ASM Sc. J., 13, 2020 https://doi.org/10.32802/asmscj.2020.sm26(5.1) 1-Normal Form for Static Watson-Crick Regular and Linear Grammars Aqilahfarhana Abdul Rahman1, Wan Heng Fong2*, Nor Haniza Sarmin3 and Sherzod Turaev4 1,2,3Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor, Malaysia. 4Sherzod Turaev Department of Computer Science & Software Engineering, College of Information Technology, United Arab Emirates University, Al Ain 15551, United Arab Emirates In DNA computing, there are various formal language theoretical approaches that involves the recombinant behavior of DNA sequences. A Watson-Crick automaton is a mathematical model that represents the biological properties of DNA based on the Watson-Crick complementarity of DNA molecules. Meanwhile, a sticker system is another DNA computing models which uses the sticker operation to form complete double-stranded sequences. Previously, Watson-Crick grammars have been introduced as the grammar counterparts of Watson-Crick automata which generate double-stranded strings using the Watson-Crick complementarity rules. Following that, static Watson-Crick grammars are introduced, where both stranded strings are generated dependently by checking for the WatsonCrick complementarity of each complete substring. In formal language theory, normal forms, such as Chomsky Normal Form (CNF) are defined by imposing the restrictions on the rules contained in context-free grammars. However, in previous research, 1-normal form for a Watson-Crick linear grammar was defined. In this research, 1-normal forms are introduced for both static Watson-Crick regular and linear grammars. Moreover, the implementation of 1-normal form is also presented by investigating the computational properties between the static Watson-Crick regular and linear grammars. The results from this research, hence, simplify the length of the rules in the grammars, which are useful for studying computational properties of Watson-Crick grammars. Keywords: DNA computing, formal languages, context-free grammars, static Watson-Crick grammars, normal form I. INTRODUCTION nitrogenous base. The four nitrogenous bases are adenine (A), thymine (T), guanine (G), and cytosine (C). The DNA (Deoxyribonucleic acid) computing contains various formal language theoretical approaches that broadly use the recombinant behavior of DNA sequences under the effect of enzymatic activities. DNA is a polymer which is constructed from monomers namely deoxyribonucleotides. Each deoxyribonucleotides adenine (A) and guanine (G) bases are double-ring molecules called purines; whereas the cytosine (C) and thymine (T) bases are single-ring molecules called pyrimidine (P aΜun et al., 1998). A DNA molecule is composed of two DNA strands which are held together by the hydrogen bonds between consists of three components; a sugar, a phosphate group, and a _________ *Corresponding author’s e-mail: fwh@utm.my the paired bases. There are two fundamental features of DNA molecules known as Watson-Crick (WK) ASM Science Journal, Volume 13, 2020 complementarity and massive parallelism of DNA strands. forms of context-free grammars are the Chomsky Normal WK complementarity is a base pairing where a purine Form and Greibach Normal Form (Levelt, 1974). For WK always binds with a pyrimidine, but each purine binds to grammars, Zulkufli et al. (2016) have introduced 1-normal one particular type of pyrimidine only; meanwhile, form for WK linear grammars and showed that for every