A Circuit Implementing Massive Parallelism in Transition P Systems

ransition P-systems are based on biological membranes and try to emulate cell behavior and its evolution due to the presence of chemical elements. These systems perform computation through transition between two consecutive configurations, which consist in a m-tuple of multisets present at any moment in the existing m regions of the system. Transition between two configurations is performed by using evolution rules also present in each region. Among main Transition P-systems characteristics are massive parallelism and non determinism. This work is part of a very large project and tries to determine the design of a hardware circuit that can improve remarkably the process involved in the evolution of a membrane. Process in biological cells has two different levels of parallelism: the first one, obviously, is the evolution of each cell inside the whole set, and the second one is the application of the rules inside one membrane. This paper presents an evolution of the work done previously and includes an improvement that uses massive parallelism to do transition between two states. To achieve this, the initial set of rules is transformed into a new set that consists in all their possible combinations, and each of them is treated like a new rule (participant antecedents are added to generate a new multiset), converting an unique rule application in a way of parallelism in the means that several rules are applied at the same time. In this paper, we present a circuit that is able to process this kind of rules and to decode the result, taking advantage of all the potential that hardware has to implement P Systems versus previously proposed sequential solutions.

HW Implementation of a Optimized Algorithm for the Application of Active Rules in a Transition P-system

P systems or Membrane Computing are a type of a distributed, massively parallel and non deterministic system based on biological membranes. They are inspired in the way cells process chemical compounds, energy and information. These systems perform a computation through transition between two consecutive configurations. As it is well known in membrane computing, a configuration consists in a m-tuple of multisets present at any moment in the existing m regions of the system at that moment time. Transitions between two configurations are performed by using evolution rules which are in each region of the system in a non-deterministic maximally parallel manner. This work is part of an exhaustive investigation line. The final objective is to implement a HW system that evolves as it makes a transition P-system. To achieve this objective, it has been carried out a division of this generic system in several stages, each of them with concrete matters. In this paper the stage is developed by obtaining the part of the system that is in charge of the application of the active rules. To count the number of times that the active rules is applied exist different algorithms. Here, it is presents an algorithm with improved aspects: the number of necessary iterations to reach the final values is smaller than the case of applying step to step each rule. Hence, the whole process requires a minor number of steps and, therefore, the end of the process will be reached in a shorter length of time.

The electrical and magnetic properties of amorphous Pd-Cu-P alloys

<p>The amorphous phases of the Pd-Cu-P system has been obtained using the technique of rapidly quenching from the liquid state. Broad maxima in the diffraction pattern were obtained in the X-ray diffraction studies which are indicative of a glass-like structure. The composition range over which the amorphous solid phase is retained for the Pd-Cu-P system is (Pd_100-xCu_x)₈₀P₂₀ with 10 ≤ x ≤ 50 and (Pd₆₅Cu₃₅)_100-yP_y with 15 ≤ y ≤ 24 and (Pd₆₀Cu₄₀)_100-yP_y with 15 ≤ y ≤ 24.p> <p>The electrical resistivity for the Pd-Cu-P alloys decreases with temperature as Tp>2p> at low temperatures and as T at high temperatures up to the crystallization temperature. The structural scattering model of the resistivity proposed by Sinha and the spin-fluctuation resistivity model proposed by Hasegawa are re-examined in the light of the similarity of this result to the Pt-Ni-P and Pd-Ni-P systems. Objections are raised to these interpretations of the resistivity results and an alternate model is proposed consistent with the new results on Pd-Cu-P and the observation of similar effects in crystalline transition metal alloys. The observed negative temperature coefficients of resistivity in these amorphous alloys are thus interpreted as being due to the modification of the density of states with temperature through the electron-phonon interaction. The weak Pauli paramagnetism of the Pd-Cu-P, Pt-Ni-P and Pd-Ni-P alloys is interpreted as being modifications of the transition d-states as a result of the formation of strong transition metal-metalloid bonds rather than a large transfer of electrons from the glass former atoms (P in this case) to the d-band of the transition metal in a rigid band picture.p>

Simulating accepting networks of evolutionary processors with filtered connections by accepting evolutionary P systems

In this work, we propose a variant of P system based on the rewriting of string-objects by means of evolutionary rules. The membrane structure of such a P system seems to be a very natural tool for simulating the filters in accepting networks of evolutionary processors with filtered connections. We discuss an informal construction supporting this simulation. A detailed proof is to be considered in an extended version of this work.

