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Molecular Physics
An International Journal at the Interface Between Chemistry and Physics
Volume 102, 2004 - Issue 9-10: Special Issue: In Honour of Ruth Lynden-Bell
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Original Articles

Some further applications of discrete path sampling to cluster isomerization

David J. Wales *
Pages 891-908 | Received 15 Jan 2004, Published online: 20 Feb 2007

Citations (175)

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Semen A. Trygubenko & David J. Wales. (2006) Kinetic analysis of discrete path sampling stationary point databases. Molecular Physics 104:9, pages 1497-1507.
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David J. Wales. (2006) Energy landscapes: calculating pathways and rates. International Reviews in Physical Chemistry 25:1-2, pages 237-282.
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Articles from other publishers (173)

Peter Schwerdtfeger & David J. Wales. (2024) 100 Years of the Lennard-Jones Potential. Journal of Chemical Theory and Computation.
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Esmae J. Woods & David J. Wales. (2024) Analysis and interpretation of first passage time distributions featuring rare events. Physical Chemistry Chemical Physics 26:3, pages 1640-1657.
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Alasdair D. Keith, Elizabeth B. Sawyer, Desmond C. Y. Choy, Yuhang Xie, George S. Biggs, Oskar James Klein, Paul D. Brear, David J. Wales & Paul D. Barker. (2024) Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins. Physical Chemistry Chemical Physics 26:2, pages 695-712.
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James Meadows & Konstantin Röder. (2023) The Effect of Pulling and Twisting Forces on Chameleon Sequence Peptides**. ChemPhysChem 24:24.
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Patryk A. Wesołowski, Adam K. Sieradzan, Michał J. Winnicki, John W.R. Morgan & David J. Wales. (2023) Energy landscapes for proteins described by the UNRES coarse-grained potential. Biophysical Chemistry 303, pages 107107.
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Gábor Csányi, John W. R. Morgan & David J. Wales. (2023) Global analysis of energy landscapes for materials modeling: A test case for C60. The Journal of Chemical Physics 159:10.
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Philipp Pracht, John W. R. Morgan & David J. Wales. (2023) Exploring energy landscapes for solid-state systems with variable cells at the extended tight-binding level. The Journal of Chemical Physics 159:6.
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James Rowe & Konstantin Röder. (2023) Chemical bonds in collagen rupture selectively under tensile stress. Physical Chemistry Chemical Physics 25:3, pages 2331-2341.
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Guowei Qi, Michail D. Vrettas, Carmen Biancaniello, Maximo Sanz-HernandezConor T. CafollaJohn W. R. MorganYifei WangAlfonso De Simone & David J. Wales. (2022) Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data. Journal of Chemical Theory and Computation 18:12, pages 7733-7750.
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Pradeep Pant. (2022) Harmonizing Interstrand Electrostatic Repulsion by Conformational Rigidity in Counterion-Deprived Z-DNA: A Molecular Dynamics Study. The Journal of Physical Chemistry B 126:48, pages 9956-9963.
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Moritz Schäffler, Mohammed Khaled & Birgit Strodel. (2022) ATRANET – Automated generation of transition networks for the structural characterization of intrinsically disordered proteins. Methods 206, pages 18-26.
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David J Wales. (2022) Dynamical Signatures of Multifunnel Energy Landscapes. The Journal of Physical Chemistry Letters 13:27, pages 6349-6358.
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Amirhossein Taghavi, Ivan Riveros, David J. Wales & Ilyas Yildirim. (2022) Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations. Journal of Chemical Theory and Computation 18:6, pages 3637-3653.
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Konstantin Röder, Amy M. Barker, Adrian Whitehouse & Samuela Pasquali. (2022) Investigating the structural changes due to adenosine methylation of the Kaposi’s sarcoma-associated herpes virus ORF50 transcript. PLOS Computational Biology 18:5, pages e1010150.
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Nicy, Debayan Chakraborty & David J. Wales. (2022) Energy Landscapes for Base-Flipping in a Model DNA Duplex. The Journal of Physical Chemistry B 126:16, pages 3012-3028.
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Konstantin Röder & David J. Wales. (2022) The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules. Frontiers in Molecular Biosciences 9.
