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)] [Group teaching VM] [Curated workshop examples (Github)]




Energy Landscapes Kalamata Greece 2nd to 9th September 2018

HOT TOPICS
Applications to spectroscopy
Landscapes for machine learning
Protein folding and misfolding
Landsapes for DNA and RNA
Designing landscapes for self-assembly and multifunctional systems
Atomic, molecular, and nanoalloy clusters
Colloids and mesoscopic systems

Organisers: David J. Wales and Sotiris Xantheas
Venue: Hotel Elite, Kalamata, Greece



buy Energy Landscapes: USA, UK


JOURNAL COVERS


Recent Publications




  • M. Eckhoff, D. Schebarchov and D.J. Wales, J. Phys. Chem. Lett., in press (2017).
    Structure and Thermodynamics of Metal Clusters on Atomically Smooth Substrates





  • J.B. Rommel and D.J. Wales, J. Phys. Chem. C, in press (2017).
    Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}





  • S.P. Niblett, M. Biedermann, D.J. Wales and V.K. de Souza, J. Chem. Phys., in press (2017).
    Pathways for Diffusion in the Potential Energy Landscape of the Network Glass Former SiO2



  • R.G. Mantell and D.J. Wales, Chem. Phys. Lett., 685, 288-293 (2017).
    Exploiting Sparsity in Free Energy Basin-Hopping



  • J.W.R. Morgan, D. Mehta and D.J. Wales, Phys. Chem. Chem. Phys., 19, 25498-25508 (2017).
    Properties of Kinetic Transition Networks for Atomic Clusters and Glassy Solids





  • M. Griffiths, S. Niblett and D.J. Wales, J. Chem. Theor. Comput., 13, 4914-4931 (2017).
    Optimal Alignment of Structures for Finite and Periodic Systems



  • D.J. Wales, Ann. Rev. Phys. Chem., 69, in press (2017).
    Exploring Energy Landscapes





  • T. Cragnolini, D. Chakraborty, J. Sponer, P. Derreumaux, S. Pasquali and D.J. Wales, J. Chem. Phys., 147, 152715 (2017).
    Multifunctional Energy Landscape for a DNA G-Quadruplex: An Evolved Molecular Switch



  • E.A. Appel, F. Biedermann, D. Hoogland, J. del Barrio, M.D. Driscoll, S. Hay, D.J. Wales and O.A. Scherman, J. Am. Chem. Soc., 139, 12985-12993 (2017).
    Decoupled Associative and Dissociative Processes in Strong yet Highly Dynamic Host-Guest Complexes





  • T. Desautels, R. Das, J. Calvert, M. Trivedi, C. Summers, D.J. Wales and A. Ercole, BMJ Open, 7, e017199 (2017).
    Predicting early unplanned intensive care unit readmission in a tertiary-care hospital: a cross-sectional machine learning approach



  • R. Das and D.J. Wales, Royal Society Open Science, 4, 170175 (2017).
    Machine Learning Landscapes and Predictions for Patient Outcomes





  • M.Sacchi, D.J. Wales and S.J. Jenkins, Phys. Chem. Chem. Phys., 19, 16600-16605 (2017).
    Energy Landscapes and Dynamics of Glycine on Cu(110)





  • I. Yildirim and D.J. Wales, J. Phys. Chem. B, 121, 2989-2999 (2017).
    Improving Computational Predictions of Single-stranded RNA Tetramers with Revised alpha/gamma Torsional Parameters for the Amber Force Field





  • J.A. Joseph, K. Roeder, D. Chakraborty, R.G. Mantell and D.J. Wales, Chem. Commun., 53, 6974-6988 (2017).
    Feature Article: Exploring Biomolecular Energy Landscapes





  • D.J. Wales, Phys. Rev. E Rapid Communication, 95, 030105(R) (2017).
    Decoding Heat Capacity Features From the Energy Landscape





  • A.J. Ballard, R. Das, S. Martiniani, D. Mehta, L. Sagun, J.D. Stevenson and D.J. Wales, Phys. Chem. Chem. Phys., 19, 12585-12603 (2017).
    Perspective: Energy Landscapes for Machine Learning



  • V. de Souza, J. Stevenson, S. Niblett, J. Farrell and D.J. Wales, J. Chem. Phys., 146, 124103 (2017).
    Defining and Quantifying Frustration in the Energy Landscape: Applications to Atomic and Molecular Clusters, Biomolecules, Jammed and Glassy Systems





  • A. Sieradzan, P. Krupa and D.J. Wales, J. Phys. Chem. B, 121, 2207-2219 (2017).
    What Makes Telomeres Unique?



  • D.J. Wales, J. Chem. Phys., 146, 054306 (2017).
    Atomic Clusters with Addressable Complexity





  • K. Roeder and D.J. Wales, J. Chem. Theor. Comput., 13, 1468-1477 (2017).
    Transforming the Energy Landscape of a Coiled-coil Peptide via Point Mutations

  • D. Chakraborty and D.J. Wales, Phys. Chem. Chem. Phys., 19, 878-892 (2016).
    Probing Helical Transitions in a DNA Duplex




  • J. Hernandez-Rojas, F. Calvo, S. Niblett and D.J. Wales, Phys. Chem. Chem. Phys., 19, 1884-1895 (2017).
    Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials

  • R. Das and D.J. Wales, Chem. Phys. Lett., 667, 158-164 (2017).
    Machine Learning Prediction for Classification of Outcomes in Local Minimisation

  • T. Xu, J. Farrell, R. Momen, A. Azizi, S.R. Kirk, S. Jenkins and D.J. Wales, Chem. Phys. Lett., 667, 25-31 (2017).
    A Stress Tensor Eigenvector Projection Space for the (H2O)5 Potential Energy Surface

  • P. Stadlbauer, L. Mazzanti, T. Cragnolini, D.J. Wales, P. Derreumaux, S. Pasquali and J. Sponer, J. Chem. Theor. Comput., 12, 6077-6097, (2016).
    Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

  • J.A. Joseph, C.S. Whittleston and D.J. Wales, J. Chem. Theor. Comput., 12, 6109-6117 (2016).
    Structure, Thermodynamics and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification



  • B. E. Husic, D. Schebarchov and D.J. Wales, Nanoscale: Hot Article, 8, 18326-18340 (2016).
    Impurity Effects on Solid-Solid Transitions in Atomic Clusters

  • R.G. Mantell, C.E. Pitt and D.J. Wales, J. Chem. Theor. Comput., 12, 6182-6191 (2016).
    GPU-Accelerated Exploration of Biomolecular Energy Landscapes

  • I.D. Seymour, D.J. Wales and C.P. Grey, J. Phys. Chem. C , 120, 19521-19530 (2016).
    Preventing Structural Rearrangements on Battery Cycling: A First-Principles Investigation of the Effect of Dopants on the Migration Barriers in Layered Li0.5MnO2

  • Y. Yoshida, H. Sato, J.W.R. Morgan and D.J. Wales, Editor's Choice: Chem. Phys. Lett., 664, 5-9 (2016) .
    Potential Energy Landscapes of Tetragonal Pyramid Molecules

  • J. Hernandez-Rojas, D. Chakrabarti and D.J. Wales, Phys. Chem. Chem. Phys., 18, 26579-26585 (2016).
    Self-Assembly of Colloidal Magnetic Particles: Energy Landscapes and Structural Transitions

  • T. Xu, J. Farrell, Y. Xu, R. Momen, S.R. Kirk, S. Jenkins and D.J. Wales, J. Comp. Chem., 37, 2712-2721 (2016) .
    QTAIM and Stress Tensor Interpretation of the (H2O)5 Potential Energy Surface

  • S. Martiniani, K.J. Schrenk, J.D. Stevenson, D.J. Wales and D. Frenkel, Phys. Rev. E, rapid communication, 94, 031301 press (2016).
    Structural Analysis of High-Dimensional Basins of Attraction

  • T. Desautels, J. Calvert, J. Hoffman, M. Jay, Y. Kerem, L. Shieh, D. Shimabukuro, U. Chettipally, M. Feldman, C. Barton, D.J Wales, R, Das, JMIR Med. Inform., 4, e28 (2016).
    A Machine Learning Approach to Sepsis Prediction in the Intensive Care Unit With Minimal Electronic Health Record Data

  • J. Sarka, A.G. Csaszar, S.C. Althorpe, D. J. Wales and E. Matyus, Phys. Chem.~Chem. Phys., 18, 22816 (2016).
    Rovibrational Transitions of the Methane-Water Dimer From Intermolecular Quantum Dynamical Computations

  • F.Y. Naumkin and D.J. Wales, Chem. Phys. Lett., 659, 282-288 (2016).
    Trapping of Hydrogen Atoms Inside Small Beryllium Clusters and Their Ions

  • S. Niblett, V. de Souza, J. Stevenson and D.J. Wales, J. Chem. Phys., 145, 024505 (2016).
    Dynamics of a Molecular Glass Former: Energy Landscapes for Diffusion in Ortho-Terphenyl

  • D. Mehta, J. Chen, D.Z. Chen, H. Kusumaatmaja and D.J. Wales, Editors' Suggestion: Phys. Rev. Lett., 117, 028301 (2016).
    Kinetic Transition Networks for the Thomson Problem and Smale's 7th Problem
    University of Notre Dame Press Release
    Researchers chip away at Smale's 7th unsolved problem in mathematics

  • V.K. de Souza and D.J. Wales, J. Stat. Phys., 7, 074001, (2016).
    The Potential Energy Landscape for Crystallisation of a Lennard-Jones Fluid

  • R. Das and D.J. Wales, Phys. Rev. E, 93, 063310 (2016).
    Energy Landscapes for a Machine Learning Prediction of Patient Discharge


  • D. Chakraborty, N. Sengupta and D.J. Wales, J. Phys. Chem. B, 120, 4331-4340 (2016).
    Conformational Energy Landscape of the Ritonavir Molecule

