The computational capability of chemical reaction automata

Abstract

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.

Enhancing Reaction Systems: A Process Algebraic Approach

“…The theory of Reaction Systems [9] was born in the field of Natural Computing to model the behaviour of biochemical reactions taking place in living cells. Despite its initial aim, this formalism has shown to be quite useful not only for modeling biological phenomena, but also for the contributions which is giving to computer science [15], theory of computing, mathematics, biology [2,14,1,3], and molecular chemistry [16]. Here we briefly review the basic notions of RSs, see [9] for more details.…”

“…Reaction Systems (RSs) [9] are a rewriting formalism inspired by the way biochemical reactions take place in living cells. This theory has already shown to be relevant in several different fields, such as computer science [15], biology [2,14,1,3], molecular chemistry [16]. Reaction Systems formalise the mechanisms of biochemical systems, such as facilitation and inhibition.…”

Finite Automata with Multiset Memory: A New Characterization of Chomsky Hierarchy

“…It has been shown, for instance, that reaction automata have the Turing universal computability in both application modes. (More results and developments in reaction automata theory may be found in recent articles [16], [17]. )…”

Natural Computing Paradigm b A Concise Introduction

“…In order to study the role of inhibitors of reactions in the computing power of RAs, we introduced and studied a restricted RA called Chemical Reaction Automaton (CRA) in which no inhibitor is allowed ( [6]). …”