Métodos acotados de aplicación de reglas de evolución para la implementación de Sistemas P de Transición

La característica fundamental de la Computación Natural se basa en el empleo de conceptos, principios y mecanismos del funcionamiento de la Naturaleza. La Computación Natural -y dentro de ésta, la Computación de Membranas- surge como una posible alternativa a la computación clásica y como resultado de la búsqueda de nuevos modelos de computación que puedan superar las limitaciones presentes en los modelos convencionales. En concreto, la Computación de Membranas se originó como un intento de formular un nuevo modelo computacional inspirado en la estructura y el funcionamiento de las células biológicas: los sistemas basados en este modelo constan de una estructura de membranas que actúan a la vez como separadores y como canales de comunicación, y dentro de esa estructura se alojan multiconjuntos de objetos que evolucionan de acuerdo a unas determinadas reglas de evolución. Al conjunto de dispositivos contemplados por la Computación de Membranas se les denomina genéricamente como Sistemas P. Hasta el momento los Sistemas P sólo han sido estudiados a nivel teórico y no han sido plenamente implementados ni en medios electrónicos, ni en medios bioquímicos, sólo han sido simulados o parcialmente implementados. Por tanto, la implantación de estos sistemas es un reto de investigación abierto. Esta tesis aborda uno de los problemas que debe ser resuelto para conseguir la implantación de los Sistemas P sobre plataformas hardware. El problema concreto se centra en el modelo de los Sistemas P de Transición y surge de la necesidad de disponer de algoritmos de aplicación de reglas que, independientemente de la plataforma hardware sobre la que se implementen, cumplan los requisitos de ser no deterministas, masivamente paralelos y además su tiempo de ejecución esté estáticamente acotado. Como resultado se ha obtenido un conjunto de algoritmos (tanto para plataformas secuenciales, como para plataformas paralelas) que se adecúan a las diferentes configuraciones de los Sistemas P. ABSTRACT The main feature of Natural Computing is the use of concepts, principles and mechanisms inspired by Nature. Natural Computing and within it, Membrane Computing emerges as an potential alternative to conventional computing and as from the search for new models of computation that may overcome the existing limitations in conventional models. Specifically, Membrane Computing was created to formulate a new computational paradigm inspired by the structure and functioning of biological cells: it consists of a membrane structure, which acts as separators as well as communication channels, and within this structure are stored multisets of objects that evolve according to certain evolution rules. The set of computing devices addressed by Membrane Computing are generically known P systems. Up to now, no P systems have been fully implemented yet in electronic or biochemical means. They only have been studied in theory, simulated or partially implemented. Therefore, the implementation of these systems is an open research challenge. This thesis addresses one of the problems to be solved in order to deploy P systems on hardware platforms. This specific problem is focused on the Transition P System model and emerges from the need of providing application rules algorithms that independently on the hardware platform on which they are implemented, meets the requirements of being nondeterministic, massively parallel and runtime-bounded. As a result, this thesis has developed a set of algorithms for both platforms, sequential and parallel, adapted to all possible configurations of P systems.

