Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.
J Chem Phys. 2019 Jun 14;150(22):220901. doi: 10.1063/1.5092590.
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.
随着分子科学家在设计纳米级分子结构方面的能力取得进展，我们在设计分子动力学（MD）和灵活性方面面临新的挑战。分子尺度上的动力学与日常物体的熟悉力学不同，因为它涉及到复杂、高度相关和三维的多体动力学编排，即使对于经过高度训练的研究人员来说，这种编排也常常是不合常理的。我们最近描述了虚拟现实中的交互式分子动力学（iMD-VR）如何帮助应对这一挑战，使研究人员能够在 3D 中操纵灵活结构的实时 MD 模拟。在本文中，我们概述了将沉浸式技术扩展到分子科学的各种努力，并介绍了“Narupa”，这是一个灵活的、开源的、多人 iMD-VR 软件框架，使研究小组能够同时居住在实时模拟环境中，以原子级精度交互可视化和操纵分子结构的动力学。我们概述了 iMD-VR 在促进分子科学领域的研究、交流和创新方法方面的几个应用领域，包括训练机器学习势能函数、生物分子构象采样、蛋白质-配体结合、使用“实时”量子化学发现反应以及材料中的输运动力学。我们涉及 iMD-VR 的各种认知和感知功能，并概述了这些功能如何为分子系统提供研究见解。通过协同结合人类的空间推理和设计洞察力与计算自动化，iMD-VR 等技术有可能提高我们理解、设计和交流微观动力学行为的能力，为设计分子和纳米结构带来新的范式提供了潜力。