  • W.T.S. Cole, J.D. Farrell, D.J. Wales and R.J. Saykally, Science, 352, 1194-1197 (2016).
    Structure and Torsional Dynamics of the Water Octamer From THz Laser Spectroscopy Near 215 micrometres-1

  • J. Hernandez-Rojas, F. Calvo and D.J. Wales, Phys. Chem. Chem. Phys. Communication, 16, 13736-13740 (2016).
    Coarse-Graining the Structure of Polycyclic Aromatic Hydrocarbon Clusters

  • S. Paquay, H. Kusumaatmaja, D.J. Wales, R. Zandi, P. van der Schoot, Soft Matter, 12, 5708-5717 (2016).
    Energetically Favoured Defects in Dense Packings of Particles on Spherical Surfaces

  • E. Matyus, D.J. Wales and S.C. Althorpe, J. Chem. Phys., 144, 114108 (2016).
    Quantum Tunneling Splittings From Path-Integral Molecular Dynamics

  • A.J. Ballard, J.D. Stevenson, R. Das and D.J. Wales, J. Chem. Phys., 144, 124119 (2016).
    Energy Landscapes for a Machine Learning Application to Series Data

  • S. Martiniani, K.J. Schrenk, J.D. Stevenson, D.J. Wales and D. Frenkel, Phys. Rev. E, 93, 012906 (2016).
    Turning Intractable Counting into Sampling: Computing the Configurational Entropy of Three-Dimensional Jammed Packings
    Cambridge University Research: How many ways can you arrange 128 tennis balls? Researchers solve an apparently impossible problem
    Sky News: Tennis Ball Experiment Could Predict Avalanches
    New Scientist: Number of ways to arrange 128 balls exceeds atoms in universe

  • P. Salamon, D.J. Wales, A. Segall, Y.A. Lai, C. Schon, K.H. Hoffmann and B. Andresen, J. Non-Equilibrium Thermodynamics, 41, 13-18 (2016).
    Rate Constants, Timescales, and Free Energy Barriers

  • J.O. Richardson, C. Perez, S. Lobsiger, A.A. Reid, B. Temelso, G.C. Shields, Z. Kisiel, D.J. Wales, B.H. Pate and S.C. Althorpe, Science, 351, 1310-1313 (2016).
    Concerted Hydrogen-Bond Breaking by Quantum Tunnelling in the Water Hexamer Prism
    D.C. Clary, Science, 351, 1267-1268 (2016).
    Perspective: Quantum dynamics in the smallest water droplet
    Science video

  • J.M. Carr, D. Mazauric, F. Cazals and D.J. Wales, J. Chem. Phys., 144, 054109 (2016).
    Energy Landscapes and Persistent Minima

  • F. Calvo, D. Schebarchov and D.J. Wales, J. Chem. Theor. Comput., 12, 902-909 (2016).
    Grand and Semi-Grand Canonical Basin-Hopping

  • D. Mehta, T. Chen, J.W.R. Morgan and D.J. Wales, J. Chem. Phys., 143, 247102, (2016)
    Response to Comment on `Exploring the potential energy landscape of the Thomson problem via Newton homotopies' [J. Chem. Phys. 143, 247101 (2015)],

  • I. Yildirim, D. Chakraborty, M.D. Disney, D.J. Wales and G.C. Schatz, J. Chem. Theor. Comput., 11, 4943-4958 (2015).
    Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1

  • C. Shang, J.M. Philpott, N. Bampos, P.D. Barker and D.J. Wales, Phys. Chem. Chem. Phys., 27, 27094-27102, (2015).
    How to make a porphyrin flip: Dynamics of asymmetric porphyrin oligomers

  • J.M. Carr, C.S. Whittleston, D.C. Wade and D.J. Wales, Phys. Chem. Chem. Phys., 15, 20250-20258 (2015).
    Energy Landscapes of a Hairpin Peptide Including NMR Chemical Shift Restraints

  • I.D. Seymour, S. Chakraborty, D.S. Middlemiss, D.J. Wales and C.P. Grey, Chemistry of Materials, 27, 5550-5561 (2015).
    Mapping Structural Changes in Electrode Materials: Application of the Hybrid Eigenvector-Following Density Functional Theory (DFT) Method to Layered Li0.5MnO2

  • 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., 5, 12556 (2015).
    Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix

  • S.N. Fejer and D.J. Wales, Soft Matter, 11(33), 6663-6668 (2015).
    Design of a Kagome lattice from soft anisotropic particles

  • D. Schebarchov and D.J. Wales, Phys. Chem. Chem. Phys., 17, 28331-28338 (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., 142, 194113 (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., 11, 2377-2384 (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, 248, 611-640 (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., 11, 2307-2314 (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., 625, 1-4 (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, 5, 273-289 (2015).
    Exploiting the Potential Energy Landscape to Sample Free Energy

  • F. Calvo and D.J. Wales, Chem. Phys. Lett., 623, 17-21 (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
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