A New Relation of Second Order Limit Language in Simple and Semi-Simple Splicing System

2014 ◽  
Vol 71 (5) ◽  
Author(s):  
Muhammad Azrin Ahmad ◽  
Nor Haniza Sarmin ◽  
Wan Heng Fong ◽  
Yuhani Yusof
Keyword(s):  
Formal Language ◽  
Theoretical Study ◽  
Second Order ◽  
Language Theory ◽  
Biological Traits ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
New Type ◽  
Limit Language ◽  
Dna Splicing

Splicing system, which is an abstraction of operations on DNA molecules, can be modelled mathematically under the framework of formal language theory and informational macromolecules. The recombinant behavior of the set of double-stranded DNA molecules under the influence of restriction enzyme and ligase further lead to the cut and paste phenomenon in splicing system. The theoretical study of splicing language has contributed to a new type of splicing language known as a second order limit language, which is an extension of limit language. Some types of splicing system can produce second order limit language. Y-G splicing system is chosen among other models to model the DNA splicing process as this model preserves the biological traits and presents the transparent behavior of the DNA splicing process. In this paper, the relation between second order limit language with simple splicing and semi-simple splicing system are presented.

A Comparison of Second Order and Non-Second Order Limit Language Generated by Yusof-Goode Splicing System

2014 ◽  
Vol 72 (1) ◽  
Author(s):  
Muhammad Azrin Ahmad ◽  
Nor Haniza Sarmin ◽  
Wan Heng Fong ◽  
Yuhani Yusof
Keyword(s):  
Mathematical Model ◽  
Restriction Enzyme ◽  
Formal Language ◽  
Laboratory Experiments ◽  
Second Order ◽  
Language Theory ◽  
Double Stranded Dna ◽  
The Difference ◽  
Splicing Systems ◽  
Limit Language

DNA splicing process is a study on the recombinant behavior of double-stranded DNA molecules with the existence of restriction enzyme and ligase. Head introduced the first mathematical model of splicing systems by using the relation of informational macromolecules and formal language theory. In addition, a few laboratory experiments have been conducted in order to verify certain types of splicing language called inert/adult, transient and limit language. Previously, researchers have focused on those types of splicing languages.   Recently, an extension of limit languages namely second order limit language has been introduced. In this paper, the difference between second order limit languages and non-second order limit languages is depicted in some examples. Then, the formations of second order limit language in Yusof-Goode splicing system are investigated. 

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 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 Logic and the Generative Power of Autosegmental Phonology

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Adam Jardine
Keyword(s):  
Formal Language ◽  
Second Order ◽  
Order Logic ◽  
Language Theory ◽  
Preliminary Conclusion ◽  
Autosegmental Phonology ◽  
Finite State ◽  
Regular Sets ◽  
Second Order Logic ◽  
Monadic Second Order Logic

<p>Autosegmental Phonology is studied in the framework of Formal Language Theory, which classifies the computational complexity of patterns. In contrast to previous computational studies of Autosegmental Phonology, which were mainly concerned with finite-state implementations of the formalism, a methodology for a model-theoretic study of autosegmental diagrams with monadic second-order logic is introduced. Monadic second order logic provides a mathematically rigorous way of studying autosegmental formalisms, and its complexity is well understood. The preliminary conclusion is that autosegmental diagrams which conform to the well-formedness constraints defined here likely describe at most regular sets of strings.</p>

scholarly journals On Special forms of Splicing on Arrays and Graphs

Triangle ◽  
2018 ◽  
pp. 119
Author(s):  
K. G. Subramanian ◽  
A. Roslin Sagaya Mary ◽  
P. Helen Chandra
Keyword(s):  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Great Depth ◽  
Formal Language Theory ◽  
Language Theory ◽  
Dna Molecules ◽  
Higher Dimensional ◽  
Theoretical Results ◽  
Theory Extension

Tom Head (1987), in his pioneering work on formal language theory applied to DNA computing, introduced a new operation of splicing on strings, while proposing a model of certain recombination behaviour of DNA molecules under the action of restriction enzymes and ligases. Since then this operation has been studied in great depth giving rise to a number of theoretical results of great interest in formal language theory. Extension of this operation of splicing to higher dimensional structures such as circular words, arrays, trees and graphs have been proposed in the literature. Here we examine the effect of certain specific forms of the splicing operation applied to arrays and graphs.

scholarly journals Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme

MATEMATIKA ◽  
2018 ◽  
Vol 34 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Fong Wan Heng ◽  
Nurul Izzaty Ismail
Keyword(s):  
Restriction Enzyme ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Potential Effect ◽  
Language Theory ◽  
Regular Expressions ◽  
Nitrogen Bases ◽  
Restriction Sites ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing system, the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and re-associated to produce further molecules is modelled mathematically.  This modelling is done in the framework of formal language theory, in which the nitrogen bases, nucleotides and restriction sites are modelled as alphabets, strings and rules respectively.  The molecules resulting from a splicing system is depicted as the splicing language.  In this research, the splicing language resulting from DNA splicing systems with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites are generalised as regular expressions.

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

Second-order nonlinear optical properties of two chalcone derivatives: insights from sum-over-states

2021 ◽  
Author(s):  
Jean Custodio ◽  
Giulio Demetrius Creazo d'Oliveira ◽  
Fernando Gotardo ◽  
Leandro Cocca ◽  
Leonardo De Boni ◽  
...  
Keyword(s):  
Optical Properties ◽  
Nonlinear Optical ◽  
Theoretical Study ◽  
Second Order ◽  
Nonlinear Optical Properties ◽  
Chalcone Derivatives

In the following study, a combined experimental and theoretical study of the nonlinear optical properties (NLO) of two chalcone derivatives, (E)-3-(2-methoxyphenyl)-1-(2-(phenylsulfonylamine)phenyl)prop-2-en-1-one (MPSP) and (E)-3-(3-nitrophenyl)-1-(2-(phenylsulfonylamine)phenyl)prop-2-en-1-one (NPSP) in DMSO is reported. Single...

QUANTUM REFLECTION, EVAPORATION, AND TRANSPORT CURRENTS AT 4He SURFACES

2006 ◽  
Vol 20 (30n31) ◽  
pp. 5047-5056
Author(s):  
V. APAJA ◽  
E. KROTSCHECK ◽  
A. RIMNAC ◽  
R. E. ZILLICH
Keyword(s):  
Excited States ◽  
Theoretical Study ◽  
Transport Phenomena ◽  
Microscopic Theory ◽  
Second Order ◽  
Quantum Liquid ◽  
Quantum Reflection ◽  
Quantum Liquids ◽  
Inhomogeneous Quantum

In this work, we study transport currents in excited states. This requires the calculation of particle currents [Formula: see text] to second order in the excitation amplitudes. For that purpose, we take a well-tested microscopic theory of inhomogeneous quantum liquids and extend it to find the mass currents created when atoms scatter off a surface or when excitations evaporate atoms. This is the first theoretical study of transport phenomena in a quantum liquid based on a quantitative microscopic theory.

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