Related papers: Coarse-graining via EDP-convergence for linear fas…
We consider nonlinear reaction systems satisfying mass-action kinetics with slow and fast reactions. It is known that the fast-reaction-rate limit can be described by an ODE with Lagrange multipliers and a set of nonlinear constraints that…
We perform a fast-reaction limit for a linear reaction-diffusion system consisting of two diffusion equations coupled by a linear reaction. We understand the linear reaction-diffusion system as a gradient flow of the free energy in the…
The theory of slow-fast gradient systems leads in a natural way to non-equilibrium steady states, because on the slow time scale the fast subsystem stays in steady states that are controlled by the interaction with the slow system. Using…
We investigate the convergence of spatial discretizations for reaction-diffusion systems with mass-action law satisfying a detailed balance condition. Considering systems on the d-dimensional torus, we construct appropriate space-discrete…
If gradient systems depend on a microstructure, we want to derive a macroscopic gradient structure describing the effective behavior of the microscopic effects. We introduce a notion of evolutionary Gamma-convergence that relates the…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
We introduce two new concepts of convergence of gradient systems $(\mathbf Q, \mathcal E_\varepsilon,\mathcal R_\varepsilon)$ to a limiting gradient system $(\mathbf Q, \mathcal E_0,\mathcal R_0)$. These new concepts are called `EDP…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Optically confined colloidal particles, when placed in close proximity, form a dissipatively coupled system through hydrodynamic interactions. The role of such interactions influencing irreversibility and energy dissipation in…
We investigate nonequilibrium steady-state dynamics in both continuous- and discrete-state stochastic processes. Our analysis focuses on planar diffusion dynamics and their coarse-grained approximations by discrete-state Markov chains.…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
We develop coarse-graining schemes for stochastic many-particle microscopic models with competing short- and long-range interactions on a d-dimensional lattice. We focus on the coarse-graining of equilibrium Gibbs states and using cluster…
Starting from a coarse-grained map of a quantum many-body system, we construct the inverse map that assigns a microscopic state to a coarse-grained state based on the maximum entropy principle. Assuming unitary evolution in the microscopic…
We formulate an effective-description framework for the dynamics of open quantum systems by extending the time-coarse-graining formalism to open systems. Our coarse-graining procedure efficiently removes high-frequency processes which are…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
We investigate the effect of coarse-graining on the energetics properties of a system, focusing on entropy production. As a case of study, we consider a one-dimensional colloidal particle in contact with a thermal bath, moving in a…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
The quantitative convergence to equilibrium for reaction-diffusion systems arising from complex balanced chemical reaction networks with mass action kinetics is studied by using the so-called entropy method. In the first part of the paper,…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…