Publication details

Instant Construction and Visualization of Crowded Biological Environments

Authors

KLEIN Tobias AUTIN Ludovic KOZLÍKOVÁ Barbora GOODSELL David S. OLSON Arthur GRÖLLER Eduard M. VIOLA Ivan

Type Article in Periodical
Magazine / Source IEEE Transactions on Visualization and Computer Graphics
MU Faculty or unit

Faculty of Informatics

Citation
Doi http://dx.doi.org/10.1109/TVCG.2017.2744258
Field Informatics
Keywords Interactive modeling;population;biological data;interactive visualization
Description 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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