基于DNA下推自动机二进制减法和乘法的实现

提出了基于DNA下推自动机二进制减法和乘法的实现方法.一位二进制借位减法,是通过预先构造好的DNA下推自动机模型在一个试管中以该模型的运行方式自动完成运算.m位二进制借位减法,是在一位二进制减法的基础上,按照从低位到高位的顺序,将低位产生的借位作为高位试管操作巾的输入符号串,从而完成高位的减法运算.两位二进制乘法中包含移位和加法操作,在两个试管中分别设计好DNA下推自动机模型,分别完成被乘数与乘数各位的移位操作,同时结合相应的生物操作,将其作为另一个试管加法操作中的输入符号串,则加法操作中产牛的结果即为所求.在此基础上,m位二进制乘法可通过移位操作的并行性和加法操作的串行性来完成运算.这些实现方法为DNA下推自动机实现基本的算术运算提供了比较完整的运算机制.     

A rapid polymerisation process realizing 3D biocompatible structures in a microfluidic channel suitable for genetic analysis

Surface probe immobilisation is a complex and time consuming task undertaken prior to microfluidic integration, this requires surface functionalisation, biomolecule spotting, incubation and blocking steps. Traditional bonding techniques (anodic, thermal, etc.) or adhesives (UV cured) used to seal fluidic systems may denature biomolecules due to high temperature or vapour effects, thus bonding techniques such as thin film laminate or PDMS are used to seal systems, with substrate-fluidic alignment required prior to bonding. We propose a technique allowing probe DNA molecules to be immobilised in a sealed microfluidic system using (3D) hydrogel structures without any alignment steps. A prepolymer solution is introduced to the channels where photo-polymerisation is undertaken forming 3D structures covalently attached to the channel surface. We use a photo-initiated prepolymer material poly-ethylene-glycol (PEG) to form structures containing probe DNA. This process is fast compared to conventional biomolecule immobilisation techniques and is also biocompatible, this direct write approach removes overnight immobilisation/incubation of the probe DNA, it also facilitates immobilisation within a sealed fluidic system where conventionally DNA probe spots must be immobilised prior to channel sealing. We consider the transport of target DNA from bulk analyte to the 3D gel structure and evaluate hybridisation within the microfluidic system.     

基于XML的DNA公共数据模型

针对目前DNA数据组织与处理中存在的数据异构问题,提出一个基于XML的DNA公共数据模型（DCDM）。该模型具有很强的可扩展性,能克服一般公共数据模型的作用范围小的缺点,可用于构建DNA研究领域统一的DNA数据描述模式。实验结果表明,该模型能解决DNA数据异构中的语义异构。     

Similarity/dissimilarity calculation methods of DNA sequences: A survey

DNA sequence similarity/dissimilarity analysis is a fundamental task in computational biology, which is used to analyze the similarity of different DNA sequences for learning their evolutionary relationships. In past decades, a large number of similarity analysis methods for DNA sequence have been proposed due to the ever-growing demands. In order to learn the advances of DNA sequence similarity analysis, we make a survey and try to promote the development of this field. In this paper, we first introduce the related knowledge of DNA similarities analysis, including the data sets, similarities distance and output data. Then, we review recent algorithmic developments for DNA similarity analysis to represent a survey of the art in this field. At last, we summarize the corresponding tendencies and challenges in this research field. This survey concludes that although various DNA similarity analysis methods have been proposed, there still exist several further improvements or potential research directions in this field.     

基于NaOH刻蚀玻碳电极的电化学传感器在检测膀胱癌DNA中的应用

制备了一种基于活化的玻碳电极的新型电化学DNA生物传感器,可用于膀胱癌DNA的检测.通过循环伏安法(CV)实现玻碳电极在NaOH溶液中的刻蚀,使电极表面负载大量官能团,为DNA提供连接位点,由Laviron方程计算得到玻碳电极表面的羧基浓度为 1.022×10-6 mol/cm2.亚甲基蓝(MB)作为电化学检测的杂交指示剂.采用原子力显微镜(AFM)对刻蚀后的电极进行了形貌表征.在最优杂交条件下,通过差分脉冲法(DPV)计算出最佳检测限为5.677×10-13 mol/L(n=5),适用目标 DNA浓度范围1×10-8 mol/L~1×10-12 mol/L.该传感器有望用于实际样品中膀胱癌DNA的快速检测.     

Polyominoes simulating arbitrary-neighborhood zippers and tilings

This paper provides a bridge between the classical tiling theory and the complex-neighborhood self-assembling situations that exist in practice.The neighborhood of a position in the plane is the set of coordinates which are considered adjacent to it. This includes classical neighborhoods of size four, as well as arbitrarily complex neighborhoods. A generalized tile system consists of a set of tiles, a neighborhood, and a relation which dictates which are the “admissible” neighboring tiles of a given tile. Thus, in correctly formed assemblies, tiles are assigned positions of the plane in accordance with this relation.We prove that any validly tiled path defined in a given but arbitrary neighborhood (a zipper) can be simulated by a simple “ribbon” of microtiles. A ribbon is a special kind of polyomino, consisting of a non-self-crossing sequence of tiles on the plane, in which successive tiles stick along their adjacent edge.Finally, we extend this construction to the case of traditional tilings, proving that we can simulate arbitrary-neighborhood tilings by simple-neighborhood tilings, while preserving some of their essential properties.     

基于DNA遗传算法的CR多载波参数优化

提出了一种基于DNA计算的非支配排序多目标遗传算法(DNA-GA)来对CR多载波传输参数进行优化。该算法通过非支配排序计算个体适应度,结合克隆操作使算法收敛于全局最优,并引入DNA基因级操作,以提高算法的搜索性能,保持种群的多样性。通过在不同服务需求情况下得到的仿真参数结果,证明了DNA-GA可以有效地优化CR传输参数。     

WindowsDNA架构模型在证券模拟交易系统开发中的应用

Windows分布式集成网络应用体系结构（Windows DNA)是Microsoft推出的旨在创建基于Microsoft Windows平台的应用程序框架的架构模型,其核心是将Web和客户机／服务器的应用开发模型通过一套公共对象模型集成起来。本文在概述Windows DNA架构的基础上,分析了其在证券模拟交易系统开发中的应用,并给出了一些经验及体会。     

Staged self-assembly: nanomanufacture of arbitrary shapes with <Emphasis Type="Italic">O</Emphasis>(1) glues

We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are motivated by a practical nanofabrication scenario through protein-based bioengineering. Staging allows us to break through the traditional lower bounds in tile self-assembly by encoding the shape in the staging algorithm instead of the tiles. All of our results are based on the practical assumption that only a constant number of glues, and thus only a constant number of tiles, can be engineered. Under this assumption, traditional tile self-assembly cannot even manufacture an n × n square; in contrast, we show how staged assembly in theory enables manufacture of arbitrary shapes in a variety of precise formulations of the model.