一种优化DNA计算模板性能的新方法

刘文斌; 朱翔鸥; 王向红; 张强; 马润年

doi:10.3724/SP.J.1146.2006.01640

一种优化DNA计算模板性能的新方法

doi: 10.3724/SP.J.1146.2006.01640

刘文斌^{①;朱翔鸥},
朱翔鸥,
王向红,
张强,
马润年

基金项目:

国家自然科学基金(60403002，60403001，30670486)，中国博士后科学基金(2004036130)和浙江省自然科学基金(Y106654，Y405553)资助课题

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出版历程
- 收稿日期: 2006-10-25
- 修回日期: 2007-03-23
- 刊出日期: 2008-05-19

A New Method to Optimize the Template Set in DNA Computing

摘要

摘要: 编码问题是目前DNA计算中的重点和难点之一,该文介绍了影响编码的各种因素及模板编码的基本思想。在此基础上分析了移位杂交出现的原因,提出了提高模板结合移位距离的一种新算法。该算法一方面降低了搜索空间,另一方面筛选了那些自身移位距离性质差的序列因而提高了算法的效率。计算结果表明模板集合的性能明显提高。此外,在保持01含量基本不变的情况下,适当扩展模板集合的搜索范围可以增加模板的数量。
- DNA计算; 编码问题; 模板编码方法
Abstract: The encoding issue is a most fundamental one in DNA based computing. In this paper, the various factors that influence the encoding problem and the general idea of the template encoding method are first introduced. Then the reason of the shift hybridisation occurred in DNA computing is presented. And a new method is proposed to search template set with high shift distance. Additionally, to increase the search space can also increase the number of template string.

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参考文献(1)

Garzon M, Neathery P, and Deaton P. A new metric for DNAcomputing [C]. In Proc. of 2nd Annual Genetic ProgrammingConference, Morgan Kaufmann, 1997: 472-47.

Adleman L. Molecular computation of solution to combinatorialproblems [J].Science.1994, 266:1021-1024[2]Garzon M, et al.. A new metric for DNA computing [C].Proceedings of the 2nd Annual Genetic ProgrammingConference GP-97, Morgan Kaufmann, Stanford University,1997: 472-487.[3]Garzon M, Deaton R, Nino L F, Stevens S E , and Wittner M.Genome encoding for DNA computing [C]. TheThirdDIMACS Workshop on DNA-based Computing,Uinversity of Pennsylvania, 1997: 230-237.[4]Baum E B. DNA sequences useful for computation [C]. Proc.Second Annual Meeting on DNABased Computers, AmericanMathematical Society, Princton University, 1996: 235-242.[5]Feldkamp, et al.. A DNA sequence compile[C]. Proceedings of6th DIMACS Workshop on DNA Based Computers,Netherlands, 2000: 253-257.[6]Suyama A, et al.. DNA chips-integrated chemical circuits forDNA diagnosis and DNA computers [C]. Proc. 3rd InternationalMicromachine Symp., Tokyo, 1997: 7-12.[7] Morey J. Encoding Choices for Error Resistant DNAComputers[OL]. www.csd.uwo.ca /~morey /dnatalk/kevin/dna/dnaerror.html.[8]Braich R, Johnson C, Rothemund P, and Adleman L.Solution of a satisfiability problem on a Gel-based DNAcomputer [C]. DNA 2000, 2001, LCNS 2054: 27-42.[9]Frutos A, et al.. Demonstration of a word design strategy forDNA computing on surface [J].Nucleic Acids Research.1997,25(23):4748-4757[10]Liu Wenbin, Wang Shudong, Gao Lin，and Xu Jin. DNAsequence design based on template strategy [J]. Chem. Info.Comput. Sci, 2003, 43(6): 2014-2018.[11]SantaLucia J, Allawi H, and Seneviratne P. Improved nearest-neighbor parameters for predicting DNA duplex stability [J].Biochemistry.1996, 35(11):3555-3562[12]刘文斌. DNA 计算中的编码问题及模型研究. [博士论文], 武汉：华中科技大学, 2004.1.Liu Wen-bin. Research on the Enconding Problem andAlgorithms of DNA Computing. [Dissertation(Doctor)],Huazhong University of Science Technology, Wuhan, China,2004.1..

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