Growth and Division in a Dynamic Protocell Model

Abstract

In this paper a new model of growing and dividing protocells is described, whose main features are (i) a lipid container that grows according to the composition of the molecular milieu (ii) a set of “genetic memory molecules” (GMMs) that undergo catalytic reactions in the internal aqueous phase and (iii) a set of stochastic kinetic equations for the GMMs. The mass exchange between the external environment and the internal phase is described by simulating a semipermeable membrane and a flow driven by the differences in chemical potentials, thereby avoiding to resort to sometimes misleading simplifications, e.g., that of a flow reactor. Under simple assumptions, it is shown that synchronization takes place between the rate of replication of the GMMs and that of the container, provided that the set of reactions hosts a so-called RAF (Reflexive Autocatalytic, Food-generated) set whose influence on synchronization is hereafter discussed. It is also shown that a slight modification of the basic model that takes into account a rate-limiting term, makes possible the growth of novelties, allowing in such a way suitable evolution: so the model represents an effective basis for understanding the main abstract properties of populations of protocells.

An Iterative Information‐Theoretic Approach to the Detection of Structures in Complex Systems

“…The RI was originally introduced to understand the actual organization of dynamical systems; to this aim, one needs to (i) properly identify meaningful organizational levels emerging from the interactions of lower-level entities (and possibly also of higher-level entities, such as groups of interacting chemical species in protocells [15]) and (ii) describe the interactions between these meso-levels. In some cases, it is possible to describe such a structure by means of a simple tree-like hierarchy, as happens in several physical systems where the levels can be identified with the space-time scales of the phenomena (microscopic and macroscopic or micromeso-macro), in inclusion hierarchies (e.g., like an organ made of tissues, which comprise cells, etc.…”

From Systems to Organisations

“…They draw on partial analogies, focus on the onset of life, or target the definition of life and organisation. Many go beyond and aim towards a theoretical biology [8,56,152,156,157]. Of the latter, two stand out: Rosen's (M,R)-systems and Gánti's Chemoton Theory [55].…”

Identifying Critical States through the Relevance Index

“…The reasons why the RI has originally been introduced were related to the difficulty in understanding the actual organization of dynamical systems, which requires (i) a proper identification of meaningful organizational "levels" that emerge from the interactions of lower level entities (and possibly also of higher-level entities, such as groups of interacting chemical species inprotocells [7,8]) and (ii) a mapping of the interactions between these meso-levels. In some cases, they can be properly described by a quite familiar tree-like hierarchical structure, as happens in several physical systems where the levels can be identified with the space-time scales of the phenomena (microscopic and macroscopic or micro-meso-macro), in inclusion hierarchies (e.g., a cell that comprises a nucleus that comprises chromosomes that comprise.…”