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  Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case

Wieczor, M., Genna, V., Aranda, J., Badia, R. M., Lluis Gelpi, J., Gapsys, V., et al. (2023). Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science, 13(1): e1622. doi:10.1002/wcms.1622.

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WIREs Comput Mol Sci - 2022 - Wiecz r.pdf (Publisher version), 6MB
 
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 Creators:
Wieczor, Milosz, Author
Genna, Vito, Author
Aranda, Juan, Author
Badia, Rosa M., Author
Lluis Gelpi, Josep, Author
Gapsys, Vytautas1, Author           
de Groot, Berend L.1, Author           
Lindahl, Erik, Author
Municoy, Marti, Author
Hospital, Adam, Author
Orozco, Modesto, Author
Affiliations:
1Research Group of Computational Biomolecular Dynamics, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, ou_3350134              

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 Abstract: Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics.

This article is categorized under:

- Data Science > Computer Algorithms and Programming
- Data Science > Databases and Expert Systems
- Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

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Language(s): eng - English
 Dates: 2022-05-302023
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/wcms.1622
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Project name : We are indebted to BioExcel partners for help and discussion and all the colleagues involved in Covid19 research for offering their research to the community. This study has been supported by the BioExcel-2. Center of Excellence for Computational Biomolecular Research” (823830), the Spanish Ministry of Science (RTI2018-096704-B-100, PID2020-116620GB-I00) and the Instituto de Salud Carlos III—Instituto Nacional de Bioinformática (ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional). Funding was also provided by the MINECO Severo Ochoa Award of Excellence from the Government of Spain (awarded to IRB Barcelona). Modesto Orozco is an ICREA (Institució Catalana de Recerca i Estudis Avancats) academia researcher and Juan Aranda is a Juan de la Cierva Fellow. Funding was also provided by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 894489. The IRB is supported by MINECO Severo Ochoa Award of Excellence from the Government of Spain. [Correction added on 25 June 2022, after first online publication: The funding provided by European Union's Horizon 2020 research and innovation programme has been added in the Acknowledgments section in this version.]
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Grant ID : 894489
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

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Title: Wiley Interdisciplinary Reviews: Computational Molecular Science
  Other : WIREs Computational Molecular Science
  Abbreviation : Wiley Interdiscip. Rev.: Comput. Mol. Sci.
Source Genre: Journal
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Publ. Info: Weinheim : Wiley Online Library
Pages: - Volume / Issue: 13 (1) Sequence Number: e1622 Start / End Page: - Identifier: ISSN: 1759-0884
CoNE: https://pure.mpg.de/cone/journals/resource/1759-0884