Erratum: “Constant-pressure and constant-surface tension simulations in dissipative particle dynamics” [J. Chem. Phys. <b>122</b>, 124901 (2005)]

The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, the conservative pairwise forces between beads of the same type in two different hydrophobic chains are chosen to be less repulsive than the water-water interaction, but the intrachain bead interactions are the same as the water-water interaction. For a certain range of parameters, the new bilayer can only be stretched up to 30% before it ruptures. Membrane tension, density profiles, and the in-plane lipid diffusion coefficient of the new bilayer are discussed in detail. They find two kinds of finite size effects that influence the membrane tension: lateral finite size effects, for which larger membranes rupture at a smaller stretch, and transverse finite size effects, for which tensionless bilayers are more compact in larger systems. These finite size effects become rather small when the simulation box is sufficiently large.

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“…To reduce the transverse finite size effects just discussed, one should use the constant pressure ensemble. 30,32,33…”

Section: B Transverse Finite Size Effectsmentioning

confidence: 99%

Improved dissipative particle dynamics simulations of lipid bilayers

Ling

Shillcock

Lipowsky

2007

The Journal of Chemical Physics

100

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“…The surface tension of a membrane was determined in our simulations from the pressure tensor using the relation 41 ,…”

Section: Macroscopic Membrane Properties and Velocity Correlation mentioning

confidence: 99%

Coarse-grain model for lipid bilayer self-assembly and dynamics: Multiparticle collision description of the solvent

Mei-Chun

Kapral

Mikhailov

et al. 2012

The Journal of Chemical Physics

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A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for the solvent. Self-assembly of a membrane from a uniform mixture of lipids is observed. Simulations at different temperatures demonstrate that it reproduces the gel and liquid phases of lipid bilayers. Investigations of lipid diffusion in different phases reveals a crossover from subdiffusion to normal diffusion at long times. Macroscopic membrane properties, such as stretching and bending elastic moduli, are determined directly from the mesoscopic simulations. Velocity correlation functions for membrane flows are determined and analyzed.

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“…Simulations were performed using the DL MESO software package in the NpT ensemble using the standard DPD thermostat and a Langevin barostat 61,62 , with a control temperature,…”

Section: Simulation Parametersmentioning

confidence: 99%

Model for the Simulation of the C_nE_m Nonionic Surfactant Family Derived from Recent Experimental Results

et al. 2020

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Using a comprehensive set of recently published experimental results for training and validation, we have developed computational models appropriate for simulations of aqueous solutions of poly(ethylene oxide) alkyl ethers, an important class of micelle-forming nonionic surfactants, usually denoted CnEm. These models are suitable for use in simulations that employ a moderate amount of coarse graining and especially for dissipative particle dynamics (DPD), which we adopt in this work. The experimental data used for training and validation were reported earlier and produced in our laboratory using dynamic light scattering (DLS) measurements performed on twelve members of the CnEm compound family yielding micelle size distribution functions and mass weighted mean aggregation numbers at each of several surfactant concentrations. The range of compounds and quality of the experimental results were designed to support the development of computational models. An essential feature of this work is that all simulation results were analysed in a way that is consistent with the experimental data. Proper account is taken of the fact that a broad distribution of micelle sizes exists, so mass weighted averages (rather than number weighted averages) over this distribution are required for the proper comparison of simulation and experimental results. The resulting DPD force field reproduces several important trends seen in the experimental critical micelle concentrations and mass averaged mean aggregation numbers with respect to surfactant characteristics and concentration. We feel it can be used to investigate a number of open questions regarding micelle sizes and shapes and their dependence on surfactant concentration for this important class of nonionic surfactants. File list (2) download file view on ChemRxiv DPDpaper-4.pdf (1.02 MiB) download file view on ChemRxiv DPDpaperSI-3.pdf (2.71 MiB)

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Erratum: “Constant-pressure and constant-surface tension simulations in dissipative particle dynamics” [J. Chem. Phys. 122, 124901 (2005)]

Cited by 23 publications

References 0 publications

Improved dissipative particle dynamics simulations of lipid bilayers

Improved dissipative particle dynamics simulations of lipid bilayers

Coarse-grain model for lipid bilayer self-assembly and dynamics: Multiparticle collision description of the solvent

Model for the Simulation of the C_nE_m Nonionic Surfactant Family Derived from Recent Experimental Results

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Erratum: “Constant-pressure and constant-surface tension simulations in dissipative particle dynamics” [J. Chem. Phys. 122, 124901 (2005)]

Cited by 23 publications

References 0 publications

Improved dissipative particle dynamics simulations of lipid bilayers

Improved dissipative particle dynamics simulations of lipid bilayers

Coarse-grain model for lipid bilayer self-assembly and dynamics: Multiparticle collision description of the solvent

Model for the Simulation of the CnEm Nonionic Surfactant Family Derived from Recent Experimental Results

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Product

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Model for the Simulation of the C_nE_m Nonionic Surfactant Family Derived from Recent Experimental Results