Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.

TitleModelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.
Publication TypeJournal Article
Year of Publication2019
AuthorsBrandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F
JournalSci Rep
Volume9
Issue1
Pagination16450
Date Published2019 Nov 11
ISSN2045-2322
Abstract

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.

DOI10.1038/s41598-019-52760-y
Alternate JournalSci Rep
Citation Key2019|2104
PubMed ID31712588
PubMed Central IDPMC6848203
Grant ListANR-11-LABX-0011-01 / / Agence Nationale de la Recherche (French National Research Agency) /
ANR-11-LABX-0011-01 / / Agence Nationale de la Recherche (French National Research Agency) /
CACSICE / / Agence Nationale de la Recherche (French National Research Agency) /
PCOFUND-GA-2013-609102 / / EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Ac /
258748 / / EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Ac /
PCOFUND-GA-2013-609102 / / EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Ac /