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A general method for determining molecular interfaces and layers.

Jiří Škvor1, Jiří Škvára1, Jan Jirsák2

  • 1Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, 400 96 Ústí nad Labem, Czechia.

Journal of Molecular Graphics & Modelling
|July 3, 2017
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Summary

A new computational method precisely identifies surfaces between molecular domains using triangulation and domain assignment. This approach defines surfaces as facets, enabling straightforward identification of molecular layers in various physical systems.

Keywords:
InterfaceMolecular layersPercolating clusterThin filmsWeighted Delaunay triangulation

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Area of Science:

  • Computational chemistry and physics
  • Materials science
  • Surface science

Background:

  • Accurate identification of interfaces between molecular domains is crucial for understanding material properties.
  • Existing methods for surface determination can be limited in scope or applicability to complex molecular arrangements.

Purpose of the Study:

  • To develop a general and direct computational scheme for locating surfaces separating arbitrarily shaped molecular domains.
  • To provide a robust method for identifying molecular layers and characterizing interfacial regions.

Main Methods:

  • A two-module scheme involving triangulation (Delaunay, regular, quasi-triangulation) and assignment of simplices to domains.
  • Assignment based on characteristic metric or touching sphere concepts.
  • Implementation and comparison with existing methods like alpha-shape and GITIM.

Main Results:

  • The scheme successfully identifies surfaces as polyhedral structures, not just discrete particles.
  • Demonstrated applicability to artificial and physical examples, including thin films, liquid water under electric fields, and at solid walls.
  • Effective identification of individual molecular layers from the interface inwards.

Conclusions:

  • The developed computational scheme offers a versatile and accurate approach to surface identification in molecular systems.
  • The method's modularity allows for flexibility and integration with existing techniques.
  • Provides a foundation for further studies on interfacial phenomena and phase behavior.