scholarly journals Mathematical Modelling of Some Null-Context and Uniform Splicing Systems

2014 ◽  
Vol 7 (2) ◽  
Author(s):  
S. J. Lim ◽  
W. H. Fong ◽  
N. H. Sarmin ◽  
F. Karimi
Keyword(s):  
Mathematical Modelling ◽  
Restriction Enzymes ◽  
Automata Theory ◽  
Dna Molecules ◽  
Specific Chemical ◽  
Language L ◽  
Different Types ◽  
Chemical Conditions ◽  
Splicing Systems

The mathematical modelling of splicing system which involves recombination of DNA molecules was first introduced by Head in 1987. 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. A splicing language, L is generated if there exists a splicing system S for which L = L(S). There are different types of splicing systems which have been discussed by various researchers. Among them are the persistent splicing system, null-context and uniform splicing system. In this paper, some molecular examples on null-context splicing system and uniform splicing systems with different initial strings and combination of restriction enzymes will be discussed. Applications of automata theory on some molecular examples of null-context and uniform splicing languages will also be presented in this paper.

scholarly journals Generalisations of Splicing Languages in DNA Splicing Systems Involving Two Palindromic Restriction Enzymes

2021 ◽  
Vol 17 (2) ◽  
pp. 128-138
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Molecules ◽  
Induction Method ◽  
Different Types ◽  
Splicing Systems ◽  
Dna Splicing

DNA splicing system is initiated by Head to mathematically model a relation between formal language theory and DNA molecules. In DNA splicing systems, DNA molecules are cut and recombined in specific ways with the existence of enzymes, which are also known as endonucleases, to produce further molecules. The resulting molecules are depicted as splicing languages by using concepts in formal languages theory. A sequence of restriction enzyme that reads the same forward and backward is called as a palindromic rule. Previously, researches on different types of splicing languages have been done. In this research, generalisations of splicing languages resulting from DNA splicing systems with non-overlapping cutting sites of two palindromic restriction enzymes are presented as theorems using the induction method. The results from this research are beneficial for researchers in the field of DNA computing since it contributes to the development of splicing languages generated from DNA splicing systems with different palindromic restriction enzymes by using these generalisations.

scholarly journals Recognition of Simple Splicing Systems using SHAutomaton

2014 ◽  
Vol 4 (2) ◽  
Author(s):  
Fong Wan Heng ◽  
Nor Haniza Sarmin ◽  
Zuwairie Ibrahim
Keyword(s):  
Mathematical Model ◽  
Regular Expression ◽  
Restriction Enzymes ◽  
Automata Theory ◽  
Dna Molecules ◽  
Deterministic Automaton ◽  
Splicing Systems ◽  
The Mathematical Model ◽  
The Given ◽  
Special Case

Splicing language is the language which results from a splicing system. Splicing system was first introduced by Tom Head in 1987 as the mathematical model of systems of restriction enzymes acting on initial DNA molecules. 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. Some examples are then given to illustrate the maximal firm subwords of a word in a simple splicing system. Taking the SH-automata concept, which is a short compact way of encoding normal non-deterministicautomata in the special case of SH systems, the maximal firm subwords of the initial words of an SH systems serve as the labels for the associated  SH-automaton. Some examples which will show the maximal firm subwords of the words in the initial set I, the regular expression for the language generated by the given splicing system and the simplest non-deterministic automaton that recognizes the corresponding splicing system are also given

scholarly journals Computation of Splicing Languages from DNA Splicing System Based on Sequences of Restriction Enzymes

2019 ◽  
Vol 8 (6S3) ◽  
pp. 31-42
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Restriction Enzymes ◽  
Visual Programming ◽  
Cleavage Pattern ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing systems, restriction enzymes and ligases cleave and recombine DNA molecules based on the cleavage pattern of the restriction enzymes. The set of molecules resulting from the splicing system depicts a splicing language. In this research, an algorithm for DNA splicing systems is developed using C++ visual programming. The splicing languages which have been characterised through some theorems based on the crossings and sequences of the restriction enzymes, are generated as the output from this computation. In order to generate the splicing languages, the algorithm detects and calculates the number of cutting sites of the restriction enzymes found in the initial molecules, determines whether the sequence of restriction enzyme is a palindrome or not, and if the restriction enzymes have the same or different crossings. The results from this research depict the splicing languages obtained from the manual computations, which contributes to the development of computational software in DNA computing.

