<i>Modeling in the Time of COVID-19:</i> Statistical and Rule-based Mesoscale Models

Nguyen, Ngan V.T.; Strnad, Ondřej; Klein, Tobias; Luo, Deng; Alharbi, Ruwayda; Wonka, Peter; Maritan, Martina; Mindek, Peter; Autin, Ludovic; Goodsell, David S.; Viola, Ivan

doi:10.1109/tvcg.2020.3030415

Cited by 33 publications

(20 citation statements)

References 90 publications

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“…Finally, we used the SARS-CoV-2 dataset (Figure 10) provided by KAUST [49]. It consists of ≈ 3,200 protein instances, ≈ 180,000 lipids, and an RNA strand.…”

Section: Resultsmentioning

confidence: 99%

Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization

Kouril

Strnad

Mindek

et al. 2023

IEEE Trans. Visual. Comput. Graphics

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We present a method for producing documentary-style content using real-time scientific visualization. We introduce molecumentaries, i. e., molecular documentaries featuring structural models from molecular biology, created through adaptable methods instead of the rigid traditional production pipeline. Our work is motivated by the rapid evolution of scientific visualization and it potential in science dissemination. Without some form of explanation or guidance, however, novices and lay-persons often find it difficult to gain insights from the visualization itself. We integrate such knowledge using the verbal channel and provide it along an engaging visual presentation. To realize the synthesis of a molecumentary, we provide technical solutions along two major production steps: (1) preparing a story structure and (2) turning the story into a concrete narrative. In the first step, we compile information about the model from heterogeneous sources into a story graph. We combine local knowledge with external sources to complete the story graph and enrich the final result. In the second step, we synthesize a narrative, i. e., story elements presented in sequence, using the story graph. We then traverse the story graph and generate a virtual tour, using automated camera and visualization transitions. We turn texts written by domain experts into verbal representations using text-to-speech functionality and provide them as a commentary. Using the described framework, we synthesize fly-throughs with descriptions: automatic ones that mimic a manually authored documentary or semi-automatic ones which guide the documentary narrative solely through curated textual input.

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“…Finally, we used the SARS-CoV-2 dataset (Figure 10) provided by KAUST [49]. It consists of ≈ 3,200 protein instances, ≈ 180,000 lipids, and an RNA strand.…”

Section: Resultsmentioning

confidence: 99%

Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization

Kouril

Strnad

Mindek

et al. 2023

IEEE Trans. Visual. Comput. Graphics

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“…The budding coronavirus image was based on previous illustrative work ( Goodsell et al, 2020b ), and incorporates a number of simplifications using a limited palette of ingredients. The coronavirus ingredients (“Coronavirus” palette) are based on the SARS-CoV-2 v.20-06 mesoscale model ( Nguyen et al, 2021 ) Cytoplasmic ingredients use the default palette developed for T-cell cytoplasm in CellPAINT ( Gardner et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

CellPAINT: Turnkey Illustration of Molecular Cell Biology

et al. 2021

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CellPAINT is an interactive digital tool that allows non-expert users to create illustrations of the molecular structure of cells and viruses. We present a new release with several key enhancements, including the ability to generate custom ingredients from structure information in the Protein Data Bank, and interaction, grouping, and locking functions that streamline the creation of assemblies and illustration of large, complex scenes. An example of CellPAINT as a tool for hypothesis generation in the interpretation of cryoelectron tomograms is presented. CellPAINT is freely available at http://ccsb.scripps.edu/cellpaint.

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“…Длина пепломеров около 20 нм. Из 3D-модели следует, что пепломеры вируса имеют особенностиони очень тонкие, гибкие и подвижные (Peering under the «hood»…, 2020; Nguyen et al, 2020).…”

Section: электрические явления при адсорбции вируса на мембране клеткиunclassified

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2021

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государственный медицинский университет имени И. М. Сеченова (Сеченовский университет) 3 Российский университет дружбы народов, Москва, Россия РЕЗЮМЕ. Рассмотрены электрически заряженные молекулярные группировки на поверхности вируса как мишени для противовирусных средств. Показана перспективность применения в качестве противовирусных средств микроэлементов в низкой степени окисления. Разработана электрическая модель SARS-CoV-2 в виде многослойной структуры, где каждой оболочке соответствуют электрически заряженные белки на поверхности вируса. Модель раскрывает роль кулоновских сил в процессах адсорбции и слияния и позволяет выявить уязвимые места коронавируса, чувствительные к электрически заряженным веществам и к электрическому полю. Раскрыт механизм противовирусного действия микроэлементов, основанный на подавлении электростатического взаимодействия вируса с клеткой путем нейтрализации зарядов на поверхности вируса и клетки. Это позволяет подбирать олигопептиды и микроэлементы в низких степенях окисления для подавления адсорбционной способности вирусов. Особая роль микроэлементов состоит в том, что многие потенциальные мишени, недоступные для антител и других больших молекул, легко доступны для микроэлементов. КЛЮЧЕВЫЕ СЛОВА: электрическая модель SARS-CoV-2, уязвимые места коронавируса, кулоновская инжекция РНК, низковалентные микроэлементы.

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Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models

Cited by 33 publications

References 90 publications

Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization

Molecumentary: Adaptable Narrated Documentaries Using Molecular Visualization

CellPAINT: Turnkey Illustration of Molecular Cell Biology

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