Related papers: Autocatalytic sets in a partitioned biochemical ne…

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…

This work concerns a many-body deterministic model that displays life-like properties as emergence, complexity, self-organization, spontaneous compartmentalization, and self-regulation. The model portraits the dynamics of an ensemble of…

The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…

We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…

At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…

We construct a simple model of a proto-cell that simulates a stochastic dynamics of abstract chemicals on a two-dimensional lattice. We assume that chemicals catalyze their reproduction through interaction with each other, and that between…

All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…

We give a self-contained introduction to the theory of directed graphs, leading up to the relationship between the Perron-Frobenius eigenvectors of a graph and its autocatalytic sets. Then we discuss a particular dynamical system on a fixed…

Life is commonly described as a self-organized, far-from-equilibrium process that maintains internal order by consuming free energy and exporting entropy. This thermodynamic view underlies diverse theoretical frameworks -- from autopoiesis…

Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…

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,…

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…

Open chemical reaction systems involve matter-exchange with the surroundings. As a result, species can accumulate inside a system during the course of the reaction. We study the role of network topology in governing the concentration…

There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…

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…

Mixtures of particles that interact through phoretic effects are known to aggregate if they belong to species that exhibit attractive self-interactions. We study self-organization in a model metabolic cycle composed of three species 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…

A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…

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…

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,…