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Archetypal energy landscapes

Author

Listed:
  • David J. Wales

    (University Chemical Laboratories)

  • Mark A. Miller

    (University Chemical Laboratories)

  • Tiffany R. Walsh

    (University Chemical Laboratories)

Abstract

Energy landscapes hold the key to understanding a wide range of molecular phenomena. The problem of how a denatured protein re-folds to its active state (Levinthal's parado1) has been addressed in terms of the underlying energy landscape2,3,4,5,6,7, as has the widely used ‘strong’ and ‘fragile’ classification of liquids8,9. Here we show how three archetypal energy landscapes for clusters of atoms or molecules can be characterized in terms of the disconnectivity graphs10 of their energy minima—that is, in terms of the pathways that connect minima at different threshold energies. First we consider a cluster of 38 Lennard–Jones particles, whose energy landscape is a ‘double funnel’ on which relaxation to the global minimum is diverted into a set of competing structures. Then we characterize the energy landscape associated with the annealing of C60 cages to buckministerfullerene, and show that it provides experimentally accessible clues to the relaxation pathway. Finally we show a very different landscape morphology, that of a model water cluster (H2O)20, and show how it exhibits features expected for a ‘strong’ liquid. These three examples do not exhaust the possibilities, and might constitute substructures of still more complex landscapes.

Suggested Citation

  • David J. Wales & Mark A. Miller & Tiffany R. Walsh, 1998. "Archetypal energy landscapes," Nature, Nature, vol. 394(6695), pages 758-760, August.
    • Handle: RePEc:nat:nature:v:394:y:1998:i:6695:d:10.1038_29487
    DOI: 10.1038/29487
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    Citations

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    Cited by:

    1. Sichun Yang & Benoît Roux, 2008. "Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms," PLOS Computational Biology, Public Library of Science, vol. 4(3), pages 1-14, March.
    2. Shiun-Jr Yang & David J. Wales & Esmae J. Woods & Graham R. Fleming, 2024. "Design principles for energy transfer in the photosystem II supercomplex from kinetic transition networks," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Livia B. Pártay & Gábor Csányi & Noam Bernstein, 2021. "Nested sampling for materials," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 94(8), pages 1-18, August.
    4. Bikulov, A.Kh. & Zubarev, A.P., 2021. "Ultrametric theory of conformational dynamics of protein molecules in a functional state and the description of experiments on the kinetics of CO binding to myoglobin," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 583(C).
    5. Michael C Prentiss & David J Wales & Peter G Wolynes, 2010. "The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein," PLOS Computational Biology, Public Library of Science, vol. 6(7), pages 1-12, July.
    6. Zúñiga-Galindo, W.A., 2022. "Ultrametric diffusion, rugged energy landscapes and transition networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 597(C).
    7. Christoph Flamm & Ivo L. Hofacker & Peter F. Stadler & Michael T. Wolfinger, 2001. "Barrier Trees of Degenerate Landscapes," Working Papers 01-09-053, Santa Fe Institute.

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