Francisco José Romero-Campero

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In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the function of living cells. We will introduce two different(More)
Quorum sensing is a cell-density-dependent gene regulation system that allows an entire population of bacterial cells to communicate in order to regulate the expression of certain or specific genes in a coordinated way depending on the size of the population. We present a model of the quorum sensing system in Vibrio fischeri using a variant of membrane(More)
In this paper P systems are used as a formal framework for the specification and simulation of biological systems. In particular, we will deal with gene regulation systems consisting of protein-protein and protein-DNA interactions that take place in different compartments of the hierarchical structure of the living cell or in different individual cells from(More)
In this paper we propose an extension of the modelling framework based on P systems which explicitly includes modularity. Modularisation in cellular systems can be produced by chemical specificity and spatial localisation in different compartments. Both these features can be easily specified and analysed in P systems using sets of rewriting rules to(More)
In this work we present a new methodology for structure and parameter estimation in cell systems biology modelling. Our modelling framework is based on P systems, an unconventional computational paradigm that abstracts from the structure and functioning of the living cell. The process of designing models, consisting of both the optimisation of the modular(More)
We introduce a variant of P systems where rules have associated a real number providing a measure for the " intrinsic reactivity " of the rule and roughly corresponding to the kinetic coefficient which, in biochemistry , is usually associated to each molecular reaction. The behaviour of these P systems is then defined according to a strategy which, in each(More)