scholarly journals Static Watson-Crick regular grammar

2018 ◽  
Vol 14 ◽  
pp. 457-462
Author(s):  
Aqilahfarhana Abdul Rahman ◽  
Wan Heng Fong ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev ◽  
Nurul Liyana Mohamad Zulkufli
Keyword(s):  
Dna Computing ◽  
Formal Language ◽  
Computational Models ◽  
Formal Language Theory ◽  
Language Theory ◽  
Chomsky Hierarchy ◽  
New Variant ◽  
Sticker System ◽  
Dna Strands ◽  
Regular Grammar

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.

scholarly journals Static Watson-Crick Linear Grammars and Its Computational Power

MATEMATIKA ◽  
2019 ◽  
Vol 35 (3) ◽  
Author(s):  
Aqilahfarhana Abdul Rahman ◽  
Fong Wan Heng ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev ◽  
Nurul Liyana Mohamad Zulkufli
Keyword(s):  
Formal Language ◽  
Computational Models ◽  
Biological Molecules ◽  
Dna Molecules ◽  
Silicon Chips ◽  
New Variant ◽  
Sticker System ◽  
Regular Grammar ◽  
Context Free ◽  
Computational Properties

DNA computing, or more generally, molecular computing, is a recent development on computations using biological molecules, instead of the traditional silicon-chips. Some computational models which are based on different operations of DNA molecules have been developed by using the concept of formal language theory. The operations of DNA molecules inspire various types of formal language tools which include sticker systems, grammars and automata. Recently, the grammar counterparts of Watson-Crick automata known as Watson-Crick grammars which consist of regular, linear and context-free grammars, are defined as grammar models that generate double-stranded strings using the important feature of Watson-Crick complementarity rule. In this research, a new variant of static Watson-Crick linear grammar is introduced as an extension of static Watson-Crick regular grammar. A static Watson-Crick linear grammar is a grammar counterpart of sticker system that generates the double-stranded strings and uses rule as in linear grammar. The main result of the paper is to determine some computational properties of static Watson-Crick linear grammars. Next, the hierarchy between static Watson-Crick languages, Watson-Crick languages, Chomsky languages and families of languages generated by sticker systems are presented.

scholarly journals On Special forms of Splicing on Arrays and Graphs

Triangle ◽  
2018 ◽  
pp. 119
Author(s):  
K. G. Subramanian ◽  
A. Roslin Sagaya Mary ◽  
P. Helen Chandra
Keyword(s):  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Great Depth ◽  
Formal Language Theory ◽  
Language Theory ◽  
Dna Molecules ◽  
Higher Dimensional ◽  
Theoretical Results ◽  
Theory Extension

Tom Head (1987), in his pioneering work on formal language theory applied to DNA computing, introduced a new operation of splicing on strings, while proposing a model of certain recombination behaviour of DNA molecules under the action of restriction enzymes and ligases. Since then this operation has been studied in great depth giving rise to a number of theoretical results of great interest in formal language theory. Extension of this operation of splicing to higher dimensional structures such as circular words, arrays, trees and graphs have been proposed in the literature. Here we examine the effect of certain specific forms of the splicing operation applied to arrays and graphs.

scholarly journals Phonological typology in Optimality Theory and Formal Language Theory: goals and future directions

Phonology ◽  
2019 ◽  
Vol 36 (2) ◽  
pp. 351-353
Author(s):  
Joe Pater
Keyword(s):  
Recent Work ◽  
Optimality Theory ◽  
Formal Language ◽  
Regular Languages ◽  
Formal Language Theory ◽  
Language Theory ◽  
Future Directions ◽  
Chomsky Hierarchy ◽  
Phonological Typology

Much recent work has studied phonological typology in terms of Formal Language Theory (e.g. the Chomsky hierarchy). This paper considers whether Optimality Theory grammars might be constrained to generate only regular languages, and also whether the tools of formal language theory might be used for constructing phonological theories similar to those within Optimality Theory. It offers reasons to be optimistic about the first possibility, and sceptical about the second.

scholarly journals A Note on Weak vs. Strong Generation in Human Language

2015 ◽  
Vol 36 (2) ◽  
pp. 59-68 ◽  
Author(s):  
Naoki Fukui
Keyword(s):  
Formal Language ◽  
Formal Language Theory ◽  
Language Theory ◽  
Human Language ◽  
Language Faculty ◽  
Brain Science ◽  
Chomsky Hierarchy ◽  
Human Language Faculty

Abstract This paper argues that various important results of formal language theory (e.g., the so-called Chomsky Hierarchy) may in fact be illusory as far as the human language faculty is concerned, as has been repeatedly emphasized by Chomsky himself. The paper takes up nested dependencies and cross-serial dependencies, the two important dependencies that typically show up in the discussion of the central classes of grammars and languages, and specifically shows that the fact that nested dependencies abound in human language while cross-serial dependencies are rather limited in human language can be naturally explained if we shift our attention from dependencies defined on terminal strings to abstract structures behind them. The paper then shows that nested dependencies are readily obtained by Merge, applying phase-by-phase, whereas cross-serial dependencies are available only as a result of copying Merge, which requires a constituency of the relevant strings. These results strongly suggest that dependencies are possible in human language only to the extent that they are the results from the structures that can be generated by Merge, leading to the conclusion that it is Merge-generability that determines various dependencies in human language, and that dependencies defined on the terminal strings are indeed illusory. A possible brain science experiment to demonstrate this point is also suggested.

THE DEVELOPMENT OF FORMAL LANGUAGE THEORY SINCE 1956

1990 ◽  
Vol 01 (04) ◽  
pp. 355-368
Author(s):  
ROBERT McNAUGHTON
Keyword(s):  
Formal Language ◽  
Formal Languages ◽  
Early Years ◽  
Formal Language Theory ◽  
Language Theory ◽  
Personal Interest

This brief survey will discuss the early years of the theory of formal languages through about 1970, treating only the most fundamental of the concepts. The paper will conclude with a brief discussion of a small number of topics, the choice reflecting only the personal interest of the author.

scholarly journals Static Watson-Crick Context-Free Grammars

2019 ◽  
Vol 15 (10) ◽  
pp. 65 ◽  
Author(s):  
Wan Heng Fong ◽  
Aqilahfarhana Abdul Rahman ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev
Keyword(s):  
Dna Computing ◽  
Biological Properties ◽  
Dna Molecules ◽  
Context Free Grammar ◽  
Double Stranded Dna ◽  
New Variant ◽  
Sticker System ◽  
Relationship Of ◽  
Context Free ◽  
Context Free Grammars

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.

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