Instant Construction and Visualization of Crowded Biological Environments

Tobias Klein, Ludovic Autin, Barbora Kozlíková, David S. Goodsell, Arthur Olson, M. Eduard Gröller, Ivan Viola

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


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 distributed according to a Halton sequence. 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.

Original languageEnglish (US)
Article number8019859
Pages (from-to)862-872
Number of pages11
JournalIEEE Transactions on Visualization and Computer Graphics
Issue number1
StatePublished - Jan 2018
Externally publishedYes


  • Interactive modeling
  • biological data
  • interactive visualization
  • population

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design


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