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Languages of Watson-Crick Petri Net

Nurhidaya Mohamad Jan, Fong Wan Heng, Nor Haniza Sarmin, Sherzod Turaev
2014 Jurnal Teknologi  
This automata work on double stranded sequences related by a complementarity relation similar with the Watson-Crick complementarity of DNA molecules.  ...  Watson-Crick automata can be related to a Petri net, which is a graphical and mathematical formalism suitable for the modeling and analysis of concurrent, asynchronous and distributed systems.  ...  The second and third authors also would like to thank the Ministry of Education (MOE) and Research Management Centre (RMC), UTM for the financial funding through Research University Fund Vote No. 07J41  ... 
doi:10.11113/jt.v70.3521 fatcat:d5alfi2dqzeenjxo4ls2i72rti

Biomolecular Implementation of Computing Devices with Unbounded Memory [chapter]

Matteo Cavaliere, Nataša Jonoska, Sivan Yogev, Ron Piran, Ehud Keinan, Nadrian C. Seeman
2005 Lecture Notes in Computer Science  
In particular, we show a procedure to implement automata with unbounded stack memory, push-down automata, using circular DNA molecules and a class IIs restriction enzyme.  ...  The same ideas are extended to show a way to implement push-down automata with two stacks (i.e, universal computing devices) using two circular molecules glued with a DX molecule and a class IIs restriction  ...  The first author is supported by a grant from the Spanish Ministry of Culture, Education and Sport under the Programa Nacional de Formación de Profesorado Universitario (FPU).  ... 
doi:10.1007/11493785_4 fatcat:iktbzimnxbc4xdlpfjrn74nyli

Mathematical Modelling of Some Null-Context and Uniform Splicing Systems

S. J. Lim, W. H. Fong, N. H. Sarmin, F. Karimi
2014 Malaysian Journal of Fundamental and Applied Sciences  
Applications of automata theory on some molecular examples of null-context and uniform splicing languages will also be presented in this paper.  ...  Splicing of DNA involves cutting of DNA molecules using the restriction enzymes and re-associating different fragments of DNA molecules using the ligase under some specific chemical conditions.  ...  ACKNOWLEDGEMENTS We would like to thank The Ministry of Education (MOHE) and the Research Management Centre (RMC), UTM for the financial funding through Research University Fund Vote No. 02J65.  ... 
doi:10.11113/mjfas.v7n2.254 fatcat:kzvrpihhevddvnmgxpbyfap5fe

Computational Power of Static Watson-Crick Context-free Grammars

Wan Heng Fong, Aqilahfarhana Abdul Rahman, Nor Haniza Sarmin, Sherzod Turaev
2019 Science Proceedings Series  
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  ...  Both are the modelings of DNA molecules in DNA computing which use the feature of Watson-Crick complementarity.  ...  R E S E A R C H H I G H L I G H T S 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 sticker  ... 
doi:10.31580/sps.v1i2.679 fatcat:2ft22npmtjftnhnposr2extzuy

Autonomous push-down automaton built on DNA [article]

Tadeusz Krasinski, Sebastian Sakowski, Tomasz Poplawski
2011 arXiv   pre-print
In this paper we propose a biomolecular implementation of the push-down automaton (one of theoretical models of computing device with unbounded memory) using DNA molecules.  ...  His interests are in analytic and algebraic geometry and recently in automata theory, formal languages and DNA computing. S.  ...  His current interests are in DNA computing, computational biology, automata theory and formal languages. T.  ... 
arXiv:1111.5807v1 fatcat:de6ubnkhfjfojfosem2s2s7evm

On the power of parallel communicating Watson–Crick automata systems

Elena Czeizler, Eugen Czeizler
2006 Theoretical Computer Science  
Automata and Formal Languages, Dobogókő, Hungary, 2005, pp. 83-96] as possible models of DNA computations.  ...  We also prove that although Watson-Crick automata are equivalent to two-head finite automata, this equivalence is not preserved when comparing parallel communicating Watson-Crick automata systems and multi-head  ...  The main result of this paper proves that PCWKS are more powerful: they recognize all languages accepted by parallel communicating finite automata systems and also some non-semilinear languages such as  ... 
doi:10.1016/j.tcs.2006.01.049 fatcat:hbd6jykrabcmtnrdhrxx35rvvq

Recognition of Simple Splicing Systems using SHAutomaton

Fong Wan Heng, Nor Haniza Sarmin, Zuwairie Ibrahim
2014 Malaysian Journal of Fundamental and Applied Sciences  
Splicing languages are closely related to automata theory. Simple splicing systems can be recognized by SH-automata diagrams due to the regularity of splicing languages.  ...  SH-automaton defines exactly one language which is the language generated by the simple splicing system. In this paper, the concept of firm and maximal firm subwords are introduced.  ...  The set of double-stranded DNA molecules that may arise from a splicing system is called the splicing language.  ... 
doi:10.11113/mjfas.v4n2.41 fatcat:fxus7mxdnvfo5jr2qalf3lbdiu

