Developing hardware and software for real-time molecular simulation of binding free energies in virtual reality

随着分子科学家在设计纳米级分子结构的能力方面取得了进展，我们在设计分子动力学（MD）和灵活性的能力方面面临着新的挑战。分子尺度上的动力学不同于我们熟悉的日常物体的力学，因为它涉及到一个复杂的、高度相关的、三维的多体动力学编排，即使是训练有素的研究人员也常常不直观。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中操纵柔性结构的实时MD模拟。在本项目中，学生将继续尝试将沉浸式技术扩展到分子科学领域。具体而言，该项目将致力于开发下一代VR数据手套，该手套使用现代导电织物制成，通过（a）拇指和食指之间的捏动作或（B）拇指和食指之间的捏动作来检测参与者何时闭合两个电路中的一个。手的绝对位置是通过在手套背面安装光学系统获得的。我们的初步结果，从我们自己的实验室进行的一小部分用户研究中获得，表明参与者发现这种手套提供的分子和原子相互作用非常直观，给他们一种“触摸”虚拟分子模拟的直接感觉。为了“触摸”一个原子并对其施加力，参与者只需伸出手去触摸他们希望触摸的原子，并将他们的拇指和食指放在一起，就像他们抓住一个正常物体一样。该项目将开发将VR数据手套应用于许多不同系统所需的软件和硬件，包括小分子与5-HT 2A血清素受体的结合。在这样做的过程中，我们将建立开源的硬件和软件框架工具，使更有效的分子模拟计算复杂系统中的结合自由能。

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 project, the student will carry on these attempts to extend immersive technologies to the molecular sciences.Specifically, the project will focus on developing a next-generation VR-data gloves, constructed using modern conductive fabrics, which detect when a participant closes one of two circuits, by making a pinching motion between (a) their thumb and index finger or (b) their thumb and forefinger. The absolute position of the hand is obtained from mounting an optical system on the back of the glove. Our preliminary results, obtained from a small set of user studies carried out in our own laboratory, suggest that participants find the molecular and atomic interaction afforded by this glove extremely intuitive, giving them a direct sense of "touching" virtual molecular simulations. To "touch" an atom and exert a force on it, the participant simply reaches out to the atom they wish to touch and brings together their thumb and forefinger as they would do if they were grasping a normal object. This project will develop the software and hardware required to apply the VR data glove to a number of different systems, including the binding of small molecules to the 5-HT2A serotonin receptors. In so doing, we will build open-source hardware and software frameworks tools which enable more efficient molecular simulation for calculating binding free energies in complex systems.