Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization

Julius Parulek, Daniel J├Ânsson, Timo Ropinski, Stefan Bruckner, Anders Ynnerman, Ivan Viola
Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization
Computer Graphics Forum, 33(6):276-287, May 2014.

Information

Abstract

Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the level-of-detail concept, where we exploit three different abstractions combined in one visualization. Firstly, molecular surface abstraction exploits three different surfaces, solvent-excluded surface (SES), Gaussian kernels and van der Waals spheres, combined as one surface by linear interpolation. Secondly, we introduce three shading abstraction levels and a method for creating seamless transitions between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation of a cluster of atoms with constant shading and without contours provide the context. Thirdly, we propose a hierarchical abstraction based on a set of clusters formed on molecular atoms. All three abstraction models are driven by one importance function classifying the scene into the near-, mid- and far-field. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.

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BibTeX

@article{Viola_Ivan_CLD,
  title =      "Continuous Levels-of-Detail and Visual Abstraction for
               Seamless Molecular Visualization",
  author =     "Julius Parulek and Daniel J{"o}nsson and Timo Ropinski and
               Stefan Bruckner and Anders Ynnerman and Ivan Viola",
  year =       "2014",
  abstract =   "Molecular visualization is often challenged with rendering
               of large molecular structures in real time. We introduce a
               novel approach that enables us to show even large protein
               complexes. Our method is based on the level-of-detail
               concept, where we exploit three different abstractions
               combined in one visualization. Firstly, molecular surface
               abstraction exploits three different surfaces,
               solvent-excluded surface (SES), Gaussian kernels and van der
               Waals spheres, combined as one surface by linear
               interpolation. Secondly, we introduce three shading
               abstraction levels and a method for creating seamless
               transitions between these representations. The SES
               representation with full shading and added contours stands
               in focus while on the other side a sphere representation of
               a cluster of atoms with constant shading and without
               contours provide the context. Thirdly, we propose a
               hierarchical abstraction based on a set of clusters formed
               on molecular atoms. All three abstraction models are driven
               by one importance function classifying the scene into the
               near-, mid- and far-field. Moreover, we introduce a
               methodology to render the entire molecule directly using the
               A-buffer technique, which further improves the performance.
               The rendering performance is evaluated on series of
               molecules of varying atom counts.",
  month =      may,
  issn =       "0167-7055",
  journal =    "Computer Graphics Forum",
  number =     "6",
  volume =     "33",
  pages =      "276--287",
  keywords =   "clustering, implicit surfaces, level of detail algorithms,
               scientific visualization, Computer Applications",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_CLD/",
}