基于自组装DNA计算的NTRU密码系统破译方案(英文)

自组装DNA计算在解决NP问题,尤其在破译密码系统方面,具有传统计算机无法比拟的优势．文中提出了一种用自组装DNA计算破译NTRU公钥密码系统的方法．针对NTRU密码系统的特点,采用DNA瓦片编码信息,借助于瓦片间的粘性末端进行自组装,给出了求解多项式卷积运算的实现方案．在此基础上,通过引入非确定性的指派瓦片,提出了一种破译NTRU系统的非确定性算法．通过创建数以亿计的参与计算的DNA瓦片,该算法可以并行地测试每个可能的密钥,以高概率地输出正确密钥．该方法最大的优点是充分利用了DNA瓦片具有的海量存储能力、生化反应的巨大并行性以及组装的自发有序性．理论分析表明,该方法具有一定的可行性．     

DNA fragment assembly using a grid-based genetic algorithm

In this paper we propose a genetic algorithm (GA) for solving the DNA fragment assembly problem in a computational grid. The algorithm, which is named GrEA, is a steady-state GA which uses a panmitic population, and it is based on computing parallel function evaluations in an asynchronous way. We have implemented GrEA on top of the Condor system, and we have used it to solve the DNA assembly problem. This is an NP-hard combinatorial optimization problem which is growing in importance and complexity as more research centers become involved on sequencing new genomes. While previous works on this problem have usually faced 30 K base pairs (bps) long instances, we have tackled here a 77 K bps long one to show how a grid system can move research forward. After analyzing the basic grid algorithm, we have studied the use of an improvement method to still enhance its scalability. Then, by using a grid composed of up to 150 computers, we have achieved time reductions from tens of days down to a few hours, and we have obtained near optimal solutions when solving the 77 K bps long instance (773 fragments). We conclude that our proposal is a promising approach to take advantage of a grid system to solve large DNA fragment assembly problem instances and also to learn more about grid metaheuristics as a new class of algorithms for really challenging problems.     

An ant colony optimization algorithm for DNA sequencing by hybridization

The reconstruction of DNA sequences from DNA fragments is one of the most challenging problems in computational biology. In recent years the specific problem of DNA sequencing by hybridization has attracted quite a lot of interest in the optimization community. Several metaheuristics such as tabu search and evolutionary algorithms have been applied to this problem. However, the performance of existing metaheuristics is often inferior to the performance of recently proposed constructive heuristics. On the basis of these new heuristics we develop an ant colony optimization algorithm for DNA sequencing by hybridization. An important feature of this algorithm is the implementation in a so-called multi-level framework. The computational results show that our algorithm is currently a state-of-the-art method for the tackled problem.     

Electrochemical DNA biosensor for the detection of interaction between di[azino-di(5,6-azafluorene)-κ-NN′]dichlormanganous and DNA

A new Mn(II) complex of MnL₂Cl₂ (L = azino-di(5,6-azafluorene)-κ²-NN′) was synthesized and utilized as an electrochemical indicator for the determination of hepatitis B virus (HBV) based on its interaction with MnL₂Cl₂. The electrochemical behavior of interaction of MnL₂Cl₂ with salmon sperm DNA was investigated on glassy carbon electrode (GCE). In the presence of salmon sperm DNA, the peak current of [MnL₂]²⁺ was decreased and the peak potential was shifted positively without appearance of new peaks. The binding ratio between [MnL₂]²⁺ and salmon sperm DNA was calculated to be 2:1 and the binding constant was 3.72 × 10⁸ mol² L⁻². The extent of hybridization was evaluated on the basis of the difference between signals of [MnL₂]²⁺ with probe DNA before and after hybridization with complementary sequence. Control experiments performed with non-complementary and mismatch sequence demonstrated the good selectivity of the biosensor. With this approach, a sequence of the HBV could be quantified over the range from 1.76 × 10⁻⁸ to 1.07 × 10⁻⁶ mol L⁻¹, with a linear correlation of r = 0.9904 and a detection limit of 6.80 × 10⁻⁹ mol L⁻¹. Additionally, the binding mechanism was preliminarily discussed. The mode of interaction between MnL₂Cl₂ and DNA was found to be primary intercalation binding.     

Pollard p-1因子分解的DNA计算机算法

如何有效地对大整数进行因子分解是数学上的一个难题.给出了基于分子生物技术的因子分解问题的DNA计算机算法.算法以Pollard p-1算法为基础,利用DNA分子生物操作完成加、减、乘、除运算,实现平方-乘以及欧几里德算法,产生并得到最终解.基于分子生物学的实验表明,该算法是可行和有效的.     

基于纳米材料的电化学生物传感器研究进展

该文主要从纳米尺寸材料电极的构建以及纳米材料作为生物分子指示剂两部分展开讨论,描述了依赖于阵列纳米管排列的生物分子与电极间的直接电子传递,纳米管、纳米颗粒为基质的纳米电极的构建,以及以金纳米颗粒、DNA量子点和蛋白为基础的多路分析技术与负载于CNT的新的纳米生物标记,特别讨论了纳米电化学方法在检测DNA和免疫传感器领域取得的研究进展.     

基于DNA技术的加密方案

DNA密码是伴随着DNA计算的研究而出现的密码学新领域。利用DNA合成技术、PCR扩增技术以及DNA数字编码技术,结合传统密码学提出了一种基于DNA技术的加密方案。方案利用引物对于PCR扩增技术的特殊作用,提出要以引物和编码方式为密钥,采用传统的加密方法对明文进行加密预处理,可有效防止可能词作为PCR引物进行攻击。生物学困难问题和密码学计算困难问题为该方案提供了双重的安全保障,安全性分析表明该加密方案具有很强的保密强度。     

一种基于无线传感器网络安全的社区卫生保健监护系统设计

设计并实现了一种基于无线传感器网络带安全机制的社区卫生保健监护系统.为了避免无线网络通信中信息泄漏和受到攻击,在现有传感器网络节点资源受限情况下,采用椭圆曲线密码体制及相关算法,有效地实现了加密系统中复杂的密钥管理功能,通过椭圆曲线加密和数字签名技术有效防止人体生理参数等敏感数据的泄漏,同时提出了一个切实可行的系统架构并加以实现.实验结果表明,系统能抵御网络潜在的无线信号窃听和内部攻击.     

时间分层的基于身份密码技术的算法和系统

基于椭圆曲线和Weil配对数学理论发明了具体可实施的基于身份密码的技术方案,但其一大缺陷就是密钥更新问题.介绍了一种时间分层的基于身份密码技术的算法和系统,其采用多个主密钥分量,逐级更新用户私钥,与PKG对接的顶级中间设备的帮助密钥更新时间相对较长,而用户终端保存的用户私钥更新时间相对较短,这样既满足了用户私钥更新频度的需要,又不引起系统频繁更新用户私钥所造成的沉重负荷.     

一种基于模糊聚类的构造进化树方法

各种生物之间的进化史可以通过构建进化树来讨论,因此进化树的研究成了一个研究热点。提出将利用DNA序列的4D表示所得相似矩阵视为模糊矩阵,再利用最大树法来构建进化树的方法。该方法不需要多序列比对,计算简单,实验验证了该方法的有效性。