scholarly journals Computation of splicing languages from DNA splicing system with one palindromic restriction enzyme

2018 ◽  
Vol 14 (2) ◽  
pp. 188-192
Author(s):  
Nurul Izzaty Ismail ◽  
Wan Heng Fong ◽  
Nor Haniza Sarmin
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
In Vitro Experiments ◽  
Dna Molecules ◽  
C Programming ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing system, the potential effects of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules are studied.  A splicing language depicts the molecules resulting from a splicing system.  In this research, a C++ programming code for DNA splicing system with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites is developed.  A graphical user interface, GUI is then designed to allow the user to insert the initial DNA string and restriction enzymes to generate the splicing languages which are the result of the computation of the C++ programming.  This interface displays the resulting splicing languages, which depict the results from in vitro experiments of the respective splicing system.  The results from this research simplify the lenghty manual computation of the resulting splicing languages of DNA splicing systems with one palindromic restriction enzyme.   

scholarly journals Automata for DNA Splicing Languages with Palindromic and Non-Palindromic Restriction Enzymes using Grammars

MATEMATIKA ◽  
2019 ◽  
Vol 35 (4) ◽  
pp. 1-14
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Dna Sequences ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Assembly ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Transition Graphs ◽  
Palindromic Sequences ◽  
Dna Splicing

In DNA splicing system, DNA molecules are cut and recombined with the presence of restriction enzymes and a ligase. The splicing system is analyzed via formal language theory where the molecules resulting from the splicing system generate a language which is called a splicing language. In nature, DNA molecules can be read in two ways; forward and backward. A sequence of string that reads the same forward and backward is known as a palindrome. Palindromic and non-palindromic sequences can also be recognized in restriction enzymes. Research on splicing languages from DNA splicing systems with palindromic and non-palindromic restriction enzymes have been done previously. This research is motivated by the problem of DNA assembly to read millions of long DNA sequences where the concepts of automata and grammars are applied in DNA splicing systems to simplify the assembly in short-read sequences. The splicing languages generated from DNA splicing systems with palindromic and nonpalindromic restriction enzymes are deduced from the grammars which are visualised as automata diagrams, and presented by transition graphs where transition labels represent the language of DNA molecules resulting from the respective DNA splicing systems.

scholarly journals DNA Splicing Systems with at Most Two Cutting Sites of a Non-Palindromic Restriction Enzyme

MATEMATIKA ◽  
2019 ◽  
Vol 35 (2) ◽  
pp. 129-137
Author(s):  
Nurul Izzaty Ismail ◽  
Fong Wan Heng ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
Dna Molecules ◽  
Dna Molecule ◽  
Splicing Systems ◽  
Palindromic Sequences ◽  
Dna Splicing

The modelling of splicing systems is simulated by the process of cleaving and recombining DNA molecules with the presence of a ligase and restriction enzymes which are biologically called as endodeoxyribonucleases.  The molecules resulting from DNA splicing systems are known as splicing languages. Palindrome is a sequence of strings that reads the same forward and backward.  Research on generalisations of splicing languages in DNA splicing system involving palindromic sequences for restriction enzymes has been done previously. In this research, the splicing languages resulting from DNA splicing systems with one non-palindromic restriction enzyme are determined using the notation from Head splicing system.  The generalisations of splicing languages for DNA splicing systems involving one and two non-overlapping cutting sites of one non-palindromic restriction enzyme are presented in the first and second theorems, respectively, which are proved using direct and induction methods.  The result from the first theorem shows a trivial string which is the initial DNA molecule; while the second theorem determines a splicing language consisting of a set of resulting DNA molecules from the respective DNA splicing system.

Ultrastructural Investigations of the Contractile Filaments of Amoebae

1974 ◽  
Vol 32 ◽  
pp. 188-189
Author(s):  
P.L. Moore
Keyword(s):  
Cytoplasmic Streaming ◽  
Three Dimensional ◽  
Freeze Fracture ◽  
Amoeboid Movement ◽  
Different Types ◽  
Chemical Conditions ◽  
Complete Interpretation

Previous freeze fracture results on the intact giant, amoeba Chaos carolinensis indicated the presence of a fibrillar arrangement of filaments within the cytoplasm. A complete interpretation of the three dimensional ultrastructure of these structures, and their possible role in amoeboid movement was not possible, since comparable results could not be obtained with conventional fixation of intact amoebae. Progress in interpreting the freeze fracture images of amoebae required a more thorough understanding of the different types of filaments present in amoebae, and of the ways in which they could be organized while remaining functional.The recent development of a calcium sensitive, demembranated, amoeboid model of Chaos carolinensis has made it possible to achieve a better understanding of such functional arrangements of amoeboid filaments. In these models the motility of demembranated cytoplasm can be controlled in vitro, and the chemical conditions necessary for contractility, and cytoplasmic streaming can be investigated. It is clear from these studies that “fibrils” exist in amoeboid models, and that they are capable of contracting along their length under conditions similar to those which cause contraction in vertebrate muscles.

