. Stevenson, D.J. Wales and D. Frenkel, Phys. Rev. X, 4, 031034 (2014).
    Superposition Enhanced Nested Sampling

  • 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

  • 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

  • D. Mehta, J.D. Hauenstein and D.J. Wales, J. Chem. Phys., 140, 224114 (2014).
    Certification and the Potential Energy Landscape

  • 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

  • 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

  • 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

  • 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

  • D. Schebarchov and D.J. Wales, J. Chem. Phys. Communications, 139, 221101 (2013).
    A New Paradigm for Structure Prediction in Multicomponent Systems

  • D.J. Wales and P. Salamon, Proc. Natl. Acad. Sci. USA, 111, 617-622, 2014.
    Observation Time Scale, Free Energy Landscapes, and Molecular Symmetry

  • 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

  • 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

  • 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

  • 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

  • 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
  • Recent Publications Archive
  • Complete Publications List
  •  
    [Back] Cambridge chemistry department homepage