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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...

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Autores principales: Sen, Samiran, Ledum, Morten, Bore, Sigbjørn Løland, Cascella, Michele
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
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.
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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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