Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware

  • John E. Stone
  • Axel Kohlmeyer
  • Kirby L. Vandivort
  • Klaus Schulten
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6454)

Abstract

Continuing advances in development of multi-core CPUs, GPUs, and low-cost six-degree-of-freedom virtual reality input devices have created an unprecedented opportunity for broader use of interactive molecular modeling and immersive visualization of large molecular complexes. We describe the design and implementation of VMD, a popular molecular visualization and modeling tool that supports both desktop and immersive virtual reality environments, and includes support for a variety of multi-modal user interaction mechanisms. A number of unique challenges arise in supporting immersive visualization and advanced input devices within software that is used by a broad community of scientists that often have little background in the use or administration of these technologies. We share our experiences in supporting VMD on existing and upcoming low-cost virtual reality hardware platforms, and we give our perspective on how these technologies can be improved and employed to enable next-generation interactive molecular simulation tools for broader use by the molecular modeling community.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L., Skeel, R., Schulten, K., Kufrin, R.: MDScope – A visual computing environment for structural biology. In: Atluri, S., Yagawa, G., Cruse, T. (eds.) Computational Mechanics 1995, vol. 1, pp. 476–481 (1995)Google Scholar
  2. 2.
    Leech, J., Prins, J., Hermans, J.: SMD: Visual steering of molecular dynamics for protein design. IEEE Comp. Sci. Eng. 3, 38–45 (1996)CrossRefGoogle Scholar
  3. 3.
    Humphrey, W., Dalke, A., Schulten, K.: VMD – Visual Molecular Dynamics. J. Mol. Graphics 14, 33–38 (1996)Google Scholar
  4. 4.
    Ihlenfeldt, W.D.: Virtual reality in chemistry. J. Mol. Mod. 3, 386–402 (1997)Google Scholar
  5. 5.
    Sharma, R., Zeller, M., Pavlovic, V.I., Huang, T.S., Lo, Z., Chu, S., Zhao, Y., Phillips, J.C., Schulten, K.: Speech/gesture interface to a visual-computing environment. IEEE Comp. Graph. App. 20, 29–37 (2000)CrossRefGoogle Scholar
  6. 6.
    Sankaranarayanan, G., Weghorst, S., Sanner, M., Gillet, A., Olson, A.: Role of haptics in teaching structural molecular biology. In: International Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, p. 363 (2003)Google Scholar
  7. 7.
    Cruz-Neira, C., Sandin, D.J., DeFanti, T.A.: Surround-screen projection-based virtual reality: The design and implementation of the CAVE. In: Proceedings of SIGGRAPH 1993, Anaheim, CA,, pp. 135–142. ACM, New York (1993)Google Scholar
  8. 8.
    Czernuszenko, M., Pape, D., Sandin, D., DeFanti, T., Dawe, G.L., Brown, M.D.: The ImmersaDesk and Infinity Wall projection-based virtual reality displays. SIGGRAPH Comput. Graph. 31, 46–49 (1997)CrossRefGoogle Scholar
  9. 9.
    Pape, D., Anstey, J., Sherman, B.: Commodity-based projection VR. In: SIGGRAPH 2004: ACM SIGGRAPH 2004 Course Notes, p. 19. ACM, New York (2004)Google Scholar
  10. 10.
    Taylor II, R.M., Hudson, T.C., Seeger, A., Weber, H., Juliano, J., Helser, A.T.: VRPN: a device-independent, network-transparent VR peripheral system. In: VRST 2001: Proceedings of the ACM Symposium on Virtual Reality Software and Technology, pp. 55–61. ACM, New York (2001)CrossRefGoogle Scholar
  11. 11.
