Improved dissipative particle dynamics simulations of lipid bilayers

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.

Section: Introductionmentioning

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

“…[4][5][6][7][8][9][10] Electrostatic interactions included in the DPD method 11 further broaden its application in biological systems. 12 To avoid strong ion pairing of soft particles in DPD potential, electrostatic field is solved locally on a grid by spreading out charges into lattice.…”

mentioning

confidence: 99%

Communications: Self-energy and corresponding virial contribution of electrostatic interactions in dissipative particle dynamics: Simulations of cationic lipid bilayers

Ling

Fang²

2010

Self Cite

General expressions of self-energy and corresponding virial terms for electrostatic interactions in dissipative particle dynamics simulations are derived in this article. In the lattice-sum electrostatics, we found the essential process is to solve the electric field equation of each individual point charge. Strong inward pressure caused by the self-energy is eliminated by subtracting the corresponding virial from the total virial. The resulting method is tested by simulating cationic lipid bilayers in constant pressure ensemble.

“…Such a study has been performed previously in Ref. 29 and revealed a size dependence of the tension of rupture. The lateral size L x = L y = 32 d used here, which is about six times the membrane thickness, was chosen as a compromise between two opposing requirements.…”

Section: A Symmetric Bilayers With Zero Bare Tensionmentioning

confidence: 95%

Membrane curvature generated by asymmetric depletion layers of ions, small molecules, and nanoparticles

Różycki

Lipowsky

2016

Self Cite

Erratum: "Membrane curvature generated by asymmetric depletion layers of ions, small molecules, and nanoparticles" [J. Chem. Phys. 145, 074117 (2016) Biomimetic and biological membranes consist of molecular bilayers with two leaflets that are typically exposed to different aqueous solutions. We consider solutions of "particles" that experience effectively repulsive interactions with these membranes and form depletion layers in front of the membrane leaflets. The particles considered here are water-soluble, have a size between a few angstrom and a few nanometers as well as a rigid, more or less globular shape, and do neither adsorb onto the membranes nor permeate these membranes. Examples are provided by ions, small sugar molecules, globular proteins, or inorganic nanoparticles with a hydrophilic surface. We first study depletion layers in a hard-core system based on ideal particle solutions as well as hard-wall interactions between these particles and the membrane. For this system, we obtain exact expressions for the coverages and tensions of the two leaflets as well as for the spontaneous curvature of the bilayer membrane. All of these quantities depend linearly on the particle concentrations. The exact results for the hard-core system also show that the spontaneous curvature can be directly deduced from the planar membrane geometry. Our results for the hard-core system apply both to ions and solutes that are small compared to the membrane thickness and to nanoparticles with a size that is comparable to the membrane thickness, provided the particle solutions are sufficiently dilute. We then corroborate the different relationships found for the hard-core system by extensive simulations of a soft-core particle system using dissipative particle dynamics. The simulations confirm the linear relationships obtained for the hard-core system. Both our analytical and our simulation results show that the spontaneous curvature induced by a single particle species can be quite large.