Diseño de un Procesador de Membranas Paralelo para los Sistemas P de Transición

La computación con membranas surge como una alternativa a la computación tradicional. Dentro de este campo se sitúan los denominados Sistemas P de Transición que se basan en la existencia de regiones que contienen recursos y reglas que hacen evolucionar a dichos recursos para poder llevar a cada una de las regiones a una nueva situación denominada configuración. La sucesión de las diferentes configuraciones conforman la computación. En este campo, el Grupo de Computación Natural de la Universidad Politécnica de Madrid lleva a cabo numerosas investigaciones al amparo de las cuales se han publicado numerosos artículos y realizado varias tesis doctorales. Las principales vías de investigación han sido, hasta el momento, el estudio del modelo teórico sobre el que se definen los Sistemas P, el estudio de los algoritmos que se utilizan para la aplicación de las reglas de evolución en las regiones, el diseño de nuevas arquitecturas que mejoren las comunicaciones entre las diferentes membranas (regiones) que componen el sistema y la implantación de estos sistemas en dispositivos hardware que pudiesen definir futuras máquinas basadas en este modelo. Dentro de este último campo, es decir, dentro del objetivo de construir finalmente máquinas que puedan llevar a cabo la funcionalidad de la computación con Sistemas P, la presente tesis doctoral se centra en el diseño de dos procesadores paralelos que, aplicando variantes de algoritmos existentes, favorezcan el crecimiento en el nivel de intra-paralelismo a la hora de aplicar las reglas. El diseño y creación de ambos procesadores presentan novedosas aportaciones al entorno de investigación de los Sistemas P de Transición en tanto en cuanto se utilizan conceptos que aunque previamente definidos de manera teórica, no habían sido introducidos en el hardware diseñado para estos sistemas. Así, los dos procesadores mantienen las siguientes características: - Presentan un alto rendimiento en la fase de aplicación de reglas, manteniendo por otro lado una flexibilidad y escalabilidad medias que son dependientes de la tecnología final sobre la que se sinteticen dichos procesadores. - Presentan un alto nivel de intra-paralelismo en las regiones al permitir la aplicación simultánea de reglas. - Tienen carácter universal en tanto en cuanto no depende del carácter de las reglas que componen el Sistema P. - Tienen un comportamiento indeterminista que es inherente a la propia naturaleza de estos sistemas. El primero de los circuitos utiliza el conjunto potencia del conjunto de reglas de aplicación así como el concepto de máxima aplicabilidad para favorecer el intra-paralelismo y el segundo incluye, además, el concepto de dominio de aplicabilidad para determinar el conjunto de reglas que son aplicables en cada momento con los recursos existentes. Ambos procesadores se diseñan y se prueban mediante herramientas de diseño electrónico y se preparan para ser sintetizados sobre FPGAs. ABSTRACT Membrane computing appears as an alternative to traditional computing. P Systems are placed inside this field and they are based upon the existence of regions called “membranes” that contain resources and rules that describe how the resources may vary to take each of these regions to a new situation called "configuration". Successive configurations conform computation. Inside this field, the Natural Computing Group of the Universidad Politécnica of Madrid develops a large number of works and researches that provide a lot of papers and some doctoral theses. Main research lines have been, by the moment, the study of the theoretical model over which Transition P Systems are defined, the study of the algorithms that are used for the evolution rules application in the regions, the design of new architectures that may improve communication among the different membranes (regions) that compose the whole system and the implementation of such systems over hardware devices that may define machines based upon this new model. Within this last research field, this is, within the objective of finally building machines that may accomplish the functionality of computation with P Systems, the present thesis is centered on the design of two parallel processors that, applying several variants of some known algorithms, improve the level of the internal parallelism at the evolution rule application phase. Design and creation of both processors present innovations to the field of Transition P Systems research because they use concepts that, even being known before, were never used for circuits that implement the applying phase of evolution rules. So, both processors present the following characteristics: - They present a very high performance during the application rule phase, keeping, on the other hand, a level of flexibility and scalability that, even known it is not very high, it seems to be acceptable. - They present a very high level of internal parallelism inside the regions, allowing several rule to be applied at the same time. - They present a universal character meaning this that they are not dependent upon the active rules that compose the P System. - They have a non-deterministic behavior that is inherent to this systems nature. The first processor uses the concept of "power set of the application rule set" and the concept of "maximal application" number to improve parallelism, and the second one includes, besides the previous ones, the concept of "applicability domain" to determine the set of rules that may be applied in each moment with the existing resources.. Both processors are designed and tested with the design software by Altera Corporation and they are ready to be synthetized over FPGAs.

A green fluorescent protein-reporter mammalian two-hybrid system with extrachromosomal maintenance of a prey expression plasmid: Application to interaction screening

An improved mammalian two-hybrid system designed for interaction trap screening is described in this paper. CV-1/EBNA-1 monkey kidney epithelial cells expressing Epstein–Barr virus nuclear antigen 1 (EBNA-1) were stably transfected with a reporter plasmid for GAL4-dependent expression of the green fluorescent protein (GFP). A resulting clone, GB133, expressed GFP strongly when transfected transiently with transcriptional activators fused to GAL4 DNA-binding domain with minimal background GFP expression. GB133 cells maintained plasmids containing the OriP Epstein–Barr virus replication origin that directs replication of plasmids in mammalian cells in the presence of the EBNA-1 protein. GB133 cells transfected stably with a model bait expressed GFP when further transfected transiently with an expression plasmid for a known positive prey. When the bait-expressing GB133 cells were transfected transiently with an OriP-containing expression plasmid for the positive prey together with excess amounts of empty vector, cells that received the positive prey were readily identified by green fluorescence in cell culture and eventually formed green fluorescent microcolonies, because the prey plasmid was maintained by the EBNA-1/Ori-P system. The green fluorescent microcolonies were harvested directly from the culture dishes under a fluorescence microscope, and total DNA was then prepared. Prey-encoding cDNA was recovered by PCR using primers annealing to the vector sequences flanking the insert-cloning site. This system should be useful in mammalian cells for efficient screening of cDNA libraries by two-hybrid interaction.

