Models of molecular computing based on molecular reactions

We discuss two models of molecular computing. The first one is based on an abstract formulation of two sorts of molecular reactions: enforcing and forbidden. The enforcing reactions are reactions that may happen, and are allowed to happen, in a given molecular system, while the forbidden reactions are detrimental for the system (e.g., leading to “incorrect” computations) and thus must be avoided. Hence computations in such a forbidding-enforcing system are driven by enforcing conditions (describing the enforcing reactions), but they are restrained by forbidding conditions (describing the forbidden reactions). The second model, called molecular landscapes, is geared towards the display of solutions. It consists of organisms (computing agents) functioning in a common environment which plays the role of a common communication medium for the organisms. When a molecular landscapes system works on a specific computational problem, each organism is working on this problem. But as soon as an organismM will get its solution to the problem, it modifies the environment, which from this moment on supports only the organisms that get the same solution asM. This is done through a selection mechanism that relies on selective competition which “kills” the losers. Since this selection mechanism interacts with the solution mechanism from the moment that computations are initiated, it can drastically increase the density of good solutions (molecules). In this way the molecular landscapes system achieves the goal of displaying solutions. Grzegorz Rozenberg, Ph.D.: He is a Professor, the Head of the Theory Group at Leiden Institute of Advanced Computer Science, and the Director of Leiden Center for Natural Computing at Leiden University, The Netherlands. He is also an Adjoint Professor of Computer Science at the Department of Computer Science, University of Colorado at Boulder, USA. He received his Engineering and Master degrees in computer science in 1965 from the Technical University of Warsaw, Poland, and his Ph.D. in mathematics in 1968 from the Polish Academy of Sciences, Warsaw, Poland. He has published about 400 papers, 5 books and edited over 50 books in formal language and automata theory, concurrent systems, graph theory and graph rewriting, computer supported cooperative work, and molecular computing. He is a performing magician, and he is possessed by paintings by Hieronymus Bosch. In his words: “I have a wonderful family, I have written many papers, I have shuffled many decks of cards, I have studied many paintings by Bosch. Life has been good to me.”     

Power control in CDMA networks based on soft computing methods

Power control is a fundamental procedure for CDMA mobile radio communication systems. In multiservice CDMA systems, power control should be used to minimise the transmission power of each connection, in order to limit the multiple access interference, while obtaining the desirable SIR levels. This paper starts from a transmitted-power allocation algorithm (TPAA) that considers a set of uplink transmissions, which should be supported by the system. In the sequel, the TPAA algorithm is used for training an Elman neural network, which, due to its internal characteristics, is applicable in the time critical context of power control. Simulations and numerical results are analysed for obtaining a solid basis for employing our scheme in the power control of CDMA systems.     

Large-scale DNA memory based on the nested PCR

A DNA Memory with over 10 million (16.8 M) addresses was achieved. The data embedded into a unique address was correctly extracted through an addressing processes based on nested PCR. The limitation of the scaling-up of the proposed DNA memory is discussed by using a theoretical model based on combinatorial optimization with some experimental restrictions. The results reveal that the size of the address space of the DNA memory presented here may be close to the theoretical limit. The high-capacity DNA memory can be also used in cryptography (steganography) or DNA ink. In decoding process, multiple data with different addresses can be also simultaneously accessed by using the mixture of some address primers. Electronic supplementary material  The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Distributed computing model for processing remotely sensed images based on grid computing

With advances in remote-sensing technology, the large volumes of data cannot be analyzed efficiently and rapidly, especially with arrival of high-resolution images. The development of image-processing technology is an urgent and complex problem for computer and geo-science experts. It involves, not only knowledge of remote sensing, but also of computing and networking. Remotely sensed images need to be processed rapidly and effectively in a distributed and parallel processing environment. Grid computing is a new form of distributed computing, providing an advanced computing and sharing model to solve large and computationally intensive problems. According to the basic principle of grid computing, we construct a distributed processing system for processing remotely sensed images. This paper focuses on the implementation of such a distributed computing and processing model based on the theory of grid computing. Firstly, problems in the field of remotely sensed image processing are analyzed. Then, the distributed (and parallel) computing model design, based on grid computing, is applied. Finally, implementation methods with middleware technology are discussed in detail. From a test analysis of our system, TARIES.NET, the whole image-processing system is evaluated, and the results show the feasibility of the model design and the efficiency of the remotely sensed image distributed and parallel processing system.     

