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Open Boundary Modeling in Molecular Dynamics with Machine Learning

Molecular-continuum flow simulations combine molecular dynamics (MD) and computational fluid dynamics for multiscale considerations. A specific challenge in these simulations arises due to the “open MD boundaries” at the molecular-continuum interface: particles close to these boundaries do not feel...

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Detalles Bibliográficos
Autores principales: Neumann, Philipp, Wittmer, Niklas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304690/
http://dx.doi.org/10.1007/978-3-030-50433-5_26
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author Neumann, Philipp
Wittmer, Niklas
author_facet Neumann, Philipp
Wittmer, Niklas
author_sort Neumann, Philipp
collection PubMed
description Molecular-continuum flow simulations combine molecular dynamics (MD) and computational fluid dynamics for multiscale considerations. A specific challenge in these simulations arises due to the “open MD boundaries” at the molecular-continuum interface: particles close to these boundaries do not feel any forces from outside which results in unphysical behavior and incorrect thermodynamic pressures. In this contribution, we apply neural networks to generate approximate boundary forces that reduce these artefacts. We train our neural network with force-distance pair values from periodic MD simulations and use this network to later predict boundary force contributions in non-periodic MD systems. We study different training strategies in terms of MD sampling and training for various thermodynamic state points and report on accuracy of the arising MD system. We further discuss computational efficiency of our approach in comparison to existing boundary force models.
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spelling pubmed-73046902020-06-22 Open Boundary Modeling in Molecular Dynamics with Machine Learning Neumann, Philipp Wittmer, Niklas Computational Science – ICCS 2020 Article Molecular-continuum flow simulations combine molecular dynamics (MD) and computational fluid dynamics for multiscale considerations. A specific challenge in these simulations arises due to the “open MD boundaries” at the molecular-continuum interface: particles close to these boundaries do not feel any forces from outside which results in unphysical behavior and incorrect thermodynamic pressures. In this contribution, we apply neural networks to generate approximate boundary forces that reduce these artefacts. We train our neural network with force-distance pair values from periodic MD simulations and use this network to later predict boundary force contributions in non-periodic MD systems. We study different training strategies in terms of MD sampling and training for various thermodynamic state points and report on accuracy of the arising MD system. We further discuss computational efficiency of our approach in comparison to existing boundary force models. 2020-05-25 /pmc/articles/PMC7304690/ http://dx.doi.org/10.1007/978-3-030-50433-5_26 Text en © Springer Nature Switzerland AG 2020 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Article
Neumann, Philipp
Wittmer, Niklas
Open Boundary Modeling in Molecular Dynamics with Machine Learning
title Open Boundary Modeling in Molecular Dynamics with Machine Learning
title_full Open Boundary Modeling in Molecular Dynamics with Machine Learning
title_fullStr Open Boundary Modeling in Molecular Dynamics with Machine Learning
title_full_unstemmed Open Boundary Modeling in Molecular Dynamics with Machine Learning
title_short Open Boundary Modeling in Molecular Dynamics with Machine Learning
title_sort open boundary modeling in molecular dynamics with machine learning
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304690/
http://dx.doi.org/10.1007/978-3-030-50433-5_26
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