Enumerating and indexing many-body intramolecular interactions:a graph theoretic approach

Penfold, Robert and Wilde, Peter J. (2015) Enumerating and indexing many-body intramolecular interactions:a graph theoretic approach. Journal of Mathematical Chemistry, 53 (7). pp. 1634-1648. ISSN 0259-9791

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The central idea observes a recursive mapping of -body intramolecular interactions to -body terms that is consistent with the molecular topology. Iterative application of the line graph transformation is identified as a natural and elegant tool to accomplish the recursion. The procedure readily generalizes to arbitrary -body potentials. In particular, the method yields a complete characterization of -body interactions. The hierarchical structure of atomic index lists for each interaction order is compactly expressed as a directed acyclic graph. A pseudo-code description of the generating algorithm is given. With suitable data structures (e.g., edge lists or adjacency matrices), automatic enumeration and indexing of -body interactions can be implemented straightforwardly to handle large bio-molecular systems. Explicit examples are discussed, including a chemically relevant effective potential model of taurocholate bile salt.

Item Type: Article
Additional Information: © The Author(s) 2015 Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Uncontrolled Keywords: computer simulation,molecular modelling,graph theory,simulations,systems
Faculty \ School: Faculty of Science > School of Mathematics
Faculty of Science > School of Pharmacy
Depositing User: Pure Connector
Date Deposited: 24 Sep 2016 00:55
Last Modified: 21 Mar 2024 01:28
URI: https://ueaeprints.uea.ac.uk/id/eprint/60286
DOI: 10.1007/s10910-015-0510-x


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