相关论文: A formal model of autocatalytic sets emerging in a…
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…
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…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
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…
This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We…
A poorly understood step in the transition from a chemical to a biological world is the emergence of self-replicating molecular systems. We study how a precursor for such a replicator might arise in a hydrothermal RNA reactor, which…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
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…
The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given a set of elements, the reactions between them (chemical or…
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…
We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…
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…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…
Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…
The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when…
The ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in origin-of-life research. Based on Kaufmann's autocatalytic sets,…
An important transition after the origin of life was the first emergence of a Darwinian population, self-reproducing entities exhibiting differential reproduction, phenotypic variation, and inheritance of phenotypic traits. The simplest…
The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key…