Static Watson-Crick Context-Free Grammars

Wan Heng Fong, Aqilahfarhana Abdul Rahman, Nor Haniza Sarmin, Sherzod Turaev
2019 International Journal of Online and Biomedical Engineering (iJOE)  
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  ...  Grammars act as language generator, and besides grammar, automata are devices for defining language which work differently from the grammar.  ... 
doi:10.3991/ijoe.v15i10.10878 fatcat:isn7z2fv7rhuzn74gxscrtbnsi

Native Chemical Computation. A Generic Application of Oscillating Chemistry Illustrated With the Belousov-Zhabotinsky Reaction. A Review

Marta Dueñas-Díez, Juan Pérez-Mercader
2021 Frontiers in Chemistry  
and rejecting words outside the language.  ...  We examine and discuss in depth the fundamental issues involved in this form of computation exclusively done by molecules.  ...  JP-M thanks Andrew Adamatzky, Jeremy England, Irving Epstein, Seth Fraden, Stein Jacobsen, Greg Kovacs, Scott Hubbard, the late Murray Gell-Mann, Seth Lloyd, Stephen Mann, Mark Ritter, and Dimitar Sasselov  ... 
doi:10.3389/fchem.2021.611120 pmid:34046394 pmcid:PMC8144498 fatcat:2xtxhr2ny5g4zoljsqlf62tbde

Static Watson-Crick regular grammar

Aqilahfarhana Abdul Rahman, Wan Heng Fong, Nor Haniza Sarmin, Sherzod Turaev, Nurul Liyana Mohamad Zulkufli
2018 Malaysian Journal of Fundamental and Applied Sciences  
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.  ...  Watson-Crick grammars and their variants can be explored using formal language theory which allows the development of new concepts of Watson-Crick grammars.  ...  The second and third authors would also like to thank the Ministry of Education (MOE) and Research Management Centre (RMC), Universiti Teknologi Malaysia (UTM) for the financial funding through Research  ... 
doi:10.11113/mjfas.v14n0.1282 fatcat:wycukfgg6rewxfuen4dpqtlgou

Automata for DNA Splicing Languages with Two Restriction Enzymes

2020 ASM Science Journal  
In this research, the relation between DNA splicing language and concepts in automata theory is discussed.  ...  In DNA splicing system, molecules are cut and recombined with the existence of restriction enzymes and a ligase to produce new molecules.  ...  The splicing system is simulated by the process of recombinant DNA where restriction enzymes and a ligase cut and recombine DNA molecules to produce further molecules.  ... 
doi:10.32802/asmscj.2020.sm26(5.5) fatcat:rymql7rtyvhhvi4lhdmezc53la

Hierarchy Results on Stateless Multicounter 5′ → 3′ Watson-Crick Automata [chapter]

Benedek Nagy, László Hegedüs, Ömer Eğecioğlu
2011 Lecture Notes in Computer Science  
We consider stateless counter machines which mix the features of one-head counter machines and a special type of two-head Watson-Crick automata (WK-automata).  ...  .: Stateless multicounter 5 → 3 Watson-Crick Automata, BIC-TA 2010).  ...  Acknowledgements The research is supported by the TÁMOP 4.2.1/B-09/1/KONV-2010-0007 project, which is implemented through the New Hungary Development Plan, co-financed by the European Social Fund and the  ... 
doi:10.1007/978-3-642-21501-8_58 fatcat:gqy4xy7ffvdyzgg4opoxztnkta

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  
The computation is carried out in an autonomous manner by one enzyme and will allow to determine whether a resulting double-stranded DNA molecule belongs to the automaton's language or not.  ...  This model is called sticker automata model as the transition rules and input data are encoded by single stranded DNA molecules (stickers).  ...  The language of the automaton is the set of all accepted input strings over the input alphabet (Fig. 1 ). The Shapiro model is composed of three parts: input data, software, and hardware.  ... 
doi:10.1504/ijbra.2009.022465 pmid:19136366 fatcat:udohgrjbqvcpdjrlc46l3mn7um

Watson—Crick Automata [chapter]

Gheorghe Păun, Grzegorz Rozenberg, Arto Salomaa
1998 DNA Computing  
In particular, we show that any finite language as well as any unary regular language can be recognized by a Watson-Crick automaton with only two and respectively three states.  ...  Watson-Crick automata are finite state automata working on double-stranded tapes, introduced to investigate the potential of DNA molecules for computing.  ...  One of the first theoretical abstractions for such nanomachines are Watson-Crick automata [2] , which are based on the idea of finite automata running on complete DNA-molecules.  ... 
doi:10.1007/978-3-662-03563-4_6 fatcat:6m2jr44najac5dhevusgxofhbq

Use of Büchi automata and randomness for the description of biological processes

Konstantinos Giannakis, Theodore Andronikos
2015 International Journal of Scientific World  
Abstract The main topic of this study is the modelling and verification of biological systems using ω-automata.  ...  Specifically, stochastic computational models with infinite input are used in this paper's approach and indicative aspects of a biological problem are presented using both ω-automata and probabilistic  ...  The set of languages recognized by probabilistic automata is called stochastic languages, having as a subset the class of the regular languages.  ... 
doi:10.14419/ijsw.v3i1.4356 fatcat:vhqsjbvl5jawlogy42oky7cxlu
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