Improved taboo search algorithm for designing DNA sequences

The design of DNA sequences is one of the most practical and important research topics in DNA computing. We adopt taboo search algorithm and improve the method for the systematic design of equal-length DNA sequences, which can satisfy certain combinatorial and thermodynamic constraints. Using taboo search algorithm, our method can avoid trapping into local optimization and can find a set of good DNA sequences satisfying required constraints.     

DNA计算及DNA计算机的研究进展

概述了DNA计算的基本原理、DNA计算的应用和DNA计算机的研究进展及存在问题，基于DNA生化反应的计算机称为DNA计算机，由于其采用一种完全不同于传统计算机的运算逻辑与存贮方式，DNA计算机在解决某些复杂问题时具有传统计算机无法比拟的优势，目前国际上关于DNA计算和DNA分子生物计算机的研究方兴未艾，极大地推进了DNA计算机的研究过程。     

图的最小顶点覆盖问题的质粒DNA计算模型

给出了图的最小顶点覆盖问题的质粒DNA算模型及其实现算法．算法的时间复杂性是O(q),编码最小覆盖问题所需的核苷酸片段种类为n,其中n,q分别是图的规模和边数．在算法中,所用酶的种类也等于图的规模．而且,算法不需要复杂的单链DNA自身退火反应和PCR扩增．     

A global heuristically search algorithm for DNA encoding

A new efficient algorithm is developed to design DNA words with equal length for DNA computing. The algorithm uses a global heuristic optimizing search approach and converts constraints to a carry number to accelerate the convergence, which can generate a DNA words set satisfying some thermodynamic and combinatorial constraints. Based on the algorithm, a software for DNA words design is developed.     

A global heuristically search algorithm for DNA encoding

A new efficient algorithm is developed to design DNA words with equal length for DNA computing. The algorithm uses a global heuristic optimizing search approach and converts constraints to a carry number to accelerate the convergence, which can generate a DNA words set satisfying some thermodynamic and combinatorial constraints. Based on the algorithm, a software for DNA words design is developed.     

DNA计算技术进展

论述DNA计算技术进展。先介绍DNA计算的基本原理,论述DNA计算的特点方法和存在的问题,接着介绍DNA计算的国内外研究现状,最后指出DNA计算研究中需要解决的问题。     

A DNA sequence alignment algorithm using quality information and a fuzzy inference method

DNA sequence alignment algorithms in computational molecular biology have been improved by diverse methods. In this paper, we propose a DNA sequence alignment that uses quality information and a fuzzy inference method developed based on the characteristics of DNA fragments and a fuzzy logic system in order to improve conventional DNA sequence alignment methods that uses DNA sequence quality information. In conventional algorithms, DNA sequence alignment scores are calculated by the global sequence alignment algo- rithm proposed by Needleman-Wunsch, which is established by using quality information of each DNA fragment. However, there may be errors in the process of calculating DNA sequence alignment scores when the quality of DNA fragment tips is low, because only the overall DNA sequence quality information are used. In our proposed method, an exact DNA sequence alignment can be achieved in spite of the low quality of DNA fragment tips by improvement of conventional algorithms using quality information. Mapping score param- eters used to calculate DNA sequence alignment scores are dynamically adjusted by the fuzzy logic system utilizing lengths of DNA fragments and frequencies of low quality DNA bases in the fragments. From the experiments by applying real genome data of National Center for Biotechnology Information, we could see that the proposed method is more efficient than conventional algorithms.     

基于生物芯片技术的地图四着色问题的DNA算法

基于先进的生物芯片技术、多种荧光标记技术和DNA计算理论提出了解决地图四着色问题的DNA算法,通过一个实例阐述了具体的DNA操作步骤,并对生化实验进行了计算机模拟,给出了所有可行的着色方案,证明了该算法的可行性。与已有的模型相比,该模型在解的准确性、计算复杂度以及操作的自动化方面都表现出了很强的优势。     

基于稀疏技术的序列运算方法

序列运算过程中经常遇到稀疏序列之间的相互运算。针对序列运算的计算优化问题,该文首先分析了序列稀疏性的成因,并分析了序列运算理论中不同类型基本运算对于序列稀疏性的影响,同时给出了相应的计算结果序列的稀疏度估算公式。然后,根据序列与序列运算的特点,将稀疏技术应用于序列运算中,提出了通用存储方法与特征存储方法等2种稀疏序列存储技术。最后,利用算例对所提出的稀疏序列存储方法加以检验,采用稀疏技术后不同类型序列运算的时间开销均有不同程度的降低,特别是卷和、交积、并积与序除运算的计算时间下降为原来的6%~38%,算例结果表明了该文工作的正确性与应用价值。     

Molecular logic computing model based on self-assembly of DNA nanoparticles

In this paper, a logic computing model was constructed using a DNA nanoparticle, combined with color change technology of DNA/Au nanoparticle conjugates, and DNA computing. Several important technologies are utilized in this molecular computing model: DNA self-assembly, DNA/Au nanoparticle conjugation, and the color change resulting from Au nanoparticle aggregation. The simple logic computing model was realized by a color change, resulting from changing of DNA self-assembly. Based on this computing model, a set of operations computing model was also established, by which a simple logic problem was solved. To enlarge the applications of this logic nanocomputing system, a molecular detection method was developed for H1N1 virus gene detection.     