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Konstantin Röder. (2022) The effects of glycine to alanine mutations on the structure of GPO collagen model peptides. Physical Chemistry Chemical Physics 24:3, pages 1610-1619.
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Konstantin Röder, Guillaume Stirnemann, Pietro Faccioli & Samuela Pasquali. (2022) Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods. QRB Discovery 3.
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Sridhar Neelamraju, Shachi Gosavi & David J. Wales. 2022. Energy Landscapes of Nanoscale Systems. Energy Landscapes of Nanoscale Systems 1 18 .
Sergey V. Gudkovskikh & Mikhail V. Kirov. (2021) Thermal stability of water polyhedra with square faces. Journal of Molecular Modeling 27:12.
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Daniel J. Sharpe & David J. Wales. (2021) Nearly reducible finite Markov chains: Theory and algorithms. The Journal of Chemical Physics 155:14.
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Debayan Chakraborty, Atreyee Banerjee & David J. Wales. (2021) Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides. The Journal of Physical Chemistry B 125:22, pages 5809-5822.
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Ruby Srivastava. (2021) Application of Optimization Algorithms in Clusters. Frontiers in Chemistry 9.
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Konstantin Röder. (2021) Is the H4 histone tail intrinsically disordered or intrinsically multifunctional?. Physical Chemistry Chemical Physics 23:9, pages 5134-5142.
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Evgeny MoermanDavid Furman & David J. Wales. (2020) Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications. Journal of Chemical Theory and Computation 17:1, pages 497-514.
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Dhagash MehtaTianran ChenTingting TangJonathan Hauenstein. (2021) The Loss Surface Of Deep Linear Networks Viewed Through The Algebraic Geometry Lens. IEEE Transactions on Pattern Analysis and Machine Intelligence, pages 1-1.
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Konstantin Röder & Samuela Pasquali. 2021. RNA Scaffolds. RNA Scaffolds 49 66 .
Pallab Dutta & Neelanjana Sengupta. (2020) Expectation maximized molecular dynamics: Toward efficient learning of rarely sampled features in free energy surfaces from unbiased simulations. The Journal of Chemical Physics 153:15, pages 154104.
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Thomas D. Swinburne, Deepti Kannan, Daniel J. Sharpe & David J. Wales. (2020) Rare events and first passage time statistics from the energy landscape. The Journal of Chemical Physics 153:13.
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David F. Burke, Rosemary G. Mantell, Catherine E. Pitt & David J. Wales. (2020) Energy Landscape for the Membrane Fusion Pathway in Influenza A Hemagglutinin From Discrete Path Sampling. Frontiers in Chemistry 8.
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K. Röder & D. J. Wales. (2020) Improving double-ended transition state searches for soft-matter systems. The Journal of Chemical Physics 153:3.
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Daniel J. Sharpe & David J. Wales. (2020) Efficient and exact sampling of transition path ensembles on Markovian networks. The Journal of Chemical Physics 153:2.
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Clovis Lapointe, Thomas D. Swinburne, Louis Thiry, Stéphane Mallat, Laurent Proville, Charlotte S. Becquart & Mihai-Cosmin Marinica. (2020) Machine learning surrogate models for prediction of point defect vibrational entropy. Physical Review Materials 4:6.
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Daniel J. Sharpe, Konstantin Röder & David J. Wales. (2020) Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers. The Journal of Physical Chemistry B 124:20, pages 4062-4068.
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Kim C. LiuKonstantin Röder, Clemens Mayer, Santosh AdhikariDavid J. Wales & Shankar Balasubramanian. (2020) Affinity-Selected Bicyclic Peptide G-Quadruplex Ligands Mimic a Protein-like Binding Mechanism. Journal of the American Chemical Society 142:18, pages 8367-8373.
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Ilda D’Annessa, Francesco Saverio Di Leva, Anna La Teana, Ettore Novellino, Vittorio Limongelli & Daniele Di Marino. (2020) Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?. Frontiers in Molecular Biosciences 7.
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Thomas D. Swinburne & David J. Wales. (2020) Defining, Calculating, and Converging Observables of a Kinetic Transition Network. Journal of Chemical Theory and Computation 16:4, pages 2661-2679.
