Real-Time Interactive Simulation and Visualization of Organic Molecules

Abstract

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.

Wielding the power of interactive molecular simulations

“…120 In the context of quantum mechanics and chemical bonding theory, VSEPR theory was the focus of a simulation to construct virtual molecules. 121 Gandhi et al 122 focused on teaching thermodynamic state variables through real-time simulations. As for interactive and reactive molecular dynamics, the InteraChem Virtual Reality Visualizer is noteworthy 123 as it combines several modern technologies such as virtual reality and speech recognition.…”

“…In the previously mentioned educational work on thermodynamic state variables, temperature is also a key focus. 122…”

Immersive Interactive Quantum Mechanics for Teaching and Learning Chemistry

“…refs. [12,29,30,32,33,[35][36][37][38][39][40]). For example, the structure of a large molecule with a complicated three-dimensional shape can easily be inspected from all possible angles, and the rearrangements of the individual atoms of this molecule as it undergoes a certain chemical reaction can be examined with great scrutiny.…”

“…For example, the structure of a large molecule with a complicated three-dimensional shape can easily be inspected from all possible angles, and the rearrangements of the individual atoms of this molecule as it undergoes a certain chemical reaction can be examined with great scrutiny. [12,20,[22][23][24][25][26][27][28][29][31][32][33]37,39] Since the person experiencing such a virtual reality is fully immersed into it, it should provide an ideal environment for teaching, learning, and, of course, research.…”

Research on the Design of Intelligent Music Teaching System Based on Virtual Reality Technology

“…Virtual Reality (VR) technology and augmented reality (AR) technology attract more and more people to engage in the research and development of related theories and technologies [ 1 ]. At present, VR technology and AR technology are widely used in entertainment [ 2 ], tourism, medical [ 3 ], games [ 4 ], education [ 5 ], etc. Many VR and AR companies and related talents [ 6 ] have emerged in the society.…”