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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 theoretical models with regard to the emergence of collectively self-replicating sets of molecule (also defined as autocatalytic sets, ACSs), a phenomenon that is often observed in nature and that is supposed to have played a major role in the emergence of the primitive forms of life. The model at issue has allowed to reveal that the emerging ACSs are characterized by a general dynamical fragility, which might explain the difficulty to observe them in lab experiments. In this work, the main results of the various analyses are reviewed, with particular regard to the factors able to affect the generic properties of catalytic reactions network, for what concerns, not only the probability of ACSs to be observed, but also the overall activity of the system, in terms of production of new species, reactions and matter.
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of randomly gener
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polyno
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation but also
Over the last few years, several computational techniques have been devised to recover protein complexes from the protein interaction (PPI) networks of organisms. These techniques model dense subnetworks within PPI networks as complexes. However, our
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step change in i