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Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the…
We investigate the multi-chain version of the Chemical Master Equation, when there are transitions between different states inside the long chains, as well as transitions between (a few) different chains. In the discrete version, such a…
Active polymeric systems exhibit a rich spectrum of non-equilibrium phenomena arising from stochastic forces that explicitly break detailed balance. Despite the rapid growth of experimental and numerical studies, analytical progress remains…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Gels in soft-matter systems are an important nonergodic state of matter. We study a colloid-polymer mixture which is quenched by increasing the polymer concentration, from a fluid to a gel. Using confocal microscopy, we study both the…
We present the energetic aspect of open systems which may exchange particles with their environments. Our attention shall be paid to the scale that the motion of the particles is described by the classical Langevin dynamics. Along a…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
We examine the long-term behaviour of non-integrable, energy-conserved, 1D systems of macroscopic grains interacting via a contact-only generalized Hertz potential and held between stationary walls. Existing dynamical studies showed the…
The article presents new model of equilibrium in open chemical systems suggesting a linear dependence of the reaction shift from equilibrium in presence of the external thermodynamic force. Basic equation of this model contains traditional…
In this paper, we study the exact dynamics of general open systems interacting with its environment through particle exchanges. The paper includes two main results. First, by taking advantage of the propagating function in the coherent…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…
The goal of the paper is to derive a revised condition of global equilibrium in complex chemical systems as variational principle in formalism of recently developed discrete thermodynamics (DTD) of chemical equilibria. In classical approach…
We investigate the heterogeneous dynamics in a model, where chemical gelation and glass transition interplay, focusing on the dynamical susceptibility. Two independent mechanisms give raise to the correlations, which are manifested in the…
We consider an interaction of charged bodies under the following simplified conditions: the distribution of charge over each body is stable; the interaction of bodies is governed by electrical forces only. Physically, these assumptions can…
We present p53-MDM2-Glucose model to study spatio-temporal properties of the system induced by glucose. The variation in glucose concentration level triggers the system at different states, namely, oscillation death (stabilized), sustain…
We present theory and simulation of simultaneous chemical demixing and phase ordering in a polymer-liquid crystal mixture in conditions where isotropic-isotropic phase separation is metastable with respect to isotropic-nematic phase…
A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Ion-conducting glasses and polymer systems show several characteristic peculiarities in their composition-dependent diffusion properties and in their dynamic response. First we give a brief review of the current understanding of the ion…