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For a family of sets we consider elements that belong to the same sets within the family as companions. The global dynamics of a reactions system (as introduced by Ehrenfeucht and Rozenberg) can be represented by a directed graph, called a transition graph, which is uniquely determined by a one-out subgraph, called the 0-context graph. We consider the companion classes of the outsets of a transition graph and introduce a directed multigraph, called an essential motion, whose vertices are such companion classes. We show that all one-out graphs obtained from an essential motion represent 0-context graphs of reactions systems with isomorphic transition graphs. All such 0-context graphs are obtained from one another by swapping the outgoing edges of companion vertices. [ABSTRACT FROM AUTHOR]

We investigate regular languages in the context of the forbidding-enforcing systems introduced by Ehrenfeucht and Rozenberg in the variant where one fe-system defines a single language. In general, these systems may have infinite sets of rules, allowing one to define arbitrary languages. On the other hand when restricted to finite sets, one obtains a strict subclass of the regular languages, between the strictly locally testable and locally testable languages. We further investigate classes of enforcing systems that characterize the regular languages. These systems have infinite sets of enforcers, but can be defined using regular languages (finite state automata). [ABSTRACT FROM AUTHOR]

Non-deterministic Constraint Logic is a family of graph games introduced by Demaine and Hearn that facilitates the construction of complexity proofs. It is very convenient for the analysis of games, providing a uniform view. We focus on the acyclic version, apply this to Klondike,Mahjong Solitaire and Nonogram (that requires planarity), and discuss the more complicated game of Dou Shou Qi. While for the first three games we reobtain known characterizations in a simple and uniform manner, the result for Dou Shou Qi is new. [ABSTRACT FROM AUTHOR]

DNA expressions constitute a formal notation for DNA molecules that may contain nicks and gaps. Different DNA expressions may denote the same DNA molecule. We describe an algorithm to rewrite a given DNA expression into a DNA expression of minimal length denoting the same molecule. [ABSTRACT FROM AUTHOR]

DNA expressions constitute a formal notation for DNA molecules that may contain nicks and gaps. Different DNA expressions may denote the same DNA molecule. We define a (minimal) normal form for the language of DNA expressions, and describe an algorithm to rewrite a given DNA expression into the normal form. [ABSTRACT FROM AUTHOR]

We show that the symmetric-difference distance measure for set systems, and more specifically for delta-matroids, corresponds to the notion of nullity for symmetric and skew-symmetric matrices. In particular, as graphs (i.e., symmetric matrices over GF(2)) may be seen as a special class of delta-matroids, this distance measure generalizes the notion of nullity in this case. We characterize delta-matroids in terms of equicardinality of minimal sets with respect to inclusion (in addition, we obtain similar characterizations for matroids). In this way, we find that, e.g., the delta-matroids obtained after loop complementation and after pivot on a single element together with the original delta-matroid fulfill the property that two of them have equal "null space" while the third has a larger dimension. [ABSTRACT FROM AUTHOR]

In a biological nervous system, astrocytes play an important role in the functioning and interaction of neurons, and astrocytes have excitatory and inhibitory influence on synapses. In this work, with this biological inspiration, a class of computation devices that consist of neurons and astrocytes is introduced, called spiking neural P systems with astrocytes (SNPA systems). The computation power of SNPA systems is investigated. It is proved that SNPA systems with simple neurons (all neurons have the same rule, one per neuron, of a very simple form) are Turing universal in both generative and accepting modes. If a bound is given on the number of spikes present in any neuron along a computation, then the computation power of SNPA systems is diminished. In this case, a characterization of semilinear sets of numbers is obtained. [ABSTRACT FROM AUTHOR]

We consider the Schur complement operation for symmetric matrices over GF(2), which we identify with graphs through the adjacency matrix representation. It is known that Schur complementation for such a matrix (i.e., for a graph) can be decomposed into a sequence of two types of elementary Schur complement operations: (1) local complementation on a looped vertex followed by deletion of that vertex and (2) edge complementation on an edge without looped vertices followed by deletion of that edge. We characterize the symmetric matrices over GF(2) that can be transformed into the empty matrix using only operations of (1). As a consequence, we find that these matrices can be inverted using local complementation. The result is applied to the theory of gene assembly in ciliates. [ABSTRACT FROM AUTHOR]

