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RNA-2QCFA: Evolving Two-way Quantum Finite Automata with Classical States for RNA Secondary Structures [article]

Amandeep Singh Bhatia, Shenggen Zheng
2020 arXiv   pre-print
Two-way quantum finite automata with classical states are more dominant than two-way probabilistic finite automata in language recognition.  ...  The main objective of this paper is on using two-way quantum finite automata with classical states to simulate, model and analyze the ribonucleic acid (RNA) sequences.  ...  Kondacs and Watrous [10] proposed the notion of two-way quantum finite automata i.e. quantum version of two-way deterministic finite automata.  ... 
arXiv:2007.06273v1 fatcat:4t5addogtrgrxgfa64ooykwc7e

Chain Reaction Systems Based on Loop Dissociation of DNA [chapter]

Keiichiro Takahashi, Satsuki Yaegashi, Atsushi Kameda, Masami Hagiya
2006 Lecture Notes in Computer Science  
States of some of those machines are represented by their conformations, such as hairpin and bulge loops, and state transitions are realized by conformational changes, in which such loops are opened.  ...  DNA automata A wide variety of ideas for implementing finite automata by DNA have been reported.  ...  And Benenson et al. has actually implemented finite automata using more sophisticated encoding techniques [15] .  ... 
doi:10.1007/11753681_27 fatcat:yrbqh2uwzjddzjogthyvuar6eu

Hairpin Structures in DNA Words [chapter]

Lila Kari, Stavros Konstantinidis, Elena Losseva, Petr Sosík, Gabriel Thierrin
2006 Lecture Notes in Computer Science  
We characterize maximal sets of hairpin-forming DNA sequences, as well as hairpin-free ones. We study their algebraic properties and their computational complexity.  ...  We formalize the notion of a DNA hairpin secondary structure, examining its mathematical properties.  ...  We assume that M and M 1 are finite automata in the case of regular languages, and pushdown automata in the case of context-free languages. Proposition 10.  ... 
doi:10.1007/11753681_12 fatcat:rcbqq7ctgffy7lbjbesvpr7sti

DNA Computing — Foundations and Implications [chapter]

Lila Kari, Shinnosuke Seki, Petr Sosík
2012 Handbook of Natural Computing  
WK-automata are more powerful than finite automata.  ...  ' sensing Watson-Crick finite automata [89] , and deterministic Watson-Crick automata [23] .  ... 
doi:10.1007/978-3-540-92910-9_33 fatcat:n3zmhzpj5rgsphmurdophcg234

Evolving state grammar for modeling DNA and RNA structures

Ajay Kumar, Nidhi Kalra, Sunita Garhwal
2017 International Journal of Engineering & Technology  
Another major advantage of the proposed approach is state grammar can be represented by deep pushdown automata, whereas no such automaton exists for matrix ins-del system.  ...  In this paper, we represent bio-molecular structures (Attenuator, Extended Pseudoknot Structure, Kissing Hairpin, Simple H-type structure, Recursive Pseudoknot and Three-knot Structure) using state grammar  ...  ( )) V Q V      I V R  where V is a finite set of symbols, V  is an alphabet of terminals,  is a finite language over V , R is a finite set of triple in a matrix format n n n n u v u v     ... 
doi:10.14419/ijet.v7i1.8627 fatcat:enlsf5es3ncsfkoertdc4bbrki

Page 6808 of Mathematical Reviews Vol. , Issue 2002I [page]

2002 Mathematical Reviews  
It is shown that, for w <a <w”, a-languages accepted by Biichi automata are locally finite a- languages.  ...  We also discuss a further use of hairpin molecules in DNA computing.” 2002i:68072 68Q45 68Q42 Wich, K. (D-KSSL-MI; Kassel) Exponential ambiguity of context-free grammars.  ... 

Page 3770 of Mathematical Reviews Vol. , Issue 2003e [page]

2003 Mathematical Reviews  
The paper examines a special kind of bisimulation relation for automata with binary output.  ...  Summary: “We further investigate here the hairpin languages defined in [G. Paun, G. Rozenberg and T. Yokomori, Internat. J. Found. Comput.  ... 

