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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…
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…
We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange…
Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…
We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary -- linear or nonlinear -- open chemical reaction networks (CRNs) operating at steady state. Our method is based on the knowledge of the…
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…
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of…
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…
Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…
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…
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…
Identifying coherent flow structures in chemical reactors is crucial for understanding the mixing dynamics, which is essential for optimizing reactor performance. We demonstrate the use of a transfer operator method to find coherent flow…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
Reaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. In…
Reaction networks are commonly used to model the evolution of populations of species subject to transformations following an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete…
Stochastic Chemical Reaction Networks are continuous time Markov chain models that describe the time evolution of the molecular counts of species interacting stochastically via discrete reactions. Such models are ubiquitous in systems and…
Continuous Stirred Tank Reactors (CSTR) are the most important and central equipment in many chemical and biochemical industry that exhibit second order complex nonlinear dynamics. The nonlinear dynamics of CSTR poses many design and…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…