Related papers: Catalysis in Reaction Networks
Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted…
Autocatalytic systems are very often incorporated in the "origin of life" models, a connection that has been analyzed in the context of the classical hypercycles introduced by Manfred Eigen. We investigate the dynamics of certain networks…
Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore…
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…
It has been known for nearly a decade that deterministically modeled reaction networks that are weakly reversible and consist of a single linkage class have trajectories that are bounded from both above and below by positive constants (so…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions…
Autocatalytic chemical reaction networks can collectively replicate or maintain their constituents despite degradation reactions only above a certain threshold, which we refer to as the decay threshold. When the chemical network has a…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks, and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be…
Autocatalysis is a fundamental concept, used in a wide range of domains. From the most general definition of autocatalysis, that is a process in which a chemical compound is able to catalyze its own formation, several different systems can…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…
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…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically…
Self-sustaining autocatalytic chemical networks represent a necessary, though not sufficient condition for the emergence of early living systems. These networks have been formalised and investigated within the framework of RAF theory, which…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…
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…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…