Related papers: Autocatalytic Sets Extended: Dynamics, Inhibition,…
The evolution of autocatalytic sets (ACS) is a widespread process in biological, chemical and ecological systems which is of great significance in many applications, such as the evolution of new species or complex chemical organizations. In…
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…
Many decision-making algorithms draw inspiration from the inner workings of individual biological systems. However, it remains unclear whether collective behavior among biological species can also lead to solutions for computational tasks.…
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to…
We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…
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…
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Catalysis, the acceleration of chemical reactions by molecules that are not consumed in the process, is essential to living organisms but currently absent in physical systems that aspire to emulate biological functionalities with artificial…
Analytical analysis of spatially extended autocatalytic and hypercyclic systems is presented. It is shown that spatially explicit systems in the form of reaction-diffusion equations with global regulation possess the same major qualitative…
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 notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
One of the main goals of Artificial Life is to research the conditions for the emergence of life, not necessarily as it is, but as it could be. Artificial Chemistries are one of the most important tools for this purpose because they provide…
Autonomous driving techniques have been flourishing in recent years while thirsting for huge amounts of high-quality data. However, it is difficult for real-world datasets to keep up with the pace of changing requirements due to their…
In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…
The aim of this work is to address issues where formal specifications cannot be realized on a given dynamical system subjected to a changing environment. Such failures occur whenever the dynamics of the system restrict the robot in such a…
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…
We demonstrate that autocatalytic reactions, where a product catalyzes its own formation, can be significantly accelerated when the product molecules are indistinguishable from each other. This ``combinatorial enhancement," analogous to the…
Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we…
Stochastic resetting, the procedure of stopping and re-initializing random processes, has recently emerged as a powerful tool for accelerating processes ranging from queuing systems to molecular simulations. However, its usefulness is…