Generalized Communicating P Systems Working in Fair Sequential Model

In this article we consider a new derivation mode for generalized communicating P systems (GCPS) corresponding to the functioning of population protocols (PP) and based on the sequential derivation mode and a fairness condition. We show that PP can be seen as a particular variant of GCPS. We also consider a particular stochastic evolution satisfying the fairness condition and obtain that it corresponds to the run of a Gillespie's SSA. This permits to further describe the dynamics of GCPS by a system of ODEs when the population size goes to the infinity.Comment: Presented at MeCBIC 201

Cellular Automata and Kan Extensions

In this paper, we formalize precisely the sense in which the application of a cellular automaton to partial configurations is a natural extension of its local transition function through the categorical notion of Kan extension. In fact, the two possible ways to do such an extension and the ingredients involved in their definition are related through Kan extensions in many ways. These relations provide additional links between computer science and category theory, and also give a new point of view on the famous Curtis-Hedlund theorem of cellular automata from the extended topological point of view provided by category theory. These links also allow to relatively easily generalize concepts pioneered by cellular automata to arbitrary kinds of possibly evolving spaces. No prior knowledge of category theory is assumed

Transformation de collections topologiques de dimension arbitraire (application à la modélisation de systèmes dynamiques)

Le projet MGS poursuit deux objectifs : l'étude de l'apport de notions topologiques dans les langages de programmation, et leur application au développement de nouvelles structures de données et de contrôle pour la simulation de systèmes dynamiques à structure dynamique. Ces objectifs ont abouti au développement d'un langage de programmation expérimental dédié à la spécification de ces systèmes : le langage MGS. Ces travaux sont organisés selon trois axes : (1) le développement de la notion de collection topologique de dimension arbitraire, une nouvelle structure de donnée fondée sur la notion de complexe cellulaire développée en topologie algébrique, (2) la spécification formelle d'une sémantique des programmes MGS et plus particulièrement des transformations, une forme originale de définition par cas de fonction sur les collections topologiques, et enfin (3) la validation de nos travaux par de nombreux exemples non triviaux dans les domaines de la biologie et de la morphogénèse.The MGS project is aimed at studying the use of topological notions for programming languages and their applications in developing new data and control structures for the simulation of dynamical systems with a dynamical structure. These goals have led to the development of an experimental programming language dedicated to the specification of such systems: the MGS language. This work is organized following three directions: (1) developing the notion of topological collection of arbitrary dimension, a new data structure based on the concept of cellular complex developed in algebraic topology, (2) specifying a formal semantics of MGS, especially for transformations, an original kind of case-based definition of functions on topological collections, and finally (3) validating our works with numerous non trivial examples in biology and morphogenesis.EVRY-Bib. électronique (912289901) / SudocSudocFranceF

From Reactive Multi-Agent models to Cellular Automata - Illustration on a Diffusion-Limited Aggregation model

International audienceThis paper deals with the synchronous implementation of situated Multi-Agent Systems (MAS) in order to have no execution bias and to allow their programming on massively parallel computing devices. For this purpose we investigate the translation of discrete MAS into Cellular Automata (CA). Contrarily to the sequential scheduling generally used in MAS simulations, CA is a model for massively parallel computing where the updating of the components is synchronous. However, CA expressivity is limited and not adapted to build models where independent entities may move and act on neighbor cells. After illustrating these issues on a simple example, we propose a generic method to translate discrete MAS into CA, called transactional CA. Our approach consists in translating MAS specified with the influence-reaction model into a transactional CA

Declarative mesh subdivision using topological rewriting in mgs.

