Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

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Publikace nespadá pod Ústav výpočetní techniky, ale pod Fakultu informatiky. Oficiální stránka publikace je na webu muni.cz.

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KUŤÁK David SELZER Matias Nicolás BYŠKA Jan GANUZA María Luján BARIŠIĆ Ivan KOZLÍKOVÁ Barbora MIAO Haichao

Rok publikování 2022
Druh Článek v odborném periodiku
Časopis / Zdroj IEEE Transactions on Visualization and Computer Graphics
Fakulta / Pracoviště MU

Fakulta informatiky

Citace
www https://ieeexplore.ieee.org/document/9523759
Doi http://dx.doi.org/10.1109/TVCG.2021.3106328
Klíčová slova Virtual reality, abstraction, DNA origami, nanostructures, visualization, focus+context, interaction, in silico modeling, nanotechnology, multiscale, magic scale lens
Popis DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.
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