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Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories

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Advances in Visual Computing (ISVC 2011)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 6939))

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Abstract

Atomistic molecular dynamics (MD) simulations of biomolecules provide insight into their physical mechanisms and potential as drug targets. Unfortunately, such simulations are extremely demanding in terms of computation, storage, and visualization. Immersive visualization environments permit fast, intuitive exploration of the pharmacological potential, but add further demands on resources. We describe the design and application of out-of-core visualization techniques for large-size and long-timescale MD simulations involving many terabytes of data, including in particular: fast regeneration of molecular representations, atom selection mechanisms, out-of-core optimized MD trajectory file formats, and multithreaded programming techniques. Our approach leverages technological advances in commodity solid state disk (SSD) devices, to enable trajectory animation rates for large structures that were previously unachievable except by in-core approaches, while maintaining full visualization flexibility. The out-of-core visualization techniques are implemented and evaluated in VMD, a widely used molecular visualization tool.

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Author information

Authors and Affiliations

  1. Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, USA

    John E. Stone, Kirby L. Vandivort & Klaus Schulten

  2. Department of Physics, University of Illinois, Urbana-Champaign, USA

    Klaus Schulten

Authors
  1. John E. Stone
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  2. Kirby L. Vandivort
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  3. Klaus Schulten
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Editor information

Editors and Affiliations

  1. University of Nevada, 89557, Reno, NV, USA

    George Bebis

  2. NASA Ames Research Center, 94035, Moffett Field, CA, USA

    Richard Boyle

  3. Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA

    Bahram Parvin

  4. Desert Research Institute, 89512, Reno, NV, USA

    Darko Koracin

  5. Department of Computer Science and Engineering, University of South Carolina, 29208, Columbia, SC, USA

    Song Wang

  6. HRL Laboratories, 3011 Malibu Canyon Road, 90265-4797, Malibu, CA, USA

    Kim Kyungnam

  7. Purdue University, West Lafayette, 47907-2021, IN, USA

    Bedrich Benes

  8. Sandia National Laboratory, 87185, Albuquerque, NM, USA

    Kenneth Moreland

  9. University of Louisiana at Lafayette, 70504, LA, USA

    Christoph Borst

  10. Adobe Systems Incorporated, San Francisco, CA, USA

    Stephen DiVerdi

  11. Polytechnic Institute of NYU, 11201, Brooklyn, NY, USA

    Chiang Yi-Jen

  12. Lawrence Livermore National Laboratory, 94551-0808, Livermore, CA, USA

    Jiang Ming

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© 2011 Springer-Verlag Berlin Heidelberg

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Stone, J.E., Vandivort, K.L., Schulten, K. (2011). Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories. In: Bebis, G., et al. Advances in Visual Computing. ISVC 2011. Lecture Notes in Computer Science, vol 6939. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24031-7_1

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  • DOI: https://doi.org/10.1007/978-3-642-24031-7_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-24030-0

  • Online ISBN: 978-3-642-24031-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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