Membrane systems with limited parallelism

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell. This work is a continuation of the investigations aiming to bridge membrane computing (where in a compartmental cell-like structure the chemicals to evolve are placed in compartments defined by membranes) and brane calculi (where one considers again a compartmental cell-like structure with the chemicals/proteins placed on the membranes themselves). We use objects both in compartments and on membranes (the latter are called proteins), with the objects from membranes evolving under the control of the proteins. Several possibilities are considered (objects only moved across membranes or also changed during this operation, with the proteins only assisting the move/change or also changing themselves). Somewhat expected, computational universality is obtained for several combinations of such possibilities. We also present a method for solving the NP-complete SAT problem using P systems with proteins on membranes. The SAT problem is solved in O(nm) time, where n is the number of boolean variables and m is the number of clauses for an instance written in conjunctive normal form. Thus, we can say that the solution for each given instance is obtained in linear time. We succeeded in solving SAT by a uniform construction of a deterministic P system which uses rules involving objects in regions, proteins on membranes, and membrane division. Then, we investigate the computational power of P systems with proteins on membranes in some particular cases: when only one protein is placed on a membrane, when the systems have a minimal number of rules, when the computation evolves in accepting or computing mode, etc. This dissertation introduces also another new variant of membrane systems that uses context-free rewriting rules for the evolution of objects placed inside compartments of a cell, and symport rules for communication between membranes. The strings circulate across membranes depending on their membership to regular languages given by means of regular expressions. We prove that these rewriting-symport P systems generate all recursively enumerable languages. We investigate the computational power of these newly introduced P systems for three particular forms of the regular expressions that are used by the symport rules. A characterization of ET0L languages is obtained in this context

Scalable Performance Analysis of Massively Parallel Stochastic Systems

The accurate performance analysis of large-scale computer and communication systems is directly inhibited by an exponential growth in the state-space of the underlying Markovian performance model. This is particularly true when considering massively-parallel architectures such as cloud or grid computing infrastructures. Nevertheless, an ability to extract quantitative performance measures such as passage-time distributions from performance models of these systems is critical for providers of these services. Indeed, without such an ability, they remain unable to offer realistic end-to-end service level agreements (SLAs) which they can have any confidence of honouring. Additionally, this must be possible in a short enough period of time to allow many different parameter combinations in a complex system to be tested. If we can achieve this rapid performance analysis goal, it will enable service providers and engineers to determine the cost-optimal behaviour which satisfies the SLAs. In this thesis, we develop a scalable performance analysis framework for the grouped PEPA stochastic process algebra. Our approach is based on the approximation of key model quantities such as means and variances by tractable systems of ordinary differential equations (ODEs). Crucially, the size of these systems of ODEs is independent of the number of interacting entities within the model, making these analysis techniques extremely scalable. The reliability of our approach is directly supported by convergence results and, in some cases, explicit error bounds. We focus on extracting passage-time measures from performance models since these are very commonly the language in which a service level agreement is phrased. We design scalable analysis techniques which can handle passages defined both in terms of entire component populations as well as individual or tagged members of a large population. A precise and straightforward specification of a passage-time service level agreement is as important to the performance engineering process as its evaluation. This is especially true of large and complex models of industrial-scale systems. To address this, we introduce the unified stochastic probe framework. Unified stochastic probes are used to generate a model augmentation which exposes explicitly the SLA measure of interest to the analysis toolkit. In this thesis, we deploy these probes to define many detailed and derived performance measures that can be automatically and directly analysed using rapid ODE techniques. In this way, we tackle applicable problems at many levels of the performance engineering process: from specification and model representation to efficient and scalable analysis

A Language-centered Approach to support environmental modeling with Cellular Automata

Die Anwendung von Methodiken und Technologien aus dem Bereich der Softwaretechnik auf den Bereich der Umweltmodellierung ist eine gemeinhin akzeptierte Vorgehensweise. Im Rahmen der "modellgetriebenen Entwicklung"(MDE, model-driven engineering) werden Technologien entwickelt, die darauf abzielen, Softwaresysteme vorwiegend auf Basis von im Vergleich zu Programmquelltexten relativ abstrakten Modellen zu entwickeln. Ein wesentlicher Bestandteil von MDE sind Techniken zur effizienten Entwicklung von "domänenspezifischen Sprachen"( DSL, domain-specific language), die auf Sprachmetamodellen beruhen. Die vorliegende Arbeit zeigt, wie modellgetriebene Entwicklung, und insbesondere die metamodellbasierte Beschreibung von DSLs, darüber hinaus Aspekte der Pragmatik unterstützen kann, deren Relevanz im erkenntnistheoretischen und kognitiven Hintergrund wissenschaftlichen Forschens begründet wird. Hierzu wird vor dem Hintergrund der Erkenntnisse des "modellbasierten Forschens"(model-based science und model-based reasoning) gezeigt, wie insbesondere durch Metamodelle beschriebene DSLs Möglichkeiten bieten, entsprechende pragmatische Aspekte besonders zu berücksichtigen, indem sie als Werkzeug zur Erkenntnisgewinnung aufgefasst werden. Dies ist v.a. im Kontext großer Unsicherheiten, wie sie für weite Teile der Umweltmodellierung charakterisierend sind, von grundsätzlicher Bedeutung. Die Formulierung eines sprachzentrierten Ansatzes (LCA, language-centered approach) für die Werkzeugunterstützung konkretisiert die genannten Aspekte und bildet die Basis für eine beispielhafte Implementierung eines Werkzeuges mit einer DSL für die Beschreibung von Zellulären Automaten (ZA) für die Umweltmodellierung. Anwendungsfälle belegen die Verwendbarkeit von ECAL und der entsprechenden metamodellbasierten Werkzeugimplementierung.The application of methods and technologies of software engineering to environmental modeling and simulation (EMS) is common, since both areas share basic issues of software development and digital simulation. Recent developments within the context of "Model-driven Engineering" (MDE) aim at supporting the development of software systems at the base of relatively abstract models as opposed to programming language code. A basic ingredient of MDE is the development of methods that allow the efficient development of "domain-specific languages" (DSL), in particular at the base of language metamodels. This thesis shows how MDE and language metamodeling in particular, may support pragmatic aspects that reflect epistemic and cognitive aspects of scientific investigations. For this, DSLs and language metamodeling in particular are set into the context of "model-based science" and "model-based reasoning". It is shown that the specific properties of metamodel-based DSLs may be used to support those properties, in particular transparency, which are of particular relevance against the background of uncertainty, that is a characterizing property of EMS. The findings are the base for the formulation of an corresponding specific metamodel- based approach for the provision of modeling tools for EMS (Language-centered Approach, LCA), which has been implemented (modeling tool ECA-EMS), including a new DSL for CA modeling for EMS (ECAL). At the base of this implementation, the applicability of this approach is shown

Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

Hybrid Behaviour of Markov Population Models

We investigate the behaviour of population models written in Stochastic Concurrent Constraint Programming (sCCP), a stochastic extension of Concurrent Constraint Programming. In particular, we focus on models from which we can define a semantics of sCCP both in terms of Continuous Time Markov Chains (CTMC) and in terms of Stochastic Hybrid Systems, in which some populations are approximated continuously, while others are kept discrete. We will prove the correctness of the hybrid semantics from the point of view of the limiting behaviour of a sequence of models for increasing population size. More specifically, we prove that, under suitable regularity conditions, the sequence of CTMC constructed from sCCP programs for increasing population size converges to the hybrid system constructed by means of the hybrid semantics. We investigate in particular what happens for sCCP models in which some transitions are guarded by boolean predicates or in the presence of instantaneous transitions