Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

Robin J Shannon; Helen M Deeks; Eleanor Burfoot; Edward Clark; Alex J Jones; Adrian J Mulholland; David R Glowacki

doi:10.1063/5.0062517

Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

Robin J Shannon, Helen M Deeks, Eleanor Burfoot, Edward Clark, Alex J Jones, Adrian J Mulholland, David R Glowacki

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

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Abstract

The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.

Original language	English
Article number	154106
Pages (from-to)	154106
Journal	The Journal of Chemical Physics
Volume	155
Issue number	15
Early online date	21 Oct 2021
DOIs	https://doi.org/10.1063/5.0062517
Publication status	Published - 21 Oct 2021

Bibliographical note

Funding Information:
First, we would like to thank the Narupa team, specifically Dr. Mike O’Connor, Dr. Jonathan Barnoud, Alexander Jamieson-Binnie, Mark Wannacott, and Rhoslyn Roebuck Williams. We would also like to thank Markus Reiher and the SCINE Sparrow team. This work was undertaken on ARC3, part of the High-Performance Computing facilities at the University of Leeds, UK, and using the computational facilities of the Advanced Computing Research Centre, University of Bristol—http://www.bris.ac.uk/acrc/. R.J.S. acknowledges support of this work through the “CHAMPS” EPSRC program (Grant No. EP/P021123/1). D.R.G. acknowledges funding from the Royal Society as a University Research Fellow, from the European Research Council through consolidator grant NANOVR 866559, and also to the Axencia Galega de Innovación for funding through the Oportunius Program. A.J.M. acknowledges support from EPSRC (Grant No. EP/M022609/1), and H.M.D. also acknowledges studentship support from the EPSRC.

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Cite this

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Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists. / Shannon, Robin J; Deeks, Helen M; Burfoot, Eleanor et al.
In: The Journal of Chemical Physics, Vol. 155, No. 15, 154106, 21.10.2021, p. 154106.

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

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AU - Deeks, Helen M

AU - Burfoot, Eleanor

AU - Clark, Edward

AU - Jones, Alex J

AU - Mulholland, Adrian J

AU - Glowacki, David R

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AB - The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.

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DO - 10.1063/5.0062517

M3 - Article (Academic Journal)

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JO - The Journal of Chemical Physics

JF - The Journal of Chemical Physics

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M1 - 154106

ER -

Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

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