massive parallelism of DNA strands allows construction of WK linear grammar, there exist an equivalent WK linear many copies of DNA strands where numerous operations grammar in 1-normal form. In this research, we are investigate the 1-normal form for each static WK regular carried out on the encoded information and linear grammars. simultaneously (P aΜun et al., 1998; Ng et al., 2007). DNA computation has been marked by Adleman This paper is organized as follows: Section 1 (1994). By using the DNA strand in his experiment, he introduces the background of the research. In Section 2, was able to solve the Hamiltonian path problem (HPP) for some preliminary concepts involve the basic terms of a simple graph with the method of sticker operation. strings, languages and grammars, sticker systems as well Then, Kari et al. (1998) proposed a mathematical model as dynamic and static WK grammars are presented. In known as a sticker system which uses the sticker Section 3, the normal forms for static WK regular and operation on DNA to form complete double-stranded linear grammars are introduced. sequences. Following that, Freund et al. (1997) proposed the Watson-Crick automata (WKA) which is one of the II. PRELIMINARIES mathematical models used in DNA computation. WKA is an extension of finite automata with the addition of two This section includes some preliminary concepts which reading heads on double-stranded sequences. involves the basic terms and definitions that are used in The grammatical studies of DNA strands started in this paper. The reader may refer to (P aΜun et al., 1998; 2012 when Subramanian et al. (2012) introduced the WK L i n z , 2 0 0 6 ) for detailed information regarding on the regular grammar, and later, modified variants for basic concepts of strings, languages, grammars and sticker different types of grammars were defined in (Zulkufli et systems. al., 2016). The research is motivated by the synthesis In this paper, the symbol ∈ denotes the membership of processes in DNA replication which can be simulated by an element to a set. Let π be an alphabet which is a derivations in the WK grammars. Although these WK nonempty finite set of abstract symbols, then π ∗ is a set of grammars use different restriction of production rules, all all strings, a finite sequence of symbols (words) over π. A of them generate double-stranded strings dynamically: string with no symbol is called the empty string and the WK complementarity can only be checked once denoted by π. The set π + is defined as the set of all generating both strands of a complete double-stranded nonempty finite strings over π, i.e., π + = π ∗ − π. string. Motivated by the WK grammars, the static WK A Chomsky grammar is defined as a quadruple πΊ = grammars are proposed as a grammar counterpart of the (π, π, π, π, π) where the alphabet π is defined as the sticker systems (Abdul Rahman et al., 2018a; 2018b). This nonterminal alphabet, π is the terminal alphabet, π ∈ π new theoretical model generates both stranded strings is the axiom or the start symbol, and π ⊆ (π ∪ π)∗ π(π ∪ dependently by checking for WK complementarity of each π)∗ is a set of production rules of πΊ. The rules (π₯, π¦) ∈ π complete substring and also illustrate the replication of are written in the form of π₯ → π¦. We say that π’ directly DNA in DNA molecules. derives π£ or π£ is derived from π’ with respect to πΊ, which is Next, a normal form is defined by imposing the written as π’ ⇒ π£, if and