KLEIN, Tobias, Ludovic AUTIN, Barbora KOZLÍKOVÁ, David S. GOODSELL, Arthur OLSON, Eduard M. GRÖLLER and Ivan VIOLA. Instant Construction and Visualization of Crowded Biological Environments. IEEE Transactions on Visualization and Computer Graphics. 2018, vol. 24, No 1, p. 862-872. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2017.2744258.
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Basic information
Original name Instant Construction and Visualization of Crowded Biological Environments
Authors KLEIN, Tobias (276 Germany, guarantor), Ludovic AUTIN (250 France), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), David S. GOODSELL (840 United States of America), Arthur OLSON (840 United States of America), Eduard M. GRÖLLER (40 Austria) and Ivan VIOLA (703 Slovakia).
Edition IEEE Transactions on Visualization and Computer Graphics, 2018, 1077-2626.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
Impact factor Impact factor: 3.780
RIV identification code RIV/00216224:14330/18:00102034
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1109/TVCG.2017.2744258
UT WoS 000418038400085
Keywords in English Interactive modeling;population;biological data;interactive visualization
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 3/5/2019 14:54.
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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