DNA计算原理及系统分析

DNA计算是一种模拟生物分子DNA的结构并借助于分子生物技术进行计算的新方法,它开创了以化学反应作为计算工具的先例,具有广阔的应用前景。DNA计算的两个主要特点是计算的高度并行性和巨大的信息存储容量。该文简要介绍了DNA计算的原理及其数学计算的基本思想;对DNA计算的特点及其系统进行了分析。比较了DNA计算机与图灵机的异同;最后对DNA计算的发展前景进行展望。     

DNA computing capabilities for game theory

Problems in game theory can be used for benchmark DNA computations. Large numbers of game strategies and chance events can be assembledinto finite state machines. These many machines perform, in parallel,distinct plays of a game. Strategies can be exposed to selection and breeding.The computational capabilities of DNA are matched with aspects of game theory, but the most interesting problems are yet to be treated.     

A high speed railway control system based on the fuzzy control method

This paper proposed a high-speed railway control system based on the fuzzy control method. The fuzzy control system of the high-speed railway is designed in the Matlab software according to the expert experience and knowledge. At first the input and output variables have been fuzzified in the fuzzification process. Then the membership function is designed and the control rules are discussed in detail bring into correspondence with expert knowledge. The parameters discussion about the maximum speed and traction effort are studied in detail. Finally, the defuzzify process can output the results directly to control the high speed railway train. The results indicated that the fuzzy control system is effective and accurate in the high speed railway control process.     

一种新的Kth最短路径搜索算法

借助于“背离”路径的概念,论文在2nd最短路径搜索算法的基础上提出了一种新的Kth最短路径搜索算法,并将其应用至实际环境中。通过K-1次2nd最短路径搜索算法的迭代,该算法可以求出网络中任意两个给定节点之间的Kth最短路径,2nd最短路径搜索算法在计算上具有简单性,因而也同样具有简洁、快速的特点。     

Evolutionary neural networks and DNA computing algorithms for dual-axis motion control

A new method is proposed to deal with the dual-axis control of a multi-variables system with two induction motors. Investigation of resolving the cross-coupling problem of dual-axis platform is addressed by a neural net-based decoupling compensator and a sufficient condition ensuring closed-loop stability is derived. An evolutionary algorithm processing the universal seeking capability is proposed for finding the optimal connecting weights of the neural decoupling compensator and the gains of PID controllers. Extensive numerical studies verify the performance and applicability of the proposed design under a variety of operating conditions.     

A Pascal program for computing the DNA concentration in cellular homogenates

The use of manual graphical methods for evaluating the results of Brunk's fluorometric DNA concentration assay was found to be subjective and time-consuming. That is why a short program (in Turbo Pascal, version 4) for fluorometric data processing was designed.     

Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes

A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is experimentally implemented and analyzed. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. In this study, real-time amplification performed using the TaqMan probes is adopted, as the TaqMan detection mechanism can be exploited for the design and development of the proposed readout approach. Double-stranded DNA molecules of length 140 base-pairs are selected as the input molecules, which represent the solving path for an HPP instance. These input molecules are prepared via the self-assembly of 20-mer and 30-mer single-stranded DNAs, by parallel overlap assembly. The proposed readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by information processing in silico to assess the results of real-time amplification, which in turn, enables extraction of the Hamiltonian path. The performance of the proposed approach is compared with that of conventional graduated PCR. Experimental results establish the superior performance of the proposed approach, relative to graduated PCR, in terms of implementation time.     

