Comparing reactions in reaction systems

Originally, reaction systems were introduced to describe in a formal way the interactions between biochemical reactions taking place in living cells. They are also investigated as an abstract model of interactive computation. A reaction system is determined by a finite background set of entities and a finite set of reactions. Each reaction specifies the entities that it needs to be able to occur, the entities which block its execution, and the entities that it produces if it occurs. Based on the entities available in a state of the system, all reactions of the system that are enabled take place and together produce the entities that form the next state. In this paper we compare reactions in terms of their enabledness and results. We investigate three partial orders on reactions that build on two definitions of equivalence of (sets of) reactions. It is demonstrated how each partial order defines a lattice (with greatest lower bounds and least upper bounds) for all nontrivial reactions. Together, these orders provide an insight in possible redundancies and (re)combinations of the reactions of a reaction system. (C) 2020 Elsevier B.V. All rights reserved.Algorithms and the Foundations of Software technolog

XML navigation and transformation by tree-walking automata and transducers with visible and invisible pebbles

Algorithms and the Foundations of Software technolog

A graph isomorphism condition and equivalence of reaction systems

Algorithms and the Foundations of Software technolog

Topologies Refining the Cantor Topology on X ω

International audienceThe space of one-sided infinite words plays a crucial rôle in several parts of Theoretical Computer Science. Usually, it is convenient to regard this space as a metric space, the Cantor-space. It turned out that for several purposes topologies other than the one of the Cantor-space are useful, e.g. for studying fragments of first-order logic over infinite words or for a topological characterisation of random infinite words. It is shown that both of these topologies refine the topology of the Cantor-space. Moreover, from common features of these topologies we extract properties which characterise a large class of topologies. It turns out that, for this general class of topologies, the corresponding closure and interior operators respect the shift operations and also, to some respect, the definability of sets of infinite words by finite automata

DNA Computing - molecular computation

Introduction. Within Computer Science the field of Natural Computation studies computational techniques inspired by natural phenomena. A wellknown example of such a technique is evolutionary computation (genetic algorithms) where properties of objects are coded using a sequence of bits (their `genetic information'), and the most suitable object emerges from a pool of candidates by a process similar to natural selection. Note that evolutionary computation is usually performed on classical `silicon' computers. With DNA computing one intends to turn the table by proposing strands of DNA as hardware, and not only as a programming paradigm. These strands are to be manipulated by biological and biotechnological methods. On the one hand nature has provided us with a large box of enzymes designed to perform specific operations on DNA, on the other hand biotechnological research leads to new and powerful lab techniques useful for genetic manipulations.

Enforcing Regular Languages

Algorithms and the Foundations of Software technolog

Enforcing Regular Languages

Algorithms and the Foundations of Software technolog

XML navigation and transformation by tree-walking automata and transducers with visible and invisible pebbles

The pebble tree automaton and the pebble tree transducer are enhanced by additionally allowing an unbounded number of "invisible" pebbles (as opposed to the usual "visible" ones). The resulting pebble tree automata recognize the regular tree languages (i.e., can validate all generalized DTD's) and hence can find all matches of MSO definable patterns. Moreover, when viewed as a navigational device, they lead to an XPath-like formalism that has a path expression for every MSO definable binary pattern. The resulting pebble tree transducers can apply arbitrary MSO definable tests to (the observable part of) their configurations, they (still) have a decidable typechecking problem, and they can model the recursion mechanism of XSLT. The time complexity of the typechecking problem for conjunctive queries that use MSO definable patterns can often be reduced through the use of invisible pebbles.Algorithms and the Foundations of Software technolog

Extracting reaction systems from function behavior

Reaction systems, introduced by Ehrenfeucht and Rozenberg, are a theoretical model of computation based on the two main features of biochemical reactions: facilitation and inhibition, which are captured by the individual reactions of the system. All reactions, acting together, determine the global behavior or the result function, res, of the system. In this paper, we study decomposing of a given result function to find a functionally equivalent set of reactions. We propose several approaches, based on identifying reaction systems with Boolean functions, Boolean formulas, and logic circuits. We show how to minimize the number of reactions and their resources for each single output individually, as a group, and when only a subset of the states are considered. These approaches work both when the reactions of the given res function are known and not known. We characterize the minimal number of reactions through the minimal number of logical terms of the Boolean formula representation of the reaction system. Finally, we make applications recommendations for our findings

Combinatorial properties of dependence graphs

Algorithms and the Foundations of Software technolog