<scp>Pre‐exascale HPC</scp> approaches for molecular dynamics simulations. Covid‐19 research: A use case

Wieczór, Miłosz; Genna, Vito; Aranda, Juan; Badía, Rosa M.; Gelpí, Josep Lluís; Gapsys, Vytautas; Groot, Bert L. de; Lindahl, Erik; Municoy, Martí; Hospital, Adam; Orozco, Modesto

doi:10.1002/wcms.1622

Cited by 14 publications

(7 citation statements)

References 229 publications

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“…The supercomputing infrastructure enabled rapid parallel processing, allowing researchers to evaluate an extensive library of antibody candidates within a short timeframe. The simulations provided valuable insights into the structural and functional characteristics of the designed antibodies, aiding in the selection of lead candidates for further experimental validation [71]. This study demonstrated how supercomputers can significantly expedite the design and optimization of therapeutic antibodies against COVID-19.…”

Section: Drug Discoverymentioning

confidence: 86%

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

Mustafa,

Makhawi

2023

Preprint

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The COVID-19 pandemic has unveiled the critical role that supercomputers play in addressing global health crises. This perspective article explores the transformative impact of supercomputing in pandemic response, highlighting how these powerful machines have transitioned from crisis management tools to essential components of preparedness strategies. In this article, we examine the key contributions of supercomputers in combating the pandemic, including their ability to accelerate scientific research, facilitate data analysis, model complex scenarios, and optimize resource allocation. Furthermore, we delve into the role of supercomputing in strengthening public health infrastructure and preparedness. We analyze the lessons learned from the pandemic and emphasize the need for proactive investment in supercomputing capabilities, data infrastructure, and computational expertise as a crucial element of pandemic preparedness efforts. By harnessing the potential of supercomputers, countries can establish robust computational frameworks that enable real-time monitoring, early detection, and effective response to future outbreaks. Moreover, we address the challenges faced by supercomputing initiatives, including the need for enhanced international collaboration, equitable access to computing resources, and the ethical considerations associated with data privacy and security. We discuss potential strategies to overcome these challenges and foster a global network of interconnected supercomputing centers dedicated to pandemic preparedness and response. Finally, we highlight ongoing research and development efforts aimed at advancing supercomputing technologies, such as exascale computing and quantum computing, and their potential to revolutionize pandemic response. We emphasize the importance of sustained investment in research and development to ensure that supercomputing remains at the forefront of future pandemic preparedness strategies.

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Section: Drug Discoverymentioning

confidence: 86%

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

Mustafa,

Makhawi

2023

Preprint

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“…In the era of exascale computing, 91,92 it is tempting to design molecular systems to study from organelles 9,93 to viruses 93,94 or even an entire cell. [95][96][97] Yet, the computing power necessary to simulate such large systems is still very huge and prevents one from reaching simulated timescales useful to decipher even simple phenomena such as the diffusion of large molecules 93 without even mentioning relevant biological time scales of milliseconds or longer.…”

Section: Discussionmentioning

confidence: 99%

There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning

Cornet,

Coulonges,

Pezeshkian

et al. 2024

Soft Matter

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“…Before presenting applications, it is important to first describe the methodological context. Methodological advances were driven by improvements both in computational power [8][9][10] and in experimental techniques capable of determining the structure of very large membrane protein assemblies [11][12][13][14]. It is currently possible to model both very large assemblies composed of millions of particles and very specific interactions between few atoms.…”

Section: -Methodological Development To Model β-Barrel Proteinsmentioning

confidence: 99%

Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies

Duncan,

Gao,

Haanappel

et al. 2023

Preprint

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Spurred by advances in AI-driven modeling and experimental methods, molecular dynamics simulations are now acting as a platform to integrate these different approaches. This combination of methods is especially useful to understand β-barrel proteins from the molecular level, e.g., identifying specific interactions with lipids or small molecules, up to assemblies comprised of hundreds of proteins and thousands of lipids. In this minireview, we will discuss recent advances, mainly from the last five years, in modeling β-barrel proteins and their assemblies. These approaches require specific kinds of modeling and potentially different model resolutions that we will first describe in Section 1. We will then focus on different aspects of β-barrel protein modeling: how different types of molecules can diffuse through β-barrel proteins (Section 2); how lipids can interact with these proteins (Section 3); how β-barrel proteins can interact with membrane partners (Section 4) or periplasmic extensions and partners (Section 5) to form large assemblies.

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

Cited by 14 publications

References 229 publications

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning

Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies

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