Abstract
Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.
Highlights
Molecular simulations are used to study the structure, function and interactions of biomolecules
We tested the capability of this tool with four systems of varied complexity: (1) the conformational dynamics of an intrinsically disordered small protein characterized through a molecular dynamics simulation (Figure 5.1); (2) the interactions of a model cell membrane with an aqueous solution of small molecules (Figure 5.2); (3) the static structure of a representative model of a high-density lipoprotein particle (Figure 5.3); and (4) the coarsegrained molecular dynamics simulation of the spontaneous formation of nanoscale lipid-droplets (Figure 5.4)
Current visualization tools are often incompatible with large screen multiuser display formats
Summary
Molecular simulations are used to study the structure, function and interactions of biomolecules. Molecular graphics systems are visualization tools that can greatly enhance the use of molecular simulations to study the behavior of biomolecules. The HIVE is a multi-user, multi-display facility which supports, encourages and enables the use of visualization technologies across a wide range of research projects across various disciplines. We aimed to explore how the use of the HIVE Cylinder display could potentially enhance the visualization and interpretation of molecular structures – both static and dynamic – for research, teaching and communication purposes. We report the development of a molecular structure and dynamics visualization tool using the Unity cross-platform game engine to deliver an immersive display experience on large scale, multi-user, stereoscopic visualization systems. It is the first known tool to allow the loading and interaction of stereoscopic molecular visualizations in real-time through a 3D user interface
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