{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Crossley-Lewis J"],"funding":["Biotechnology and Biological Sciences Research Council","Engineering and Physical Sciences Research Council"],"pagination":["108606"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7616772"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["125"],"pubmed_abstract":["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."],"journal":["Journal of molecular graphics & modelling"],"pubmed_title":["Interactive molecular dynamics in virtual reality for modelling materials and catalysts."],"pmcid":["PMC7616772"],"funding_grant_id":["1274908","EP/G007705/1","EP/M015378/1","BB/L018756/1","GR/R86119/01","EP/N024117/1","EP/M027546/1","BB/T017066/1","EP/W013738/1","EP/J010588/1","EP/R029407/1","EP/R029407/2","EP/L000253/1","EP/G042853/1","EP/V028537/1","EP/M022609/1","BB/V016768/1","EP/I030395/1","BB/L01386X/1","BB/K016601/1","BB/R016445/1","EP/X035859/1","EP/E022197/1","BB/RO16445/1","EP/G002843/1"],"pubmed_authors":["Glowacki DR","Todorov IT","Allan NL","Yong CW","Mulholland AJ","Dunn J","Sunley GJ","Crossley-Lewis J","Buda C","Elena AM"],"additional_accession":[]},"is_claimable":false,"name":"Interactive molecular dynamics in virtual reality for modelling materials and catalysts.","description":"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.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Dec","modification":"2025-04-03T23:23:48.668Z","creation":"2025-04-03T23:23:48.668Z"},"accession":"S-EPMC7616772","cross_references":{"pubmed":["37660615"],"doi":["10.1016/j.jmgm.2023.108606"]}}