Related papers: A Hessian Geometric Structure of Chemical Thermody…
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow.…
The theory of chemical kinetics form the basis to describe the dynamics of chemical systems. Owing to physical and thermodynamic constraints, chemical reaction systems possess various structures, which can be utilized to characterize…
Recently, Hessian geometry - an extension of information geometry - has emerged as a framework to naturally connect the geometries appearing in the theory of chemical reaction networks (CRN) to their inherent thermodynamical and kinetic…
Information geometry is based on classical Legendre duality but allows to incorporate additional structure such as algebraic constraints and Bregman divergence functions. It is naturally suited, and has been successfully used, to describe…
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…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…
This article deals with the problem of maximizing the production of a species for a chemical network by controlling the temperature. Under the so-called mass kinetics assumption the system can be modeled as a single-input control system…
We consider growing open chemical reaction systems (CRSs), in which autocatalytic chemical reactions are encapsulated in a finite volume and its size can change in conjunction with the reactions. The thermodynamics of growing CRSs is…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Power law dynamics is used to describe the stability behavior in metabolic networks such as chemical reaction networks (CRN's). These systems allow multiple steady states within a single stoichiometric class. On the other side thermodynamic…
It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas…
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
In this note we report some advances in the study of thermodynamic formalism for a class of partially hyperbolic system -- center isometries, that includes regular elements in Anosov actions. The techniques are of geometric flavor (in…
We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of…