Related papers: A mesoscale model for quantitative phospholipid mo…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
A three-dimensional model of polydisperse reactive sedimentation is developed by means of a multilayer shallow water approach. The model consists of a variety of solid particles of different sizes and densities, and substrates diluted in…
Understanding the phase behaviour of pheromones and other messaging molecules remains a significant and largely unexplored challenge, even though it plays a central role in chemical communication. Here, we present all-atom molecular…
Cholesterol (CHOL) is one of the most important components of plasma membranes of higher cells and one of the main factors for the formation of (nano)domains. In this work, molecular dynamics simulations of mixtures of CHOL with DPPC…
Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for…
The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the…
We report on atomistic simulations of DPPC lipid monolayers using the CHARMM36 lipid force field and four-point OPC water model. The entire two-phase region where domains of the `liquid-condensed' (LC) phase coexist with domains of the…
We have studied the composition dependence of density of liquid water-DMSO mixtures at different temperatures by using the isobaric-isothermal (NPT) molecular dynamics computer simulations. The non-polarizable semi-flexible, P1 and P2…
We study self-diffusion and sedimentation in colloidal suspensions of nearly-hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
The miscibility in several polymer blend mixtures (polymethylmethacrylate/polystyrene, (1,4-cis) polyisoprene/polystyrene, and polymethylmethacrylate/polyoxyethylene) has been investigated using Molecular Dynamics simulations for atomistic…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
Various experiments have found a boundary slip in hydrophobic microchannel flows, but a consistent understanding of the results is still lacking. While Molecular Dynamics (MD) simulations cannot reach the low shear rates and large system…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
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…
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes reveal a membrane phase transition dictated drastic growth in the interface water (IW) heterogeneity length scales. It acts as an…
We have revisited the composition dependence of principal properties of liquid water-DMSO mixtures by using the isobaric-isothermal molecular dynamics computer simulations. A set of non-polarizable semi-flexible models for the DMSO molecule…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
We have calculated the electron density maps of the ripple phase of dimyristoylphosphatidylcholine (DMPC) and palmitoyl-oleoyl phosphatidylcholine (POPC) multibilayers at different temperatures and fixed relative humidity. Our analysis…