Related papers: Autocatalytic sets in a partitioned biochemical ne…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
It has been proposed that cultural evolution was made possible by a cognitive transition brought about by onset of the capacity for self-triggered recall and rehearsal. Here we develop a novel idea that models of collectively autocatalytic…
This paper describes a 2D particle system in which autopoietic vesicles that are able to grow, repair, and reproduce can emerge from an initial random distribution of individual components. The reproduction process also exhibits inheritance…
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that…
One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit…
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…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical…
We introduce an autocatalytic aggregation model in which the rate at which two clusters merge to form a cluster is controlled by the presence of a third "catalytic" cluster whose mass must equal to the mass of one of the reaction partners.…
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 consider a scheme of equiprobable allocation of particles into cells by sets. The Edgeworth type asymptotic expansion in the local central limit theorem for a number of empty cells left after allocation of all sets of particles is…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in inflow and outflow, containing one non-flow (reversible or…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
The managed-metabolism hypothesis suggests that a cooperation barrier must be overcome if self-producing chemical organizations are to transition from non-life to life. This barrier prevents un-managed, self-organizing, autocatalytic…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
We study a model for the evolution of chemical species under a combination of population dynamics on a short time scale and a selection mechanism on a longer time scale. Least fit nodes are replaced by new nodes whose links are attached to…
This paper is an invited layperson summary for The Academic of the paper referenced on the last page. We summarize how the formal framework of autocatalytic networks offers a means of modeling the origins of self-organizing, self-sustaining…