Reaction Automata Research Articles

The computational capability of chemical reaction automata

We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant of reaction automata (RAs) studied in recent literature (Okubo in RAIRO Theor Inform Appl 48:23---38 2014; Okubo et al. in Theor Comput Sci 429:247---257 2012a, Theor Comput Sci 454:206---221 2012b). We show that CRAs in maximally parallel manner are computationally equivalent to Turing machines, while the computational power of CRAs in sequential manner coincides with that of the class of Petri nets, which is in marked contrast to the result that RAs (in both maximally parallel and sequential manners) have the computing power of Turing universality (Okubo 2014; Okubo et al. 2012a). Intuitively, CRAs are defined as RAs without inhibitor functioning in each reaction, providing an offline model of computing by chemical reaction networks (CRNs). Thus, the main results in this paper not only strengthen the previous result on Turing computability of RAs but also clarify the computing powers of inhibitors in RA computation.

Reaction automata working in sequential manner

Based on the formal framework of reaction systems by Ehrenfeucht and Rozenberg [Fund. Inform. 75 (2007) 263–280], reaction automata (RAs) have been introduced by Okubo et al. [Theoret. Comput. Sci. 429 (2012) 247–257], as language acceptors with multiset rewriting mechanism. In this paper, we continue the investigation of RAs with a focus on the two manners of rule application: maximally parallel and sequential. Considering restrictions on the workspace and the λ-input mode, we introduce the corresponding variants of RAs and investigate their computation powers. In order to explore Turing machines (TMs) that correspond to RAs, we also introduce a new variant of TMs with restricted workspace, called s(n)-restricted TMs. The main results include the following: (i) for a language L and a function s(n), L is accepted by an s(n)-bounded RA with λ-input mode in sequential manner if and only if L is accepted by a log s(n)-bounded one-way TM; (ii) if a language L is accepted by a linear-bounded RA in sequential manner, then L is also accepted by a P automaton [Csuhaj−Varju and Vaszil, vol. 2597 of Lect. Notes Comput. Sci. Springer (2003) 219–233.] in sequential manner; (iii) the class of languages accepted by linear-bounded RAs in maximally parallel manner is incomparable to the class of languages accepted by RAs in sequential manner.

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 (Okubo et al. (2012) [19]). Reaction automata are language acceptors with multiset rewriting mechanism whose basic frameworks are based on reaction systems introduced in Ehrenfeucht and Rozenberg (2007) [8].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 linear-bounded reaction automata (LRAs) and exponentially-bounded reaction automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by λ-LRAs) by allowing λ-moves in the accepting process of reaction, and investigate the closure properties of language classes accepted by both LRAs and λ-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 λ-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.

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.