基于DNA Tiles自组装的布尔逻辑运算

大量研究工作表明,DNA tiles自组装现象是分子生物计算过程中一个很重要的计算方式.分子自组装的基本特点在于由许多小分子在一定机理的作用下,自动形成更大规模的超级分子结构的过程.自组装用于计算,在于这种组装模式可以抽象成一个自动化的系统,只需根据问题的需要设计好输入,再将其输入到运算系统,经过分子自组装过程,最后能生成问题的解.文中基于这样的运算机理,在DNA tiles自组装这个计算平台上,尝试做布尔逻辑运算,针对4变量4句子的布尔逻辑问题,提出一个DNA tiles自组装自动化运算系统.     

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.

Efficient automatic exact motif discovery algorithms for biological sequences

ObjectiveThis paper presents an algorithm for the solution of the motif discovery problem (MDP).Methods and materialsMotif discovery problem can be considered in two cases: motifs with insertions/deletions, and motifs without insertions/deletions. The first group motifs can be found by stochastic and approximated methods. The second group can be found by using stochastic and approximated methods, but also deterministic method. We proved that the second group motifs can be found with a deterministic algorithm, and so, it can be said that the second motifs finding is a P-type problem as proved in this paper.Results and conclusionsAn algorithm was proposed in this paper for motif discovery problem. The proposed algorithm finds all motifs which are occurred in the sequence at least two times, and it also finds motifs of various sizes. Due to this case, this algorithm is regarded as Automatic Exact Motif Discovery Algorithm. All motifs of different sizes can be found with this algorithm, and this case was proven in this paper. It shown that automatic exact motif discovery is a P-type problem in this paper. The application of the proposed algorithm has been shown that this algorithm is superior to MEME, MEME3, Motif Sampler, WEEDER, CONSENSUS, AlignACE.     

基于虚拟仪器的瓷砖平整度自动检测系统

为实现瓷砖表面平整度误差的自动检测和产品质量的自动分级，探讨了瓷砖表面平整度检测的原理和方法。将虚拟仪器技术应用于瓷砖表面平整度的自动检测研究，以非接触式光纤位移传感器、数据采集卡、PC机作为硬件配置，以LabVIEW作为软件开发平台，设计了瓷砖表面平整度自动检测系统：实际应用表明，该系统可以自动检测瓷砖表面平整度，并对产品进行分级，适合于实际生产过程的质量控制.     

DNA algorithms for fractal construction—an application of the SInsDelP system

The SInsDelP system with single contextual insertion and (u, v)-contextual deletion was introduced by Murugan and Easwarakumar. In this paper we discuss an application of the SInsDelP system for the construction of fractal images. The fractal images considered are of self-similar types, such as Koch Snowflake, Anti-Koch Snowflake, Fractal Tree and Sierpinski Triangle. This is performed in two stages. A DNA sequence for the fractal image is generated first by a sequence of SInsDelP operations, and then the respective image is produced through the specialized recognition algorithm.     

Self-Assembling Rulers for Approximating Generalized Sierpinski Carpets

Discrete self-similar fractals have been used as test cases for self-assembly, both in the laboratory and in mathematical models, ever since Winfree exhibited a tile assembly system in which the Sierpinski triangle self-assembles. For strict self-assembly, where tiles are not allowed to be placed outside the target structure, it is an open question whether any self-similar fractal can self-assemble. This has motivated the development of techniques to approximate fractals with strict self-assembly. Ideally, such an approximation would produce a structure with the same fractal dimension as the intended fractal, but with specially labeled tiles at positions corresponding to points in the fractal. We show that the Sierpinski carpet, along with an infinite class of related fractals, can approximately self-assemble in this manner. Our construction takes a set of parameters specifying a target fractal and creates a tile assembly system in which the fractal approximately self-assembles. This construction introduces rulers and readers to control the self-assembly of a fractal structure without distorting it. To verify the fractal dimension of the resulting assemblies, we prove a result on the dimension of sets embedded into discrete fractals. We also give a conjecture on the limitations of approximating self-similar fractals.     