    Bierbaum, A., Just, C., Hartling, P., Meinert, K., Baker, A., Cruz-Neira, C.: VR Juggler: a virtual platform for virtual reality application development. In: Proceedings of IEEE Virtual Reality, pp. 89–96 (2001)Google Scholar
  12. 12.
    Martens, J.B., Qi, W., Aliakseyeu, D., Kok, A.J.F., van Liere, R.: Experiencing 3D interactions in virtual reality and augmented reality. In: EUSAI 2004: Proceedings of the 2nd European Union Symposium on Ambient Intelligence, pp. 25–28. ACM, New York (2004)Google Scholar
  13. 13.
    Stone, J., Gullingsrud, J., Grayson, P., Schulten, K.: A system for interactive molecular dynamics simulation. In: Hughes, J.F., Séquin, C.H. (eds.) 2001 ACM Symposium on Interactive 3D Graphics, New York. ACM SIGGRAPH, pp. 191–194 (2001)Google Scholar
  14. 14.
    Kreylos, O.: Environment-independent VR development. In: Bebis, G., Boyle, R., Parvin, B., Koracin, D., Remagnino, P., Porikli, F., Peters, J., Klosowski, J., Arns, L., Chun, Y.K., Rhyne, T.-M., Monroe, L. (eds.) ISVC 2008, Part I. LNCS, vol. 5358, pp. 901–912. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  15. 15.
    Angus, I.G., Sowizral, H.A.: Embedding the 2D interaction metaphor in a real 3D virtual environment, vol. 2409, pp. 282–293. SPIE, San Jose (1995)Google Scholar
  16. 16.
    Watsen, K., Darken, R.P., Capps, M.V.: A handheld computer as an interaction device to a virtual environment. In: Proceedings of the Third Immersive Projection Technology Workshop (1999)Google Scholar
  17. 17.
    Hartling, P.L., Bierbaum, A.D., Cruz-Niera, C.: Tweek: Merging 2D and 3D interaction in immersive environments. In: Proceedings of the 6th World Multiconference on Systemics, Cybernetics, and Informatics, Orlando, FL, USA, vol. VI, pp. 1–5 (2002)Google Scholar
  18. 18.
    Férey, N., Delalande, O., Grasseau, G., Baaden, M.: A VR framework for interacting with molecular simulations. In: VRST 2008: Proceedings of the 2008 ACM Symposium on Virtual Reality Software and Technology, pp. 91–94. ACM, New York (2008)CrossRefGoogle Scholar
  19. 19.
    Grayson, P., Tajkhorshid, E., Schulten, K.: Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Biophys. J. 85, 36–48 (2003)CrossRefGoogle Scholar
  20. 20.
    Hamdi, M., Ferreira, A., Sharma, G., Mavroidis, C.: Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality. Microelectronics Journal 39, 190–201 (2008)CrossRefGoogle Scholar
  21. 21.
    Phillips, J.C., Stone, J.E., Schulten, K.: Adapting a message-driven parallel application to GPU-accelerated clusters. In: SC 2008: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, Piscataway, NJ, USA. IEEE Press, Los Alamitos (2008)Google Scholar
  22. 22.
    Anderson, J.A., Lorenz, C.D., Travesset, A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Chem. Phys. 227, 5342–5359 (2008)MATHGoogle Scholar
  23. 23.
    Stone, J.E., Hardy, D.J., Ufimtsev, I.S., Schulten, K.: GPU-accelerated molecular modeling coming of age. J. Mol. Graph. Model. 29, 116–125 (2010)CrossRefGoogle Scholar
  24. 24.
    Hachet, M., Kitamura, Y.: 3D interaction with and from handheld computers. In: Proceedings of IEEE VR 2005 Workshop: New Directions in 3D User Interfaces. IEEE, Los Alamitos (2005)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • John E. Stone
    • 1
  • Axel Kohlmeyer
    • 2
  • Kirby L. Vandivort
    • 1
  • Klaus Schulten
    • 3
  1. 1.Beckman Institute for Advanced Science and TechnologyUniversity of IllinoisUrbana-ChampaignUSA
  2. 2.Center for Molecular ModelingTemple UniversityUSA
  3. 3.Department of PhysicsUniversity of IllinoisUrbana-ChampaignUSA

Personalised recommendations