Cargando…
Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics
In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems....
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848203/ https://www.ncbi.nlm.nih.gov/pubmed/31712588 http://dx.doi.org/10.1038/s41598-019-52760-y |
_version_ | 1783469045936291840 |
---|---|
author | F. Brandner, Astrid Timr, Stepan Melchionna, Simone Derreumaux, Philippe Baaden, Marc Sterpone, Fabio |
author_facet | F. Brandner, Astrid Timr, Stepan Melchionna, Simone Derreumaux, Philippe Baaden, Marc Sterpone, Fabio |
author_sort | F. Brandner, Astrid |
collection | PubMed |
description | In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments. |
format | Online Article Text |
id | pubmed-6848203 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68482032019-11-19 Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics F. Brandner, Astrid Timr, Stepan Melchionna, Simone Derreumaux, Philippe Baaden, Marc Sterpone, Fabio Sci Rep Article In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments. Nature Publishing Group UK 2019-11-11 /pmc/articles/PMC6848203/ /pubmed/31712588 http://dx.doi.org/10.1038/s41598-019-52760-y Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article F. Brandner, Astrid Timr, Stepan Melchionna, Simone Derreumaux, Philippe Baaden, Marc Sterpone, Fabio Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title | Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title_full | Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title_fullStr | Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title_full_unstemmed | Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title_short | Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics |
title_sort | modelling lipid systems in fluid with lattice boltzmann molecular dynamics simulations and hydrodynamics |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848203/ https://www.ncbi.nlm.nih.gov/pubmed/31712588 http://dx.doi.org/10.1038/s41598-019-52760-y |
work_keys_str_mv | AT fbrandnerastrid modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics AT timrstepan modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics AT melchionnasimone modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics AT derreumauxphilippe modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics AT baadenmarc modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics AT sterponefabio modellinglipidsystemsinfluidwithlatticeboltzmannmoleculardynamicssimulationsandhydrodynamics |