On Hairpin-Free Words and Languages [chapter]

Lila Kari, Stavros Konstantinidis, Petr Sosík, Gabriel Thierrin
2005 Lecture Notes in Computer Science  
We study elementary properties and finiteness of hairpin (-free) languages w.r.t. the involutions a) and c). Maximal length of hairpinfree words is also examined.  ...  Finally, descriptional complexity of maximal hairpin-free languages is determined.  ...  Problems related to the finite-ness of hairpin-free languages are addressed in Section 4.  ... 
doi:10.1007/11505877_26 fatcat:kbxk2sac3vc2tmtlpxtsjmvbd4

Grammatical inference of directed acyclic graph languages with polynomial time complexity

Antonio-Javier Gallego, Damián López, Jorge Calera-Rubio
2018 Journal of computer and system sciences (Print)  
That model takes into account the work by Potthoff et al. in [36] , where the authors present three models of finite graph automata.  ...  The simplest secondary structures that are present in RNA molecules are called hairpins or 485 hairpin loops.  ... 
doi:10.1016/j.jcss.2017.12.002 fatcat:mewnslgipzfodhmzwh5yd4p3xa

It Is NL-complete to Decide Whether a Hairpin Completion of Regular Languages Is Regular [article]

Volker Diekert, Steffen Kopecki
2011 arXiv   pre-print
The hairpin completion is an operation on formal languages which is inspired by the hairpin formation in biochemistry. Hairpin formations occur naturally within DNA-computing.  ...  This complexity bound holds for both, the one-sided and the two-sided hairpin completions.  ...  The hairpin completion H k (L 1 , L 2 ) is a finite union of regular languages and hence it is regular itself.  ... 
arXiv:1101.4824v1 fatcat:gaghkjovinehdf5igvuzaaoxky

M-ITRS: Mathematical Model for Identification of Tandem Repeats in DNA Sequence

Ajay Kumar, Sunita Garhwal
2018 IAES International Journal of Artificial Intelligence (IJ-AI)  
In this paper, we have designed deep pushdown automata for k-continuous copies of the pattern for <!  ...  [6] and Mcmurray [7] investigated the repeat of tandem repeats play a significant role in the formation of hairpin structures.  ...  Def. 1: A deep pushdown automaton [16] is a septuple ( , , , , , , ) Q s S R F  where Q is a finite set of states,  is an alphabet,  is a set of stack symbol such that    , s is a start state,  ... 
doi:10.11591/ijai.v7.i4.pp179-184 fatcat:7zpikbr2qfbn5kc5bbmitcbguu

An autonomous DNA model for finite state automata

Israel M. Martinez Perez, Karl Heinz Zimmermann, Zoya Ignatova
2009 International Journal of Bioinformatics Research and Applications  
In this paper we introduce an autonomous DNA model for finite state automata.  ...  The sticker automata model will allow (theoretically) to implement all kind of applications for finite automata at the molecular level.  ...  If we suceed, the generality of the model would allow to implement all kinds of applications for finite automata at the molecular level (at least in theory).  ... 
doi:10.1504/ijbra.2009.022465 pmid:19136366 fatcat:udohgrjbqvcpdjrlc46l3mn7um

On iterated hairpin completion

Steffen Kopecki
2011 Theoretical Computer Science  
Here we show that this is true by providing a more general result which applies to all classes of languages which are closed under finite union, intersection with regular sets, and concatenation with regular  ...  (Bounded) hairpin completion and its iterated versions are operations on formal languages which have been inspired by hairpin formation in DNA biochemistry.  ...  A common way to describe regular languages is by non-deterministic finite automata (NFAs).  ... 
doi:10.1016/j.tcs.2011.03.009 fatcat:436hewi47jcdfmfviagpy3pxeu

Foreword

Costas S. Iliopoulos, Alessio Langiu
2017 Mathematics in Computer Science  
Palindromic Subsequence Automata and Longest Common Palindromic Subsequence presents a novel weighted finite automata, which is a compact representation of all the palindromic subsequences of a string,  ...  to the Longest Common Palindromic Subsequence problem, which is generally used in predicting the secondary structure of viruses and proteins, especially in discovering binding structures such as the hairpins  ... 
doi:10.1007/s11786-017-0323-3 fatcat:fwxwq2gdvvh5zjcp62gqs3saye

On the Iterated Hairpin Completion [article]

Steffen Kopecki
2011 arXiv   pre-print
Here we show that this is true by providing a more general result which applies to all the classes of languages which are closed under finite union, intersection with regular sets, and concatenation with  ...  The (bounded) hairpin completion and its iterated versions are operations on formal lan- guages which have been inspired by the hairpin formation in DNA-biochemistry.  ...  A common way to describe regular languages are non-deterministic finite automata (NFAs).  ... 
arXiv:1010.3640v3 fatcat:bn4mhp5uw5hplc7b53fgudnuqq
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