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

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.

Základní údaje

Originální název

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

Autoři

KUŤÁK, David (203 Česká republika, domácí), Matias Nicolás SELZER, Jan BYŠKA (203 Česká republika, domácí), María Luján GANUZA, Ivan BARIŠIĆ, Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Haichao MIAO

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.200

Kód RIV

RIV/00216224:14330/22:00124972

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1109/TVCG.2021.3106328

UT WoS

000873836400062

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 3. 2023 17:03, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

MUNI/A/1230/2021, interní kód MU

Název: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 22 (Akronym: SKOMU)

Investor: Masarykova univerzita, Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 22

MUNI/A/1549/2020, interní kód MU

Název: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 21 (Akronym: SKOMU)

Investor: Masarykova univerzita, Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 21

Citovat

KUŤÁK, David, Matias Nicolás SELZER, Jan BYŠKA, María Luján GANUZA, Ivan BARIŠIĆ, Barbora KOZLÍKOVÁ a Haichao MIAO. Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures. IEEE Transactions on Visualization and Computer Graphics. 2022, roč. 28, č. 12, s. 4825-4838. ISSN 1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2021.3106328.

@article{1788657,
   author = {Kuťák, David and Selzer, Matias Nicolás and Byška, Jan and Ganuza, María Luján and Barišić, Ivan and Kozlíková, Barbora and Miao, Haichao},
   article_number = {12},
   doi = {http://dx.doi.org/10.1109/TVCG.2021.3106328},
   keywords = {Virtual reality; abstraction; DNA origami; nanostructures; visualization; focus+context; interaction; in silico modeling; nanotechnology; multiscale; magic scale lens},
   language = {eng},
   issn = {1077-2626},
   journal = {IEEE Transactions on Visualization and Computer Graphics},
   title = {Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures},
   url = {https://ieeexplore.ieee.org/document/9523759},
   volume = {28},
   year = {2022}
}

TY  - JOUR
ID  - 1788657
AU  - Kuťák, David - Selzer, Matias Nicolás - Byška, Jan - Ganuza, María Luján - Barišić, Ivan - Kozlíková, Barbora - Miao, Haichao
PY  - 2022
TI  - Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures
JF  - IEEE Transactions on Visualization and Computer Graphics
VL  - 28
IS  - 12
SP  - 4825-4838
EP  - 4825-4838
SN  - 10772626
KW  - Virtual reality
KW  - abstraction
KW  - DNA origami
KW  - nanostructures
KW  - visualization
KW  - focus+context
KW  - interaction
KW  - in silico modeling
KW  - nanotechnology
KW  - multiscale
KW  - magic scale lens
UR  - https://ieeexplore.ieee.org/document/9523759
N2  - 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.
ER  -

KUŤÁK, David, Matias Nicolás SELZER, Jan BYŠKA, María Luján GANUZA, Ivan BARIŠI$\backslash$'C, Barbora KOZLÍKOVÁ a Haichao MIAO. Vivern – A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures. \textit{IEEE Transactions on Visualization and Computer Graphics}. 2022, roč.~28, č.~12, s.~4825-4838. ISSN~1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2021.3106328.

Podrobný výpis o publikaci