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Debayan Chakraborty, Yassmine Chebaro & David J. Wales. (2020) A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide. Physical Chemistry Chemical Physics 22:3, pages 1359-1370.
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Konstantin Röder, Guillaume Stirnemann, Anne-Catherine Dock-Bregeon, David J Wales & Samuela Pasquali. (2019) Structural transitions in the RNA 7SK 5′ hairpin and their effect on HEXIM binding. Nucleic Acids Research.
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Shiyan Xiao, Daniel J. Sharpe, Debayan Chakraborty & David J. Wales. (2019) Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes. The Journal of Physical Chemistry Letters 10:21, pages 6771-6779.
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Daniel J. Sharpe & David J. Wales. (2019) Identifying mechanistically distinct pathways in kinetic transition networks. The Journal of Chemical Physics 151:12.
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Sridhar Neelamraju, David J. Wales & Shachi Gosavi. (2019) Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins. Journal of Chemical Information and Modeling 59:5, pages 1703-1708.
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Konstantin Röder, Jerelle A. Joseph, Brooke E. Husic & David J. Wales. (2019) Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. Advanced Theory and Simulations 2:4.
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Debayan Chakraborty & David J. Wales. (2019) Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling. The Journal of Chemical Physics 150:12.
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Ruby Srivastava. 2019. Density Functional Theory. Density Functional Theory.
David J. Wales, Matthew D. Disney & Ilyas Yildirim. (2018) Computational Investigation of RNA A-Bulges Related to the Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism. The Journal of Physical Chemistry B 123:1, pages 57-65.
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Jerelle A. Joseph, Debayan Chakraborty & David J. Wales. (2018) Energy Landscape for Fold-Switching in Regulatory Protein RfaH. Journal of Chemical Theory and Computation 15:1, pages 731-742.
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Sridhar Neelamraju, Shachi Gosavi & David J. Wales. (2018) Energy Landscape of the Designed Protein Top7. The Journal of Physical Chemistry B 122:51, pages 12282-12291.
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Addie Kingsland & Lutz Maibaum. (2018) DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. The Journal of Physical Chemistry B 122:51, pages 12251-12259.
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Jerelle A. Joseph & David J. Wales. (2018) Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide. The Journal of Physical Chemistry B 122:50, pages 11906-11921.
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Konstantin Röder & David J. Wales. (2018) Evolved Minimal Frustration in Multifunctional Biomolecules. The Journal of Physical Chemistry B 122:49, pages 10989-10995.
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Konstantin Röder & David J. Wales. (2018) Analysis of the Ub to Ub-CR Transition in Ubiquitin. Biochemistry 57:43, pages 6180-6186.
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S. P. Niblett, V. K. de Souza, R. L. Jack & D. J. Wales. (2018) Effects of random pinning on the potential energy landscape of a supercooled liquid. The Journal of Chemical Physics 149:11.
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Yinjiang Cai & Longjiu Cheng. (2018) Single-root networks for describing the potential energy surface of Lennard-Jones clusters. The Journal of Chemical Physics 149:8.
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Konstantin Röder & David J. Wales. (2018) Predicting Pathways between Distant Configurations for Biomolecules. Journal of Chemical Theory and Computation 14:8, pages 4271-4278.
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Justin E. Elenewski, Kirill A. Velizhanin & Michael Zwolak. (2018) A spin-1 representation for dual-funnel energy landscapes. The Journal of Chemical Physics 149:3.
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James S. Klimavicz, Konstantin Röder & David J. Wales. (2018) Energy Landscapes of Mini-Dumbbell DNA Octanucleotides. Journal of Chemical Theory and Computation 14:7, pages 3870-3876.
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David J. Wales. (2018) Exploring Energy Landscapes. Annual Review of Physical Chemistry 69:1, pages 401-425.
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Konstantin Röder & David J. Wales. (2018) Energy Landscapes for the Aggregation of Aβ 17–42 . Journal of the American Chemical Society 140:11, pages 4018-4027.
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Debayan Chakraborty & David J. Wales. (2017) Energy Landscape and Pathways for Transitions between Watson–Crick and Hoogsteen Base Pairing in DNA. The Journal of Physical Chemistry Letters 9:1, pages 229-241.
