Watson-Crick conjugates of words and languages (2208.03123v2)
Abstract: This paper explores the concept of Watson-Crick conjugates, also known as $\theta$-conjugates, of words and languages. This concept extends the classical idea of conjugates by incorporating the Watson-Crick complementarity of DNA sequences, from the perspective of DNA computing. Our investigation initially focuses on the properties of $\theta$-conjugates of words. We then define $\theta$-conjugates of a language and study closure properties of certain families of languages under the $\theta$-conjugate operation. Furthermore, we analyze the iterated $\theta$-conjugate of both words and languages. Finally, we delve into the idea of $\theta$-conjugate-free languages and examine the decidability problems surrounding $\theta$-conjugate-freeness for different classes of languages
- L. M. Adleman. Molecular computation of solutions to combinatorial problems. science, 266(5187):1021–1024, 1994.
- Solution of the knapsack problem by deoxyribonucleic acid computing. Japanese journal of applied physics, 37(10R):5839 – 5841, 1998.
- Introducing two low-latency cipher families: Sonic and supersonic. Cryptology ePrint Archive, 2023.
- Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing. Biosensors and Bioelectronics, 83:281–286, 2016.
- Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 296(5567):499–502, 2002.
- A. Brandstädt. Closure properties of certain families of formal languages with respect to a generalization of cyclic closure. RAIRO. Informatique théorique, 15(3):233–252, 1981.
- Pseudo-power avoidance. In Developments in Language Theory, volume 6224 of Lecture Notes in Computer Science, pages 432–433. Springer, 2010.
- On a special class of primitive words. Theoretical Computer Science, 411(3):617–630, 2010.
- Undecidability and finite automata. In Developments in Language Theory, volume 10396 of Lecture Notes in Computer Science, pages 160–172. Springer, 2017.
- Testing generalised freeness of words. In 31st International Symposium on Theoretical Aspects of Computer Science (STACS 2014), volume 25 of Leibniz International Proceedings in Informatics (LIPIcs), pages 337–349, 2014.
- Computing with DNA by operating on plasmids. Biosystems, 57(2):87–93, 2000.
- DNA computing of solutions to knapsack problems. Biosystems, 88(1-2):156–162, 2007.
- Protein output for DNA computing. Natural Computing, 4:1–10, 2005.
- I. Jeddi and L. Saiz. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. Scientific reports, 7(1):1178, 2017.
- G. Jirásková and A. Okhotin. State complexity of cyclic shift. RAIRO-Theoretical Informatics and Applications, 42(2):335–360, 2008.
- C. R. Johnson. Automating the DNA computer: solving n-variable 3-SAT problems. Natural Computing, 7:239–253, 2008.
- L. Kari and M. S. Kulkarni. Generating the pseudo-powers of a word. Journal of Automata, Languages and Combinatorics, 19(1-4):157–171, 2014.
- L. Kari and M. S. Kulkarni. Pseudo-identities and bordered words. In Discrete Mathematics and Computer Science, pages 207–222. Editura Academiei Române, Romania, 2014.
- L. Kari and M. S. Kulkarni. Disjunctivity and other properties of sets of pseudo-bordered words. Acta Informatica, 54(4):379–398, 2017.
- L. Kari and K. Mahalingam. Involutively bordered words. International Journal of Foundations of Computer Science, 18(05):1089–1106, 2007.
- L. Kari and K. Mahalingam. Watson-crick bordered words and their syntactic monoid. International Journal of Foundations of Computer Science, 19(05):1163–1179, 2008.
- L. Kari and K. Mahalingam. Watson-Crick conjugate and commutative words. In DNA Computing, volume 4848 of Lecture Notes in Computer Science, pages 273–283. Springer, 2008.
- L. Kari and K. Mahalingam. Watson-Crick palindromes in DNA computing. Natural Computing, 9(2):297–316, 2010.
- L. Kari and T. Ng. State complexity of pseudocatenation. In Language and Automata Theory and Applications, volume 11417 of Lecture Notes in Computer Science, pages 203–214. Springer, 2019.
- L. Kari and S. Seki. On pseudoknot-bordered words and their properties. Journal of Computer and System Sciences, 75(2):113–121, 2009.
- P. Linz. An introduction to formal languages and automata (5th edition). Jones & Bartlett Learning, 2012.
- M. Lothaire. Combinatorics on words. Cambridge University Press, 1997.
- The equation aM=bNcPsuperscript𝑎𝑀superscript𝑏𝑁superscript𝑐𝑃a^{M}=b^{N}c^{P}italic_a start_POSTSUPERSCRIPT italic_M end_POSTSUPERSCRIPT = italic_b start_POSTSUPERSCRIPT italic_N end_POSTSUPERSCRIPT italic_c start_POSTSUPERSCRIPT italic_P end_POSTSUPERSCRIPT in a free group. Michigan Mathematical Journal, 9:289–298, 1962.
- Counting (Watson-Crick) palindromes in Watson-Crick conjugates. Information and Computation, 285:104863, 2022.
- T. Oshiba. Closure property of the family of context-free languages under the cyclic shift operation. Electronics & communications in Japan, 55(4):119–122, 1972.
- DNA solution of the maximal clique problem. Science, 278(5337):446–449, 1997.
- E. L. Post. A variant of a recursively unsolvable problem. Bulletin of the American Mathematical Society, 52(4):264–268, 1946.
- G. Rozenberg and A. Salomaa(Eds.). Handbook of Formal Languages, volume 1. Springer, 1997.
- Molecular computation by DNA hairpin formation. Science, 288(5469):1223–1226, 2000.
- J. Shallit. A second course in formal languages and automata theory. Cambridge University Press, 2008.
- Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorganic & medicinal chemistry letters, 27(3):361–369, 2017.
- Š. Starosta. On theta-palindromic richness. Theoretical Computer Science, 412(12-14):1111–1121, 2011.
- Consistent testing for recurrent genomic aberrations. Biometrika, 102(4):783–796, 2015.
- Solving the SAT problem using a DNA computing algorithm based on ligase chain reaction. Biosystems, 91(1):117–125, 2008.
- D. Y. Zhang and G. Seelig. Dynamic DNA nanotechnology using strand-displacement reactions. Nature chemistry, 3(2):103–113, 2011.