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)
This paper investigates a hybrid approach to modeling molecular interactions in biology. P systems, π-calculus, and Petri nets models , and two tools, Daikon, used in software reverse-engineering, and PRISM, a probabilistic model checker, are investigated for their expres-siveness and complementary roles in describing and analyzing biological systems. A… (More)
This paper presents two approaches based on metabolic and stochastic P systems, together with their associated analysis methods, for modelling biological systems and illustrates their use through two case studies.
In contrast to differential equations, P systems are an unconven-tional model of computation which takes into consideration the discrete character of the quantity of components and the inherent randomness that exists in biological phenomena. The key feature of P systems is their compartmentalised structure which represents the heterogeneity of the… (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)