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Tristan Cragnolini, Debayan Chakraborty, Jiří Šponer, Philippe Derreumaux, Samuela Pasquali & David J. Wales. (2017) Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch. The Journal of Chemical Physics 147:15.
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Matthew Griffiths, Samuel P. Niblett & David J. Wales. (2017) Optimal Alignment of Structures for Finite and Periodic Systems. Journal of Chemical Theory and Computation 13:10, pages 4914-4931.
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G. Henkelman. (2017) Atomistic Simulations of Activated Processes in Materials. Annual Review of Materials Research 47:1, pages 199-216.
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David J. Wales & Ilyas Yildirim. (2017) Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field. The Journal of Physical Chemistry B 121:14, pages 2989-2999.
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J. Hernández-Rojas, F. Calvo, S. Niblett & D. J. Wales. (2017) Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials. Physical Chemistry Chemical Physics 19:3, pages 1884-1895.
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David J. Wales & Joanne M. Carr. (2012) Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations. Journal of Chemical Theory and Computation 8:12, pages 5020-5034.
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Nathan Eidelson & Baron Peters. (2012) Transition path sampling for discrete master equations with absorbing states. The Journal of Chemical Physics 137:9.
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David J. WalesTeresa Head-Gordon. (2012) Evolution of the Potential Energy Landscape with Static Pulling Force for Two Model Proteins. The Journal of Physical Chemistry B 116:29, pages 8394-8411.
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David J. Wales. (2012) Decoding the energy landscape: extracting structure, dynamics and thermodynamics. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 370:1969, pages 2877-2899.
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F. Calvo, E. Yurtsever & D. J. Wales. (2012) Energy landscapes of ion clusters in isotropic quadrupolar and octupolar traps. The Journal of Chemical Physics 136:2.
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Florent Calvo, Jonathan P. K. Doye & David J. Wales. (2012) Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms. Nanoscale 4:4, pages 1085-1100.
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Konstantin Klenin, Birgit Strodel, David J. Wales & Wolfgang Wenzel. (2011) Modelling proteins: Conformational sampling and reconstruction of folding kinetics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1814:8, pages 977-1000.
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Massimiliano Picciani, Manuel Athènes, Jorge Kurchan & Julien Tailleur. (2011) Simulating structural transitions by direct transition current sampling: The example of LJ38. The Journal of Chemical Physics 135:3.
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William Challacombe, Jim Chelikowsky, Jeffrey Grossman, Arkady V. Krasheninnikov, Fedor Y. Naumkin, George C. Schatz, Gotthard Seifert, Jayant K Singh, David Wales, Mark Wilson, Alessandro Fortunelli, Stefano Sanvito, Malcolm Heggie & Eva ZurekDwaipayan Chakrabarti, Szilard N. Fejer & David J. Wales. 2011. Computational Nanoscience. Computational Nanoscience 58 81 .
Dwaipayan Chakrabarti, Tim S. Totton, Markus Kraft & David J. Wales. (2011) A survey of the potential energy surface for the (benzene)13 cluster. Physical Chemistry Chemical Physics 13:48, pages 21362.
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David J. Wales. 2010. Modern Methods of Crystal Structure Prediction. Modern Methods of Crystal Structure Prediction 29 54 .
Edyta Małolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer & David J. Wales. (2010) Symmetrization of the AMBER and CHARMM force fields. Journal of Computational Chemistry 31:7, pages 1402-1409.
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Dimitrios G. Tsalikis, Nikolaos Lempesis, Georgios C. Boulougouris & Doros N. Theodorou. (2010) Efficient Parallel Decomposition of Dynamical Sampling in Glass-Forming Materials Based on an “On the Fly” Definition of Metabasins. Journal of Chemical Theory and Computation 6:4, pages 1307-1322.
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Marianne S. Bauer, Birgit Strodel, Szilard N. Fejer, Elena F. Koslover & David J. Wales. (2010) Interpolation schemes for peptide rearrangements. The Journal of Chemical Physics 132:5, pages 054101.
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T. Okushima, T. Niiyama, K. S. Ikeda & Y. Shimizu. (2009) Graph-based analysis of kinetics on multidimensional potential-energy surfaces. Physical Review E 80:3.
