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).     

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.     

最大独立集问题的表面计算模型

DNA计算是解决一类难于计算问题的一种新方法,最大独立集问题是一个著名的NP完全问题,最大团问题及最小覆盖问题等价于最大独立集问题。本文中,我们尝试将最大独立集转化为0-1规化问题,利用0-1规化问题的表面计算模型求解最大独立集。本文充分说明了NP-完全问题可以相互转化的性质。     

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。     

基于粘贴和删除系统求解旅行商问题的DNA算法

旅行商问题（Traveling Salesman Problem,TSP）是一个典型的NP完全问题.粘贴和删除模型是DNA计算的两个基本计算模型.结合上述两个模型的优点,构造粘贴-删除模型,并利用该模型给出求解旅行商问题一种新的DNA算法.     

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．     

A novel DNA computing model based on RecA-mediated triple-stranded DNA structure

The field of DNA computing emerged in 1994 after Adleman’s paper was published. Henceforth,a few scholars solved some noted NP-complete problems in this way. And all these methods of DNA computing are based on conventional Watson-Crick hydrogen bond of doublehelical DNA molecule. In this paper, we show that the triple-stranded DNA structure mediated by RecA protein can be used for solving computational problems. Sequence-specific recognition of double-stranded DNA by oligonucleotide-directed triple helix (triplex) formation is used to carry out the algorithm. We present procedure for the 3-vertex-colorability problems. In our proposed procedure, it is suggested that it is possible to solve more complicated problems with more variables by this model.     

DNA computing on surfaces

DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the 'NP-complete' or non-deterministic polynomial time complete problems). The principle of the technique has been demonstrated experimentally for a simple example of the hamiltonian path problem (in this case, finding an airline flight path between several cities, such that each city is visited only once). DNA computational approaches to the solution of other problems have also been investigated. One technique involves the immobilization and manipulation of combinatorial mixtures of DNA on a support. A set of DNA molecules encoding all candidate solutions to the computational problem of interest is synthesized and attached to the surface. Successive cycles of hybridization operations and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions. Upon completion of all the multistep cycles, the solution to the computational problem is identified using a polymerase chain reaction to amplify the remaining molecules, which are then hybridized to an addressed array. The advantages of this approach are its scalability and potential to be automated (the use of solid-phase formats simplifies the complex repetitive chemical processes, as has been demonstrated in DNA and protein synthesis). Here we report the use of this method to solve a NP-complete problem. We consider a small example of the satisfiability problem (SAT), in which the values of a set of boolean variables satisfying certain logical constraints are determined.     

Modified PSO algorithm for solving planar graph coloring problem

The graph coloring is a classic NP-complete problem. Presently there is no effective method to solve this problem. Here we propose a modified particle swarm optimization （PSO） algorithm in which a disturbance factor is added to a particle swarm optimizer for improving its performance. When the current global best solution cannot be updated in a certain time period that is longer than the disturbance factor, a certain number of particles will be chosen according to probability and their velocities will be reset to force the particle swarm to get rid of local minimizers. It is found that this operation is helpful to improve the performance of particle swarm. Classic planar graph coloring problem is resolved by using modified particle swarm optimization algorithm. Numerical simulation results show that the performance＇of the modified PSO is superior to that of the classical PSO.     

Modified PSO algorithm for solving planar graph coloring problem

The graph coloring is a classic NP-complete problem. Presently there is no effective method to solve this problem. Here we propose a modified particle swarm optimization (PSO) algorithm in which a disturbance factor is added to a particle swarm optimizer for improving its performance. When the current global best solution cannot be updated in a certain time period that is longer than the disturbance factor, a certain number of particles will be chosen according to probability and their velocities will be reset to force the particle swarm to get rid of local minimizers. It is found that this operation is helpful to improve the performance of particle swarm. Classic planar graph coloring problem is resolved by using modified particle swarm optimization algorithm. Numerical simulation results show that the performance of the modified PSO is superior to that of the classical PSO.     

BWC着色问题的一种启发式算法研究

无向图的BWC着色问题是给定两个正整数b和w,判断是否存在这样的着色方案:对b个顶点着黑色,对w个顶点着白色,其它顶点不着色,着黑色顶点集合与着白色顶点集合之间没有任何边相连。BWC的最优化问题,是找出一种最优化着色方案,使得与所有黑色顶点不相连接的着白色顶点数最大。该问题被证明是NP-完全问题。提出了一种基于禁忌表和局部搜索机制的混合启发式算法(BTLSBWC),通过对部分网络图进行测试,结果达到了现有文献计算出的最好值。     

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 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 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 development of molecular biology technique, the field of DNA computation has made a great progress. By using an advance technique of biochip, laboratory-on-a-chip, in this paper a new DNA computing model was presented to solve a simple timetabling problem, which is a special version of the optimization problems and plays an important role in education. 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 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.     

关于合取范式可满足性问题的复杂性分析

合取范式可满足性问题(简称SAT问题)是典型的NP完全问题,本文引入了一个饱和子句集的新概念,利用饱和子句集的特性,研究了SAT问题的复杂性,证明了SAT问题复杂性为多项式的一个充分条件,并揭示了二元可满足性问题与三元可满足性问题的本质差别。因此,通过变换来提炼出SAT问题的复杂性的本质特征,并加以研究的方法,是SAT问题的复杂性研究的一种有效方法。     

脱氧核糖核酸在案例分析中的应用

用脱氧核糖核酸(DNA)作为信息处理的工具,运用图论方法,解决案例分析 中较为复杂的逻辑计算问题,展示了DNA分子计算的光明前景。     

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。     

染色的装箱问题及其近似算法

给出了染色装箱问题和染色覆盖问题的数学描述,得到了给定颜色限制的染色装箱问题和染色覆盖问题的两个近似算法.