In a biological nervous system, astrocytes play an important role in the functioning and interaction of neurons, and astrocytes have excitatory and inhibitory influence on synapses. In this work, with this biological inspiration, a class of computation devices that consist of neurons and astrocytes is introduced, called spiking neural P systems with astrocytes (SNPA systems). The computation power of SNPA systems is investigated. It is proved that SNPA systems with simple neurons (all neurons have the same rule, one per neuron, of a very simple form) are Turing universal in both generative and acceptingmodes. If a bound is given on the number of spikes present in any neuron along a computation, then the computation power of SNPA systems is diminished. In this case, a characterization of semilinear sets of numbers is obtained. [ABSTRACT FROM AUTHOR]

In a biological system, if a long enough time interval is given, an enabled chemical reaction will finish its reaction in the given time interval. With this motivation, it is natural to impose a bound on the time interval when an enabled spiking rule in a spiking neural P system (SN P system, for short) remains unused. In this work, a new working mode of SN P systems is defined, which is called limited asynchronous mode. In an SN P system working in limited asynchronous mode, if a rule is enabled at some step, this rule is not obligatorily used. From this step on, if the unused rule may be used later, it should be used in the given time interval. If further spikes make the rule non-applicable, then the computation continues in the new circumstances. The computation result of a computation in an SN P system working in limited asynchronous mode is defined as the total number of spikes sent into the environment by the system. It is proved that limited asynchronous SN P systems with standard spiking rules are universal. If the number of spikes present in each neuron of a limited asynchronous SN P system with standard spiking rules is bounded during a computation, then the power of a limited asynchronous SN P system with standard spiking rules falls drastically, and we get a characterization of semilinear sets of numbers. [ABSTRACT FROM AUTHOR]

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: (i) its results are valid for a broad range of systems based on multiset rewriting; (ii) it allows to know the computational power of abstract computing devices without tedious proofs; (iii) it links computational power to topology and, in this way, it opens a broad range of questions. In this paper we summarise the known results on this topic and we list a few suggestions for research together with the relevance of possible outcomes. [ABSTRACT FROM AUTHOR]

The article focuses on the selection of DNA markers and primers. The authors begin by describing an algorithm designed to detect substrings that have edit distances to a fixed substring at most equal to a given error, followed by proposing an algorithm which finds the set of all substrings that have edit distances larger than errors to all others. Then, the authors provide their practical applications and implications, focusing on biological issues such as hairpins and guanine-cytosine percentage. They conclude that primers and DNA markers, which have high chance of performing well in experiments and microarrays, can be selected.

Membrane systems with carriers holding only a single passenger are known to be computationally complete, although this result does not bound the number of membranes and the number of carriers. We show that actually two membranes suffice. [ABSTRACT FROM AUTHOR]

The hierarchy of arbitrary compositions of two-way nondeterministic finite-state transductions collapses when restricted to finitary transductions, i.e., transductions that produce a finite set of outputs for each input. The hierarchy collapses to the class of nondeterministic MSO definable transductions, which is inside the second level of that hierarchy. It is decidable whether a composition of two-way nondeterministic finite-state transducers realizes a finitary transduction (i.e., is MSO definable). [ABSTRACT FROM AUTHOR]

The generative capability of several variants of P systems with symport/antiport is studied via the simulation of counter automata. This leads to the reduction of the complexity, expressed in number of membranes and weight of rules, of P systems generating recursively enumerable sets. [ABSTRACT FROM AUTHOR]

In the popular computer game of Tetris, the player is given a sequence of tetromino pieces and must pack them into a rectangular gameboard initially occupied by a given configuration of filled squares; any completely filled row of the gameboard is cleared and all filled squares above it drop by one row. We prove that in the offline version of Tetris, it is $\mathsf{NP}$-complete to maximize the number of cleared rows, maximize the number of tetrises (quadruples of rows simultaneously filled and cleared), minimize the maximum height of an occupied square, or maximize the number of pieces placed before the game ends. We furthermore show the extreme inapproximability of the first and last of these objectives to within a factor of p1-ε, when given a sequence of p pieces, and the inapproximability of the third objective to within a factor of 2-ε, for any ε>0. Our results hold under several variations on the rules of Tetris, including different models of rotation, limitations on player agility, and restricted piece sets. [ABSTRACT FROM AUTHOR]

Presents a direct universal P system based on splicing. Overview of splicing and P systems; Definition of a universal splicing system; Description of operations that can be performed by a system.

Abstract. Codings of fair sticker languages are characterized as languages accepted by blind one-counter automata. [ABSTRACT FROM AUTHOR]