42,265 research outputs found
Developing Tools for Networks of Processors
A great deal of research eort is currently being made in the realm of so called natural computing. Natural computing mainly focuses on the denition, formal description, analysis, simulation and programming of new models of computation (usually with the same expressive power as Turing Machines) inspired by Nature, which makes them particularly suitable for the simulation of complex systems.Some of the best known natural computers are Lindenmayer systems (Lsystems, a kind of grammar with parallel derivation), cellular automata, DNA computing, genetic and evolutionary algorithms, multi agent systems, arti- cial neural networks, P-systems (computation inspired by membranes) and NEPs (or networks of evolutionary processors). This chapter is devoted to this last model
(Tissue) P Systems with Anti-Membranes
The concept of a matter object being annihilated when meeting its corresponding
anti-matter object is taken over for membranes as objects and anti-membranes
as the corresponding annihilation counterpart in P systems. Natural numbers can be
represented by the corresponding number of membranes with a speci c label. Computational
completeness in this setting then can be obtained with using only elementary
membrane division rules, without using objects. A similar result can be obtained for tissue
P systems with cell division rules and cell / anti-cell annihilation rules. In both cases,
as derivation modes we may take the standard maximally parallel derivation modes as
well as any of the maximally parallel set derivation modes (non-extendable (multi)sets of
rules, (multi)sets with maximal number of rules, (multi)sets of rules a ecting the maximal
number of objects)
Computing with cells: membrane systems - some complexity issues.
Membrane computing is a branch of natural computing which abstracts computing models from the structure and the functioning of the living cell. The main ingredients of membrane systems, called P systems, are (i) the membrane structure, which consists of a hierarchical arrangements of membranes which delimit compartments where (ii) multisets of symbols, called objects, evolve according to (iii) sets of rules which are localised and associated with compartments. By using the rules in a nondeterministic/deterministic maximally parallel manner, transitions between the system configurations can be obtained. A sequence of transitions is a computation of how the system is evolving. Various ways of controlling the transfer of objects from one membrane to another and applying the rules, as well as possibilities to dissolve, divide or create membranes have been studied. Membrane systems have a great potential for implementing massively concurrent systems in an efficient way that would allow us to solve currently intractable problems once future biotechnology gives way to a practical bio-realization. In this paper we survey some interesting and fundamental complexity issues such as universality vs. nonuniversality, determinism vs. nondeterminism, membrane and alphabet size hierarchies, characterizations of context-sensitive languages and other language classes and various notions of parallelism
Membrane Systems and Petri Net Synthesis
Automated synthesis from behavioural specifications is an attractive and
powerful way of constructing concurrent systems. Here we focus on the problem
of synthesising a membrane system from a behavioural specification given in the
form of a transition system which specifies the desired state space of the
system to be constructed. We demonstrate how a Petri net solution to this
problem, based on the notion of region of a transition system, yields a method
of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
Playing with Derivation Modes and Halting Conditions
In the area of P systems, besides the standard maximally parallel derivation
mode, many other derivation modes have been investigated, too. In this paper, many
variants of hierarchical P systems and tissue P systems using different derivation modes
are considered and the effects of using di erent derivation modes, especially the maximally
parallel derivation modes and the maximally parallel set derivation modes, on the
generative and accepting power are illustrated. Moreover, an overview on some control
mechanisms used for (tissue) P systems is given.
Furthermore, besides the standard total halting mode, we also consider different halting
conditions such as unconditional halting and partial halting and explain how the use
of different halting modes may considerably change the computing power of P systems
and tissue P systems
Catalytic and communicating Petri nets are Turing complete
In most studies about the expressiveness of Petri nets, the focus has been put either on adding suitable arcs or on assuring that a complete snapshot of the system can be obtained. While the former still complies with the intuition on Petri nets, the second is somehow an orthogonal approach, as Petri nets are distributed in nature. Here, inspired by membrane computing, we study some classes of Petri nets where the distribution is partially kept and which are still Turing complete
P Systems: from Anti-Matter to Anti-Rules
The concept of a matter object being annihilated when meeting its corresponding
anti-matter object is taken over for rule labels as objects and anti-rule labels
as the corresponding annihilation counterpart in P systems. In the presence of a corresponding
anti-rule object, annihilation of a rule object happens before the rule that the
rule object represents, can be applied. Applying a rule consumes the corresponding rule
object, but may also produce new rule objects as well as anti-rule objects, too. Computational
completeness in this setting then can be obtained in a one-membrane P system
with non-cooperative rules and rule / anti-rule annihilation rules when using one of the
standard maximally parallel derivation modes as well as any of the maximally parallel
set derivation modes (i.e., non-extendable (multi)sets of rules, (multi)sets with maximal
number of rules, (multi)sets of rules a ecting the maximal number of objects). When
using the sequential derivation mode, at least the computational power of partially blind
register machines is obtained
A Process Algebraical Approach to Modelling Compartmentalized Biological Systems
This paper introduces Protein Calculus, a special modeling language designed for encoding and calculating the behaviors of compartmentilized biological systems. The formalism combines, in a unified framework, two successful computational paradigms - process algebras and membrane systems. The goal of Protein Calculus is to provide a formal tool for transforming collected information from in vivo experiments into coded definition of the different types of proteins, complexes of proteins, and membrane-organized systems of such entities. Using this encoded information as input, our calculus computes, in silico, the possible behaviors of a living system. This is the preliminary version of a paper that was published in Proceedings of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2: 642-646, 2007 (http://scitation.aip.org/dbt/dbt.jsp?KEY=APCPCS&Volume=963&Issue=2)
A Calculus of Looping Sequences with Local Rules
In this paper we present a variant of the Calculus of Looping Sequences (CLS
for short) with global and local rewrite rules. While global rules, as in CLS,
are applied anywhere in a given term, local rules can only be applied in the
compartment on which they are defined. Local rules are dynamic: they can be
added, moved and erased. We enrich the new calculus with a parallel semantics
where a reduction step is lead by any number of global and local rules that
could be performed in parallel. A type system is developed to enforce the
property that a compartment must contain only local rules with specific
features. As a running example we model some interactions happening in a cell
starting from its nucleus and moving towards its mitochondria.Comment: In Proceedings DCM 2011, arXiv:1207.682
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