J 2022

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

KUŤÁK, David, Matias Nicolás SELZER, Jan BYŠKA, María Luján GANUZA, Ivan BARIŠIĆ et. al.

Basic information

Original name

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

Authors

KUŤÁK, David (203 Czech Republic, belonging to the institution), Matias Nicolás SELZER, Jan BYŠKA (203 Czech Republic, belonging to the institution), María Luján GANUZA, Ivan BARIŠIĆ, Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Haichao MIAO

Edition

IEEE Transactions on Visualization and Computer Graphics, 2022, 1077-2626

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 5.200

RIV identification code

RIV/00216224:14330/22:00124972

Organization unit

Faculty of Informatics

UT WoS

000873836400062

Keywords in English

Virtual reality; abstraction; DNA origami; nanostructures; visualization; focus+context; interaction; in silico modeling; nanotechnology; multiscale; magic scale lens

Tags

International impact, Reviewed
Změněno: 27/3/2023 17:03, RNDr. Pavel Šmerk, Ph.D.

Abstract

V originále

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.

Links

MUNI/A/1230/2021, interní kód MU
Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 22 (Acronym: SKOMU)
Investor: Masaryk University
MUNI/A/1549/2020, interní kód MU
Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 21 (Acronym: SKOMU)
Investor: Masaryk University