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
Folding and misfolding of proteins, DNA and RNA
Designing landscapes for self-assembly and multifunctional systems
Landscapes for machine learning
Atomic, molecular, colloidal and nanoalloy clusters


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



buy Energy Landscapes: USA, UK

JOURNAL COVERS

Recent Publications




  • S.N. Fejer, R.G. Mantell and D.J. Wales, Mol. Phys., in press (2018).
    Designing Hierarchical Molecular Complexity: Icosahedra of Addressable Icosahedra


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  • D. Schebarchov, F. Baletto and D.J. Wales, Nanoscale, in press (2017).
    Structure, Thermodynamics, and Rearrangement Mechanisms in Gold Clusters - Insights From the Energy Landscapes Framework


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  • D. Chakraborty and D.J. Wales, J. Phys. Chem. Lett., in press (2017).
    Perspective: Energy Landscape and Pathways for Transitions Between Watson-Crick and Hoogsteen Base Pairing in DNA



  • 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


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  • 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}


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  • 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


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  • 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


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  • 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



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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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

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  • D. Chakraborty, N. Sengupta and D.J. Wales, J. Phys. Chem. B, 120, 4331-4340 (2016).
    Conformational Energy Landscape of the Ritonavir Molecule
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  • 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
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  • 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
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  • 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
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  • E. Matyus, D.J. Wales and S.C. Althorpe, J. Chem. Phys., 144, 114108 (2016).
    Quantum Tunneling Splittings From Path-Integral Molecular Dynamics
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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  • K.H. Sutherland-Cash, D. Chakrabarti and D.J. Wales, Chem. Phys. Lett., 625, 1-4 (2015).
    Free Energy Basin-Hopping
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  • 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
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  • F. Calvo and D.J. Wales, Chem. Phys. Lett., 623, 17-21 (2015).
    Harmonic Superposition Method for Grand-Canonical Ensembles
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  • 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
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  • 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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