Parallel Graph Rewriting Systems

In this paper we introduce a new theoretical paradigm, called PGR systems, which can be used to model in a discrete manner some natural phenomena occurring in-vivo/in-vitro en- vironments. PGR systems make use of graphs to describe the spatial structure of space of individuals, while the system dynamics caused by the movement/interaction of individuals is captured by the parallel applications of some graph rewriting rules. In this frame, an il- lustrative example is studied and based on it, an eloquent comparison between the abstract rewriting machines and PGR systems is done. Several further ideas to overcome the global computational effort needed for simulations, but still maintaining the overall ability for mod- eling are finally proposed

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

A bioinspired computing approach to model complex systems

The use of models is intrinsic to any scientific activity. In particular, formal/mathematical models provide a relevant tool for scientific investigation. This paper presents a new Membrane Computing based computational paradigm as a framework for modelling processes and real-life phenomena. P systems, devices in Membrane Computing, are not used as a computing paradigm, but rather as a formalism for describing the behaviour of the system to be modelled. They offer an approach to the development of models for biological systems that meets the requirements of a good modelling framework: relevance, understandability, extensibility and computability.Ministerio de Economía y Competitividad TIN2012-3743

Complex event types for agent-based simulation

This thesis presents a novel formal modelling language, complex event types (CETs), to describe behaviours in agent-based simulations. CETs are able to describe behaviours at any computationally represented level of abstraction. Behaviours can be specified both in terms of the state transition rules of the agent-based model that generate them and in terms of the state transition structures themselves. Based on CETs, novel computational statistical methods are introduced which allow statistical dependencies between behaviours at different levels to be established. Different dependencies formalise different probabilistic causal relations and Complex Systems constructs such as ‘emergence’ and ‘autopoiesis’. Explicit links are also made between the different types of CET inter-dependency and the theoretical assumptions they represent. With the novel computational statistical methods, three categories of model can be validated and discovered: (i) inter-level models, which define probabilistic dependencies between behaviours at different levels; (ii) multi-level models, which define the set of simulations for which an inter-level model holds; (iii) inferred predictive models, which define latent relationships between behaviours at different levels. The CET modelling language and computational statistical methods are then applied to a novel agent-based model of Colonic Cancer to demonstrate their applicability to Complex Systems sciences such as Systems Biology. This proof of principle model provides a framework for further development of a detailed integrative model of the system, which can progressively incorporate biological data from different levels and scales as these become available

Domain-specific languages for modeling and simulation

Simulation models and simulation experiments are increasingly complex. One way to handle this complexity is developing software languages tailored to specific application domains, so-called domain-specific languages (DSLs). This thesis explores the potential of employing DSLs in modeling and simulation. We study different DSL design and implementation techniques and illustrate their benefits for expressing simulation models as well as simulation experiments with several examples.Simulationsmodelle und -experimente werden immer komplexer. Eine Möglichkeit, dieser Komplexität zu begegnen, ist, auf bestimmte Anwendungsgebiete spezialisierte Softwaresprachen, sogenannte domänenspezifische Sprachen (\emph{DSLs, domain-specific languages}), zu entwickeln. Die vorliegende Arbeit untersucht, wie DSLs in der Modellierung und Simulation eingesetzt werden können. Wir betrachten verschiedene Techniken für Entwicklung und Implementierung von DSLs und illustrieren ihren Nutzen für das Ausdrücken von Simulationsmodellen und -experimenten anhand einiger Beispiele

Natural Computing and Beyond

This book contains the joint proceedings of the Winter School of Hakodate (WSH) 2011 held in Hakodate, Japan, March 15–16, 2011, and the 6th International Workshop on Natural Computing (6th IWNC) held in Tokyo, Japan, March 28–30, 2012, organized by the Special Interest Group of Natural Computing (SIG-NAC), the Japanese Society for Artificial Intelligence (JSAI). This volume compiles refereed contributions to various aspects of natural computing, ranging from computing with slime mold, artificial chemistry, eco-physics, and synthetic biology, to computational aesthetics

Formal Modelling for Population Dynamics

The spirit of sustainable development has inspired our research work. Ecologically sus- tainable development needs preventative strategies and measures against environmental degradation. In our work we focus on constructing a formalism that enables modellers to model the population dynamics within an ecosystem and to analyse them. Furthermore, preventative strategies can be put into the model so that their effectiveness for ecosystems can be measured. An ecosystem consists of many interacting components. These components have many behaviours which are not easy to put together in a model. Work on such modelling started a long time ago, and even more has been done recently. These approaches have been taken from ordinary differential equations to stochastic processes. There are also some existing formalisms that have already been used for this modelling. In ecosystems there are several important aspects that need to be incorporated into the model, especially: stochasticity, spatiality and parallelism. One formalism has strengths in a certain aspect but weaknesses in others. Being motivated by this situation our work is to construct a formalism that could accommodate these aspects. Besides this, the formalism is intended to facilitate the modellers, who are generally biologists, to define the behaviours in the model in a more intuitive way. This has led our work to adopt features from existing formalisms: Cellular Automata and P Systems. Then, after adding new features, our work results in a new formalism called Grid Systems. Grid Systems have the spatiality of Cellular Automata but also provide a way to define behaviours differently in each cell (also called membrane) according to the reaction rules of P Systems. Therefore, Grid Systems have a richer spatiality compared to CA and the parallelism and stochaticity of P Systems. Besides these, we incorporate stochastic reaction duration for the reaction rules so that Grid Systems have stochasticity in rule selection and stochasticity in reaction termination. This enables us to define scheduled external events which are important aspects in modelling ecosystems. In addition to these, we extend Grid Systems with a new feature called ‘links’. A link is an object that can carry pointers. The pointer of a link can be used in the rule to transfer objects to another membrane. Because a link is also an object, its existence as well as its pointer are dynamic. By using the links, the membranes of Grid Systems can be structured as a tree to imitate the membrane structure of P Systems, or even more as a graph for a more general computation. The property of the links enables the structure to be dynamic, in a similar way to the dissolving membrane in the P Systems. The features of Grid Systems are defined in terms of syntax and semantics. The syntax describes how the model should be expressed by the modeller. The semantics describes what will happen to the model when the model evolves. From the semantics a software tool can be developed for analysing the model. In our research work we have developed the models in two case studies. In the first case study, we focus on the interacting events and external events that affect the population dynamics of mosquitoes. We observe how the impacts of events are propagated in space and time. In the second case study, we focus on the spatiality movement created by the seasonal migration of wildebeests. We observe that the pathways in the migration can be modelled well using links. The models of both case studies are analysed by using our simulation tool. From both case studies we conclude that our formalism can be used as a modelling framework especially for population dynamics, and in general for analysing the models of ecosystems