Related papers: Minimal autocatalytic networks
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…
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…
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…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
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…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
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…
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species $X$ catalyzes its own formation. From the perspective of chemical kinetics, autocatalysts show a regime of super-linear growth. Given a…
Autocatalysis, the ability of a chemical system to make more of itself, is a crucial feature in metabolism and is speculated to have played a decisive role in the origin of life. Nevertheless, how autocatalytic systems behave far from…
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…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
I analyse a model of an evolving network represented as a directed graph; each node corresponds to one molecular species and the links to catalytic interactions between species. Over short timescales the graph remains fixed while relative…
It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and…
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…
Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears both as reactant and product in the same reaction, they are…
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…
This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…
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…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Biochemical models that exhibit bistability are of interest to biologists and mathematicians alike. Chemical reaction network theory can provide sufficient conditions for the existence of bistability, and on the other hand can rule out the…