Related papers: Parametrization of coarse grained force fields for…
We propose a method to parameterize a coarse grained model for the hydrodynamic friction between nearly touching rough spheres in suspension flows. The frictional resistance due to surface roughness primarily alters the sliding and rolling…
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…
Simple homogeneous shear flows of frictionless, deformable particles are studied by particle simulations at large shear rates and for differently soft, deformable particles. The particle stiffness sets a time-scale that can be used to scale…
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
The results of modeling shear flows in classical two-dimensional dipole systems are presented. We used the method of non-equilibrium molecular dynamics to calculate the viscosity at various shear rates. The coefficients of shear viscosity…
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling:…
The continuum theory of partially fluidized shear granular flows is tested and calibrated using two dimensional soft particle molecular dynamics simulations. The theory is based on the relaxational dynamics of the order parameter that…
A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics,…
The limited availability of accurate experimental data in wide ranges of pressure, temperature, and composition is the main constraining factor for the proper development and assessment of thermodynamic models and equations of state. In the…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
We report on measurements of self-diffusion coefficients in discrete numerical simulations of steady, homogeneous, collisional shearing flows of nearly identical, frictional, inelastic spheres. We focus on a range of relatively high solid…
We use molecular dynamics simulations of a model three-dimensional particulate gel, to investigate the linear viscoelastic response. The numerical simulations are combined with a novel test protocol (the optimally- windowed chirp or OWCh),…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
Various volatile aerosols have been associated with adverse health effects; however, characterization of these aerosols is challenging due to their dynamic nature. Here we present a method that directly measures the volatility of…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results.…