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Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble
[Image: see text] Hamiltonian hybrid particle–field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091448/ https://www.ncbi.nlm.nih.gov/pubmed/36976890 http://dx.doi.org/10.1021/acs.jcim.3c00186 |
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author | Sen, Samiran Ledum, Morten Bore, Sigbjørn Løland Cascella, Michele |
author_facet | Sen, Samiran Ledum, Morten Bore, Sigbjørn Løland Cascella, Michele |
author_sort | Sen, Samiran |
collection | PubMed |
description | [Image: see text] Hamiltonian hybrid particle–field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer. |
format | Online Article Text |
id | pubmed-10091448 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100914482023-04-13 Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble Sen, Samiran Ledum, Morten Bore, Sigbjørn Løland Cascella, Michele J Chem Inf Model [Image: see text] Hamiltonian hybrid particle–field molecular dynamics is a computationally efficient method to study large soft matter systems. In this work, we extend this approach to constant-pressure (NPT) simulations. We reformulate the calculation of internal pressure from the density field by taking into account the intrinsic spread of the particles in space, which naturally leads to a direct anisotropy in the pressure tensor. The anisotropic contribution is crucial for reliably describing the physics of systems under pressure, as demonstrated by a series of tests on analytical and monatomic model systems as well as realistic water/lipid biphasic systems. Using Bayesian optimization, we parametrize the field interactions of phospholipids to reproduce the structural properties of their lamellar phases, including area per lipid, and local density profiles. The resulting model excels in providing pressure profiles in qualitative agreement with all-atom modeling, and surface tension and area compressibility in quantitative agreement with experimental values, indicating the correct description of long-wavelength undulations in large membranes. Finally, we demonstrate that the model is capable of reproducing the formation of lipid droplets inside a lipid bilayer. American Chemical Society 2023-03-28 /pmc/articles/PMC10091448/ /pubmed/36976890 http://dx.doi.org/10.1021/acs.jcim.3c00186 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Sen, Samiran Ledum, Morten Bore, Sigbjørn Løland Cascella, Michele Soft Matter under Pressure: Pushing Particle–Field Molecular Dynamics to the Isobaric Ensemble |
title | Soft Matter under
Pressure: Pushing Particle–Field
Molecular Dynamics to the Isobaric Ensemble |
title_full | Soft Matter under
Pressure: Pushing Particle–Field
Molecular Dynamics to the Isobaric Ensemble |
title_fullStr | Soft Matter under
Pressure: Pushing Particle–Field
Molecular Dynamics to the Isobaric Ensemble |
title_full_unstemmed | Soft Matter under
Pressure: Pushing Particle–Field
Molecular Dynamics to the Isobaric Ensemble |
title_short | Soft Matter under
Pressure: Pushing Particle–Field
Molecular Dynamics to the Isobaric Ensemble |
title_sort | soft matter under
pressure: pushing particle–field
molecular dynamics to the isobaric ensemble |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10091448/ https://www.ncbi.nlm.nih.gov/pubmed/36976890 http://dx.doi.org/10.1021/acs.jcim.3c00186 |
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