Four-to-one coarse-grained polarisable water model for dissipative particle dynamics

Electroosmotic Flow Grows with Electrostatic Coupling in Confining Charged Dielectric Surfaces

In this work, the effects of polarization of confining charged planar dielectric surfaces on induced electroosmotic flow are investigated. To this end, we use dissipative particle dynamics to model solvent and ionic particles together with a modified Ewald sum method to model electrostatic interactions and surfaces polarization. A relevant difference between counterions number density profiles, velocity profiles, and volumetric flow rates obtained with and without surface polarization for moderate and high electrostatic coupling parameters is observed. For low coupling parameters, the effect is negligible. An increase of almost 500% in volumetric flow rate for moderate/high electrostatic coupling and surface separation is found when polarizable surfaces are considered. The most important result is that the increase in electrostatic coupling substantially increases the electroosmotic flow in all studied range of separations when the dielectric constant of electrolytes is much higher than the dielectric constant of confining walls. For the higher separation simulated, an increase of around 340% in volumetric flow rate when the electrostatic coupling is increased by a factor of two orders of magnitude is obtained.

Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

Establishing an Electrostatics Paradigm for Membrane Electroporation in the Framework of Dissipative Particle Dynamics

With an exclusive aim to looking into a mechanism of membrane electroporation on mesoscopic length and time scales, we report the dissipative particle dynamics (DPD) simulation results for systems with and without electrolytes. A polarizable DPD model of water is employed for accurate modeling of long-range electrostatics near the water-lipid interfaces. A great deal of discussion on field induced change in dipole moments of water and lipids together with the special variation of electric field is made in order to understand the dielectrophoretic movement of water, initiating a pore formation via an intrusion through the bilayer core. The presence of salt alters the dipolar arrangement of lipids and water, and thereby it reduces the external field required to create a pore in the membrane. The species fluxes through the pore, distributions for bead density, electrostatic potential, stresses across the membrane, etc. are used to answer some of the key questions pertaining to mechanism of electroporation. The findings are compared with the molecular dynamics simulation results found in the literature, and the comparison successfully establishes an electrostatics paradigm for biomembrane studies using DPD simulations.

Electroporation Using Dissipative Particle Dynamics with a Novel Protocol for Applying Electric Field

In molecular dynamics simulations of membrane electroporation, the bilayer is subjected to an electric field E either by direct addition of a force f = qE on the charge-bearing species or by imposing an ion imbalance in the salt solutions on the two sides of the bilayer. The former is believed to mimic electroporation with high fields over nanosecond pulse period, during which the membrane is almost uncharged, especially in the low salt limit. Conversely, the ion imbalance method elucidates a low electric field-induced poration over a longer period of micro- to milliseconds with a fully charged membrane. Both these methods of applying electric field have disadvantages while investigating electroporation using dissipative particle dynamics (DPD) simulations. The method involving direct addition of force fails to address the presence of a nonuniform dielectric background for ions embedded in nonpolarizable DPD water and those found in the core of the bilayer. The ion imbalance method in DPD simulations suffers from its unavoidable use of a wall potential to prevent the movement of ions across the periodic boundaries. To address the above issues, we propose a simple method for imposing a desired transmembrane potential (TMV) by placing oppositely but uniformly charged plates on either side of the bilayer. Our DPD simulations demonstrate that the profiles for bead density, mechanical stress, electrical potential, as well as the transient responses in the dipole moment and species fluxes obtained from the proposed method utilizing charged plates are quite similar to those obtained using the ion imbalance method. The proposed protocol is free from the aforementioned drawbacks of the direct force addition and ion imbalance methods.