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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Abstract
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 |
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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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