Sampling molecular conformations and dynamics in a multi-user virtual reality framework

Abstract

We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures 'on the fly', and to interact with other users in the same virtual environment. A series of controlled studies, wherein participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw-sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modelling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically 3d. This framework should accelerate progress in nanoscale molecular engineering areas such as drug development, synthetic biology, and catalyst design. More broadly, our findings highlight VR's potential in scientific domains where 3d dynamics matter, spanning research and education.

5 pages, 3 figures, 19 pages Supporting Info

References in corpus (2)

• PLUMED: a portable plugin for free-energy calculations with molecular dynamics
• Interactive Chemical Reactivity Exploration

Cited by in corpus (22)

• On scientific understanding with artificial intelligence
• FCHL revisited: faster and more accurate quantum machine learning
• Exploration of Reaction Pathways and Chemical Transformation Networks
• The Exploration of Chemical Reaction Networks
• Neural Network Potentials for Chemistry: Concepts, Applications and Prospects
• Training neural nets to learn reactive potential energy surfaces using interactive quantum chemistry in virtual reality
• Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework
• Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis
• Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking
• Isness: Using Multi-Person VR to Design Peak Mystical-Type Experiences Comparable to Psychedelics
• Expansive Quantum Mechanical Exploration of Chemical Reaction Paths
• Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS
• Training atomic neural networks using fragment-based data generated in virtual reality
• Immersive Interactive Quantum Mechanics for Teaching and Learning Chemistry
• Free energy along drug-protein binding pathways interactively sampled in virtual reality
• Measuring the limit of perception of bond stiffness of interactive molecules in VR via a gamified psychophysics experiment
• Virtual Reality for Understanding Artificial-Intelligence-driven Scientific Discovery with an Application in Quantum Optics
• Dissolving yourself in connection to others: shared experiences of ego attenuation and connectedness during group VR experiences can be comparable to psychedelics
• OMG-VR: Open-source Mudra Gloves for Manipulating Molecular Simulations in VR
• Towards Commodity, Web-Based Augmented Reality Applications for Research and Education in Chemistry and Structural Biology
• Somatic Practices for Understanding Real, Imagined, and Virtual Realities
• Continuous evaluation of the performance of cloud infrastructure for scientific applications