only if π’ = π’1 π₯π’2 , π£ = π’1 π¦π’2 , for restrictions of the rules contained in the grammar. In some π’1 , π’2 ∈ (π ∪ π)∗ and π₯ → π¦ ∈ π. The reflexive and Chomsky grammars, the normal forms are implemented for context-free grammars and transitive closure of ⇒ is denoted by ⇒∗ . context-sensitive A grammar can normally generate many strings by grammars (Ito et al., 2010). The most important normal applying the rules in arbitrary order. The set of all 2 ASM Science Journal, Volume 13, 2020 terminal strings is the language generated by the grammar πΏπ (π) = (( which is defined by πΏ(πΊ) = {π€ ∈ π ∗ : π ⇒∗ π€}. π ∗ π π∗ π π (π) = [ ] (( ∗ ) ∪ ( )), ππ π π The Chomsky grammars are classified depending on their respective form of production rules. A grammar πΊ = (π, π, π, π, π) is called context-sensitive, if each rule π’ → πΏπ π (π) = (( π£ ∈ π has π’ = π’1 π΄π’2 , π£ = π’1 π₯π’2 for π’1 , π’2 ∈ (π ∪ π)∗ , π΄ ∈ according to our grammar, where has π’ ∈ π; linear, if each rule π’ → π£ ∈ π has π’ ∈ π and π£ ∈ πΏπ π∗ (π) = (( π ∗ ∪ π ∗ ππ ∗ ; regular, if each rule π’ → π£ ∈ π has π’ ∈ π and π£ ∈ π ∪ ππ ∪ {π} (P aΜun et al., 1998). πΏπ π+ (π) = (( All those families of languages generated by contextsensitive, context-free, linear and regular grammars are π∗ π π∗ π π∗ ∗ ) ∪ ( )) [π ] (( ∗ ) ∪ ( )), π π π π π π+ π π∗ π π∗ ) ∪ ( )) [ ] (( ∗ ) ∪ ( )), ππ π π∗ π π and the alphabet π which is defined in ππ (π) is changed to denoted as CS, CF, LIN and REG respectively. Other alphabet π according to the definition in the Chomsky than that, RE and FIN represent the family of recursive grammar. enumerable languages, i.e., arbitrary languages and finite Next, we recall the definition of static WK regular languages. grammar and static WK linear grammar. Since static WK Further, we recall the definitions of Watson-Crick regular grammar consists of right-linear and left-linear grammars: grammar, then we state only for right-linear grammar (Rahman et al., 2018a) in this paper. Definition 1. (Zulkufli et al., 2016) A Watson-Crick (WK) grammar πΊ = (π, π, π, π, π) is called Definition 2. (Rahman et al., 2018a) regular, if each production has the form π΄ → 〈π’/π£〉 where A static Watson-Crick right-linear grammar is a 5-tuple π΄, π΅ ∈ π and 〈π’/π£〉 ∈ 〈π ∗ /π ∗ 〉; linear, if each production πΊ = (π, π, π, π, π) where π, π are disjoint nonterminal and has the form π΄ → 〈π’1 /π£1 〉π΅〈π’2 /π£2 〉 or π΄ → 〈π’/π£〉 where and 〈π’/π£〉, 〈π’1 /π£1 〉, 〈π’2 /π£2 〉 ∈ 〈π ∗ /π ∗ 〉; terminal alphabets respectively, π ∈ π × π is a symmetric context- relation (Watson-Crick complementarity), π ∈ π is a start free, if each production has the form π΄ → πΌ where π΄ ∈ π symbol (axiom) and π is a finite set of production rules in and πΌ ∈ (π ∪ 〈π ∗ /π ∗ 〉)∗ . the form of π’ π₯ π’ π₯ (i) π → [ ] (π¦) π΄ where π΄ ∈ π − {π}, [ ] (π¦) ∈ π π (π); π£ π£ π₯ π₯ (ii) π΄ → (π¦) π΅ where π΄, π΅ ∈ π − {π}, (π¦) ∈ πΏπ π ∗ (π); or In order to generate or form a complete doublestranded sequence of DNA, the sticker system uses a sticker π + π π∗ π π∗ ∗ ) ∪ ( )) [π ] (( ∗ ) ∪ ( )). π π π π π In this research, the definition of πΏπ π (π) is modified π and π₯ ∈ (π ∪ π)+ ; context-free, if each rule π’ → π£ ∈ π π΄, π΅ ∈ π π ∗ π π∗ ∗ ) ∪ ( )) [π ] , π π π operation on DNA molecules (P aΜun and π₯ π’ π₯ π’ (iii) π΄ → (π¦) [ ] where π΄ ∈ π − {π}, (π¦) [ ] ∈ πΏπ (π). π£ π£ Rozenberg, 1998). Let π be an alphabet for a symmetric π ∗ relation π ∈ π × π over π. The set ππΎπ (π) = [ ] where ππ Definition 