Computing with Membranes and Picture Arrays

Splicing systems were introduced by Tom Head [3] on biological considerations to model certain recombinant behaviour of DNA molecules. An effective extension of this operation to images was introduced by Helen Chandra et al. [5] and H array splicing systems were considered. A new method of applying the splicing operation on images of hexagonal arrays was introduced by Thomas et al. [12] and generated a new class of hexagonal array languages HASSL. On the other hand, P systems, introduced by Paun [6] generating rectangular arrays and hexagonal arrays have been studied in the literature, bringing together the two areas of theoretical computer science namely membrane computing and picture languages. P system with array objects and parallel splicing operation on arrays is introduced as a simple and effective extension of P system with operation of splicing on strings and this new class of array languages is compared with the existing families of array languages. Also we propose another P system with hexagonal array objects and parallel splicing operation on hexagonal arrays is introduced and this new class of hexagonal array languages is compared with the existing families of hexagonal array languages

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

Four-Brane and Six-Brane Interactions in M(atrix) Theory

We discuss the proposed description of configurations with four-branes and six-branes in m(atrix) theory. Computing the velocity dependent potential between these configurations and gravitons and membranes, we show that they agree with the short distance string results computed in type IIa string theory. Due to the ``closeness'' of these configuration to a supersymmetric configuration the m(atrix) theory reproduces the correct long distance behavior.Comment: 14 pages, late

Complexity Classes in Cellular Computing with Membranes

In this paper we introduce the complexity class PMC∗ F of all decision problems solvable in polynomial time by a family of P systems belonging to a prefixed class of recognizer membrane systems, F.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Dictionary Search and Update by P Systems with String-Objects and Active Membranes

Membrane computing is a formal framework of distributed parallel computing. In this paper we implement working with the prefix tree by P systems with strings and active membranes

Evolution-Communication P Systems: Time-Freeness

Membrane computing is a (biologically motivated) theoretical framework of distributed parallel computing. If symbol-objects are considered, then membrane sys- tems (also called P systems) are distributed multiset processing systems. In evolution- communication (EC) P systems the computation is carried out with the use of non- cooperative rewriting rules and with (usually the minimally cooperative) transport rules. The goal of this article is to improve the existing results on evolution-communication P systems. It is known that EC P systems with 2 membranes are universal, and so are time-free EC P systems with targets with 3 membranes. We prove that any recursively enumerable set of vectors of nonnegative integers can be generated by time-free EC P systems (without targets) with 2 membranes, thus improving both results

Membrane systems with limited parallelism

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell. This work is a continuation of the investigations aiming to bridge membrane computing (where in a compartmental cell-like structure the chemicals to evolve are placed in compartments defined by membranes) and brane calculi (where one considers again a compartmental cell-like structure with the chemicals/proteins placed on the membranes themselves). We use objects both in compartments and on membranes (the latter are called proteins), with the objects from membranes evolving under the control of the proteins. Several possibilities are considered (objects only moved across membranes or also changed during this operation, with the proteins only assisting the move/change or also changing themselves). Somewhat expected, computational universality is obtained for several combinations of such possibilities. We also present a method for solving the NP-complete SAT problem using P systems with proteins on membranes. The SAT problem is solved in O(nm) time, where n is the number of boolean variables and m is the number of clauses for an instance written in conjunctive normal form. Thus, we can say that the solution for each given instance is obtained in linear time. We succeeded in solving SAT by a uniform construction of a deterministic P system which uses rules involving objects in regions, proteins on membranes, and membrane division. Then, we investigate the computational power of P systems with proteins on membranes in some particular cases: when only one protein is placed on a membrane, when the systems have a minimal number of rules, when the computation evolves in accepting or computing mode, etc. This dissertation introduces also another new variant of membrane systems that uses context-free rewriting rules for the evolution of objects placed inside compartments of a cell, and symport rules for communication between membranes. The strings circulate across membranes depending on their membership to regular languages given by means of regular expressions. We prove that these rewriting-symport P systems generate all recursively enumerable languages. We investigate the computational power of these newly introduced P systems for three particular forms of the regular expressions that are used by the symport rules. A characterization of ET0L languages is obtained in this context

Mass-Gaps and Spin Chains for (Super) Membranes

We present a method for computing the non-perturbative mass-gap in the theory of Bosonic membranes in flat background spacetimes with or without background fluxes. The computation of mass-gaps is carried out using a matrix regularization of the membrane Hamiltonians. The mass gap is shown to be naturally organized as an expansion in a 'hidden' parameter, which turns out to be $\frac{1}{d}$: d being the related to the dimensionality of the background space. We then proceed to develop a large $N$ perturbation theory for the membrane/matrix-model Hamiltonians around the quantum/mass corrected effective potential. The same parameter that controls the perturbation theory for the mass gap is also shown to control the Hamiltonian perturbation theory around the effective potential. The large $N$ perturbation theory is then translated into the language of quantum spin chains and the one loop spectra of various Bosonic matrix models are computed by applying the Bethe ansatz to the one-loop effective Hamiltonians for membranes in flat space times. Apart from membranes in flat spacetimes, the recently proposed matrix models (hep-th/0607005) for non-critical membranes in plane wave type spacetimes are also analyzed within the paradigm of quantum spin chains and the Bosonic sectors of all the models proposed in (hep-th/0607005) are diagonalized at the one-loop level.Comment: 36 Page

Affine Buildings and Tropical Convexity

The notion of convexity in tropical geometry is closely related to notions of convexity in the theory of affine buildings. We explore this relationship from a combinatorial and computational perspective. Our results include a convex hull algorithm for the Bruhat--Tits building of SL$_d(K)$ and techniques for computing with apartments and membranes. While the original inspiration was the work of Dress and Terhalle in phylogenetics, and of Faltings, Kapranov, Keel and Tevelev in algebraic geometry, our tropical algorithms will also be applicable to problems in other fields of mathematics.Comment: 22 pages, 4 figure