基于闭环DNA的边着色问题DNA算法

提出一种新的DNA计算模型——闭环DNA计算模型。引进了批删除实验。讨论了其实现过程;提出并证明了边着色问题的基本定理,设计并实现了闭环DNA计算算法．该算法将边的DNA编码分为两部分,一部分存储边和色位置的二维数据,另一部分存储色号值;在DNA计算的主体部分用批删除实验得到全部正常的边着色,并通过电泳实验和检测实验获得χ′^-正常边着色．举例说明了算法的有效性和可行性．     

DNA序列的一种分类方法

基于小波变换和相关技术,提出了一种DNA序列的分类方法.首先将DNA序列转换成数字序列,然后对此序列进行Matlab快速分解,计算未知类别序列与已知类别序列的相关系数,由此判定序列的类别.结果表明,该方法是切实可行的.     

A surface-based DNA algorithm for the minimal vertex cover problem

Abstract DNA computing was proposed for solving a class of intractable computational problems, of which the computing timewill grow exponentially with the problem size. Up to now, many achievements have been made to improve its performance and increase itsreliability. It has been shown many times that the surface-based DNA computing technique has very low error rate, but the technique hasnot been widely used in the DNA computing algorithms design. In this paper, a surface-based DNA computing algorithm for minimal ver-tex cover problem, a problem well-known for its exponential difficulty, is introduced. This work provides further evidence for the abilityof surface-based DNA computing in solving NP-complete problems.     

基于BIT位运算的N皇后问题解法

皇后问题是一经典的回溯算法问题,本文使用B IT位运算对非递归的回溯算法进行优化,取得了较好的效果,对其他类似问题的算法的优化有一定指导意义。     

路径排序问题基于表面的DNA算法

提出了路径排序问题表面DNA算法三步骤：a．找出两端点的所有链,b．筛选出所有的路,c．得到路序．指出编码问题在DNA计算中的重要性．在算法实现过程中,用保护两端点对应的DNA片段3’端或5’端的办法得到所有的链,并用电泳的方法对链进行排序以及去掉链长大于图权值总和的链;对探针进行生物素标记并且采用观察、记录亮点强度的办法筛选出所有的路;分析实验记录得到路序．将算法推广到最短（长）路问题的不同之处在第三步,即只需分析在表面上排在最前（最后）的DNA链的实验记录就得到最短（长）路．     

A new DNA algorithm to solve graph coloring problem

Using a small quantity of DNA molecules and little experimental time to solve complex problems successfully is a goal of DNA computing. Some NP-hard problems have been solved by DNA computing with lower time complexity than conventional computing. However, this advantage often brings higher space complexity and needs a large number of DNA encoding molecules. One example is graph coloring problem. Current DNA algorithms need exponentially increasing DNA encoding strands with the growing of problem size. Here we propose a new DNA algorithm of graph coloring problem based on the proof of four-color theorem. This algorithm has good properties of needing a relatively small number of operations in polynomial time and needing a small number of DNA encoding molecules (we need only 6R DNA encoding molecules if the number of regions in a graph is R).     

A new DNA algorithm to solve graph coloring problem

Using a small quantity of DNA molecules and little experimental time to solve complex problems successfully is a goal of DNA computing. Some NP-hard problems have been solved by DNA computing with lower time complexity than conventional computing. However, this advantage often brings higher space complexity and needs a large number of DNA encoding molecules. One example is graph coloring problem. Current DNA algorithms need exponentially increasing DNA encoding strands with the growing of problem size. Here we propose a new DNA algorithm of graph coloring problem based on the proof of four-color theorem. This algorithm has good properties of needing a relatively small number of operations in polynomial time and needing a small number of DNA encoding molecules (we need only 6R DNA encoding molecules if the number of regions in a graph is R).     

新一代网络计算模式分析

论述了目前引起广泛关注的新一代网络计算模式，即Web服务、P2P和网格计算，阐述了它们的体系结构，重点分析了它们的应用前景，即Web服务能够让用户直接获得所需要的服务结果，从而构造出个性化的、能适应业务变化并满足用户即时需求的网络应用；P2P能够实现空闲计算资源的共享；网格计算则能够在智能教育、机械、军事、医药等领域得到广泛应用。     

质粒DNA计算模型的计算体系

首先从具体实例入手抽象和归纳出质粒DNA计算模型的概念,并对质粒DNA计算模型计算体系的2个基本要素———计算物质和计算手段进行研究,由此形成了质粒DNA计算模型完备的计算体系;然后针对质粒DNA计算模型计算体系的应用,分析和解决了经常出现的关键问题.讨论了初始质粒DNA重新合成的重要性,并给出了重新合成的方法;接着对计算体系的2个基本实验(酶切和酶连实验)的成功率问题进行了分析,并提出了解决的方案;最后对检测实验进行了分析,提出了检测多种DNA序列的检测方法.对这些问题的分析和解决有利于质粒DNA计算模型理论的完善和应用的拓广.     

一种基于进化博弈论的云计算虚拟计算资源配置模型

目前针对云计算的资源配置策略研究多关注于云计算资源提供商状况,研究云计算资源提供商的虚拟资源调度管理策略,可以提高云计算资源的可靠性和资源利用率.本文针对云应用提供商,提出基于进化博弈论的自适应资源配置模型,以性能目标为进化博弈目标,通过该模型得到最优的资源分配策略.对比实验结果显示,本模型能有效减少资源的使用.