DNA粘接计算模型及其应用

DNA计算是应用分子生物技术进行计算的新方法。应用形式语言及自动机理论技术研究DNA计算理论,有利于推动理论计算科学的发展。本文根据DNA分子的结构及特点给出了DNA分子的形式化描述,介绍了DNA粘接计算模型的文法结构和计算能力,并应用DNA计算方法求解3-SAT问题。     

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).     

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．     

解决NP问题的DNA编码技术

NP问题是密码学中的一个难题,用DNA计算解决NP问题是目前DNA密码研究的一个热点。文章阐述了DNA编码问题及约束条件,归纳出用DNA计算解决NP问题的基本步骤,分析了Adleman解决哈密尔顿回路问题的实验中DNA编码的质量,提出了可选的更好的编码,并总结了目前DNA编码研究中存在的问题。     

DNA computing model based on lab-on-a-chip and its application to solving the timetabling problem

The essential characteristic of DNA computation is its massive parallelism in obtaining and managing information.With the development of molecular biology technique,the field of DNA computation has made a great progress.By using an advanced biochip technique,laboratory-on-a-chip,a new DNA computing model is presented in the paper to solve a simple timetabling problem,which is a special version ofthe optimization problems.It also plays an important role in education and other industries.With a simulated biological experiment,the result suggested that DNA computation with lab-on-a-chip has the potential to solve a real complex timetabling problem.     

DNA computing model based on lab-on-a-chip and its application on solving the timetabling problem

The essential characteristic of DNA computation is its massive parallelism in obtaining and managing information. With the develop- ment of molecular biology technique, the field of DNA computation has made a great progress. By using an advanced biochip technique, laboratory-on-a-chip, a new DNA computing model is presented in the paper to solve a simple timetabling problem, which is a special version of the optimization problems. It also plays an important role in education and other industries. With a simulated biological experiment, the result snggested that DNA comnutation with lab-on-a-chin has the notential to solve a real comtplex timetabling problem.     

DNA计算原理与发展

DNA计算是一种摸拟生物分子DNA的结构并借助分子生物技术进行计算的新方法,为NP完全问题的解决提供了一种全新的途径,具有广阔的应用前景。本文首先介绍了DNA计算的基本思想;然后综述了DNA算例及其模型;指出了DNA计算的应用及目前存在的问题;最后对DNA计算的发展前景进行展望。     

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.     

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。     

最大匹配问题Tile自组装模型

Tile自组装模型凭借其自组装、可编程等特性在解决NP问题方面具有巨大优势.文中提出了一种求解最大匹配问题的Tile自组装新模型,该模型主要由初始配置子系统、选择子系统及检测子系统3大部分构成.新模型中首先设计Tile分子存储问题信息,其次通过Tile分子自组装操作生成最大匹配问题解空间,最后通过Tile检测分子筛选得到最大匹配问题的解.对模型从所需Tile分子种类、计算时间和计算空间3个方面进行性能分析,并通过实验模拟论证了模型的有效性和正确性.     

三维DNA自组装在多维背包问题中的应用研究

利用DNA自组装执行计算的思想已从实验上被证明了其可行性．已有多种理论模型被提出用以解决各种NP问题．基于DNA Tile自组装模型理论在二维下的扩展,本文设计了可以实现这一算法的三维DNA Tile组装系统,提出了一种用于解决多维背包问题的三维DNA自组装模型．该模型可以非确定性的输出可行性解决方案．分析表明系统可以在线性组装步骤内完成计算,所需的Tile种类数与问题维数无关．为探索三维DNA自组装的计算能力进行了一次有意义的尝试．     

背包问题的三链DNA计算模型

背包问题是组合优化中很重要的NP问题。因为三链DNA的特殊结构在参与反应时可以减少计算模型的错解率,且在生化反应中利用磁珠分离法对解进行分离较方便准确,文章利用三链模型求解0-1背包问题和完全背包问题。首先将背包问题的约束条件进行分解,再将物品质量编码为DNA片段,链接反应后,利用凝胶电泳技术和三链模型检测所包含的物品组合,得到满足约束条件的物品组合,再利用此方法检测价值最大的组合,即问题的解。其他的背包问题也可用此方法来解决。     

分子计算机的诞生与现状

介绍了计算机领域的一项最新成果———分子计算机 .分子计算机利用脱氧核糖核酸 (DNA)来进行计算 .腺嘌呤、鸟嘌呤、胞密啶、胸腺密啶 (核苷酸 )在计算中起了重要的作用 .使用限制内切酶、接合酶、转移酶、外切核酸酶、修饰酶来实现计算所需要的各种操作 .介绍了分子计算机完成的第 1个计算———解哈密顿通路问题的方法 ,用这种方法使NP完全问题在很短的时间内就得到解决     

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。     

基于粘贴系统求解无向图最短路径问题的DNA计算模型

提出了用粘贴系统求解赋权无向图中固定端点最短路径的DNA算法。该算法首先将无向图中每条边用两条方向相反的有向边代替,将无向图转化为有向图,同时利用粘贴系统的巨大并行性得到两端点间的所有路径,最后通过探针、电泳等分子生物技术手段获得最短路径,并通过实例说明算法的可行性。     

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．     

一类特殊整数规划问题的DNA计算

通过22种荧光标记DNA链的办法,在基于表面方式的实验环境中,将变量用变异的二进制变量组来表示,提出一种基于DNA计算的特殊整数规划问题的求解算法.算法通过将上述问题转化为特殊的-1-0-1规划问题,解决了运筹学中特殊的整数规划问题,并为最终解决一般的整数规划问题奠定了基础.