Cargando…

Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme

In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divi...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Xiaoxu, Gao, Lianghui, Fang, Weihai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4854440/
https://www.ncbi.nlm.nih.gov/pubmed/27137463
http://dx.doi.org/10.1371/journal.pone.0154568
_version_ 1782430223454699520
author Li, Xiaoxu
Gao, Lianghui
Fang, Weihai
author_facet Li, Xiaoxu
Gao, Lianghui
Fang, Weihai
author_sort Li, Xiaoxu
collection PubMed
description In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop.
format Online
Article
Text
id pubmed-4854440
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-48544402016-05-07 Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme Li, Xiaoxu Gao, Lianghui Fang, Weihai PLoS One Research Article In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop. Public Library of Science 2016-05-03 /pmc/articles/PMC4854440/ /pubmed/27137463 http://dx.doi.org/10.1371/journal.pone.0154568 Text en © 2016 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Li, Xiaoxu
Gao, Lianghui
Fang, Weihai
Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title_full Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title_fullStr Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title_full_unstemmed Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title_short Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme
title_sort dissipative particle dynamics simulations for phospholipid membranes based on a four-to-one coarse-grained mapping scheme
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4854440/
https://www.ncbi.nlm.nih.gov/pubmed/27137463
http://dx.doi.org/10.1371/journal.pone.0154568
work_keys_str_mv AT lixiaoxu dissipativeparticledynamicssimulationsforphospholipidmembranesbasedonafourtoonecoarsegrainedmappingscheme
AT gaolianghui dissipativeparticledynamicssimulationsforphospholipidmembranesbasedonafourtoonecoarsegrainedmappingscheme
AT fangweihai dissipativeparticledynamicssimulationsforphospholipidmembranesbasedonafourtoonecoarsegrainedmappingscheme