A dynamical model of genetic networks describes cell differentiation

Cell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of cellular noise in differentiation, which has never been hypothesized so far, and leads to non trivial predictions which could be subject to experimental testing

Sviluppo di cicli innovativi per lo sfruttamento di risorse geotermiche a bassa entalpia

Il lavoro svolto ha trattato l’analisi, lo sviluppo e l’ottimizzazione di sistemi per lo sfruttamento di risorse geotermiche a bassa entalpia, operanti con fluidi di lavoro diversi dal fluido geotermico. Possono essere individuate tre macrosezioni per schematizzare meglio gli argomenti trattati. Nella prima, dopo aver individuato i fluidi ausiliari compatibili con le nostre condizioni ed aver fatto un breve stato dell’arte sulle tecnologie utilizzate negli impianti operanti nei principali siti geotermici a bassa entalpia, ci siamo concentrati sull’analisi termodinamica del ciclo di potenza. Sono state studiate le prestazioni dei possibili cicli di recupero in relazione alle condizioni in ingresso ed ai fluidi di lavoro utilizzati. La seconda parte è stata incentrata sul dimensionamento dei principali apparati di scambio termico per due casi significativi riscontrati nell’analisi termodinamica. Sono stati dimensionati sia lo scambiatore a recupero, suddiviso nelle sezioni di preriscaldamento, evaporazione e surriscaldamento, sia il condensatore; quest’ultimo è stato studiato sia ad acqua che ad aria, con la temperatura dell’aria variabile con la stagione. La terza ed ultima parte ha visto lo studio e l’applicazione di una funzione obiettivo che contenesse sia indicatori termodinamici puramente prestazionali, sia indicatori legati alle dimensioni degli organi di scambio termico ed alla potenza assorbita dagli ausiliari, in particolare pompe e ventilatori

Evolution, complexity and artificial life

Evolution and complexity characterize both biological and artificial life – by direct modeling of biological processes and the creation of populations of interacting entities from which complex behaviors can emerge and evolve. This edited book includes invited chapters from leading scientists in the fields of artificial life, complex systems, and evolutionary computing. The contributions identify both fundamental theoretical issues and state-of-the-art real-world applications. The book is intended for researchers and graduate students in the related domains

Analysis of attractor distances in Random Boolean Networks

We study the properties of the distance between attractors in Random Boolean Networks, a prominent model of genetic regulatory networks. We define three distance measures, upon which attractor distance matrices are constructed and their main statistic parameters are computed. The experimental analysis shows that ordered networks have a very clustered set of attractors, while chaotic networks' attractors are scattered; critical networks show, instead, a pattern with characteristics of both ordered and chaotic networks.Comment: 9 pages, 6 figures. Presented at WIRN 2010 - Italian workshop on neural networks, May 2010. To appear in a volume published by IOS Pres

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

On the dynamical properties of a model of cell differentiation

One of the major challenges in complex systems biology is that of providing a general theoretical framework to describe the phenomena involved in cell differentiation, i.e., the process whereby stem cells, which can develop into different types, become progressively more specialized. The aim of this study is to briefly review a dynamical model of cell differentiation which is able to cover a broad spectrum of experimentally observed phenomena and to present some novel results

Mechanism for the formation of density gradients through semipermeable membranes

We describe and theoretically analyze here a phenomenon which can take place in a system with two different compartments, each containing the same chemicals, which undergo reactions on the surface of both sides of the membrane which separates the two compartments, in the case where the membrane permeabilities to the various chemicals are different and diffusion is fast. There are two main reasons of interest for this kind of system. First, if the overall system is isolated, starting from the case where the initial concentrations of the chemicals are the same in the two phases, one observes the formation of a transient concentration difference. This difference eventually vanishes, although it might last for a long time, depending upon the value of the relevant parameters. The second reason of interest is that, in the case of an open system, one can achieve a steady-state value of the concentration of some chemicals in the smaller compartment which is higher than that in the external one. These results may prove important, inter alia, to understand the behavior of lipid vesicles in water, a topic which is important for studies on the origin of life as well as for possible future applications

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