Evidence map›Paper›PMID 37660615›Full record

ArticleJournal of molecular graphics & modelling2023

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

Joe Crossley-Lewis, Josh Dunn, Corneliu Buda, Glenn J Sunley, Alin M Elena, Ilian T Todorov, Chin W Yong, David R Glowacki, Adrian J Mulholland, Neil L Allan

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular graphics & modelling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
6.1field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 12 citations in OpenAlex.

  1. Review
  2. Elements and roadmap for interactive molecular graphics and modeling "in the Holodeck".Protein science : a publication of the Protein Society · 2026
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 3 institutions in 1 country.

Joe Crossley-LewisCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
Josh DunnCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
Corneliu BudaApplied Sciences, bp Innovation and Engineering, BP plc, 150 West Warrenville Road, Naperville, IL, 60563, USA.
Glenn J SunleyApplied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK.
Alin M ElenaScientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK.
Ilian T TodorovScientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK.
Chin W YongScientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK.
David R GlowackiCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
Adrian J MulhollandCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
Neil L AllanCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. Electronic address: neil.allan@bristol.ac.uk.
University of Bristol · GBDaresbury Laboratory · GBBP (United Kingdom) · GB

Funding

Biotechnology and Biological Sciences Research Council BB/L01386X/1Biotechnology and Biological Sciences Research Council BB/R016445/1Biotechnology and Biological Sciences Research Council BB/RO16445/1
6 · The paper itself

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.

Indexed as

Molecular Dynamics SimulationVirtual RealityCatalysisDiffusionEstersLithiumEstersLithiumDefectsFast-ion conductionInteractive molecular dynamics in virtual reality zeolite catalysisMaterialsMolecular dynamicsVirtual reality

Identifiers

PMID37660615
PMCPMC7616772
OpenAlexW4386319351

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.