Instant Construction and Visualization of Crowded Biological Environments

Tobias Klein, Ludovic Autin, Barbora Kozlikova, David Goodsell, Arthur Olson, Meister Eduard Gröller, Ivan Viola
Instant Construction and Visualization of Crowded Biological Environments
IEEE Transactions on Visualization and Computer Graphics, (), 2017. [paper]

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Abstract

We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments using the Halton sequence for their distribution. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.

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BibTeX

@article{klein_2017_IM,
  title =      "Instant Construction and Visualization of Crowded Biological
               Environments",
  author =     "Tobias Klein and Ludovic Autin and Barbora Kozlikova and
               David Goodsell and Arthur Olson and Meister Eduard
               Gr{"o}ller and Ivan Viola",
  year =       "2017",
  abstract =   "We present the first approach to integrative structural
               modeling of the biological mesoscale within an interactive
               visual environment. These complex models can comprise up to
               millions of molecules with defined atomic structures,
               locations, and interactions. Their construction has
               previously been attempted only within a non-visual and
               non-interactive environment. Our solution unites the
               modeling and visualization aspect, enabling interactive
               construction of atomic resolution mesoscale models of large
               portions of a cell. We present a novel set of GPU algorithms
               that build the basis for the rapid construction of complex
               biological structures. These structures consist of multiple
               membrane-enclosed compartments including both soluble
               molecules and fibrous structures. The compartments are
               defined using volume voxelization of triangulated meshes.
               For membranes, we present an extension of the Wang Tile
               concept that populates the bilayer with individual lipids.
               Soluble molecules are populated within compartments using
               the Halton sequence for their distribution. Fibrous
               structures, such as RNA or actin filaments, are created by
               self-avoiding random walks. Resulting overlaps of molecules
               are resolved by a forced-based system. Our approach opens
               new possibilities to the world of interactive construction
               of cellular compartments. We demonstrate its effectiveness
               by showcasing scenes of different scale and complexity that
               comprise blood plasma, mycoplasma, and HIV.",
  journal =    "IEEE Transactions on Visualization and Computer Graphics",
  pages =      "--",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2017/klein_2017_IM/",
}