Researching Framework for Simulating/Implementating P Systems

Researching simulation/implementation of membranes systems is very recent. Present literature gathers new publications frequently about software/hardware, data structures and algorithms for implementing P system evolution. In this context, this work presents a framework which goal is to make tasks of researchers of this field easier. Hence, it establishes the set of cooperating classes that form a reusable and flexible design for the customizable evaluation with new data structures and algorithms. Moreover, it includes customizable services for correcting, monitoring and logging the evolution and edition, recovering, automatic generating, persistence and visualizing P systems.

Static Analysis of Usefulness States in Transition P Systems

Transition P Systems are a parallel and distributed computational model based on the notion of the cellular membrane structure. Each membrane determines a region that encloses a multiset of objects and evolution rules. Transition P Systems evolve through transitions between two consecutive configurations that are determined by the membrane structure and multisets present inside membranes. Moreover, transitions between two consecutive configurations are provided by an exhaustive non-deterministic and parallel application of evolution rules. But, to establish the rules to be applied, it is required the previous calculation of useful, applicable and active rules. Hence, computation of useful evolution rules is critical for the whole evolution process efficiency, because it is performed in parallel inside each membrane in every evolution step. This work defines usefulness states through an exhaustive analysis of the P system for every membrane and for every possible configuration of the membrane structure during the computation. Moreover, this analysis can be done in a static way; therefore membranes only have to check their usefulness states to obtain their set of useful rules during execution.

Decision Trees for Applicability of Evolution Rules in Transition P Systems

Transition P Systems are a parallel and distributed computational model based on the notion of the cellular membrane structure. Each membrane determines a region that encloses a multiset of objects and evolution rules. Transition P Systems evolve through transitions between two consecutive configurations that are determined by the membrane structure and multisets present inside membranes. Moreover, transitions between two consecutive configurations are provided by an exhaustive non-deterministic and parallel application of active evolution rules subset inside each membrane of the P system. But, to establish the active evolution rules subset, it is required the previous calculation of useful and applicable rules. Hence, computation of applicable evolution rules subset is critical for the whole evolution process efficiency, because it is performed in parallel inside each membrane in every evolution step. The work presented here shows advantages of incorporating decision trees in the evolution rules applicability algorithm. In order to it, necessary formalizations will be presented to consider this as a classification problem, the method to obtain the necessary decision tree automatically generated and the new algorithm for applicability based on it.

P Systems Goedelization

This paper presents a method for assigning natural numbers to Transition P systems based on a Gödelization process. The paper states step by step the way for obtaining Gödel numbers for each one of the fundamental elements of Transition P systems –multisets of objects, evolution rules, priorities relation, membrane structure- until defining the Gödel number of a given Transition P system.

Fast Linear Algorithm for Active Rules Application in Transition P Systems

Transition P systems are computational models based on basic features of biological membranes and the observation of biochemical processes. In these models, membrane contains objects multisets, which evolve according to given evolution rules. In the field of Transition P systems implementation, it has been detected the necessity to determine whichever time are going to take active evolution rules application in membranes. In addition, to have time estimations of rules application makes possible to take important decisions related to the hardware / software architectures design. In this paper we propose a new evolution rules application algorithm oriented towards the implementation of Transition P systems. The developed algorithm is sequential and, it has a linear order complexity in the number of evolution rules. Moreover, it obtains the smaller execution times, compared with the preceding algorithms. Therefore the algorithm is very appropriate for the implementation of Transition P systems in sequential devices.

Analysis of P-Systems under a Multiagent Systems Perspective

Membrane computing is a recent area that belongs to natural computing. This field works on computational models based on nature's behavior to process the information. Recently, numerous models have been developed and implemented with this purpose. P-systems are the structures which have been defined, developed and implemented to simulate the behavior and the evolution of membrane systems which we find in nature. What we show in this paper is an application capable to simulate the P-systems based on a multiagent systems (MAS) technology. The main goal we want to achieve is to take advantage of the inner qualities of the multiagent systems. This way we can analyse the proper functioning of any given p-system. When we observe a P-system from a different perspective, we can be assured that it is a particular case of the multiagent systems. This opens a new possibility, in the future, to always evaluate the P-systems in terms of the multiagent systems technology.