Instant Construction and Visualization of Crowded Biological Environments
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F18%3A00102034" target="_blank" >RIV/00216224:14330/18:00102034 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1109/TVCG.2017.2744258" target="_blank" >http://dx.doi.org/10.1109/TVCG.2017.2744258</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1109/TVCG.2017.2744258" target="_blank" >10.1109/TVCG.2017.2744258</a>
Alternative languages
Result language
angličtina
Original language name
Instant Construction and Visualization of Crowded Biological Environments
Original language 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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
IEEE Transactions on Visualization and Computer Graphics
ISSN
1077-2626
e-ISSN
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Volume of the periodical
24
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
862-872
UT code for WoS article
000418038400085
EID of the result in the Scopus database
2-s2.0-85028725673