Real-Time Interactive Simulation and Visualization of Organic Molecules
Real-Time Interactive Simulation and Visualization of Organic Molecules
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DOI：
10.1021/acs.jchemed.9b01161
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发表时间：
2020-11-10
影响因子：
3
通讯作者：
White, Andrew D.
中科院分区：
文献类型：
--
作者：
Gandhi, Heta A.;Jakymiw, Sebastian;White, Andrew D.
虚拟现实（VR）中分子模拟的三维可视化是化学教育中新兴的教学工具。这项工作描述了一个 VR 应用程序，它可以从任意分子结构生成 3D 分子动力学 (MD) 模拟，并在 VR 耳机上实时渲染该 MD 模拟轨迹。该系统使用 ZeroMQ (ZMQ) 消息传递框架来实现 MD 模拟的多重模拟到多客户端 VR 可视化。所有 MD 模拟均在 HOOMD-blue 模拟引擎中完成，VR 图形在 Unity3D 中渲染。该软件与以前的 3D 查看器程序不同的关键功能是实时模拟，因此能够实时操纵温度等热力学变量。这使得观看者能够以亲身实践的方式直观地理解热力学状态变量的影响。该应用程序被用作高中生的教学工具，所使用的课程以及活动的结果已在此处介绍。该应用程序可以为热力学和统计力学教学提供交互式工具，甚至可以作为用于研究目的的 MD 模拟的诊断工具。
Three-dimensional visualization of molecular simulations in virtual reality (VR) is an emerging teaching tool in chemical education. This work describes a VR application which can generate a 3D molecular dynamics (MD) simulation from arbitrary molecular structures and renders that MD simulation trajectory on a VR headset in real-time. This system uses the ZeroMQ (ZMQ) message passing framework for multisimulation to multiclient VR visualization of MD simulation. All MD simulations are done in the HOOMD-blue simulation engine, and the graphics for the VR are rendered in Unity3D. The key feature that sets this software apart from previous 3D viewer programs is the real-time simulation and thus the ability to manipulate thermodynamic variables like temperature on the fly. This allows viewers to build an intuitive understanding of the effects of thermodynamics state variables in a hands-on way. This application was used as a pedagogical tool with high school students, and the curriculum used, along with outcomes of the activity, has been presented here. This application can provide an interactive tool for teaching thermodynamics and statistical mechanics, and even as a diagnostic tool for MD simulations for research purposes.