Related papers: Semigroup models for biochemical reaction networks
The ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in origin-of-life research. Based on Kaufmann's autocatalytic sets,…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
Developing a mathematical understanding of autocatalysis in reaction networks has both theoretical and practical implications. We review definitions of autocatalytic networks and prove some properties for minimal autocatalytic subnetworks…
Recent research in both the experimental and mathematical communities has focused on biochemical interaction systems that satisfy an "absolute concentration robustness" (ACR) property. The ACR property was first discovered experimentally…
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…
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…
Autocatalysis lies at the heart of many (bio)chemical processes and is key to processes leading up to the origin of life. Two seemingly very different formalisms have emerged that define autocatalysis. Kauffman introduced collective…
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.…
This paper presents novel decomposition classes of chemical reaction networks (CRNs) derived from S-system kinetics. Based on the network decomposition theory initiated by Feinberg in 1987, we introduce the concept of incidence independent…
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…
Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two…
We delve into growing open chemical reaction systems (CRSs) characterized by autocatalytic reactions within a variable volume, which changes in response to these reactions. Understanding the thermodynamics of such systems is crucial for…
The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modelling how living systems first arose. It has been known for several decades that such networks will form…
Complex systems can be advantageously modeled by formal reaction systems (RS), a.k.a. chemical reaction networks in chemistry. Reaction-based models can indeed be interpreted in a hierarchy of semantics, depending on the question at hand,…
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…
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…
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in inflow and outflow, containing one non-flow (reversible or…
Over the last years, analyses performed on a stochastic model of catalytic reaction networks have provided some indications about the reasons why wet-lab experiments hardly ever comply with the phase transition typically predicted by…