Catálogo de publicaciones - libros

P systems offer the possibility to appropriately describe discrete processes performed by: i) single objects: catalytic molecules (= enzymes), supramolecular structures (MscL, porins, ionic channels etc.), single cells, and ii) a small number of objects occurring in the sample, e.g., several mechanosensitive channels occurring within a membrane patch. Thus P systems could offer the possibility to capture and model the plethora of experimental data obtained in the emerging and rapidly growing field of single cell or single molecule or atom studies.

Furthermore, it is suggested that implementation of P systems could be done by the use of artificial membranes, a step forward computations with artificial membranes.

We present a formalization of membrane structure by using a parametric 2-dimensional spherical surface, where membrane proteins reside and can move, according to prescribed operations. A more detailed formalization of membrane proteins acting as transporters is also given, thus possibly allowing a global scale analysis of ion flows across a membrane. Several other applications, both biology and computation oriented, are proposed.

One of the most important mechanisms for bacterial cell-to-cell communication and behavior coordination under changing environments is often referred to as “quorum sensing” (QS). QS relies on the activation of a sensor kinase or response regulator protein by, in many cases, a diffusible, low molecular weight signal molecule (a “pheromone” or “autoinducer”) (Cámara et al., 2002). Consequently, in QS, the concentration of the signal molecule reflects the number of bacterial cells in a particular niche and perception of a threshold concentration of that signal molecule indicates that the population is “quorated”, i.e. ready to make a behavioral decision. Bacteria cell-to-cell communication is perhaps the most important tool in the battle for survival; they employ communication to trigger transcriptional regulation resulting in sexual exchange and niche protection in some cases, to battle host’ defences and coordinate population migration. Ultimately, bacteria cell-to-cell communication is used to effect phenotypic change. The importance of coordinated gene-expression (and hence phenotypic change) in bacteria can be understood if one realizes that only by pooling together the activity of a quorum of cells can a bacterium be successful. It is increasingly apparent that, in nature, bacteria function less as individuals and more as coherent groups that are able to inhabit multiple ecological niches (Lazdunski et al., 2004). Within quorum sensing process several key elements must be considered: (i) the gene(s) involved in signal synthesis, (ii) the gene(s) involved in signal transduction, and (iii) the QS signal molecule(s).

This paper presents a general framework for modelling with membrane systems that is based on a computational paradigm where rules have associated a finite set of attributes and a corresponding function. Attributes and functions are meant to provide those extra features that allow to define different strategies to run a P system. Such a strategy relying on a bounded parallelism is presented using an operational approach and applying it for a case study presenting the basic model of quorum sensing for bacteria.

We consider synchrony and asynchrony in the behavior of various models of membrane systems, which may differ in the way individual reactions are defined as well as in the way multisets of these reactions can be executed in a single computational step. We concentrate on the properties of ongoing computations, including the unbounded ones. Our focus is on the properties of system states involved in such computations as well as on concurrency and causality relationships between executed reactions. This should be contrasted with the approach which investigates different notions of ‘results’ produced through halting computations of membrane systems. As a formal behavioral model we use Petri nets and their processes which are very well suited to capture the notion of an execution in a concurrent context. We continue our earlier work reported in [15], where a systematic and structural link has been established between a basic class of membrane systems and Petri nets. Here, we look at some natural extensions of this basic class of membrane systems and investigate the ways in which they can be represented within the behavioral model provided by Petri nets.

Metabolic P systems are a special class of P systems which seem to be adequate for expressing biological phenomena related to metabolism and signaling transduction in biological systems. We give the basic motivation for their introduction and some ideas about their applicability to some basic biological oscillators.

Cellular signalling pathways are fundamental to the control and regulation of cell behavior. Understanding of biosignalling network functions is crucial to the study of different diseases and to the design of effective therapies. In this paper we present P systems as a feasible computational modeling tool for cellular signalling pathways that takes into consideration the discrete character of the components of the system and the key role played by membranes in their functioning. We illustrate these cellular models simulating the epidermal growth factor receptor (EGFR) signalling cascade and the FAS–induced apoptosis using a deterministic strategy for the evolution of P systems.

We consider extended variants of spiking neural P systems and show how these extensions of the original model allow for easy proofs of the computational completeness of extended spiking neural P systems and for the characterization of semilinear sets and regular languages by finite extended spiking neural P systems (defined by having only finite checking sets in the rules assigned to the cells) with only a bounded number of neurons.

We prove that any set of numbers containing zero generated by symport/antiport P systems with two membranes and minimal cooperation is finite (for both symport/antiport P systems and for purely symport P systems). On the other hand, one additional object in the output membrane allows symport/antiport P systems (purely symport P systems) with two membranes and minimal cooperation generate any recursively enumerable sets of natural numbers without zero. Thus we improve our previous results for symport/antiport P systems with two membranes and minimal cooperation from three “garbage” objects down to one object and for purely symport P systems from six objects down to one object. Thus we show the optimality of these results.

In this paper we present a rewriting semantics of membrane systems based on strategies. We use strategies to describe the control mechanisms in membranes. We provide strategies for maximally parallel rewriting, and for maximally parallel rewriting with priorities between rules. Maximally parallel rewriting with promoters or inhibitors requires an additional encoding of the rules.