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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2020
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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. |
format | Online Article Text |
id | pubmed-7304690 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT neumannphilipp openboundarymodelinginmoleculardynamicswithmachinelearning AT wittmerniklas openboundarymodelinginmoleculardynamicswithmachinelearning |