The Complexity of Flood Filling Games

We study the complexity of the popular one player combinatorial game known as Flood-It. In this game the player is given an n×n board of tiles where each tile is allocated one of c colours. The goal is to make the colours of all tiles equal via the shortest possible sequence of flooding operations. In the standard version, a flooding operation consists of the player choosing a colour k, which then changes the colour of all the tiles in the monochromatic region connected to the top left tile to k. After this operation has been performed, neighbouring regions which are already of the chosen colour k will then also become connected, thereby extending the monochromatic region of the board. We show that finding the minimum number of flooding operations is NP-hard for c≥3 and that this even holds when the player can perform flooding operations from any position on the board. However, we show that this ‘free’ variant is in P for c=2. We also prove that for an unbounded number of colours, Flood-It remains NP-hard for boards of height at least 3, but is in P for boards of height 2. Next we show how a (c−1) approximation and a randomised 2c/3 approximation algorithm can be derived, and that no polynomial time constant factor, independent of c, approximation algorithm exists unless P=NP. We then investigate how many moves are required for the ‘most demanding’ n×n boards (those requiring the most moves) and show that the number grows as fast as Q(?c n)\Theta(\sqrt{c}\, n). Finally, we consider boards where the colours of the tiles are chosen at random and show that for c≥2, the number of moves required to flood the whole board is Ω(n) with high probability.     

A route to fractal DNA-assembly

Crystallization is periodic self-assembly onthe molecular scale. Individual DNA componentshave been used several times to achieveself-assembled crystalline arrangements in twodimensions. The design of a fractal system isa much more difficult goal to achieve withmolecular components. We present DNAcomponents whose cohesive portions arecompatible with a fractal assembly. Thesecomponents are DNA parallelograms that havebeen used previously to produce two dimensionalarrays. To obtain a fractal arrangement,however, we find it necessary to combine theseparallelograms with glue-like constructs. Theassembly of the individual parallelograms and aseries of glues and protecting groups appear toensure the fractal growth of the system in twodimensions. Synthetic protocols are suggestedfor the implementation of this approach tofractal assembly.     

3D Fractal DNA Assembly from Coding,Geometry and Protection

We present DNA components whose 3D geometry and cohesive portions are compatible with a fractal 3D assembly. DNA parallelograms have been proposed in Carbone and Seeman [(2002b) Natural Computing 1: 469–480; (2003) Natural Computing 2: 133–151] as suitable building blocks for a 2D fractal assembly of the Sierpinski carpet. Here we use Mao 3D triangles, which are 3D geometrically trigonal molecules, to construct basic building blocks and we obtain a simplified version of the 2D assembly design. As in the previous 2D construction, we utilize the interplay of coding in the form of cohesive ends, geometrical complementarity and protection of potentially undesirable sites of reactivity. The schema we propose works for trigonal symmetries and the Mao triangle is one example of a possible DNA trigonal tile.     

A novel compact self‐similar fractal UWB MIMO antenna

A novel compact self‐similar fractal ultra‐wideband (UWB) multiple‐input‐multiple‐output (MIMO) antenna is presented. This fractal geometry is designed by using iterated function system (IFS). Self‐similar fractal geometry is used here to achieve miniaturization and wideband performance. The self‐similarity dimension of proposed fractal geometry is 1.79, which is a fractional dimension. The antenna consists of two novel self‐similar fractal monopole‐antenna elements and their metallic area is minimized by 29.68% at second iteration. A ground stub of T‐shape with vertical slot enhances isolation and impedance bandwidth of proposed MIMO antenna. This antenna has a compact dimension of 24 × 32 mm² and impedance bandwidth (S₁₁ < ?10 dB) of 9.4 GHz ranging from 3.1 to 12.5 GHz with an isolation better than 16 dB. The various diversity performance parameters are also determined. There is good agreement between measured and simulated results, which confirms that the proposed antenna is acceptable for UWB applications.     

