Mathematical modelling of persistent splicing systems in DNA computing

Splicing system is a bio-inspired computational model that interprets the cutting and pasting behavior of DNA molecules in the presence of restriction enzymes. Splicing system is defined under the framework of formal language theory. In this research the relation between different types of splicing...

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Main Author:	Karimi, Fariba
Format:	Thesis
Language:	English
Published:	2013
Subjects:	QA Mathematics
Online Access:	http://eprints.utm.my/id/eprint/36644/1/FaribaKarimiPFS2013.pdf
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id	my-utm-ep.36644
record_format	uketd_dc
spelling	my-utm-ep.366442017-09-19T04:19:08Z Mathematical modelling of persistent splicing systems in DNA computing 2013 Karimi, Fariba QA Mathematics Splicing system is a bio-inspired computational model that interprets the cutting and pasting behavior of DNA molecules in the presence of restriction enzymes. Splicing system is defined under the framework of formal language theory. In this research the relation between different types of splicing systems and languages such as uniform, null-context, permanent, persistent and strictly locally testable languages are investigated. Then, the characteristics of persistent and permanent splicing systems are explored in detail. The interesting point about these two systems is that if restriction enzymes are chosen from actual biological sense, then the resulting systems are often persistent and permanent. Their main feature is that the property of crossing of a site is preserved and consequently, the enzymes cleavage process persists. Some sufficient conditions are provided for splicing systems to be persistent and permanent. New concepts of self-closed, crossingpreserved and extended crossing-preserved are introduced. These new concepts are closely connected to the notions of persistent and permanent systems. Moreover, fuzzy splicing system is introduced as an extension of splicing systems. In fact, by considering the threshold languages generated by fuzzy splicing systems, their computational power is increased. In other words, there are some fuzzy splicing systems that generate non-regular languages, while splicing systems with finite components can only generate regular languages. At the end of this research, a laboratory experiment has been conducted to biologically validate the behavior of persistent splicing systems. 2013 Thesis http://eprints.utm.my/id/eprint/36644/ http://eprints.utm.my/id/eprint/36644/1/FaribaKarimiPFS2013.pdf application/pdf en public phd doctoral Universiti Teknologi Malaysia, Faculty of Science Faculty of Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	QA Mathematics
spellingShingle	QA Mathematics Karimi, Fariba Mathematical modelling of persistent splicing systems in DNA computing
description	Splicing system is a bio-inspired computational model that interprets the cutting and pasting behavior of DNA molecules in the presence of restriction enzymes. Splicing system is defined under the framework of formal language theory. In this research the relation between different types of splicing systems and languages such as uniform, null-context, permanent, persistent and strictly locally testable languages are investigated. Then, the characteristics of persistent and permanent splicing systems are explored in detail. The interesting point about these two systems is that if restriction enzymes are chosen from actual biological sense, then the resulting systems are often persistent and permanent. Their main feature is that the property of crossing of a site is preserved and consequently, the enzymes cleavage process persists. Some sufficient conditions are provided for splicing systems to be persistent and permanent. New concepts of self-closed, crossingpreserved and extended crossing-preserved are introduced. These new concepts are closely connected to the notions of persistent and permanent systems. Moreover, fuzzy splicing system is introduced as an extension of splicing systems. In fact, by considering the threshold languages generated by fuzzy splicing systems, their computational power is increased. In other words, there are some fuzzy splicing systems that generate non-regular languages, while splicing systems with finite components can only generate regular languages. At the end of this research, a laboratory experiment has been conducted to biologically validate the behavior of persistent splicing systems.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Karimi, Fariba
author_facet	Karimi, Fariba
author_sort	Karimi, Fariba
title	Mathematical modelling of persistent splicing systems in DNA computing
title_short	Mathematical modelling of persistent splicing systems in DNA computing
title_full	Mathematical modelling of persistent splicing systems in DNA computing
title_fullStr	Mathematical modelling of persistent splicing systems in DNA computing
title_full_unstemmed	Mathematical modelling of persistent splicing systems in DNA computing
title_sort	mathematical modelling of persistent splicing systems in dna computing
granting_institution	Universiti Teknologi Malaysia, Faculty of Science
granting_department	Faculty of Science
publishDate	2013
url	http://eprints.utm.my/id/eprint/36644/1/FaribaKarimiPFS2013.pdf
_version_	1747816437731295232

Mathematical modelling of persistent splicing systems in DNA computing

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