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)
In this paper we propose a new way to represent recognizer P systems with active membranes based on Production Systems techniques. This representation allows us to express the set of rules and the configurations in each step of the evolution as facts in a knowledge base. We provide a CLIPS program to simulate the evolutions of this variant of P systems.
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 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)
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 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)
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)