sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

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Authors

ULBRICH Pavol WALDNER Manuela FURMANOVÁ Katarína MARQUES Sérgio Manuel BEDNÁŘ David KOZLÍKOVÁ Barbora BYŠKA Jan

Year of publication 2023
Type Article in Periodical
Magazine / Source IEEE Transactions on Visualization and Computer Graphics
MU Faculty or unit

Faculty of Informatics

Citation
Web https://ieeexplore.ieee.org/abstract/document/9903280
Doi http://dx.doi.org/10.1109/TVCG.2022.3209411
Keywords Molecular dynamics;structure;node-based visualization;progressive analytics
Description We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case studies illustrate that even with relatively few sMolBoxes, it is possible to express complex analytical tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods.
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