Related papers: Particle-based membrane model for mesoscopic simul…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
The interaction potential between supported floating bilayers has been determined by grazing incidence specular and off-specular scattering using synchrotron radiation. Our measurements demonstrate that floating bilayers are significantly…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
We present a meshless numerical method for simulating the dynamics of axisymmetric vesicles in a viscous medium. Key innovations include: (1) adaptive reparameterization based on local length scales, reducing the number of required…
Kinetic plasma processes, such as magnetic reconnection, collisionless shocks, and turbulence, are fundamental to the dynamics of astrophysical and laboratory plasmas. Simulating these processes often requires particle-in-cell (PIC)…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle…
The issue of the stability of Pickering emulsions is tackled at a mesoscopic level using dissipative particle dynamics simulations within the Adiabatic Biased Molecular Dynamics framework. We consider the early stage of the coalescence…
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use…
We propose a particle-based method to simulate thin-film fluid that jointly facilitates aggressive surface deformation and vigorous tangential flows. We build our dynamics model from the surface tension driven Navier-Stokes equation with…
We review recent molecular dynamics simulations of thermally activated undulations and defects in the lamellar $L_\alpha$ phase of a binary amphiphile-solvent mixture, using an idealized molecular coarse-grained model: Solvent particles are…
We study the settling of solid particles within a viscous incompressible fluid contained in a two-dimensional channel, where the mass density of the particles is slightly greater than that of the fluid. The fluid-structure interaction…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
In this paper, we present an Eulerian-Lagrangian methodology to simulate the interaction between a fluid-fluid interface and a solid particle in the presence of wetting effects. The target physical problem is represented by ternary phase…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…