Related papers: Autocatalytic sets in a partitioned biochemical ne…
Autocatalytic processes underlie diverse systems in which replication is triggered at interfaces, including heterogeneous catalysis on solid substrates, enzyme activity at membranes, viral infections, biofilm growth, and spatially…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…
We present a geometric framework to study the growth-division dynamics of cells and protocells, and demonstrate that self-reproduction emerges only when a system's growth dynamics and division strategy are mutually compatible. Using several…
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…
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 reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions.…
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…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Over the last years, analyses performed on a stochastic model of catalytic reaction networks have provided some indications about the reasons why wet-lab experiments hardly ever comply with the phase transition typically predicted by…
We propose a novel definition of life in terms of which its emergence in the universe is expected, and its ever-creative open-ended evolution is entailed by no law. Living organisms are Kantian Wholes that achieve Catalytic Closure,…
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…
Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears both as reactant and product in the same reaction, they are…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Phase separation drives the formation of biomolecular condensates in cells, which comprise many components and sometimes possess multiple phases. The equilibrium physics of phase separation is well understood, but many components in…
The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…
The origin of heredity is studied as a recursive state in a replicating proto-cell consisting of many molecule species in mutually catalyzing reaction networks. Protocells divide when the number of molecules, increasing due to replication,…
The concept of (auto)catalytic systems has become a cornerstone in understanding evolutionary processes in various fields. The common ground is the observation that for the production of new species/goods/ideas/elements etc. the…
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal…
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acids, and lipids to "molecular food sources" that have likely…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…