Interactive molecular dynamics in virtual reality for modelling materials and catalysts.

Autor: Crossley-Lewis J; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK., Dunn J; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK., Buda C; Applied Sciences, bp Innovation and Engineering, BP plc, 150 West Warrenville Road, Naperville, IL, 60563, USA., Sunley GJ; Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK., Elena AM; Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK., Todorov IT; Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK., Yong CW; Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK., Glowacki DR; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK., Mulholland AJ; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK., Allan NL; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. Electronic address: neil.allan@bristol.ac.uk.
Jazyk: angličtina
Zdroj: Journal of molecular graphics & modelling [J Mol Graph Model] 2023 Dec; Vol. 125, pp. 108606. Date of Electronic Publication: 2023 Aug 24.
DOI: 10.1016/j.jmgm.2023.108606
Abstrakt: Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.
Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Joe Crossley-Lewis reports financial support was provided by BP Plc. Josh Dunn reports financial support was provided by BP Plc.
(Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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