How Does a P System Sound?

P systems are computational devices versatile enough to represent many real-life scenarios. In this paper, we present a first interpretation for P systems where a computation produces a set of sounds. The idea is to associate sounds to the application of specific rules in the P system. The application of such rules produces sounds of one time unit. Different rules produce different sounds. The combination of such sounds along time can be interpreted as music.Ministerio de Ciencia e Innovación TIN2008-04487-EMinisterio de Ciencia e Innovación TIN-2009-13192Junta de Andalucía P08-TIC-0420

Simulating Large-Scale ENPS Models by Means of GPU

Enzymatic Numerical P Systems (ENPS), an extension of Numerical P Systems, have been successfully applied to model robot controllers. GPGPU is an innovative technological paradigm which applies the parallel architecture of graphic cards to solve parallel, general{purpose problems. In previous work, a GPU simulator for ENPS was introduced. In this paper, a performance analysis on the simulator is performed in order to experimentally measure the speed-up factors resulting from the simulations.Ministerio de Ciencia e Innovación TIN2009-13192Junta de Andalucía P08-TIC-0420

Solving Sudoku with Membrane Computing

Sudoku is a very popular puzzle which consists on placing several numbers in a squared grid according to some simple rules. In this paper we present an efficient family of P systems which solve sudokus of any order verifying a specific property. The solution is searched by using a simple human-style method. If the sudoku cannot be solved by using this strategy, the P system detects this drawback and then the computations stops and returns No. Otherwise, the P system encodes the solution and returns Yes in the last computation step.Ministerio de Ciencia e Innovación TIN2008-04487-EMinisterio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

Modeling Diel Vertical Migration with Membrane Computing

Diel vertical migration (DVM) is an important ecological phenomenon in which zooplankton migrate vertically to deal with trade-offs associated with greater food availability in shallow waters and lower predator risk in deep waters due to lower light availability. Because of these trade-offs, DVM dynamics are particularly sensitive to changes in light intensity at the water surface. Therefore, changes in the proportion of cloudy and sunny days have the potential to disrupt DVM dynamics. We propose a new membrane computing model that captures the effect of cloud cover on DVM in Daphnia, and we use it to explore the impacts of an increased proportion of cloudy days that are predicted to occur with climate change. Our 2-dimensional, spatially explicit model integrates multiple trophic levels from abiotic nutrients to Daphnia predators. We analyzed the effect that different proportions of cloudy and sunny days throughout the summer have on our model. The model simulations suggest that an increase in sunny days promotes a high phytoplankton concentration near the surface but does not necessarily promote an increased abundance of Daphnia. Our model also suggests that a higher proportion of cloudy days would increase Daphnia abundance due to a shift in the vertical distribution of Daphnia populations towards superficial waters. Our results highlight that climate changes in multiple regions will affect animal migrations leading to altered food web dynamics in freshwater ecosystems, and emphasize the potential of membrane computing as a modeling framework for spatially and temporally explicit ecological processes

P-Lingua 2.0: New Features and First Applications

P-Lingua is a programming language for membrane computing. It was rst presented in Edinburgh, during the Ninth Workshop on Membrane Computing (WMC9). In this paper, the models, simulators and formats included in P-Lingua in version 2.0 are explained. We focus on the stochastic model, associated simulators and updated features. Finally, we present two new applications based on P-Lingua 2.0: a tool for describing and simulating ecosystems and a framework (currently under development) for P systems design.Ministerio de Educación y Ciencia TIN2006–13425Junta de Andalucía P08-TIC-0420

Analysing Gene Networks with PDP Systems. Arabidopsis thaliana, a Case Study

Gene Regulatory Networks (GRNs) are a useful tool for biologists to understand the interactions among genes in living organisms. A special kind of GRNs known as Logic Networks (LNs) has been recently introduced. These networks consider that the state of one or more genes can in uence another one. In a previous work, we proposed a Membrane Computing model which simulates the dynamics of LNs by drawing on the improved LAPP algorithm. In this paper we provide a case study for our LN model on a network which regulates the circadian rhythms of long{term studied plant Arabidopsis thaliana. We outline the software tools employed and propose a methodology for analysing LNs on our Membrane Computing model. At the end of the paper, some conclusions and future work are included.Ministerio de Ciencia e Innovación TIN2012-37434Junta de Andalucía P08-TIC-0420

Kernel P Systems - Version 1

A basic P system, called kernel P system4 (kP system for short), combining features of di erent P systems introduced and studied so far is de ned and discussed. The structure of such systems is de ned as a dynamic graph, similar to tissue-like P systems, the objects are organised as multisets, and the rules in each compartment, rewriting and communication together with system structure changing rules, are applied in accordance with a speci c execution strategy. The de nition of kP systems is introduced and some examples illustrate this concept. Two classes of P systems, namely neural-like and generalised communicating P systems are simulated by kP systems. Some case studies prove the expressive power of these systems.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08-TIC-0420

An Overview of P-Lingua 2.0

P–Lingua is a programming language for membrane computing which aims to be a standard to define P systems. In order to implement this idea, a Java library called pLinguaCore has been developed as a software framework for cell–like P systems. It is able to handle input files (either in XML or in P–Lingua format) defining P systems from a number of different cell–like P system models. Moreover, the library includes several built–in simulators for each supported model. For the sake of software portability, pLinguaCore can export a P system definition to any convenient output format (currently XML and binary formats are available). This software is not a closed product, but it can be extended to accept new input or output formats and also new models or simulators. The term P–Lingua 2.0 refers to the software package consisting of the above mentioned library together with a user interface called pLinguaPlugin (more details can be found at http://www.p-lingua.org). Finally, in order to illustrate the software, this paper includes an application using pLinguaCore for describing and simulating ecosystems by means of P systems.Ministerio de Educación y Ciencia TIN2006-13425Junta de Andalucía TIC04200

A Cellular Sudoku Solver

Sudoku is a very popular puzzle which consists on placing several numbers in a squared grid according to some simple rules. In this paper we present an efficient family of P systems which solve sudoku puzzles of any order verifying a specific property. The solution is searched by using a simple human-style method. If the sudoku cannot be solved by using this strategy, the P system detects this drawback and then the computations stops and returns No. Otherwise, the P system encodes the solution and returns Yes in the last computation step.Ministerio de Ciencia e Innovación TIN2008-04487-EMinisterio de Ciencia e Innovación TIN-2009-13192Junta de Andalucía P08-TIC-0420

3-Col problem modelling using simple kernel P systems

This paper presents the newly introduced class of (simple) kernel P systems ((s)kP systems) and investigates through a 3-colouring problem case study the expressive power and efficiency of kernel P systems. It describes two skP systems that model the problem and analyses them in terms of efficiency and complexity. The skP models prove to be more succinct (in terms of number of rules, objects, number of cells and execution steps) than the corresponding tissue P system, available in the literature, that solves the same problem, at the expense of a greater length of the rules.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420