Related papers: Random autocatalytic networks
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
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…
Template directed replication of nucleic acids is at the essence of all living beings and a major milestone for any origin of life scenario. We here present an idealized model of prebiotic sequence replication, where binary polymers act as…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Power law systems have been studied extensively due to their wide-ranging applications, particularly in chemistry. In this work, we focus on power law systems that can be decomposed into stoichiometrically independent subsystems. We show…
Diagrammatic models of feeding choices reveal fundamental robotic behaviors. Successful choices are reinforced by positive feedback, while unsuccessful ones by negative feedback. This paper will address robotic feeding by casually relating…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
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 paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
Two alternative views of an economy are combined and studied. The first view is that of technological evolution as a process of combinatorial innovation. Recently a simple mathematical model (TAP) was introduced to study such a…
In this paper, we derive two sufficient conditions to diagnose the persistence of two classes of delayed complex balanced chemical reaction network systems equipped with mass-action kinetics. One class is identified by $\dim…
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…
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…
The research concerns the dynamics of complex autonomous Kauffman networks. The article defines and shows using simulation experiments half-chaotic networks, which exhibit features much more similar to typically modeled systems like a…
Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
The directed polymerization of actin networks is an essential element of many biological processes, including cell migration. Different theoretical models considering the interplay between the underlying processes of polymerization, capping…