A novel method for concentration evaluation of reading behaviors with electrical activity recorded on the scalp

In this paper, a concentration evaluation of reading behaviors with electrical signal detection on the head is presented. The electrode signal is extracted by brain–computer-interface (BCI) to monitor the user's degree of concentration, where the user is reminded by sound to concentrate, or teaching staffs are reminded to help users improve reading habits, in order to facilitate the user's ability to concentrate. The digital signal processing methods, such as the Kalman Filter, Fast Fourier Transform, the Hamming window, the average value of the total energy of a frame, correlation coefficient, and novel judgment algorithm are used to obtain the corresponding parameters of concentration evaluation. Users can correct their manner of reading with reminders. The repeated test results may be expected to lie with a probability of 95%. Such model training results in better learning effect.     

A novel text and image encryption method based on chaos theory and DNA computing

In today’s world, the security of information is associated with valid and reliable encryption algorithms that we have used in our systems. Today, the latest methods for data encryption are based on DNA computing. In this paper, we consider a reliable data encryption algorithm (OTP) which is theoretically unbreakable, but it experiences some disadvantages in its algorithm. These drawbacks have prevented the common use of its scheme in modern cryptosystems. In this research, we include a logistic chaotic map as an input of OTP algorithm. So, the obtained result of ‘Matlab Simulation’ could prove the efficiency of proposed algorithm in image encryption. In addition to the cryptography of text files, we can propose an interesting encryption algorithm based on a chaotic selection between original message DNA strands and OTP DNA strands. Finally, the empirical results of our proposed algorithm will be compared with AES Open SSl algorithm.     

移动自组网QoS路由的DNA计算模型

QoS路由问题是移动自组网应用面临的一个重要问题,其中如何根据移动自组网动态拓扑结构和单向链路的特点来设计路由算法是关键。DNA计算是一种基于生化反应的新型计算方法,高度的并行性和海量存储能力是其最大的特点。文章首先给出了QoS路由问题模型,然后介绍了DNA的分子结构和DNA计算的基本原理,最后依据Adleman进行DNA计算的编码方法,给出了移动自组网QoS路由问题的DNA计算模型,为解决多约束QoS路由问题提供了一种新的思路。     

Improving the design of sequences for DNA computing: A multiobjective evolutionary approach

Designing oligonucleotide strands that selectively hybridize to reduce undesired reactions is a critical step for successful DNA computing. To accomplish this, DNA molecules must be restricted to a wide window of thermodynamical and logical conditions, which in turn facilitate and control the algorithmic processes implemented by chemical reactions. In this paper, we propose a multiobjective evolutionary algorithm for DNA sequence design that, unlike preceding evolutionary approaches, uses a matrix-based chromosome as encoding strategy. Computational results show that a matrix-based GA along with its specific genetic operators may improve the performance for DNA sequence optimization compared to previous methods.     

一种Windows Services进程控制方法的探讨与实现

Win32平台下的Windows Services是一种强大的后台程序管理模式。如果将服务程序要执行的内容与服务程序剥离写成若干单独的可执行程序,而只在服务程序里面生成它们的进程,则不但可以实现后台程序的开机启动,还可以更加有效地管理它们。     

A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem

This paper describes a tissue P system for solving the Shortest Common Superstring Problem in linear time. This tissue P system is well suited for parallel and distributed implementation using a microfluidic device working with DNA strands. The approach is not based on the usual brute force generate/test technique applied in DNA computing, but it builds the space solution gradually. The possible solutions/superstrings are build step by step through the parallel distributed combination of strings using the overlapping concatenation operation. Moreover, the DNA microfluidic device solves the problem autonomously, without the need of external control or manipulation.An erratum to this article can be found at     

DNA计算模型发展分析

概述了DNA计算的起源和发展,对几种常用的DNA计算模型,如剪接模型、粘贴模型、等同检测模型等进行了介绍和分析,展望了今后DNA计算模型发展的趋势。     

一种基于远程控制技术的网上培训系统

分析了远程控制技术的应用原理,针对远程培训的应用特点设计并实现了一种基于虚拟网络计算(Virtial Network Computing,VNC)的网上培训系统,为网上培训提供了一条便捷有效的解决方案.重点阐述了系统架构的设计理念和关键技术,并进行了身份认证及安全机制等相关特性分析.