Erratum: “Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules” [J. Chem. Phys. <b>116</b>, 5842 (2002)]

Yamamoto, Satoru; Maruyama, Yutaka; Hyodo, Shi‐aki

doi:10.1063/1.1494416

Cited by 117 publications

(181 citation statements)

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“…As with the Smit model, springs define molecular architecture. The DPD technique has found recent applications in the area of lipids and surfactants, with simulations of bilayer structure, 12 elastic properties, 13 self-assembly, 14 pore formation, 15 vesicle formation and fusion, 16 and the construction of a complete phase diagram for a simple AB type surfactant. 17 Although the current CG models used in MD and DPD are becoming very powerful in understanding structural aspects of lipid and surfactant phases and the relative phase stabilities, the models cited above are qualitative rather than quantitative in their predictions.…”

Section: Introductionmentioning

confidence: 99%

Coarse Grained Model for Semiquantitative Lipid Simulations

2003

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This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of magnitude can be achieved. Micrometer length scales or millisecond time scales are therefore within reach. To encourage applications, the model is kept very simple. Only a small number of coarse grained atom types are defined, which interact using a few discrete levels of interaction. Despite the computational speed and the simplistic nature of the model, it proves to be both versatile in its applications and accurate in its predictions. We show that densities of liquid alkanes from decane up to eicosane can be reproduced to within 5%, and the mutual solubilities of alkanes in water and water in alkanes can be reproduced within 0.5 kT of the experimental values. The CG model for dipalmitoylphosphatidylcholine (DPPC) is shown to aggregate spontaneously into a bilayer. Structural properties such as the area per headgroup and the phosphate-phosphate distance match the experimentally measured quantities closely. The same is true for elastic properties such as the bending modulus and the area compressibility, and dynamic properties such as the lipid lateral diffusion coefficient and the water permeation rate. The distribution of the individual lipid components along the bilayer normal is very similar to distributions obtained from atomistic simulations. Phospholipids with different headgroup (ethanolamine) or different tail lengths (lauroyl, stearoyl) or unsaturated tails (oleoyl) can also be modeled with the CG force field. The experimental area per headgroup can be reproduced for most lipids within 0.02 nm 2 . Finally, the CG model is applied to nonbilayer phases. Dodecylphosphocholine (DPC) aggregates into small micelles that are structurally very similar to ones modeled atomistically, and DOPE forms an inverted hexagonal phase with structural parameters in agreement with experimental data.

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Section: Introductionmentioning

confidence: 99%

Coarse Grained Model for Semiquantitative Lipid Simulations

2003

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“…[21][22][23][24] Besides the proposition of coarse-grained models, hybrid methodologies have been proposed to study large micellar systems. [25][26][27] More recently, implicit solvent model using dissipative particle dynamics (DPD) and Monte Carlo (MC), 28,29 have been carried out. We chose the MARTINI CG model, because of the simplicity of it.…”

Section: Introductionmentioning

confidence: 99%

Investigating the spontaneous formation of SDS micelle in aqueous solution using a coarse-grained force field

Pires¹,

Moura²,

Freitas³

2012

Quím. Nova

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Recebido em 19/8/11; aceito em 5/12/11; publicado na web em 31/1/12 A 1µs Molecular Dynamic simulation was performed with a realistic model system of Sodium Dodecyl Sulfate (SDS) micelles in aqueous solution, comprising of 360 DS -, 360 Na + and 90000 water particles. After 300 ns three different micellar shapes and sizes 41, 68 and 95 monomers, were observed. The process led to stabilization in the total number of SDS clusters and an increase in the micellar radius to 2.23 nm, in agreement with experimental results. An important conclusion, is be aware that simulations employed in one aggregate, should be considered as a constraint. Size and shape distribution must be analyzed.

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“…The equilibrium properties of membrane with open edges were also studied by this method. 29,30 In the second group, the bilayer structure is modeled on an atomic [31][32][33] or molecular [33][34][35][36][37][38][39][40][41] scale, and the solvent is on the moving least-squares ͑MLS͒ method. 44,45 This model is well suitable to study membrane dynamics accompanied by topological changes.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of vesicle self-assembly and dissolution

Noguchi

Gompper

2006

The Journal of Chemical Physics

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The dynamics of membranes is studied on the basis of a particle-based meshless surface model, which was introduced earlier ͓Phys. Rev. E 73, 021903 ͑2006͔͒. The model describes fluid membranes with bending energy and-in the case of membranes with boundaries-line tension. The effects of hydrodynamic interactions are investigated by comparing Brownian dynamics with a particle-based mesoscale solvent simulation ͑multiparticle collision dynamics͒. Particles self-assemble into vesicles via disk-shaped membrane patches. The time evolution of assembly is found to consist of three steps: particle assembly into discoidal clusters, aggregation of clusters into larger membrane patches, and finally vesicle formation. The time dependence of the cluster distribution and the mean cluster size is evaluated and compared with the predictions of Smoluchowski rate equations. On the other hand, when the line tension is suddenly decreased ͑or the temperature is increased͒, vesicles dissolve via pore formation in the membrane. Hydrodynamic interactions are found to speed up the dynamics in both cases. Furthermore, hydrodynamics makes vesicle more spherical in the membrane-closure process.

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Erratum: “Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules” [J. Chem. Phys. 116, 5842 (2002)]

Cited by 117 publications

References 1 publication

Coarse Grained Model for Semiquantitative Lipid Simulations

Coarse Grained Model for Semiquantitative Lipid Simulations

Investigating the spontaneous formation of SDS micelle in aqueous solution using a coarse-grained force field

Dynamics of vesicle self-assembly and dissolution

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