Interactive molecular dynamics in virtual reality for modelling materials and catalysts

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

doi:10.1016/j.jmgm.2023.108606

Interactive molecular dynamics in virtual reality for modelling materials and catalysts

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

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

9 Citations (Scopus)

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.

Original language	English
Article number	108606
Number of pages	9
Journal	Journal of Molecular Graphics and Modelling
Volume	125
Early online date	24 Aug 2023
DOIs	https://doi.org/10.1016/j.jmgm.2023.108606
Publication status	Published - 1 Dec 2023

Bibliographical note

Funding Information:
BP plc is thanked for financial support of J.C-L and J.D. through industrial CASE studentships in partnership with the Engineering and Physical Sciences Research Council (EPSRC) . Dr Simon Bennie assisted at the start of this project and participated in some discussions. JC-L acknowledges support from a 2019 summer bursary awarded by CCP5 (under EPSRC Grant EP/M022617/1 ) to Dr Bennie. The work has also been supported by EPSRC Grant, EP/M022609/1 (AJM) and BBSRC Grant BB/RO16445/1 (AJM).

Research Groups and Themes

Physical & Theoretical

Keywords

Virtual Reality
Materials
Molecular Dynamics
Zeolites
Fast Ion Conductors
Simulation and Modelling
Catalysis

Access to Document

10.1016/j.jmgm.2023.108606Licence: CC BY

Handle.net

Persistent link

Molecular Modelling of Methyl Ester-Promoted Dimethyl Ether Formation from Methanol: Enhancing Routes to Renewable Fuels in MFI Zeolite through Reactivity and Dynamics
Crossley-Lewis, J. M. (Author), Allan, N. (Supervisor) & Mulholland, A. (Supervisor), 1 Oct 2024
Student thesis: Doctoral Thesis › Doctor of Philosophy (PhD)

File

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities
Alam, S. R. (Manager), Williams, D. A. G. (Manager), Eccleston, P. E. (Manager) & Greene, D. (Manager)
Facility/equipment: Facility

Cite this

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title = "Interactive molecular dynamics in virtual reality for modelling materials and catalysts",

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.",

keywords = "Virtual Reality, Materials, Molecular Dynamics, Zeolites, Fast Ion Conductors, Simulation and Modelling, Catalysis",

author = "Crossley-Lewis, \{Joe M\} and Josh Dunn and Corneliu Buda and Sunley, \{Glenn J\} and Alin Elena and IT Todorov and Chin Yong and Glowacki, \{David R\} and Mulholland, \{Adrian J\} and Allan, \{Neil L\}",

note = "Funding Information: BP plc is thanked for financial support of J.C-L and J.D. through industrial CASE studentships in partnership with the Engineering and Physical Sciences Research Council (EPSRC) . Dr Simon Bennie assisted at the start of this project and participated in some discussions. JC-L acknowledges support from a 2019 summer bursary awarded by CCP5 (under EPSRC Grant EP/M022617/1 ) to Dr Bennie. The work has also been supported by EPSRC Grant, EP/M022609/1 (AJM) and BBSRC Grant BB/RO16445/1 (AJM).",

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doi = "10.1016/j.jmgm.2023.108606",

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AU - Crossley-Lewis, Joe M

AU - Dunn, Josh

AU - Buda, Corneliu

AU - Sunley, Glenn J

AU - Elena, Alin

AU - Todorov, IT

AU - Yong, Chin

AU - Glowacki, David R

AU - Mulholland, Adrian J

AU - Allan, Neil L

N1 - Funding Information: BP plc is thanked for financial support of J.C-L and J.D. through industrial CASE studentships in partnership with the Engineering and Physical Sciences Research Council (EPSRC) . Dr Simon Bennie assisted at the start of this project and participated in some discussions. JC-L acknowledges support from a 2019 summer bursary awarded by CCP5 (under EPSRC Grant EP/M022617/1 ) to Dr Bennie. The work has also been supported by EPSRC Grant, EP/M022609/1 (AJM) and BBSRC Grant BB/RO16445/1 (AJM).

PY - 2023/12/1

Y1 - 2023/12/1

N2 - 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.

AB - 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.

KW - Virtual Reality

KW - Materials

KW - Molecular Dynamics

KW - Zeolites

KW - Fast Ion Conductors

KW - Simulation and Modelling

KW - Catalysis

U2 - 10.1016/j.jmgm.2023.108606

DO - 10.1016/j.jmgm.2023.108606

M3 - Article (Academic Journal)

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SN - 1093-3263

VL - 125

JO - Journal of Molecular Graphics and Modelling

JF - Journal of Molecular Graphics and Modelling

M1 - 108606

ER -

Interactive molecular dynamics in virtual reality for modelling materials and catalysts

Abstract

Bibliographical note

Research Groups and Themes

Keywords

Access to Document

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Student theses

Molecular Modelling of Methyl Ester-Promoted Dimethyl Ether Formation from Methanol: Enhancing Routes to Renewable Fuels in MFI Zeolite through Reactivity and Dynamics

Equipment

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities

Cite this