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Languages of Watson-Crick Petri Net
2014
Jurnal Teknologi
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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]
2005
Lecture Notes in Computer Science
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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
2014
Malaysian Journal of Fundamental and Applied Sciences
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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
2019
Science Proceedings Series
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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]
2011
arXiv
pre-print
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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
2006
Theoretical Computer Science
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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
2014
Malaysian Journal of Fundamental and Applied Sciences
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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
2019
International Journal of Online and Biomedical Engineering (iJOE)
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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
2021
Frontiers in Chemistry
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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
2018
Malaysian Journal of Fundamental and Applied Sciences
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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
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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]
2011
Lecture Notes in Computer Science
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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
2009
International Journal of Bioinformatics Research and Applications
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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]
1998
DNA Computing
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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
2015
International Journal of Scientific World
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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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