Giancarlo Mauri

Solving NP-Complete Problems Using P Systems with Active Membranes

A recently introduced variant of P-systems considers membranes which can multiply by division. These systems use two types of division: division for elementary membranes (Le. membranes not containing other membranes inside) and division for non-elementary membranes. In two recent papers it is shown how to solve the Satisfiability problem and the Hamiltonian Path problem (two well known NP complete problems) in linear time with respect to the input length, using both types of division. We show in this paper that P-systems with only division for elementary membranes suffice to solve these two problems in linear time. Is it possible to solve NP complete problems in polynomial time using P-systems without membrane division? We show, moreover, that (if P ≠ NP) deterministic P-systems without membrane division are not able to solve NP complete problems in polynomial time.

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes

Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. The server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites (TFBSs) in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved TFBSs and distal regulatory modules in sequences from homologous genes; RNAProfile, for the discovery of conserved secondary structure motifs in unaligned RNA sequences whose secondary structure is not known. In this way, a given gene can be compared with other co-regulated genes or with its homologs, or its mRNA can be analyzed for conserved motifs regulating its post-transcriptional fate. The web server thus provides researchers with different strategies and methods to investigate the regulation of gene expression, at both the transcriptional and post-transcriptional levels. Available at and .

Cellular automata: from a theoretical parallel computational model to its application to complex system

This introductory paper gives a short survey of cellular automata (CAs), from different points of view. It starts with the main definitions and theoretical results about CAs as an abstract model of computation or as discrete dynamical systems. Then, the main applications of CAs in different fields (biology, physics, etc.) as a model of complex systems are illustrated. Finally, implementations of the CA model on parallel computing platforms are surveyed.

On-Line Construction of Compact Directed Acyclic Word Graphs

Many different index structures, providing efficient solutions to problems related to pattern matching, have been introduced so far. Examples of these structures are suffix trees and directed acyclic word graphs (DAWGs), which can be efficiently constructed in linear time and space. Compact directed acyclic word graphs (CDAWGs) are an index structure preserving some features of both suffix trees and DAWGs, and require less space than both of them. An algorithm which directly constructs CDAWGs in linear time and space was first introduced by Crochemore and Verin, based on McCreights algorithm for constructing suffix trees. In this work, we present a novel on-line linear-time algorithm that builds the CDAWG for a single string as well as for a set of strings, inspired by Ukkonens on-line algorithm for constructing suffix trees.

Uniform solutions to SAT and Subset Sum by spiking neural P systems

We continue the investigations concerning the possibility of using spiking neural P systems as a framework for solving computationally hard problems, addressing two problems which were already recently considered in this respect:

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

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Modelling metapopulations with stochastic membrane systems

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