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Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

O’Connor, Michael B.; Bennie, Simon J.; Deeks, Helen M.; Jamieson-Binnie, Alexander; Jones, Alex J.; Shannon, Robin J.; Walters, Rebecca; Mitchell, Thomas J.; Mulholland, Adrian J.; Glowacki, David R.

Authors

Michael B. O’Connor

Simon J. Bennie

Helen M. Deeks

Alexander Jamieson-Binnie

Alex J. Jones

Robin J. Shannon

Rebecca Walters

Tom Mitchell Tom.Mitchell@uwe.ac.uk
Associate Professor in Creative Technologies

Adrian J. Mulholland

David R. Glowacki



Abstract

© 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.

Citation

O’Connor, M. B., Bennie, S. J., Deeks, H. M., Jamieson-Binnie, A., Jones, A. J., Shannon, R. J., …Glowacki, D. R. (2019). Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework. Journal of Chemical Physics, 150(22), https://doi.org/10.1063/1.5092590

Journal Article Type Article
Acceptance Date May 2, 2019
Online Publication Date Jun 10, 2019
Publication Date Jun 14, 2019
Publicly Available Date Nov 30, -0001
Journal The Journal of Chemical Physics
Print ISSN 0021-9606
Publisher AIP Publishing
Peer Reviewed Peer Reviewed
Volume 150
Issue 22
DOI https://doi.org/10.1063/1.5092590
Keywords sonificatioon, VR, molecular dynamics, immersive
Public URL https://uwe-repository.worktribe.com/output/847404
Additional Information Additional Information : The following article has been submitted accepted by The Journal of Chemical Physics. After it is published, it will be found at https://aip.scitation.org/journal/jcp

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