Abstract. Mesh subdivision algorithms are usually specified informally using graphical schemes defining local mesh refinements. These algorithms are then implemented efficiently in an imperative framework. The implementation is cumbersome and implies some tricky indices management

Arbitrary Nesting of Spatial Computations

International audienceModern programming languages allow the definition and the use of arbitrary nested data structures but this is not generally considered in unconventional programming models. In this paper, we present arbitrary nesting in MGS, a spatial comput- ing language. By considering different classes of neighborhood relationships, MGS can emulate several unconventional computing models from a programming point of view. The use of arbitrary nested spatial structures allows a hierarchical form of coupling between them. We propose an extension of the MGS pattern- matching facilities to handle directly nesting. This makes possible the straightforward emulation of a larger class of unconventional programming models

Spatial Computing as Intensional Data Parallelism

International audienceIn this paper, we show that various concepts and tools developed in the 90's in the field of data-parallelism provide a relevant spatial programming framework. It allows high level spatial computation specifications to be translated into efficient low-level operations on processing units. We provide some short examples to illustrate this statement

Gardening Cyber-Physical Systems

cote interne IRCAM: Stepney12aNational audienceToday’s artefacts, from small devices to buildings and cities, are, or are becoming, cyber-physical socio-technical systems, with tightly interwoven material and computational parts. Currently, we have to la- boriously build such systems, component by component, and the results are often difficult to maintain, adapt, and reconfigure. Even “soft”ware is brittle and non-trivial to adapt and change. If we look to nature, how- ever, large complex organisms grow, adapt to their environment, and repair themselves when damaged. In this position paper, we present Gro-CyPhy, an unconventional computational framework for growing cyber-physical systems from com- putational seeds, and gardening the growing systems, in order to adapt them to specific needs. The Gro-CyPhy architecture comprises: a Seed Factory, a process for designing specific computational seeds to meet cyber-physical system requirements; a Growth Engine, providing the computational processes that grow seeds in simulation; and a Computational Garden, where mul- tiple seeds can be planted and grown in concert, and where a high-level gardener can shape them into complex cyber-physical systems. We outline how the Gro-CyPhy architecture might be applied to a significant exemplar application: a (simulated) skyscraper, comprising several mutually interdependent physical and virtual subsystems, such as the shell of exterior and interior walls, electrical power and data net- works, plumbing and rain-water harvesting, heating and air-conditioning systems, and building management control systems

Virus effects on plant quality and vector behavior are species specific and do not depend on host physiological phenotype

There is growing evidence that plant viruses manipulate host plants to increase transmission-conducive behaviors by vectors. Reports of this phenomenon frequently include only highly susceptible, domesticated annual plants as hosts, which constrains our ability to determine whether virus effects are a component of an adaptive strategy on the part of the pathogen or simply by-products of pathology. Here, we tested the hypothesis that transmission-conducive effects of a virus (Turnip yellows virus [TuYV]) on host palatability and vector behavior (Myzus persicae) are linked with host plant tolerance and physiological phenotype. Our study system consisted of a cultivated crop, false flax (Camelina sativa) (Brassicales: Brassicaceae), a wild congener (C. microcarpa), and a viable F1 hybrid of these two species. We found that the most tolerant host (C. microcarpa) exhibited the most transmission-conducive changes in phenotype relative to mock-inoculated healthy plants: Aphids preferred to settle and feed on TuYV-infected C. microcarpa and did not experience fitness changes due to infection—both of which will increase viruliferous aphid numbers. In contrast, TuYV induced transmission-limiting phenotypes in the least tolerant host (C. sativa) and to a greater degree in the F1 hybrid, which exhibited intermediate tolerance to infection. Our results provide no evidence that virus effects track with infection tolerance or physiological phenotype. Instead, vector preferences and performance are driven by host-specific changes in carbohydrates under TuYV infection. These results provide evidence that induction of transmission-enhancing phenotypes by plant viruses is not simply a by-product of general pathology, as has been proposed as an explanation for putative instances of parasite manipulation by viruses and many other taxa

Interaction-based programming: A review of MGS

The modeling and simulation of morphogenetic phenomena require to take into account the coupling between the processes that take place in a space and the modification of that space due to those processes, leading to a chicken-and-egg problem. To address this issue, we proposed to consider a growing structure as the byproduct of a multitude of interactions between its constitutive elements. An interaction-based model of computation relying on spatial relationships has then been developed leading to an original style of programming implemented in the MGS programming language. Contributions of MGS include a generic programming mechanism that captures most of the unconventional computing models by simply varying the underlying structure of interactions. I will introduce the interaction-based way of programming and review some current works taking roots in the fertile ground of MGS.Non UBCUnreviewedAuthor affiliation: University of Paris-Est CreteilFacult