The surface-based DNA computing is one of the methods of DNA computing which uses DNA strands immobilized on a solid surface. In this paper, we applied surface-based DNA computing for solving the dominating set proble...The surface-based DNA computing is one of the methods of DNA computing which uses DNA strands immobilized on a solid surface. In this paper, we applied surface-based DNA computing for solving the dominating set problem. At first step, surface-based DNA solution space was constructed by using appropriate DNA strands. Then, by application of a DNA parallel algorithm, dominating set problem was resolved in polynomial time.展开更多
The exponential growth of data necessitates an effective data storage scheme,which helps to effectively manage the large quantity of data.To accomplish this,Deoxyribonucleic Acid(DNA)digital data storage process can b...The exponential growth of data necessitates an effective data storage scheme,which helps to effectively manage the large quantity of data.To accomplish this,Deoxyribonucleic Acid(DNA)digital data storage process can be employed,which encodes and decodes binary data to and from synthesized strands of DNA.Vector quantization(VQ)is a commonly employed scheme for image compression and the optimal codebook generation is an effective process to reach maximum compression efficiency.This article introduces a newDNAComputingwithWater StriderAlgorithm based Vector Quantization(DNAC-WSAVQ)technique for Data Storage Systems.The proposed DNAC-WSAVQ technique enables encoding data using DNA computing and then compresses it for effective data storage.Besides,the DNAC-WSAVQ model initially performsDNA encoding on the input images to generate a binary encoded form.In addition,aWater Strider algorithm with Linde-Buzo-Gray(WSA-LBG)model is applied for the compression process and thereby storage area can be considerably minimized.In order to generate optimal codebook for LBG,the WSA is applied to it.The performance validation of the DNAC-WSAVQ model is carried out and the results are inspected under several measures.The comparative study highlighted the improved outcomes of the DNAC-WSAVQ model over the existing methods.展开更多
In this paper, the sticker based DNA computing was used for solving the independent set problem. At first, solution space was constructed by using appropriate DNA memory complexes. We defined a new operation called “...In this paper, the sticker based DNA computing was used for solving the independent set problem. At first, solution space was constructed by using appropriate DNA memory complexes. We defined a new operation called “divide” and applied it in construction of solution space. Then, by application of a sticker based parallel algorithm using biological operations, independent set problem was resolved in polynomial time.展开更多
Molecular programming is applied to minimum spanning problem whose solution requires encoding of real values in DNA strands. A new encoding scheme is proposed for real values that is biologically plausible and has a f...Molecular programming is applied to minimum spanning problem whose solution requires encoding of real values in DNA strands. A new encoding scheme is proposed for real values that is biologically plausible and has a fixed code length. According to the characteristics of the problem, a DNA algorithm solving the minimum spanning tree problem is given. The effectiveness of the proposed method is verified by simulation. The advantages and disadvantages of this algorithm are discussed.展开更多
Recently, the possibility of using DNA as a computing tool arouses wide interests of many researchers. In this paper, we first explored the mechanism of DNA computing and its biological mathematics based on the mechan...Recently, the possibility of using DNA as a computing tool arouses wide interests of many researchers. In this paper, we first explored the mechanism of DNA computing and its biological mathematics based on the mechanism of biological DNA. Then we integrated DNA computing with evolutionary computation, fuzzy systems, neural networks and chaotic systems in soft computing technologies. Finally, we made some prospects on the further work of DNA bio soft computing.展开更多
To solve job shop scheduling problem, a new approach-DNA computing is used in solving job shop scheduling problem. The approach using DNA computing to solve job shop scheduling is divided into three stands. Finally, o...To solve job shop scheduling problem, a new approach-DNA computing is used in solving job shop scheduling problem. The approach using DNA computing to solve job shop scheduling is divided into three stands. Finally, optimum solutions are obtained by sequencing A small job shop scheduling problem is solved in DNA computing, and the ＂operations＂ of the computation were performed with standard protocols, as ligation, synthesis, electrophoresis etc. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.展开更多
As rule-based systems (RBS) technology gains wider acceptance, the need to create and maintain large knowledge bases will assume greater importance. Demonstrating a rule base to be free from error remains one of the o...As rule-based systems (RBS) technology gains wider acceptance, the need to create and maintain large knowledge bases will assume greater importance. Demonstrating a rule base to be free from error remains one of the obstacles to the adoption of this technology. In the past several years, a vast body of research has been carried out in developing various graphical techniques such as utilizing Petri Nets to analyze structural errors in rule-based systems, which utilize propositional logic. Four typical errors in rule-based systems are redundancy, circularity, incompleteness, and inconsistency. Recently, a DNA-based computing approach to detect these errors has been proposed. That paper presents algorithms which are able to detect structural errors just for special cases. For a rule base, which contains multiple starting nodes and goal nodes, structural errors are not removed correctly by utilizing the algorithms proposed in that paper and algorithms lack generality. In this study algorithms mainly based on Adleman’s operations, which are able to detect structural errors, in any form that they may arise in rule base, are presented. The potential of applying our algorithm is auspicious giving the operational time complexity of O(n*(Max{q, K, z})), in which n is the number of fact clauses;q is the number of rules in the longest inference chain;K is the number of tubes containing antecedents which are comprised of distinct number of starting nodes;and z denotes the maximum number of distinct antecedents comprised of the same number of starting nodes.展开更多
DNA computing is a novel method for solving a class of intractable computationalproblems in which the computing can grow exponentially with problem size. Up to now, manyaccomplishments have been achieved to improve it...DNA computing is a novel method for solving a class of intractable computationalproblems in which the computing can grow exponentially with problem size. Up to now, manyaccomplishments have been achieved to improve its performance and increase its reliability.Hamilton Graph Problem has been solved by means of molecular biology techniques. A smallgraph was encoded in molecules of DNA, and the “operations” of the computation wereperformed with standard protocols and enzymes. This work represents further evidence forthe ability of DNA computing to solve NP-complete search problems.展开更多
This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA ...This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.展开更多
Data encryption is essential in securing exchanged data between connected parties.Encryption is the process of transforming readable text into scrambled,unreadable text using secure keys.Stream ciphers are one type of...Data encryption is essential in securing exchanged data between connected parties.Encryption is the process of transforming readable text into scrambled,unreadable text using secure keys.Stream ciphers are one type of an encryption algorithm that relies on only one key for decryption and as well as encryption.Many existing encryption algorithms are developed based on either a mathematical foundation or on other biological,social or physical behaviours.One technique is to utilise the behavioural aspects of game theory in a stream cipher.In this paper,we introduce an enhanced Deoxyribonucleic acid(DNA)-coded stream cipher based on an iterated n-player prisoner’s dilemma paradigm.Our main goal is to contribute to adding more layers of randomness to the behaviour of the keystream generation process;these layers are inspired by the behaviour of multiple players playing a prisoner’s dilemma game.We implement parallelism to compensate for the additional processing time that may result fromadding these extra layers of randomness.The results show that our enhanced design passes the statistical tests and achieves an encryption throughput of about 1,877 Mbit/s,which makes it a feasible secure stream cipher.展开更多
文摘The surface-based DNA computing is one of the methods of DNA computing which uses DNA strands immobilized on a solid surface. In this paper, we applied surface-based DNA computing for solving the dominating set problem. At first step, surface-based DNA solution space was constructed by using appropriate DNA strands. Then, by application of a DNA parallel algorithm, dominating set problem was resolved in polynomial time.
基金This research was supported in part by Basic Science Research Program through the National Research Foundation of Korea(NRF)funded by the Ministry of Education(NRF-2021R1A6A1A03039493)in part by the NRF grant funded by the Korea government(MSIT)(NRF-2022R1A2C1004401)in part by the 2022 Yeungnam University Research Grant.
文摘The exponential growth of data necessitates an effective data storage scheme,which helps to effectively manage the large quantity of data.To accomplish this,Deoxyribonucleic Acid(DNA)digital data storage process can be employed,which encodes and decodes binary data to and from synthesized strands of DNA.Vector quantization(VQ)is a commonly employed scheme for image compression and the optimal codebook generation is an effective process to reach maximum compression efficiency.This article introduces a newDNAComputingwithWater StriderAlgorithm based Vector Quantization(DNAC-WSAVQ)technique for Data Storage Systems.The proposed DNAC-WSAVQ technique enables encoding data using DNA computing and then compresses it for effective data storage.Besides,the DNAC-WSAVQ model initially performsDNA encoding on the input images to generate a binary encoded form.In addition,aWater Strider algorithm with Linde-Buzo-Gray(WSA-LBG)model is applied for the compression process and thereby storage area can be considerably minimized.In order to generate optimal codebook for LBG,the WSA is applied to it.The performance validation of the DNAC-WSAVQ model is carried out and the results are inspected under several measures.The comparative study highlighted the improved outcomes of the DNAC-WSAVQ model over the existing methods.
文摘In this paper, the sticker based DNA computing was used for solving the independent set problem. At first, solution space was constructed by using appropriate DNA memory complexes. We defined a new operation called “divide” and applied it in construction of solution space. Then, by application of a sticker based parallel algorithm using biological operations, independent set problem was resolved in polynomial time.
文摘Molecular programming is applied to minimum spanning problem whose solution requires encoding of real values in DNA strands. A new encoding scheme is proposed for real values that is biologically plausible and has a fixed code length. According to the characteristics of the problem, a DNA algorithm solving the minimum spanning tree problem is given. The effectiveness of the proposed method is verified by simulation. The advantages and disadvantages of this algorithm are discussed.
文摘Recently, the possibility of using DNA as a computing tool arouses wide interests of many researchers. In this paper, we first explored the mechanism of DNA computing and its biological mathematics based on the mechanism of biological DNA. Then we integrated DNA computing with evolutionary computation, fuzzy systems, neural networks and chaotic systems in soft computing technologies. Finally, we made some prospects on the further work of DNA bio soft computing.
基金This Project was supported by the National Nature Science Foundation (60274026 ,30570431) China Postdoctoral Sci-ence Foundation Natural +1 种基金Science Foundation of Educational Government of Anhui Province of China Excellent Youth Scienceand Technology Foundation of Anhui Province of China (06042088) and Doctoral Foundation of Anhui University of Scienceand Technology
文摘To solve job shop scheduling problem, a new approach-DNA computing is used in solving job shop scheduling problem. The approach using DNA computing to solve job shop scheduling is divided into three stands. Finally, optimum solutions are obtained by sequencing A small job shop scheduling problem is solved in DNA computing, and the ＂operations＂ of the computation were performed with standard protocols, as ligation, synthesis, electrophoresis etc. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.
文摘As rule-based systems (RBS) technology gains wider acceptance, the need to create and maintain large knowledge bases will assume greater importance. Demonstrating a rule base to be free from error remains one of the obstacles to the adoption of this technology. In the past several years, a vast body of research has been carried out in developing various graphical techniques such as utilizing Petri Nets to analyze structural errors in rule-based systems, which utilize propositional logic. Four typical errors in rule-based systems are redundancy, circularity, incompleteness, and inconsistency. Recently, a DNA-based computing approach to detect these errors has been proposed. That paper presents algorithms which are able to detect structural errors just for special cases. For a rule base, which contains multiple starting nodes and goal nodes, structural errors are not removed correctly by utilizing the algorithms proposed in that paper and algorithms lack generality. In this study algorithms mainly based on Adleman’s operations, which are able to detect structural errors, in any form that they may arise in rule base, are presented. The potential of applying our algorithm is auspicious giving the operational time complexity of O(n*(Max{q, K, z})), in which n is the number of fact clauses;q is the number of rules in the longest inference chain;K is the number of tubes containing antecedents which are comprised of distinct number of starting nodes;and z denotes the maximum number of distinct antecedents comprised of the same number of starting nodes.
基金Supported by the CNSF(60274026 60174047+1 种基金 30370356) Supported by the Anhui Provinc'e Educational Committee Foundation(2003Kj098)
文摘DNA computing is a novel method for solving a class of intractable computationalproblems in which the computing can grow exponentially with problem size. Up to now, manyaccomplishments have been achieved to improve its performance and increase its reliability.Hamilton Graph Problem has been solved by means of molecular biology techniques. A smallgraph was encoded in molecules of DNA, and the “operations” of the computation wereperformed with standard protocols and enzymes. This work represents further evidence forthe ability of DNA computing to solve NP-complete search problems.
基金This work was supportedin part by the National Nature Science Foundation of China (No.60474037and60004006) Programfor NewCentury Excellent Talents in University (NCET04 415) +1 种基金Specialized Research Fund for the Doctoral Programof Higher Educationfrom Educational Committee of China (No.20030255009) the Youth Foundation fromEducational Committee of Anhui Province(No.2005jql043) .
文摘This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.
文摘Data encryption is essential in securing exchanged data between connected parties.Encryption is the process of transforming readable text into scrambled,unreadable text using secure keys.Stream ciphers are one type of an encryption algorithm that relies on only one key for decryption and as well as encryption.Many existing encryption algorithms are developed based on either a mathematical foundation or on other biological,social or physical behaviours.One technique is to utilise the behavioural aspects of game theory in a stream cipher.In this paper,we introduce an enhanced Deoxyribonucleic acid(DNA)-coded stream cipher based on an iterated n-player prisoner’s dilemma paradigm.Our main goal is to contribute to adding more layers of randomness to the behaviour of the keystream generation process;these layers are inspired by the behaviour of multiple players playing a prisoner’s dilemma game.We implement parallelism to compensate for the additional processing time that may result fromadding these extra layers of randomness.The results show that our enhanced design passes the statistical tests and achieves an encryption throughput of about 1,877 Mbit/s,which makes it a feasible secure stream cipher.