Modelling of a Twin-Track Vehicle Model with Modular Wheel Suspensions

2012 ◽  
Vol 165 ◽  
pp. 214-218
Author(s):  
Michael Unterreiner ◽  
Dieter Schramm
Keyword(s):  
Mathematical Modelling ◽  
Jacobian Matrix ◽  
Vehicle Model ◽  
Different Types ◽  
Multi Body ◽  
Modelling Approach

A mathematical modelling approach of a multi-body wheel suspension is presented. The wheel suspension is modelled in a modular manner so that different types of vehicles can be simulated. The inter-changeability of the wheel suspensions is achieved by calculating the translational and rotational Jacobian matrix and its partial time derivatives for the wheel carrier and the wheel. The results of modelling the kinematics of a McPherson wheel suspension are shown.

Fibre deformations induced by different mechanical treatments and their effect on zero-span strength

2012 ◽  
Vol 27 (2) ◽  
pp. 335-342 ◽  
Author(s):  
Xiling Zeng ◽  
Shiyu Fu ◽  
Elias Retulainen ◽  
Sabine Heinemann
Keyword(s):  
Tensile Strength ◽  
Mechanical Treatment ◽  
Kraft Pulp ◽  
Fibre Surface ◽  
Wall Structure ◽  
Fibre Strength ◽  
Different Types ◽  
Chemical Conditions ◽  
Mechanical Devices ◽  
High Consistency

Abstract Fibre deformations have a significant effect on fibre strength and sheet properties. There is little information, however, on the kinds of deformations different types of treatments induce and how they affect the fibre strength. In the present study, first-thinning bleached pine kraft pulp was treated with three mechanical devices: a wing defibrator (high consistency treatment), an E-compactor (high consistency treatment) and a conventional Valley beater (low consistency treatment). The fibre properties were determined with a fibre analyser. The fibre cutting induced by the hydrochloric acid (HCl) treatment (‘cleavage index’) was used for the quantification of the fibre defects. The zero-span tensile strength of dry and wet paper was used to estimate the fibre strength. Each mechanical treatment induced fibre deformations in its own characteristic way. The wing defibrator induced fibre kinks and curl whereas the E-compactor, in addition to fibre cutting, favoured kinks. Low consistency Valley beating straightened the fibres and released fibre deformations. The fibre deformations, especially the number of kinks, correlated well with the wet zero-span tensile strength. The cleavage index had some correlation with the zero-span tensile strength, but the results indicated that the cleavage index may not be directly related to the mechanical defects in fibres but depend more on the chemical conditions on the fibre surface and the wall structure.

Probabilistic Semi–Simple Splicing System and Its Characteristics

2013 ◽  
Vol 62 (3) ◽  
Author(s):  
Mathuri Selvarajoo ◽  
Fong Wan Heng ◽  
Nor Haniza Sarmin ◽  
Sherzod Turaev
Keyword(s):  
Regular Languages ◽  
Computational Power ◽  
Dna Molecules ◽  
Finite Sets ◽  
Generative Power ◽  
Recursively Enumerable ◽  
Splicing Systems ◽  
Recursively Enumerable Languages

The concept of splicing system was first introduced by Head in 1987. This model has been introduced to investigate the recombinant behavior of DNA molecules. Splicing systems with finite sets of axioms only generate regular languages. Hence, different restrictions have been considered to increase the computational power up to the recursively enumerable languages. Recently, probabilistic splicing systems have been introduced where probabilities are initially associated with the axioms, and the probability of a generated string is computed by multiplying the probabilities of all occurrences of the initial strings in the computation of the string. In this paper, some properties of probabilistic semi-simple splicing systems, which are special types of probabilistic splicing systems, are investigated. We prove that probabilistic semi-simple splicing systems can also increase the generative power of the generated languages.

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