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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F22%3A00124972" target="_blank" >RIV/00216224:14330/22:00124972 - isvavai.cz</a>

Result on the web

<a href="https://ieeexplore.ieee.org/document/9523759" target="_blank" >https://ieeexplore.ieee.org/document/9523759</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/TVCG.2021.3106328" target="_blank" >10.1109/TVCG.2021.3106328</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_imp - 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)

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

IEEE Transactions on Visualization and Computer Graphics

ISSN

1077-2626

e-ISSN

—

Volume of the periodical

28

Issue of the periodical within the volume

12

Country of publishing house

US - UNITED STATES

Number of pages

14

Pages from-to

4825-4838

UT code for WoS article

000873836400062

EID of the result in the Scopus database

2-s2.0-85113898010