Related papers: Glucans monomer-exchange dynamics as an open chemi…
In this paper we discuss some examples of systems composed of $N$ units, which exchange a conserved quantity $x$ according to some given stochastic rule, from some standard kinetic model of condensed matter physics to the kinetic exchange…
At the microscopic scale, open chemical reaction networks are described by stochastic reactions that follow mass-action kinetics and are coupled to chemostats. We show that closed chemical reaction networks -- with specific stoichiometries…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
Nonreciprocity, a hallmark of nonequilibrium systems, can generate dynamics not possible near thermodynamic equilibrium, including oscillatory and rotating patterns. The onset of temporal oscillations is often evident in linearized…
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations satisfying mass action law. Our most general framework…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Dynamic properties of chemical reactions and appropriate relationships for open chemical equilibrium are discussed in approach of the chemical dynamics. New way to calculate composition of chemical systems in open equilibrium, based on the…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
A microscopic theory for cation diffusion in polymer electrolytes is presented. Based on a thorough analysis of molecular dynamics simulations on PEO with LiBF$_4$ the mechanisms of cation dynamics are characterised. Cation jumps between…
In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first…
We consider networks of massive particles connected by non-linear springs. Some particles interact with heat baths at different temperatures, which are modeled as stochastic driving forces. The structure of the network is arbitrary, but the…
These lecture notes describe a basic theory of chemically active droplets, which are droplets kept away from equilibrium by driven chemical reactions. The notes assume a basic familiarity with equilibrium thermodynamics of phase separation,…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
We design several examples of constrained, symmetric quantum circuit dynamics that generate non-equilibrium steady states. The qubit networks maintain local memory of the initial conditions and display inhomogeneous subsystem dynamics over…