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

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.

A Brave New World: Virtual Reality and Augmented Reality in Systems Biology

“…Barriers for access to VR/AR visualizations in systems biology will likely remain, however, for researchers from underdeveloped countries, and which will need to be addressed. At the same time, with the increasing trends in gamification within the VR environments (Shannon et al, 2021), barriers for scientists with low computational expertise and non-scientists in conducting their own virtual experiments will decrease. As user community grows and commercial VR/AR technologies expand, we expect the range of their systems biology applications will also continue to grow, opening possibilities for significant advancements in understanding and communicating disease-associated mechanisms, running virtual experiments, and education, and help boost the development of new therapies.…”

“…VR environments open exciting new possibilities of such gamification of virtual scientific problems both for scientists with little coding experience, as well as for non-scientists, and the communication between these two communities. We have already started to observe the first examples of such tools in computational chemistry, where Shannon et al have introduced molecular dynamics VR game to encourage users to explore the reactivity of a specific chemical system (Shannon et al, 2021), and an intuitive VR platform called Nanome presented by Kingsley et al, where the users explore and modify chemical structures collaboratively to work on structural biology and molecular drug design problems (Kingsley et al, 2019). The next several years will witness an increasing number of tools that gamify virtual experiments in the VR environments.…”

Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery

“…Most VR molecular visualization programs run as dedicated desktop applications [ 60 , 95 , 96 , 97 ]. The desktop approach is ideal in many cases because it enables innovative navigation methods [ 95 ], resource-intensive molecular-editing tools [ 97 ], and real-time user interactions with ongoing molecular dynamics simulations [ 96 , 98 , 99 , 100 , 101 , 102 , 103 ]. However, many situations call for quick, easily accessible VR visualization, and desktop programs require download, installation, and experience to use effectively.…”

Wielding the power of interactive molecular simulations

“…In the latter case, scientific problems are reformulated as playful activities, games, or puzzles to leverage human problem-solving capacity. This approach has already been applied to remote optimization of an experiment with ultracold atoms, 165 IMD exploration of chemical reaction networks, 166 molecular docking, 167 RNA folding, 34 computational enzyme design, 168 and protein structure prediction. 35,169 The approach can be taken a step further by attempting to discover the underlying algorithms used by humans in interactive simulations in order to incorporate them into novel modeling algorithms, as described by Khatib et al 170 Similarly, data harvested from reactive potential energy surface IMD have been used to train neural networks.…”

“…In the latter case, scientific problems are reformulated as playful activities, games, or puzzles to leverage human problem‐solving capacity. This approach has already been applied to remote optimization of an experiment with ultracold atoms, 165 IMD exploration of chemical reaction networks, 166 molecular docking, 167 RNA folding, 34 computational enzyme design, 168 and protein structure prediction 35,169 …”