Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications

P Colony Automata with LL(k)-like Conditions

We investigate the possibility of the deterministic parsing (that is, parsing without backtracking) of languages characterized by (generalized) P colony automata. We de ne a class of P colony automata satisfying a property which resembles the LL(k) property of context-free grammars, and study the possibility of parsing the characterized languages using a k symbol lookahead, as in the LL(k) parsing method for context-free languages

Dependencies and Simultaneity in Membrane Systems

Membrane system computations proceed in a synchronous fashion: at each step all the applicable rules are actually applied. Hence each step depends on the previous one. This coarse view can be refined by looking at the dependencies among rule occurrences, by recording, for an object, which was the a rule that produced it and subsequently (in a later step), which was the a rule that consumed it. In this paper we propose a way to look also at the other main ingredient in membrane system computations, namely the simultaneity in the rule applications. This is achieved using zero-safe nets that allows to synchronize transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into occurrence nets in a classical way, and to this unfolding an event structure can be associated. The capability of capturing simultaneity of zero-safe nets is transferred on the level of event structure by adding a way to express which events occur simultaneously

First Steps Towards Linking Membrane Depth and the Polynomial Hierarchy

In this paper we take the first steps in studying possible connections between non-elementary division with limited membrane depth and the levels of the Polynomial Hierarchy. We present a uniform family with a membrane structure of depth d + 1 that solves a problem complete for level d of the Polynomial Hierarchy

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

A Formal Framework for P Systems with Dynamic Structure

This article introduces a formalism/framework able to describe different variants of P systems having a dynamic structure. This framework can be useful for the definition of new variants of P systems with dynamic structure, for the comparison of existing definitions as well as for their extension. We give a precise definition of the formalism and show how existing variants of P systems with dynamic structure can be translated to it

Computationally Complete Generalized Communicating P Systems with Three Cells

International audienc

Towards P Colonies Processing Strings

In this paper we introduce and study P colonies where the environment is given as a string. These variants of P colonies, called Automaton-like P systems or APCol systems, behave like automata: during functioning, the agents change their own states and process the symbols of the string. After introducing the concept of APCol systems, we examine their computational power. It is shown that the family of languages accepted by jumping nite automata is properly included in the family of languages accepted by APCol systems with one agent, and it is proved that any recursively enumerable language can be obtained as a projection of a language accepted by an Automaton-like P colony with two agents

Automaton-like P Colonies

In this paper we study P colonies where the environment is given as a string. These variants, called automaton-like P systems or APCol systems, behave like automata: during functioning, the agents change their own states and process the symbols of the string. We develop the concept of APCol systems by introducing the notion of their generating working mode. We then compare the power of APCol systems working in the generating mode and that of register machines and context-free matrix grammars with and without appearance checking