Related papers: Coarse-graining strategy for modeling effective, h…
Using molecular dynamics simulation, we examine the dynamics of crystal, polycrystal, and glass in a Lennard-Jones binary mixture composed of small and large particles in two dimensions. The crossovers occur among these states as the…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
We present the conceptual and technical background required to describe and understand the correlations and fluctuations of the empirical density and current of steady-state diffusion processes on all time scales -- observables central to…
Complex physical dynamics can often be modeled as a Markov jump process between mesoscopic configurations. When jumps between mesoscopic states are mediated by thermodynamic reservoirs, the time-irreversibility of the jump process is a…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
In this study, a coarse-graining framework for discrete models is formulated on the basis of multiscale homogenization. The discrete model considered in this paper is the Lattice Discrete Particle Model (LDPM), which simulates concrete at…
Some basic questions about the hydrodynamical approach to relativistic heavy ion collisions are discussed aiming to clarify how far we can go with such an approach to extract useful information on the properties and dynamics of the QCD…
We investigate by Molecular Dynamics simulation a system of $N$ particles moving on the surface of a two-dimensional sphere and interacting by a Lennard-Jones potential. We detail the way to account for the changes brought by a nonzero…
We present a single-particle Lennard-Jones (L-J) model for CO2 and N2. Simplified L-J models for other small polyatomic molecules can be obtained following the methodology described herein. The phase-coexistence diagrams of single-component…
A lubrication model can be used to describe the dynamics of a weakly volatile viscous fluid layer on a hydrophobic substrate. Thin layers of the fluid are unstable to perturbations and break up into slowly evolving interacting droplets. A…
Successful computer studies of glass-forming materials need to overcome both the natural tendency to structural ordering and the dramatic increase of relaxation times at low temperatures. We present a comprehensive analysis of eleven…
Granular gaseous mixtures under rapid flow conditions are usually modeled by a multicomponent system of smooth inelastic hard spheres with constant coefficients of normal restitution. In the low density regime an adequate framework is…
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise…
An expression for the stress tensor near an external boundary of a discrete mechanical system is derived explicitly in terms of the constituents' degrees of freedom and interaction forces. Starting point is the exact and general coarse…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
Granular systems confined in a shallow box and driven by vertical vibration provide a simple geometry to study fluidized granular media. Grains gain kinetic energy vertically through collisions with the walls and redistribute it…
New insights into phase separation in colloidal suspensions are provided via a new dynamical theory based on the Polydisperse Lattice-Gas model. The model gives a simplified description of polydisperse colloids, incorporating a hard-core…