基于神经网络的字牌识别系统

设计基于BP神经网络的字牌识别系统,可用于实现字牌自动发牌机,以克服字牌比赛中人工洗牌的弊端。为提高系统的识别正确率,对字牌图像进行特定处理：（1）对图像像素数据通过闭运算、膨胀运算和腐蚀运算衍生出多种标准特征矩阵以增加训练样本,（2）挖掘图像特征数据规律提取颜色特征值和大小写特征值,组成特征向量并依此对图像进行分类编组,用特定编组的特征矩阵训练对应编组的BP神经网络。仿真结果表明,该系统识别正确率高,适应字牌比赛对自动发牌机的要求。     

Decentralized consensus in distributed networks

Abstract

We consider the decentralised consensus optimization problem in this paper. A fast decentralised gradient-based algorithm is proposed for a general class of problems with convex and differentiable objective functions. The developed method guarantees that all the nodes in the network would reach consensus on the global variable eventually. Based on the proposed decentralised algorithm, a broadcast-based protocol is designed, which is capable of providing solution for real-time in situ seismic imaging. Extensive numerical experiments on both synthetic and real sensor network seismic data sets validate the superior efficiency of the proposed algorithm over the other benchmarks.     

二维瓦片矢量基对二次映射分布方法

针对基于对象存储系统中各个存储设备的性能差异,提出了一种二维瓦片矢量基对二次映射分布方法。首先,构建一组性能相同、容量无限的虚拟设备,并根据矢量基对分布模板将二维瓦片分布到M个虚拟设备中;然后,通过伪随机数发生器将M个虚拟设备中的瓦片均匀映射到[0,1）区间的M个等分区间;最后,根据真实设备的瓦片分布百分比将[0,1）区间划分成M个区间,并将映射到各个区间的二维瓦片分布到对应的真实设备中。     

Health surveillance under adverse ergonomics conditions – validity of a screening method adapted for the occupational health service

A new health surveillance protocol for work-related upper-extremity musculoskeletal disorders has been validated by comparing the results with a reference protocol. The studied protocol, Health Surveillance in Adverse Ergonomics Conditions (HECO), is a new version of the reference protocol modified for application in the Occupational Health Service (OHS). The HECO protocol contains both a screening part and a diagnosing part. Sixty-three employees were examined. The screening in HECO did not miss any diagnosis found when using the reference protocol, but in comparison to the reference protocol considerable time savings could be achieved. Fair to good agreement between the protocols was obtained for one or more diagnoses in neck/shoulders (86%, k = 0.62) and elbow/hands (84%, k = 0.49). Therefore, the results obtained using the HECO protocol can be compared with a reference material collected with the reference protocol, and thus provide information of the magnitude of disorders in an examined work group.

Practitioner Summary: The HECO protocol is a relatively simple physical examination protocol for identification of musculoskeletal disorders in the neck and upper extremities. The protocol is a reliable and cost-effective tool for the OHS to use for occupational health surveillance in order to detect workplaces at high risk for developing musculoskeletal disorders.     

It started with Watson and Crick,but it sure didn't end there: Pitfalls and possibilities beyond the classic double helix

The Watson-Crick double helix is perhaps themost predictable and programmable of allintermolecular interactions. In addition toits biological role in the cell, double helicalDNA is used for DNA-based computation and forDNA nanotechnology. The success of theseapplications has been based on the reliabilityof Watson-Crick base pairing, and, in thelatter case, circumventing the linearity of thedouble helix. We survey some of thealternative base pairing structures that can befound in synthetic systems, indicating motifsthat can be propagated and giving examples ofmispairing that can occur within the doublehelical context. We discuss some of the morecommon covalent modifications of nucleic acids. We also indicate the structural interplay ofspecial sequences and negative supercoiling. In addition to the caveats that wepresent involving unexpected results in nucleicacid systems, we show that the process ofreciprocal exchange and the generalization ofcomplementarity can be used to generatebranched DNA motifs for use in DNAnanotechnology or DNA-based computation. Weshow that these motifs can be used for thedirected construction of DNA objects, for thegeneration of specific designed patterns intwo-dimensional lattices, for computation byself-assembly, and for the fabrication ofDNA-based nanodevices. The use ofnon-Watson-Crick DNA leads inherently both toerrors and to thrilling possibilities. Successfully juggling these aspects ofgeneralized nucleic acid structure is anexciting challenge to investigators in thearea.     

