Related papers: Coarse-graining via EDP-convergence for linear fas…
We propose a general coarse-graining method to derive a continuity equation that describes any dissipative system of repulsive particles interacting through short-ranged potentials. In our approach, the effect of particle-particle…
Granular systems present surprisingly complicated dynamics. In particular, nonlinear interactions and energy dissipation play important roles in these dynamics. Usually, constant coefficients of restitution are introduced phenomenologically…
This paper proposes a novel reaction-diffusion system approximation tailored for singular diffusion problems, typified by the fast diffusion equation. While such approximation methods have been successfully applied to degenerate parabolic…
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 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 a system of two coupled nonlinear parabolic equations. It constitutes a variant of the Keller-Segel model for chemotaxis, i.e. it models the behaviour of a population of bacteria that interact by means of a signalling substance. We…
Exchange-driven growth (EDG) is a process in which pairs of clusters interact by exchanging single unit with a rate given by a kernel $K(j,k)$. Despite EDG model's common use in the applied sciences, its rigorous mathematical treatment is…
We consider a family of drift-diffusion-recombination systems, where the recombination of electrons and holes is facilitated by an intermediate energy-level for electrons in so-called trapped states. In particular, it has been proven in…
We investigate both analytically and by numerical simulation the kinetics of a microscopic model of hard rods adsorbing on a linear substrate, a model which is relevant for compaction of granular materials. The computer simulations use an…
Constrained quantum dynamics is used to propose a nonlinear dynamical equation for pure states of a generalized coarse-grained system. The relevant constraint is given either by the generalized purity or by the generalized invariant…
Mathematical modelling of biological population dynamics often involves proposing high fidelity discrete agent-based models that capture stochasticity and individual-level processes. These models are often considered in conjunction with an…
We present a model for sticky particles in which cluster sizes after a reaction have $\ell$ fewer total particles than the sum of their reactants. The finite particle system is modeled as a Markov process under a mean-field assumption 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.…
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,…
We discuss a coarse-grained approach to the computation of rare events in the context of grand canonical Monte Carlo (GCMC) simulations of self-assembly of surfactant molecules into micelles. The basic assumption is that the {\it…
Large eddy approximation of turbulent flow is given a natural setting within the DSC framework of computational fluid dynamics. Periodic cellular coarse-graining prevents the nodal flow from piling up and preserves its large patterns. The…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
The group classification of a class of variable coefficient reaction-diffusion equations with exponential nonlinearities is carried out up to both the equivalence generated by the corresponding generalized equivalence group and the general…
Inspired by holographic Wilsonian renormalization, we consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, coupled via the Hamiltonian. Observations using purely long distance…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…