3. (Rahman et al., 2018b) π π π [ ] = {[ ] | π, π ∈ π, ( ) ∈ π} denotes the Watson-Crick π π ππ A static Watson-Crick linear grammar is a 5-tuple πΊ = (π, π, π, π, π) where π, π are disjoint nonterminal and domain associated to alphabet π and the complementarity terminal alphabets respectively, π ∈ π × π is a symmetric π€1 relation π. The elements [π€ ] ∈ ππΎπ (π) are called well2 relation (Watson-Crick complementarity), π ∈ π is a start formed double-stranded sequences. The strings π€1 is the symbol (axiom) and π is a finite set of production rules in upper strand and π€2 is the lower strand of the molecule. the form of π₯2 π’2 π’1 π₯1 (i) π → [π£ ] (π¦ ) π΄ (π¦ ) [π£ ] Apart from that, the set of incomplete molecules are 1 denoted as ππ (π) = πΏπ (π) ∪ π (π) ∪ πΏπ π (π), where 1 2 2 where π₯2 π’2 π’1 π₯1 [π£ ] (π¦ ) ∈ π π (π), (π¦ ) [π£ ] ∈ πΏπ (π); 1 2 1 2 3 π΄ ∈ π − {π}, ASM Science Journal, Volume 13, 2020 π₯1 π₯2 π₯1 π₯2 (ii) π΄ → (π¦ ) π΅ (π¦ ) where π΄, π΅ ∈ π − {π}, (π¦ ) , (π¦ ) ∈ 1 2 1 2 π₯ π’ π₯ π’ (iii) π3 = {π΄ → (π¦) [ ] ∈ π | (π¦) [ ] ∈ πΏπ (π), π΄ ∈ π − π£ π£ πΏπ π ∗ (π); or {π}}; π₯1 π₯1 (iii) π΄ → (π¦ ) where π΄ ∈ π − {π}, (π¦ ) ∈ πΏπ π ∗ (π). 1 1 i.e., π = π1 ∪ π2 ∪ π3 . Without loss of generality, consider Next, the 1-normal form for static WK regular and π₯ π₯ π π β― ππ ) π: π΄ → (π¦) π΅ where (π¦) = ( 1 2 π linear grammars are discussed in the following section. π π β― ππ π [ 1 2 ]( ). We construct the sequence of π1 π2 β― ππ π1 π2 β― ππ III. RESULTS AND DISCUSSIONS new The normal form represents the standardized form for the production rules in the grammars. Therefore in this section, we define a 1-normal form for static WK regular grammar as stated ππ π π ) π΅ π , π΅π π → [ 1 ] πΆπ 1 , β― , πΆπ π−1 → [ π ] πΆπ π , πΆπ π → π1 ππ π π ( π π1 ) π·π 1 , β― , π·π π−1 → ( π ) π΅ where π΅π π , πΆπ π and π·π π are π π (π′, π, π, π, π′) where π′ contains the nonterminals of π 1, |π£π | ≤ 1. The following s h o w s a 1 - n o r m a l f o r m f or regular ( Next, we define a static WK regular grammar πΊ′ = lower strand is less than or equal to one, such that |π’π | ≤ WK π {π}: π΄ → ( 1 ) π΅π 1 , β― , π΅π π−1 → π new nonterminals that are only used in the rule π. and linear grammars where the order of each upper and st a t i c productions and all new nonterminals introduced above and π′ in contains the productions constructed above. Hence, every Definition 4 and Lemma 1. production π in π can be replaced with the corresponding Definition 4. sequence {π} of productions in π′ and vice versa. A static WK regular grammar πΊ = Therefore, πΏ(πΊ) = πΏ(πΊ ′ ). (π, π, π, π, π) is said to be in 1-normal form if each Next, the following definition and lemma of 1- production in π has one of the following forms: normal form for static WK linear grammars are given. π π (i) π΄ → ( ) π΅ | ( ), π π π π (ii) π΄ → ( ) π΅ | ( ), π π Definition 5. A static WK linear grammar πΊ = (π, π, π, π, π) is said to be in 1-normal form if each π π (iii) π΄ → ( ) π΅ | ( ), π π π π (iv) π΄ → [ ] π΅ | [ ], π π production in π has one of the following forms: π π π (i) π΄ → ( ) π΅ | π΅ ( ) | ( ), π π π where π΄, π΅ ∈ π and (π, π) ∈ π. π π π (ii) π΄ → ( ) π΅ | π΅ ( ) | ( ), π π π π π π (iii) π΄ → ( ) π΅ | π΅ ( ) | ( ), π π π π π π (iv) π΄ → [ ] π΅ | π΅ [ ] | [ ], π π π Lemma 1. For every static WK regular grammar, there exists a static WK regular grammar in 1-normal form. Proof. β Let πΊ = (π, π, π, π, π) be a static WK regular where π΄, π΅ ∈ π and (π, π) ∈ π. grammar. By definition, π can be divided into three subsets: Lemma 2. For every static WK linear grammar, there π’ π₯ π’ π₯ (i) π1 = {π → [ ] (π¦) π΄ ∈ π | [ ] (π¦) ∈ π π (π), π΄ ∈ π£ π£ exists a static WK linear grammar in 1-normal form. Proof. π − {π}}; Let πΊ = (π, π, π, π, π) be a static WK linear grammar. By definition, π can be divided into three π₯ π₯ (ii) π2 = {π΄ → (π¦) π΅ ∈ π | (π¦) ∈ πΏπ π ∗ (π), π΄, π΅ ∈ π − subsets: π₯2 π’2 π’1 π₯1 π’1 π₯1 (i) π1 = {π → [π£ ] (π¦ ) π΄ (π¦ ) [π£ ] ∈ π | [π£ ] (π¦ ) ∈ 1 2 1 1 2 1 {π}}; or π₯2 π’2 π π (π), (π¦ ) [π£ ] ∈ πΏπ (π) and π΄ ∈ π − {π}}; 2 4 2 ASM Science Journal, Volume 13, 2020 grammar, where π consists of the following rules: π₯1 π₯2 π₯1 π₯2 (ii) π2 = {π΄ → (π¦ ) π΅ (π¦ ) ∈ π | (π¦ ) , (π¦ ) ∈ 1 2 1 2 π π π → [ ]π΄[ ] π π ∗ πΏπ π (π), π΄, π΅ ∈ π − {π}}; or π = π1 ∪ π2 ∪ π3 . π·→ Without loss of π+1 π π ππ π ππ π π ⇒ [ ] π΄ [ ] ⇒∗ [ ] ( ) π΅ ( ) [ ] ⇒∗ [ππ+1 ] π π π π π π π generality, π+1 π+1 π π π+1 ππ πΆ [ππ+1 ] ⇒∗ [ππ+1 ] ( ) πΆ ( ) [ππ+1 ] ⇒∗ π π π π π 1 1 2 2 π+1 π π π+1 π+1 π π π+1 [ππ+1 π π ] πΈ [π π ππ+1 ] ⇒ [ππ+1 π π π π ππ+1 ]. π π π π π π π π π1 π2 β― ππ π π β― ππ π π β― ππ π1 π2 β― ππ )π΄( 1 2 )[ [π π β― π ] ( 1 2 ]. π π1 π2 β― ππ 1 2 π π Therefore, πΏ(πΊ) = {ππ π π π π ππ | π, π ≥ 1}. We construct the sequence of new productions Next, we need to show that πΏ(πΊ) = {ππ π π π π ππ | π, π ≥ π π {π}: π → [π1 ] π΅π 1 , π΅π 1 → [π2 ] π΅π 2 , β―, 1 2 1} ∉ SREG. By contradiction, suppose that πΏ(πΊ) can be ππ π → [π ] π΅π π , π΅π π → ( 1 ) πΆπ 1 , πΆπ 1 → π π generated by a static WK regular grammar πΊ′ = (π′, {π, π, π, π}, π, π, π′). Without loss of generality, assume π π π ( 2 ) πΆπ 2 , β― , πΆπ π−1 → ( π ) πΆπ π , πΆπ π → π·π 1 [ π ] , β― , ππ π π π·π π−1 → π·π π [ π΅→ From this, we obtain the derivation: π₯2 π’2 π’1 π₯1 consider π: π → [π£ ] (π¦ ) π΄ (π¦ ) [π£ ] = π΅π , π π π π π ( )π·( ) | ( )πΈ( ) , πΈ → ( ) . π π π π π {π}}; π−1 π π π π π΄ → ( )π΄( )|( )π΅( ) π π π π π π π π π π π π ( )π΅( )|( )πΆ ( ) , πΆ → ( )πΆ ( )|( )π·( ) , π π π π π π π π π₯1 π₯1 (iii) π3 = {π΄ → (π¦ ) ∈ π | (π¦ ) ∈ πΏπ π ∗ (π), π΄ ∈ π − 1 1 i.e., , that πΊ′ is in 1-normal form. Let π€ = π π π π π π π π be a string π π π1 ] , π·π π → π΄π 1 ( π ) , β― , π΄π π−1 → π΄ ( 1 ) π π π1 in πΏ(πΊ). Then, the grammar πΊ′ can generate the complete where π΄π π , π΅π π , πΆπ π and π·π π are new nonterminals that are π π π π sequences [π π π π π π π π ] as follows: π π π π used in this production with 1 ≤ π ≤ π − 1, 1 ≤ π ≤ π, 1 ≤ Case 1: In the derivation of the string, the first π can π ≤ π and 1 ≤ π ≤ π. occur in the upper (or lower) strand if π π has already been Next, we define a static WK linear grammar πΊ′ = generated in the upper (or lower) strand. Then, some of (π′, π, π, π, π′) where π′ contains the nonterminals of π the possible derivations are: and all new nonterminals introduced above and π′ contains the productions constituted above. Hence, every production π in π can be replaced with the corresponding sequence {π} of productions in π′ and vice versa. ′ Therefore, πΏ(πΊ) = πΏ(πΊ ). π ππ π π ⇒∗ [ππ ] ( ) ( ); or π π π (5) π π π π ⇒∗ [π π ] ( ) or π ⇒∗ [π π π] , π π π π (6) where π + π = π. For derivation (5), we can β continue the derivation by using the lower strand of π and upper strand of π to generate the upper strand of π π : To further investigate on the computational properties π π π ππ π π ⇒∗ [ππ ] ( ) ( ) ⇒∗ [π π ] (π ). π π π π π between the static WK regular and linear