多尺度有理分形的图像插值算法

目的图像插值是图像处理中的重要问题,为了提高纹理图像的放大质量,结合以往的有理函数的插值算法,提出一种新的基于有理分形函数的图像插值算法。方法对于输入图像,首先,运用中值滤波和直方图均衡化对输入图像预处理;其次,通过毯子覆盖法求出图像的多尺度分形特征值,进行纹理区域和平滑区域的划分;最后,在纹理区域采用有理分形插值函数,在平滑区域采用有理插值函数。结果对于一般图像,本文算法与NARM(nonlocal autoregressive model),NEDI(new edge-directed interpolation)相当,在纹理区域较多的图像中,本文算法在峰值信噪比(PSNR)和结构相似性(SSIM)数值上较对比算法进一步提高,在视觉效果上,图像对比度明显增强,在Barbara,Truck等的对比图像中,峰值信噪比均提高了0.5 1 dB。结论本文插值算法利用多尺度分形特征将图像划分区域,在不同区域采用不同的插值模型。优化模型参数使得插值质量进一步提高。实验表明本文算法能够对纹理和非纹理区域有效划分对纹理的信息保持优于传统算法,获得了较好的主客观效果。     

基于相关系数的快速分形图像编码算法

自Jacquin提出的分形块编码以来,各种改进算法不断出现,不同程度地减少了编码时间.该文基于相关系数的快速分形图像编码算法,从理论上研究了图像块匹配误差度量和图像块相关系数之间的关系,论证了极小化图像块的均方误差等价于极大化图像块的相关系数,提出了基于相关系数的分形图像编码算法,实现了在解码图像不降质的情况下大大地缩短了编码时间.     

面向瓦当文字识别的改进水平集骨架提取

目的 瓦当是珍贵的历史文化遗产。为了进行瓦当的数字化保护和瓦当文字的自动识别,针对瓦当图像高磨损、高噪声和拓扑复杂的特点,提出基于梯度矢量流场改进的level set骨架提取算法。方法 算法在传统level set骨架算法的基础上对中间函数进行改进,引入基于修正梯度矢量流场的中间函数替代传统的基于欧氏距离场的中间函数,主要通过两次速度不同的波传播实现,因此提高了算法的自动性和精确性。结果 面对构建的标准模型,算法所提骨架线与标准骨架线的平均匹配度为98.03%,骨架均为单像素宽,居中性良好。面对各种噪声,本文算法所提骨架线与不加噪声骨架线的平均匹配度为99.15%,算法的抗噪性强。面对拓扑复杂模型,算法得到的骨架与原图像拓扑一致性、连通性、光滑性良好。结论 实验结果表明,本文算法提取的骨架性能良好,算法抗噪性强,对拓扑复杂物体亦有较好结果,是一种有效的骨架提取算法。     

Simulations of DNA Computing with In Vitro Selection

An attractive feature of DNA-based computers is the large number of possible sequences (4 ⁿ ) of a given length n with which to represent information. The problem, however, is that any given sequence is not necessarily independent of the other sequences, and thus, reactions among them can interfere with the reliability and efficiency of the computation. Independent sequences might be manufactured in the test tube using evolutionary methods. To this end, an in vitro selection has been developed that selects maximally mismatched DNA sequences. In order to understand the behavior of the protocol, a computer simulation of the protocol was done, results of which showed that Watson-Crick pairs of independent oligonucleotides were preferentially selected. In addition, to explore the computational capability of the selection protocol, a design is presented that generates the Fibonacci sequence of numbers.     

Universal forgery on Sekhar's signature scheme with message recovery

Owing to the abundance of electronic applications of digital signatures, many additional properties are needed. Recently, Sekhar [Sekhar, M. R. (2004). Signature scheme with message recovery and its application. Int. J. Comput. Math., 81(3), 285–289.] proposed three signature schemes with message recovery designed to protect the identity of the signer. In this setting, only a specific verifier can check the validity of a signature, and he can transmit this conviction to a third party. In this note, we show that this protocol is totally insecure, as it is universally forgeable under a no-message attack. In other words, we show that anyone can forge a valid signature of a user on an arbitrary message. The forged signatures are unconditionally indistinguishable (in an information theoretical sense) from properly formed signatures.