Sticker systems and Watson-Crick automata are two modellings of DNA molecules in DNA computing. A sticker system is a computational model which is coded with single and double-stranded DNA molecules; while Watson-Crick automata is the automata counterpart of sticker system which represents the biological properties of DNA. Both of these models use the feature of Watson-Crick complementarity in DNA computing. Previously, the grammar counterpart of the Watson-Crick automata have been introduced, known as Watson-Crick grammars which are classified into three classes: Watson-Crick regular grammars, Watson-Crick linear grammars and Watson-Crick context-free grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick context-free grammar, which is a grammar counterpart of sticker systems that generates the double-stranded strings and uses rule as in context-free grammar, is introduced. The static Watson-Crick context-free grammar differs from a dynamic Watson-Crick context-free grammar in generating double-stranded strings, as well as for regular and linear grammars. The main result of the paper is to determine the generative powers of static Watson-Crick context-free grammars. Besides, the relationship of the families of languages generated by Chomsky grammars, sticker systems and Watson-Crick grammars are presented in terms of their hierarchy.
Sticker system is a computer model which is coded with single and double-stranded molecules of DNA; meanwhile, Watson-Crick automata is the automata counterpart of the sticker system representing the biological properties of DNA. Both are the modelings of DNA molecules in DNA computing which use the feature of Watson-Crick complementarity. Formerly, Watson-Crick grammars which are classified into three classes have been introduced [1]. In this research, a grammar counterpart of sticker systems that uses the rule as in context-free grammar is introduced, known as a static Watson-Crick context-free grammar. The research finding on the computational power of these grammar shows that the family of context-free languages is strictly included in the family of static Watson-Crick context-free languages; the static Watson-Crick context-free grammars can generate non context-free languages; the family of Watson-Crick context-free languages is included in the family of static Watson-Crick context-free languages which are presented in terms of their hierarchy.
DNA computing, or more generally, molecular computing, is a recent development at the interface of computer science and molecular biology. In DNA computing, many computational models have been proposed in the framework of formal language theory and automata such as Watson-Crick grammars and sticker systems. A Watson-Crick grammar is a grammar model that generates double stranded strings, whereas a sticker system is a DNA computing model of the ligation and annealing operations over DNA strands using the Watson-Crick complementarity to form a complete double stranded DNA sequence. Most of the proposed DNA computing models make use of this concept, including the Watson-Crick grammars and sticker systems. Watson-Crick grammars and their variants can be explored using formal language theory which allows the development of new concepts of Watson-Crick grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick regular grammar is introduced as an analytical counterpart of sticker systems. The computation of a sticker system starts from a given set of incomplete double stranded sequence to form a complete double stranded sequence. Here, a static Watson-Crick regular grammar differs from a dynamic Watson-Crick regular grammar in generating double stranded strings: the latter grammar produces each strand string “independently” and only check for the Watson-Crick complementarity of a generated complete double stranded string at the end, while the former grammar generates both strand strings “dependently”, i.e., checking for the Watson-Crick complementarity for each complete substring. In this paper, computational properties of static Watson-Crick regular grammars are investigated to correlate with the Chomsky hierarchy and hierarchy of the families of dynamic Watson-Crick regular languages. The relationship between families of languages generated by static Watson-Crick regular grammars with several variants of sticker systems, Watson-Crick regular grammars and Chomsky grammars are presented by showing the hierarchy.
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