P Systems and Topology: Some Suggestions for Research

Lately, some studies linked the computational power of abstract computing systems based on multiset rewriting to Petri nets and the computation power of these nets to their topology. In turn, the computational power of these abstract computing devices can be understood just looking at their topology, that is, information flow. This line of research is very promising for several aspects: its results are valid for a broad range of systems based on multiset rewriting; it allows to know the computational power of abstract computing devices without tedious proofs based on simulations; it links computational power to topology and, in this way, it opens a broad range of questions. In this note we summarize the known result on this topic and we list a few suggestions for research together with the relevance of possible outcomes

Modeling Reaction Kinetics in Low-dimensional Environments with Conformon P Systems: Comparison with Cellular Automata and New Rate Laws

Recently it has been shown that simulations of complex biological systems using conformon P systems and cellular automata do not necessarily give the same pre- dictions. To further elucidate these di®erences we simulate a simple model of intracellular reactions involving a single bimolecular reaction occurring on a biological membrane us- ing conformon P systems. We ¯nd that the predictions broadly agree with results from both the theory of ran- dom walks in low-dimensional environments and with previously published simulations using cellular automata. Moreover, a re-analysis of the data enables us to deduce novel rate laws for the kinetics of reactions occurring on biological membranes

No Cycles in Compartments. Starting from Conformon-P Systems

Starting from proofs of results about the computing power of conformon- P systems, we infer several results about the power of certain classes of tissue-like P systems with (cooperative) rewriting rules used in an asynchronous way, without cycles in compartments. This last feature is related to an important restriction appearing when dealing with lab implementations of P systems, that of avoiding local evolution loops of objects

Dynamics of Randomly Constructed Computational Systems

We studied Petri nets with five places constructed in a pseudo-random way: their underlying net is composed of join and fork. We report initial results linking the dynamical properties of these systems to the topology of their underlying net. The obtained results can be easily related to the computational power of some abstract models of computation

On Languages Accepted by P/T Systems Composed of joins

Recently, some studies linked the computational power of abstract computing systems based on multiset rewriting to models of Petri nets and the computation power of these nets to their topology. In turn, the computational power of these abstract computing devices can be understood by just looking at their topology, that is, information flow. Here we continue this line of research introducing J languages and proving that they can be accepted by place/transition systems whose underlying net is composed only of joins. Moreover, we investigate how J languages relate to other families of formal languages. In particular, we show that every J language can be accepted by a log n space-bounded non-deterministic Turing machine with a one-way read-only input. We also show that every J language has a semilinear Parikh map and that J languages and context-free languages (CFLs) are incomparable

Infobiotics workbench: a P systems based tool for systems and synthetic biology

This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework. The Workbench incorporates three important features, simulation, model checking and optimisation. Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and synthetic biology research

On Two Variants of Splicing Super-Cell Systems

. New computability models, called super-cell systems or P systems, based on the evolution of objects in a membrane structure, were recently introduced. The seminal paper of Gheorghe Paun describes three ways to look at them: transition, rewriting and splicing super-cell systems having different properties. Here we investigate two variants of splicing super-cell systems improving results concerning their generative capability. This is obtained with a variant of the "rotate-and-simulate" technique classical in H systems area. 1 Introduction Super-cell systems (also called P systems) were recently introduced in [5] as distributed parallel computing models. In the seminal paper the author considers systems based on a hierarchical arranged, finite cell-structure consisting of several cell-membranes embedded in a main membrane called skin. The membranes delimit regions where objects, elements of a finite set or alphabet, and evolution rules can be placed. The objects evolve acco..

Conformon-P systems with negative values

Summary. Some initial results on the study of conformon-P systems with negative values are reported. One model of these conformon-P systems is proved to be computationally universal while another is proved to be at least as powerful as partially blind program machines.