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Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression
We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-sca...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404643/ https://www.ncbi.nlm.nih.gov/pubmed/30930707 http://dx.doi.org/10.1007/s10404-018-2164-z |
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author | Stephenson, David Kermode, James R. Lockerby, Duncan A. |
author_facet | Stephenson, David Kermode, James R. Lockerby, Duncan A. |
author_sort | Stephenson, David |
collection | PubMed |
description | We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging–diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate—around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required. |
format | Online Article Text |
id | pubmed-6404643 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-64046432019-03-27 Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression Stephenson, David Kermode, James R. Lockerby, Duncan A. Microfluid Nanofluidics Research Paper We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging–diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate—around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required. Springer Berlin Heidelberg 2018-11-16 2018 /pmc/articles/PMC6404643/ /pubmed/30930707 http://dx.doi.org/10.1007/s10404-018-2164-z Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Research Paper Stephenson, David Kermode, James R. Lockerby, Duncan A. Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title | Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title_full | Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title_fullStr | Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title_full_unstemmed | Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title_short | Accelerating multiscale modelling of fluids with on-the-fly Gaussian process regression |
title_sort | accelerating multiscale modelling of fluids with on-the-fly gaussian process regression |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404643/ https://www.ncbi.nlm.nih.gov/pubmed/30930707 http://dx.doi.org/10.1007/s10404-018-2164-z |
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