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

Abstract

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.

Effects of Electrostatic Interactions on the Translocation of Polymers Through a Narrow Pore Under Different Solvent Conditions: A Dissipative Particle Dynamics Simulation Study

“…There have been some successful attempts to tackle this problem60–62; most proposed the replacement of the point charge at the center of the DPD particle with a charge distribution smeared across the particle. Groot developed a particle/particle–particle/mesh (PPPM) algorithm to spread out charges into the lattice 60.…”

Nanodomain Formation of Ganglioside GM1 in Lipid Membrane: Effects of Cholera Toxin-Mediated Cross-Linking

“…31 The initial configuration of a single phospholipid or ganglioside lipid is obtained from an MD simulation. To prepare bilayer membranes, 1568 (or 512) phospholipid molecules (DPPC or DOPC) are placed on square grids in the center of an L x × L y × L z sized box with the head groups on the outside of the membrane and the alkyl chains inside the membrane (Fig.…”

“…14,15 For example, in a recent work with AAMD simulation, 15 only one CTB, which was binding to a monolayer membrane composed of five GM1 molecules and a hundred phospholipids, was investigated. To handle the entire perspective of phenomena in complex materials, various coarse-grained (CG) methods, including coarse-grained Molecular Dynamics (CGMD) [16][17][18][19][20] and dissipative particle dynamics (DPD) simulations, [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] have been developed. The CG model groups a few atoms into one mesoscopic pseudoatom and thus can reach the biologically relevant time and length scales efficiently.…”

Effects of Antimicrobial Peptide Revealed by Simulations: Translocation, Pore Formation, Membrane Corrugation and Euler Buckling

“…In addition, for polymeric molecules, such as lipids and peptides, beads are connected by harmonic Hookean spring forces, and bending stiffness forces are also included [11,12]. Electrostatic interactions between charged beads are calculated by using the method introduced by Groot [17] and recently further developed by us [18], where the charges are distributed on a lattice and the electrostatic field is solved locally on the grid. Some of the here reported simulations are performed in constant particle number, surface tension, normal pressure and temperature ( Nγ s P ⊥ T ), assembled by using the Langevin piston method to control the pressure [19].…”

“…Already at the early times, the peptides bind onto the surface of the membrane and disorder the lipids around them. Such binding induces local compression on the peptide-rich leaflet of the membrane and a tension on the peptide-poor leaflet [18]. Some peptides then tend to intrude into the membrane interior to release the local tension; see the circled region in Figure 2a.…”