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

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

doi:10.1063/5.0062517

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.

Highlights

In recent years, the closely related concepts of “gamification”1–3 of scientific problems and utilizing “citizen scientists”4 to gather data have become increasingly used as research tools in the molecular science literature
The utility of this iMD-virtual reality (VR) framework has been demonstrated in other applications: It has been shown to be effective at sampling drug binding poses32 and has recently been utilized for a study on SARSCoV-2 docking,33 it has been used to aid the sampling of molecular geometries for fitting to a neural network,34,35 and the enhanced perception of users in iMD-VR toward subtle dynamical changes in molecular simulations is an area of ongoing research
IV, where we analyze the reaction game data in the context of three separate questions: Does the user-generated reaction network capture the important process that has been identified in the literature, does the user-generated network find anything new, and can we identify any difference in strategy between human-guided molecular dynamics and molecular dynamics biased through some algorithmic method

Summary

Introduction

The closely related concepts of “gamification” of scientific problems and utilizing “citizen scientists” to gather data have become increasingly used as research tools in the molecular science literature. The growing body of work in this field clearly demonstrates that if scientific problems are formulated in the right way and the game is engineered to engage a lay audience with these questions, scitation.org/journal/jcp utilizing data from the public can be highly effective Another emerging tool in the molecular sciences is the use of virtual reality (VR) technologies, and the manner in which VR can aid the teaching/learning of computational chemistry tasks has been well documented.. This “interactive” molecular dynamics approach extended to virtual reality (iMD-VR) has been described in several recent papers. It has been shown that a VR environment offers an intuitive way for nonexperts to understand and manipulate molecular motion, and it was demonstrated that users in a 3D VR environment were significantly more efficient at performing complex computational chemistry tasks when compared to a 2D mouse-based or touchscreen interface. The utility of this iMD-VR framework has been demonstrated in other applications: It has been shown to be effective at sampling drug binding poses and has recently been utilized for a study on SARSCoV-2 docking, it has been used to aid the sampling of molecular geometries for fitting to a neural network, and the enhanced perception of users in iMD-VR toward subtle dynamical changes in molecular simulations is an area of ongoing research. Other work has explored the addition of sonic elements to add another perceptive layer to users’ experience in VR. These successes coupled with the user interface (UI) elements and the immersive experience afforded by VR and potential sonification make iMD-VR an ideal basis for a gamification interface

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