P and dP Automata: A Survey

This is a quick survey of basic notions and results related to P automata (P systems with symport/antiport rules working in the accepting mode), with some emphasis on the recently introduced dP automata (a distributed version of the standard P automata), ending with some open problems and research topics which we find of interest in this area.Junta de Andalucía P08 – TIC 0420

生化学反応による計算能力の研究

早大学位記番号:新6514早稲田大

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

Limits of the power of Tissue P systems with cell division

Tissue P systems generalize the membrane structure tree usual in original models of P systems to an arbitrary graph. Basic opera- tions in these systems are communication rules, enriched in some variants with cell division or cell separation. Several variants of tissue P systems were recently studied, together with the concept of uniform families of these systems. Their computational power was shown to range between P and NP ? co-NP , thus characterizing some interesting borderlines between tractability and intractability. In this paper we show that com- putational power of these uniform families in polynomial time is limited by the class PSPACE . This class characterizes the power of many clas- sical parallel computing model

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

Language generating alphabetic flat splicing P systems

An operation on strings, called at splicing was introduced, inspired by a splicing operation on circular strings considered in the study of modelling of the recombinant behaviour of DNA molecules. A simple kind of at splicing, called alphabetic at splicing, allows insertion of a word with a specified start symbol and/or a specified end symbol, between two pre-determined symbols in a given word. In this work, we consider a P system with only alphabetic at splicing rules as the evolution rules and strings of symbols as objects in its regions. We examine the language generative power of the resulting alphabetic at splicing P systems (AFS P systems, for short). In particular, we show that AFS P systems with two membranes are more powerful in generative power than AFS P systems with a single membrane. We also construct AFS P systems with at most three membranes to generate languages that do not belong to certain other language classes and show an application to generation of chain code pictures

(Leftmost-Outermost) Beta Reduction is Invariant, Indeed

Slot and van Emde Boas' weak invariance thesis states that reasonable machines can simulate each other within a polynomially overhead in time. Is lambda-calculus a reasonable machine? Is there a way to measure the computational complexity of a lambda-term? This paper presents the first complete positive answer to this long-standing problem. Moreover, our answer is completely machine-independent and based over a standard notion in the theory of lambda-calculus: the length of a leftmost-outermost derivation to normal form is an invariant cost model. Such a theorem cannot be proved by directly relating lambda-calculus with Turing machines or random access machines, because of the size explosion problem: there are terms that in a linear number of steps produce an exponentially long output. The first step towards the solution is to shift to a notion of evaluation for which the length and the size of the output are linearly related. This is done by adopting the linear substitution calculus (LSC), a calculus of explicit substitutions modeled after linear logic proof nets and admitting a decomposition of leftmost-outermost derivations with the desired property. Thus, the LSC is invariant with respect to, say, random access machines. The second step is to show that LSC is invariant with respect to the lambda-calculus. The size explosion problem seems to imply that this is not possible: having the same notions of normal form, evaluation in the LSC is exponentially longer than in the lambda-calculus. We solve such an impasse by introducing a new form of shared normal form and shared reduction, deemed useful. Useful evaluation avoids those steps that only unshare the output without contributing to beta-redexes, i.e. the steps that cause the blow-up in size. The main technical contribution of the paper is indeed the definition of useful reductions and the thorough analysis of their properties.Comment: arXiv admin note: substantial text overlap with arXiv:1405.331

Voicing Transformations and a Linear Representation of Uniform Triadic Transformations (Preprint name)

Motivated by analytical methods in mathematical music theory, we determine the structure of the subgroup $\mathcal{J}$ of $GL(3,\mathbb{Z}_{12})$ generated by the three voicing reflections. We determine the centralizer of $\mathcal{J}$ in both $GL(3,\mathbb{Z}_{12})$ and the monoid ${Aff}(3,\mathbb{Z}_{12})$ of affine transformations, and recover a Lewinian duality for trichords containing a generator of $\mathbb{Z}_{12}$. We present a variety of musical examples, including Wagner's hexatonic Grail motive and the diatonic falling fifths as cyclic orbits, an elaboration of our earlier work with Satyendra on Schoenberg, String Quartet in $D$ minor, op. 7, and an affine musical map of Joseph Schillinger. Finally, we observe, perhaps unexpectedly, that the retrograde inversion enchaining operation RICH (for arbitrary 3-tuples) belongs to the setwise stabilizer $\mathcal{H}$ in $\Sigma_3 \ltimes \mathcal{J}$ of root position triads. This allows a more economical description of a passage in Webern, Concerto for Nine Instruments, op. 24 in terms of a morphism of group actions. Some of the proofs are located in the Supplementary Material file, so that this main article can focus on the applications