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

Abstract

As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing 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 non-intuitive 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 efforts to extend immersive technologies to the molecular sciences, and we introduce 'Narupa', a flexible, open-source, multi-person 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 reactive potential energy surfaces (PESs), 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 how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies like 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.

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Cited by in corpus (9)

• 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
• Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS
• Training atomic neural networks using fragment-based data generated in virtual reality
• Free energy along drug-protein binding pathways interactively sampled in virtual reality
• Subtle Sensing: Detecting Differences in the Flexibility of Virtually Simulated Molecular Objects
• Virtual Reality for Understanding Artificial-Intelligence-driven Scientific Discovery with an Application in Quantum Optics
• Measuring the limit of perception of bond stiffness of interactive molecules in VR via a gamified psychophysics experiment
• AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems