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Temperature gradientbased DNA computing for graph problems with weighted edges
 Lecture Notes in Computer Science
, 2003
"... Abstract. We propose an encoding method of numerical data in DNA using temperature gradient. We introduce melting temperature (Tm) for this purpose. Melting temperature is a unique characteristic to manipulate the hybridization and denaturation processes that used in the key steps in DNA computing s ..."
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Abstract. We propose an encoding method of numerical data in DNA using temperature gradient. We introduce melting temperature (Tm) for this purpose. Melting temperature is a unique characteristic to manipulate the hybridization and denaturation processes that used in the key steps in DNA computing such as the solution generation step and the amplification step. DNA strands of lower melting temperature tend to denature with ease and also be easily amplified by slightly modified polymerase chain reaction, called denaturation temperature gradient polymerase chain reaction. Using these properties, we implement a local search molecular algorithm using temperature gradient, which is contrasted to conventional exhaustive search molecular algorithms. The proposed methods are verified by solving an instance of the travelling salesman problem. We could effectively amplify the correct solution and the use of temperature gradient made the detection of solutions easier. 1
Fast Parallel Molecular Algorithms for DNABased Computation: Factoring Integers
"... Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two la ..."
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Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNAbased algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using publickey are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations. Index Terms—Biological parallel computing, DNAbased algorithms, DNAbased computing, factoring integers, RSA publickey cryptosystem. I.
The Design of Sorters Based on DNA for BioComputers
 International Computer Symposium, Workshop on Algorithms and Computational Molecular Biology, National Dong Hwa
, 2002
"... devoted to the study of molecular computing based on DNA in order to implement algorithms for solving some NPcomplete problems and simulate logic gates in siliconbased computers. A great deal of effort has been made on using DNA to implement simple logic gates, such as simple 1bit comparators and ..."
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devoted to the study of molecular computing based on DNA in order to implement algorithms for solving some NPcomplete problems and simulate logic gates in siliconbased computers. A great deal of effort has been made on using DNA to implement simple logic gates, such as simple 1bit comparators and simple adders, or to solve NPcomplete problems, such as the Hamiltonian path problem, the travelling salesperson problem and the satisfiability problem. All of the methods rely on the capability of DNA computing which could perform computation in huge parallelism to produce all possible solutions where the answer may be derived from. In this paper, we will first design a full bitserial comparator that can perform the feedback operation. Then, we will design a wordparallel bitserial sorter which uses our comparators as the elementary building components. Our design of sorters can be applied to any sorting network, such as bitonic sorter and oddeven merge sorter.
Fast parallel molecular solution to the dominatingset problem on massively parallel biocomputing
, 2004
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Solving the Maximum Independent Set Problem based on Molecule Parallel Supercomputing
"... Abstract: The maximum independent set Problem is to find a biggest vertex independent set in a given undirected graph. It is a vitally important NP problem in graph theory and applied mathematics, having numerous real life applications. It can be difficultly solved by the electronic computer in expo ..."
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Abstract: The maximum independent set Problem is to find a biggest vertex independent set in a given undirected graph. It is a vitally important NP problem in graph theory and applied mathematics, having numerous real life applications. It can be difficultly solved by the electronic computer in exponential level time. Simultaneity in previous studies DNA molecular computation usually be used to solve NPcomplete continuous path search problems (for example HPP, traveling salesman problem), rarely for NP problems with discrete vertex or path solutions result, such as the maximum independent set problem, graph coloring problem and so on. In this paper, we present a new algorithm for solving the maximum independent set problem with DNA molecular operations. For an undirected graph with n vertices, We reasonably design fixed length DNA strands representing the vertices and edges of graph, take appropriate steps and get the solutions of the problem in proper length range using O(n 2) time. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation.
1 A DNA computing approach to solve Task Assignment problem in Real Time Distributed computing System
"... Early attention has focused on DNA because its properties are extremely attractive as a basis for a computational system. In this paper, we have proposed a new framework for assigning task in heterogeneous Real time distributed system(RTDS) including the cost of path connecting the nodes. The propos ..."
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Early attention has focused on DNA because its properties are extremely attractive as a basis for a computational system. In this paper, we have proposed a new framework for assigning task in heterogeneous Real time distributed system(RTDS) including the cost of path connecting the nodes. The proposed approach is based upon a DNA replication technique using fixed length coding to select the computing node to which task to be assigned in RTDS.
Fast parallel molecular solution to the
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Towards solution of the setsplitting problem on gelbased DNA computing
, 2003
"... Adleman wrote the first paper that demonstrated that DNA (DeoxyriboNucleic Acid) strands could be applied for dealing with solutions of the NPcomplete Hamiltonian path problem (HPP). Lipton wrote the second paper that showed that the Adleman techniques could also be used to solve the NPcomplete sa ..."
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Adleman wrote the first paper that demonstrated that DNA (DeoxyriboNucleic Acid) strands could be applied for dealing with solutions of the NPcomplete Hamiltonian path problem (HPP). Lipton wrote the second paper that showed that the Adleman techniques could also be used to solve the NPcomplete satisfiability (SAT) problem (the first NPcomplete problem). Adleman and his coauthors proposed sticker for enhancing the Adleman–Lipton model. In this paper, it proves how to apply sticker in the stickerbased model to construct solution space of DNA in the setsplitting problem and how to apply DNA operations in the Adleman–Lipton model to solve that problem from the solution space of sticker. © 2004 Elsevier B.V. All rights reserved.