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David J. Wales. (2009) Calculating rate constants and committor probabilities for transition networks by graph transformation. The Journal of Chemical Physics 130:20.
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Joanne M. Carr & David J. Wales. (2009) Refined kinetic transition networks for the GB1 hairpin peptide. Physical Chemistry Chemical Physics 11:18, pages 3341.
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Birgit Strodel & David J. Wales. (2008) Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide. Chemical Physics Letters 466:4-6, pages 105-115.
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Birgit Strodel, Anthony W. Fitzpatrick, Michele Vendruscolo, Christopher M. Dobson & David J. Wales. (2008) Characterizing the First Steps of Amyloid Formation for the ccβ Peptide. The Journal of Physical Chemistry B 112:32, pages 9998-10004.
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Quoc Chinh Nguyen, Yew Soon Ong, Harold Soh & Jer-Lai Kuo. (2008) Multiscale Approach to Explore the Potential Energy Surface of Water Clusters (H 2 O) n n ≤ 8 . The Journal of Physical Chemistry A 112:28, pages 6257-6261.
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Joanne M. Carr & David J. Wales. (2008) Folding Pathways and Rates for the Three-Stranded β-Sheet Peptide Beta3s using Discrete Path Sampling. The Journal of Physical Chemistry B 112:29, pages 8760-8769.
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Pavel A. Frantsuzov & Vladimir A. Mandelshtam. (2008) Equilibrium properties of quantum water clusters by the variational Gaussian wavepacket method. The Journal of Chemical Physics 128:9.
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Mey Khalili & David J. Wales. (2008) Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling. The Journal of Physical Chemistry B 112:8, pages 2456-2465.
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Chengju Wang & Richard M. Stratt. (2007) Global perspectives on the energy landscapes of liquids, supercooled liquids, and glassy systems: Geodesic pathways through the potential energy landscape. The Journal of Chemical Physics 127:22.
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Birgit StrodelChris S. WhittlestonDavid J. Wales. (2007) Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide. Journal of the American Chemical Society 129:51, pages 16005-16014.
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Elena F. Koslover & David J. Wales. (2007) Comparison of double-ended transition state search methods. The Journal of Chemical Physics 127:13.
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T. Okushima, T. Niiyama, K. S. Ikeda & Y. Shimizu. (2007) Connectivity graph: Multiple connectivity on potential energy surface does affect the dynamics. Physical Review E 76:3.
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F. Calvo & P. Parneix. (2007) Accurate modeling of sequential decay in clusters over long time scales: Insights from phase space theory. The Journal of Chemical Physics 126:3.
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David J. Wales & Tetyana V. Bogdan. (2006) Potential Energy and Free Energy Landscapes. The Journal of Physical Chemistry B 110:42, pages 20765-20776.
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Graham Cox, R. Stephen Berry & Roy L. Johnston. (2006) Characterizing Potential Surface Topographies through the Distribution of Saddles and Minima. The Journal of Physical Chemistry A 110:40, pages 11543-11550.
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G. Adjanor, M. Athènes & F. Calvo. (2006) Free energy landscape from path-sampling: application to the structural transition in LJ38. The European Physical Journal B 53:1, pages 47-60.
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Vladimir A. Mandelshtam, Pavel A. Frantsuzov & Florent Calvo. (2005) Structural Transitions and Melting in LJ 74 - 78 Lennard-Jones Clusters from Adaptive Exchange Monte Carlo Simulations . The Journal of Physical Chemistry A 110:16, pages 5326-5332.
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David J. Wales, Joanne M. Carr & Tim James. 2006. New Algorithms for Macromolecular Simulation. New Algorithms for Macromolecular Simulation 73 87 .
Joanne M. Carr & David J. Wales. (2005) Global optimization and folding pathways of selected α-helical proteins. The Journal of Chemical Physics 123:23.
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David J Wales. (2005) Energy landscapes and properties of biomolecules. Physical Biology 2:4, pages S86-S93.
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Claire P. Massen & Jonathan P. K. Doye. (2005) Identifying communities within energy landscapes. Physical Review E 71:4.
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