grammars, the (7) next lemma shows that there exist a static WK linear Following that, derivation (7) is continued by generating language which cannot be generated by static WK regular the first π in the upper strand and use the lower strand of grammar. π to control their number of occurrences: We consider a language πΏ(πΊ) = π π π π π π ⇒∗ [π π ] (π ) ⇒∗ [π π π π ] (π ). π π π π π {π π π π π π ππ | π, π ≥ 1} where the idea of 1-normal form is used to simplify the length of the rules in the grammars as Next, derivation (8) is continued by generating the first π shown in Lemma 3. Lemma 3. in the upper strand and use the strand of π to control their number of occurrences: πΏ(πΊ) = {ππ π π π π ππ | π, π ≥ 1} ∈ SLIN− π π π π π π π π ⇒∗ [π π π π ] (π ) ⇒∗ [π π π π π π ] (π ). π π π π π π π SREG. Proof. (8) Let (9) The derivation can be completed by generating the lower πΊ = ({π, π΄, π΅, πΆ, π·, πΈ}, {π, π, π, π}, {(π, π), (π, π), (π, π), (π, π)}, π, π) be a static WK linear 5 ASM Science Journal, Volume 13, 2020 π π π π strand of π. Thus, [π π π π π π π π ] where π ≠ π. For derivation π π π π (6), we can continue the derivation by using the same idea as in (5) and get the possible derivation as in (7) until (9). Case 2: The number of π in the lower strand is controlled by the upper strand of π. In this case, the number of π′s cannot be related to the number of π such π π π that π ⇒∗ [π π ] (π π ). Thus, we can conclude that πΏ(πΊ) ∉ π π SREG since the number of π, π and π are difficult to control at the same time using SREG rules. IV. CONCLUSION In this paper, the 1-normal form for static WK regular and linear grammars are defined. We show that for each grammar, there exists the equivalent grammars by using the concept of 1-normal form. In addition, the implementation of 1-normal form has been shown in Lemma 3 to investigate the computational properties between the static WK regular and linear grammars. It has been found that there exist a static WK linear language which cannot be generated by static WK regular grammar. There are some interesting topic that can be explored in the future research such as to study the computational properties for the static WK grammars, define static WK context-free grammar and introduce the normal forms for static WK context-free grammar. V. ACKNOWLEDGEMENT The first author would like to thank UTM Zamalah for funding her studies at Universiti Teknologi Malaysia (UTM) under the Zamalah Scholarship. The second and third authors would also like to thank the Ministry of Education (MOE) and Research Management Centre (RMC), UTM for the financial funding through Fundamental Research Grant Scheme (FRGS) Vote No. 5F022. 6 ASM Science Journal, Volume 13, 2020 VI. REFERENCES Linz, P. (2006). An introduction to formal languages and Adleman, L. M. (1994). Molecular computation of solutions automata, Jones and Bartlett Publishers, USA. to combinatorial problems. Science, 266 (5187), 10211024. P aΜun, G. & Rozenberg, G. (1998). Sticker systems. Theoretical Computer Science, 204, 183-203. Freund, R., P aΜun, G., Rozenberg, G. & Salomaa, A. (1997). Watson-Crick finite automata. Proceeding 3rd DIMACS P aΜun, G., Rozenberg, G. & Salomaa, A. (1998). DNA Workshop on DNA based Computers, Philadelphia, 297- computing: new computing paradigms. Springer-Verlag 328. & Business Media. Hg, W. D. & Wong, C. K. B. (2007). Self-Recognition of DNA Rahman, A. A., Fong, W. H., Sarmin, N. 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