On the Properties of Language Classes Defined by Bounded Reaction Automata

Reaction automata are a formal model that has been introduced to investigate the computing powers of interactive behaviors of biochemical reactions([14]). Reaction automata are language acceptors with multiset rewriting mechanism whose basic frameworks are based on reaction systems introduced in [4]. In this paper we continue the investigation of reaction automata with a focus on the formal language theoretic properties of subclasses of reaction automata, called linearbounded reaction automata (LRAs) and exponentially-bounded reaction automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by lambda-LRAs) by allowing lambda-moves in the accepting process of reaction, and investigate the closure properties of language classes accepted by both LRAs and lambda-LRAs. Further, we establish new relationships of language classes accepted by LRAs and by ERAs with the Chomsky hierarchy. The main results include the following : (i) the class of languages accepted by lambda-LRAs forms an AFL with additional closure properties, (ii) any recursively enumerable language can be expressed as a homomorphic image of a language accepted by an LRA, (iii) the class of languages accepted by ERAs coincides with the class of context-sensitive languages.Comment: 23 pages with 3 figure

Reaction Systems: a Formal Framework for Processes Based on Biochemical Interactions

This paper presents a formal framework for investigating processes driven by interactions between biochemical reactions in living cells. These interactions are based on the mechanisms of facilitation and inhibition, which underlie the definition of reaction systems - the central construct of our framework. We discuss in this paper the basic setup for reaction systems, and its motivation. We also present an important extension of reaction systems as well as some research topics and results

Towards Bridging Two Cell-Inspired Models: P Systems and R Systems

We examine, from the point of view of membrane computing, the two basic assumptions of reaction systems, the "threshold" and "no permanence" ones. In certain circumstances (e.g., defining the successful computations by local halting), the second assumption can be incorporated in a transition P system or in a symport/antiport P system without losing the universality. The case of the first postulate remains open: the reaction systems deal, deterministically, with finite sets of symbols, which is not of much interest for computing; three ways to introduce nondeterminism are suggested and left as research topics.Junta de Andalucía P08 – TIC 0420

Bridging Membrane and Reaction Systems - Further Results and Research Topics

This paper continues an investigation into bridging two research areas con- cerned with natural computing: membrane computing and reaction systems. More specif- ically, the paper considers a transfer of two assumptions/axioms of reaction systems, non- permanency and the threshold assumption, into the framework of membrane computing. It is proved that: SN P systems with non-permanency of spikes assumption charac- terize the semilinear sets of numbers, and symport/antiport P systems with threshold assumption (translated as ! multiplicity of objects) can solve SAT in polynomial time. Also, several open research problems are stated.Junta de Andalucía P08 – TIC 0420

A visual language for temporal specifications based on Spider diagrams

Spider Diagrams are a well-established visual language to specify sets, their relationships, and constraints on their cardinalities. However, they do not support evolution of specifications, where one wants to state that under certain circumstances a specification becomes invalid and a new one must be used, nor transformation of specifications, where one needs operators to manipulate specifications. In this paper, we attack the first problem by developing a new system of timed Spider Diagrams which allow modellers to indicate the temporal range of validity of a specification. The approach is illustrated with examples of policies for library management

Reaction Automata

Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their language classes are compared to the ones in the Chomsky hierarchy.Comment: 19 pages, 6 figure

Investigating dynamic causalities in reaction systems

Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Moreover, reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozenberg investigated dynamic causalities in reaction systems by introducing the idea of predictors. A predictor of a molecule s, for a given n, is the set of molecules to be observed in the environment in order to determine whether s is produced or not by the system at step n. In this paper, we continue the investigation on dynamic causalities by defining an abstract interpretation framework containing three different notions of predictor: Formula based predictors, that is a propositional logic formula that precisely characterizes environments that lead to the production of s after n steps; Multi-step based predictors, that consist of n sets of molecules to be observed in the environment, one for each step; and Set based predictors, that are those proposed by Brijder, Ehrenfeucht and Rozenberg, and consist of a unique set of molecules to be observed in all steps. For each kind of predictor we define an effective operator that allows predictors to be computed for any molecule s and number of steps n. The abstract interpretation framework allows us to compare the three notions of predictor in terms of precision, to relate the three defined operators and to compute minimal predictors. We also discuss a generalization of this approach that allows predictors to be defined independently of the value of n, and a tabling approach for the practical use of predictors on reaction systems models. As an application, we use predictors, generalization and tabling to give theoretical grounds to previously obtained results on a model of gene regulation

Reaction Systems and Synchronous Digital Circuits

A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause-effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design