相关论文: Coupling a nano-particle with isothermal fluctuati…
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 study coarse-grained density fluctuations in the disordered phase of the paradigmatic Vicsek-like models of self-propelled particles with alignment interactions and random self-propulsion velocities. By numerically integrating a…
We study the dynamics of membrane vesicle motor transport into dendritic spines, which are bulbous intracellular compartments in neurons that play a key role in transmitting signals between neurons. We consider the stochastic analog of the…
Confocal microscopy of fluorescent labeled particles has been used to study the dynamical and structural properties of colloidal and granular matter in real space. Localization algorithms allow for a fully automatized determination of the…
Segregation induced by a thermal gradient of an impurity in a driven low-density granular gas is studied. The system is enclosed between two parallel walls from which we input thermal energy to the gas. We study here steady states occurring…
We describe the thermodynamic state of a highly confined single-phase and single-component fluid in a slit pore using Hill's thermodynamics of small systems. This theory was more recently named nanothermodynamics. We start by constructing…
Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
Weakly-compressible particle-based discretization methods, utilized for the solution of the subsonic Navier-Stokes equation, are gaining increasing popularity in the fluid dynamics community. One of the most popular among these methods is…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
By considering general Markov stochastic dynamics and its coarse-graining, we study the framework of stochastic thermodynamics for the original and reduced descriptions corresponding to different scales. We are especially concerned with the…
We present a numerical formulation for the solution of non-isothermal, compressible, Navier-Stokes equations with thermal fluctuations to describe mesoscale transport phenomena in multispecies fluid mixtures. The novelty of our numerical…
Capturing the correct dynamics at the Coarse-Grained (CG) scale remains a central challenge in the advancement of systematic CG models for soft matter simulations. The Generalized Langevin Equation (GLE), rooted in the Mori-Zwanzig…
In this work, we derive particle schemes, based on micro-macro decomposition, for linear kinetic equations in the diffusion limit. Due to the particle approximation of the micro part, a splitting between the transport and the collision part…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel…
This work presents a rigorous framework based on coarse-graining to analyze highly compressible turbulence. We show how the requirement that viscous effects on the dynamics of large-scale momentum and kinetic energy be negligible ---an…
The construction of coarse-grained descriptions of a system's kinetics is well established in biophysics. One prominent example is Markov state models in protein folding dynamics. In this paper, we develop a coarse-grained, discrete state…
We propose to couple a state-resolved rovibrational coarse-grain model to a stochastic particle method for simulating internal energy excitation and dissociation of a molecular gas. An existing coarse-grain model based on the NASA Ames ab…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…