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Parallel computation and interactive visualization of time-varying solvent excluded surfaces

Published: 02 August 2010 Publication History

Abstract

Molecular dynamics simulations are a principal tool in the study of molecules. The efficient investigation of the structure and dynamics of the simulated molecular systems benefits from interactive high-quality visualizations. Molecular surfaces are among the most common representations for visual analysis of the properties of these molecules, especially when studying proteins and other biomolecules. In this paper we evaluate the suitability of parallel graphics hardware (GPUs) for interactive computation and visualization of the Solvent Excluded Surface. This surface consists of spherical and toroidal geometric primitives, which can be rendered using ray casting on the GPU, thereby obtaining unsurpassed visual quality at interactive frame rates. The key, however, is the efficient calculation of the Reduced Surface that defines the occurrence and location of these primitives. The Reduced Surface can be computed quite efficient and allows for a partial update of the surface in regions where changes occur. However, the original algorithm to construct the Reduced Surface cannot be parallelized straightforward. We introduce a novel, parallel algorithm, leveraging programmable GPUs, for computing the Reduced Surface. This allows the high-quality rendering and interactive exploration of complex molecules and time-varying molecular datasets.

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Cited By

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  • (2018)Improving perception of molecular surface visualizations by incorporating translucency effectsProceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine10.2312/vcbm.20181244(185-195)Online publication date: 20-Sep-2018
  • (2017)Interactive Analysis of Connolly Surfaces for Various ProbesComputer Graphics Forum10.1111/cgf.1287036:6(160-172)Online publication date: 1-Sep-2017
  • (2011)Interactive exploration of protein cavitiesProceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization10.1111/j.1467-8659.2011.01916.x(673-682)Online publication date: 1-Jun-2011

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cover image ACM Conferences
BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
August 2010
705 pages
ISBN:9781450304382
DOI:10.1145/1854776
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 02 August 2010

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Author Tags

  1. GPU
  2. isosurfaces
  3. molecular visualization
  4. point-based data
  5. ray casting
  6. surface extraction
  7. time-varying data

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Cited By

View all
  • (2018)Improving perception of molecular surface visualizations by incorporating translucency effectsProceedings of the Eurographics Workshop on Visual Computing for Biology and Medicine10.2312/vcbm.20181244(185-195)Online publication date: 20-Sep-2018
  • (2017)Interactive Analysis of Connolly Surfaces for Various ProbesComputer Graphics Forum10.1111/cgf.1287036:6(160-172)Online publication date: 1-Sep-2017
  • (2011)Interactive exploration of protein cavitiesProceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization10.1111/j.1467-8659.2011.01916.x(673-682)Online publication date: 1-Jun-2011

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