Related papers: Coarse-graining via EDP-convergence for linear fas…
We expand on a previous study of fronts in finite particle number reaction-diffusion systems in the presence of a reaction rate gradient in the direction of the front motion. We study the system via reaction-diffusion equations, using the…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard…
Recently-derived high-order splitting schemes with complex coefficients are shown to exhibit reduced convergence rates for certain parabolic evolution equations. When applied to semilinear reaction-diffusion equations with periodic boundary…
We introduce a definition of coarse-grained entropy that unifies measurement-based (observational entropy) and max-entropy-based (Jaynes) approaches to coarse-graining, by identifying physical constraints with information theoretic priors.…
We present a new approach to coarse-graining of variables describing dust flow in GR. It is based on assigning quasi-local shear, twist and expansion to 2-dimensional surfaces with the help of isometric embeddings into the 3-dimensional…
We discuss a Bayesian formulation to coarse-graining (CG) of PDEs where the coefficients (e.g. material parameters) exhibit random, fine scale variability. The direct solution to such problems requires grids that are small enough to resolve…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
We study the motion of an overdamped particle connected to a thermal heat bath in the presence of an external periodic potential in one dimension. When we coarse-grain, i.e., bin the particle positions using bin sizes that are larger than…
The minimum energy path (MEP) describes the mechanism of reaction, and the energy barrier along the path can be used to calculate the reaction rate in thermal systems. The nudged elastic band (NEB) method is one of the most commonly used…
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,…
We develop a rigorous error analysis for coarse-graining of defect-formation free energy. For a one-dimensional constrained atomistic system, we establish the thermodynamic limit of the defect-formation free energy and obtain explicitly the…
For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a…
We introduce a high dimensional symplectic map, modeling a large system consisting of weakly interacting chaotic subsystems, as a toy model to analyze the interplay between single-particle chaotic dynamics and particles interactions in…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
We provide a derivation of the fourth-order DLSS equation based on an interpretation as a chemical reaction network. We consider the rate equation on the discretized circle for a process in which pairs of particles occupying the same site…
Sand production is an important issue for many hydrocarbon recovery applications in unconsolidated reservoirs. The model using the Computational Fluid Dynamics coupled with Discrete Element Method (CFD-DEM) can capture micro-scale features…
We derive the exchange-driven growth (EDG) equations as the mean-field limit of interacting particle systems on the complete graph. Extending previous work, we consider symmetric exchange kernels $c(k, l) = c(l, k)$ satisfying super-linear…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…