51 research outputs found
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks
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 generated reaction schemes highlight remarkable
differences between this very simple protocell description model and the
classical case of the continuous stirred-tank reactor (CSTR). In particular, in
the CSTR case, distinct simulations with the same reaction scheme reach the
same dynamical equilibrium, whereas, in the protocell case, simulations with
identical reaction schemes can reach very different dynamical states, despite
starting from the same initial conditions.Comment: In Proceedings Wivace 2013, arXiv:1309.712
A stochastic model of catalytic reaction networks in protocells
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 self-replicating molecules for granted, or (ii) describe the
emergence of the aforementioned sets from an ensemble of random molecules in a
simple experimental setting (e.g. a closed system or a steady-state flow
reactor) that does not properly describe a protocell. In this paper we present
a model that goes beyond these limitations by describing the dynamics of sets
of replicating molecules within a lipid vesicle. We adopt the simplest possible
protocell architecture, by considering a semi-permeable membrane that selects
the molecular types that are allowed to enter or exit the protocell and by
assuming that the reactions take place in the aqueous phase in the internal
compartment. As a first approximation, we ignore the protocell growth and
division dynamics. The behavior of catalytic reaction networks is then
simulated by means of a stochastic model that accounts for the creation and the
extinction of species and reactions. While this is not yet an exhaustive
protocell model, it already provides clues regarding some processes that are
relevant for understanding the conditions that can enable a population of
protocells to undergo evolution and selection.Comment: 20 pages, 5 figure
Dynamical criticality: overview and open questions
Systems that exhibit complex behaviours are often found in a particular dynamical condition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states that systems in a dynamical regime between order and disorder attain the highest level of computational capabilities and achieve an optimal trade-off between robustness and flexibility. Recent results in cellular and evolutionary biology, neuroscience and computer science have revitalised the interest in the criticality hypothesis, emphasising its role as a viable candidate general law in adaptive complex systems. This paper provides an overview of the works on dynamical criticality that are - to the best of our knowledge - particularly relevant for the criticality hypothesis. The authors review the main contributions concerning dynamics and information processing at the edge of chaos, and illustrate the main achievements in the study of critical dynamics in biological systems. Finally, the authors discuss open questions and propose an agenda for future work
The role of backward reactions in a stochastic model of catalytic reaction networks
We investigate the role of backward reactions in a stochastic model of catalytic reaction network, with specific regard to the influence on the emergence of autocatalytic sets (ACSs), which are supposed to be one of the pre-requisites in the transition between non-living to living matter.
In particular, we analyse the impact that a variation in the kinetic rates of forward and backward reactions may have on the overall dynamics.
Significant effects are indeed observed, provided that the intensity of backward reactions is sufficiently high. In spite of an invariant activity of the system in terms of production of new species, as backward reactions are intensified, the emergence of ACSs becomes more likely and an increase in their number, as well as in the proportion of species belonging to them, is observed. Furthermore, ACSs appear to be more robust to fluctuations than in the usual settings with no backward reaction.
This outcome may rely not only on the higher average connectivity of the reaction graph, but also on the distinguishing property of backward reactions of recreating the substrates of the corresponding forward reactions
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