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A global heuristically search algorithm for DNA encoding

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Progress in Natural science:Materials International 2007年第6期17卷 745-749页

作者： Zhang Kai, Pan Linqiang and Xu Jin (The key laboratory of image processing and intelligent control, department of control science and engineering, huazhong university of science and technology, wuhan 430074, china) The key laboratory of image processing and intelligent control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China department of Superconductivity University of Tokyo Bunkyo-ku Tokyo 113 Japan

A new efficient algorithm is developed to design DNA words with equal length for DNA computing. The algorithm uses a global heuristic optimizing search approach and converts constraints to a carry number to accelerate the convergence, which can generate a DNA words set satisfying some thermodynamic and combinatorial constraints. Based on the algorithm, a software for DNA words design is developed.

关键词： DNA computing encoding heuristic optimizing search

Multi-objective carrier chaotic evolutionary algorithm for DNA sequences design

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Progress in Natural science:Materials International 2007年第12期17卷 1515-1520页

作者： Xiao Jianhua, Xu Jin, Geng Xiutang and Pan Linqiang(key laboratory of image processing and intelligent control, department of control science and engineering, huazhong university of science and technology, wuhan 430074, china) key laboratory of image processing and intelligent control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China

DNA computing is a new vista of computation, which is of biochemical type. Since each piece of information is encoded in biological sequences, their design is crucial for successful DNA computation. DNA sequence design is involved with a number of design criteria, which is difficult to be solved by the traditional optimization methods. In this paper, the multi-objective carrier chaotic evolution algorithm (MCCEA) is introduced to solve the DNA sequence design problem. By merging the chaotic search base on power function carrier, a set of good DNA sequences are generated. Furthermore, the simulation results show the efficiency of our method.

关键词： DNA computing carrier chaotic search multi-objective evolutionary algorithm DNA sequences design.

Sufficient and necessary conditions for Lyapunov stability of Lorenz system and their application

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science china(Information sciences) 2010年第8期53卷 1574-1583页

作者： LUO Qi 1 , LIAO XiaoXin 2 & ZENG ZhiGang 2 1 College of Information and control, Nanjing university of Information science and technology, Nanjing 210044, china 2 department of control science and engineering, huazhong university of science and technology, image processing and intelligent control key laboratory of education ministry of china, wuhan 430074, china College of Information and control Nanjing University of Information Science and Technology Nanjing China department of control science and engineering Huazhong University of Science and Technology Image Processing and Intelligent Control Key Laboratory of Education Ministry of China Wuhan China

The sufficient and necessary conditions for Lyapunov stability of the zero equilibrium point of Lorenz system are discussed, and some brief criteria are presented for globally exponential stability, globally asymptotical stability and instability. Furthermore, the behavior of the non-zero equilibrium point of Lorenz system is also investigated, and several sufficient and necessary conditions are provided for locally exponential stability and instability. The established theorems in this paper develop and extend the existing achievements on Lyapunov stability of Lorenz system. In conclusion, by applying the obtained results, some less conservative feedback-control laws are derived to guarantee the globally exponential stability of the chaos control of Chen system, Lu¨ system, Yang-Chen system and Yu-Xia Li system.

关键词： Lorenz system Lyapunov stability sufficient and necessary condition bifurcation values globally exponential synchronization

A fast algorithm for color image enhancement with total variation regularization

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science china(Information sciences) 2010年第9期53卷 1913-1916页

作者： LI Ming1,2 1School of Computer science and technology,huazhong university of science and technology,wuhan 430074,china 2key laboratory of education ministry for image processing and intelligent control,wuhan 430074,china School of Computer science and technology Huazhong University of Science and Technology Wuhan China key laboratory of education ministry for image processing and intelligent control Wuhan China

In this paper,a novel algorithm for color image enhancement is *** proposed method,which is based on Retinex theory and total variational framework,improves the original variational method by using a TV penalty term to force spatial smoothness on the reflectance *** split Bregman algorithm is employed to solve the proposed *** practical experiments,it is verified that our method obtains better enhancement performance and much better calculation efficiency.

关键词： color image enhancement Retinex theory total variational model split Bregman algorithm

Improved taboo search algorithm for designing DNA sequences

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Progress in Natural science:Materials International 2008年第5期18卷 623-627页

作者： Kai Zhang a, Jin Xu a,b, Xiutang Geng a, Jianhua Xiao a, Linqiang Pana, a The key laboratory of image processing and intelligent control, department of control science and engineering, huazhong university of science and technology, wuhan 430074, china b School of Electronic engineering and Computer science, Peking university, Beijing 100871, china The key laboratory of image processing and intelligent control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China School of Electronic engineering and Computer science Peking University Beijing 100871 China

The design of DNA sequences is one of the most practical and important research topics in DNA computing. We adopt taboo search algorithm and improve the method for the systematic design of equal-length DNA sequences, which can satisfy certain combinatorial and thermodynamic constraints. Using taboo search algorithm, our method can avoid trapping into local optimization and can nd a set of good DNA sequences satisfying required constraints.

关键词： DNA computing Taboo search algorithm DNA sequence design

Arithmetic computation using self-assembly of DNA tiles:subtraction and division

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Progress in Natural science:Materials International 2009年第3期19卷 377-388页

作者： Xuncai Zhang a,b, Yanfeng Wang b, Zhihua Chen a, Jin Xu a,*, Guangzhao Cui b a The key laboratory of image processing and intelligent control, department of control science and engineering, huazhong university of science and technology, wuhan 430074, china b School of Electrical and Electronic engineering, Zhengzhou university of Light Industry, Zhengzhou 450002, china The key laboratory of image processing and intelligent control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China School of Electrical and Electronic engineering Zhengzhou University of Light Industry Zhengzhou 450002 China

Recently, experiments have demonstrated that simple binary arithmetic and logical operations can be computed by the process of self- assembly of DNA tiles. In this paper, we show how the tile assembly process can be used for subtraction and division. In order to achieve this aim, four systems, including the comparator system, the duplicator system, the subtraction system, and the division system, are pro- posed to compute the difference and quotient of two input numbers using the tile assembly model. This work indicates that these systems can be carried out in polynomial time with optimal O(1) distinct tile types in parallel and at very low cost. Furthermore, we provide a scheme to factor the product of two prime numbers, and it is a breakthrough in basic biological operations using a molecular computer by self-assembly.

关键词： Self-assembly Subtractor Divider Tile assembly model DNA tiles DNA computing

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

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Progress in Natural science:Materials International 2007年第6期17卷 708-711页

作者： Fang Gang1, Zhang Shemin2, Dong Yafei1 and Xu Jin1(1. The key laboratory of image processing and intelligent control, department of control science & engineering, huazhong university of science and technology, wuhan 430074, china 2. Shaanxi university of technology, Hanzhong 723000, china) The key laboratory of image processing and intelligent control Department of Control Science & Engineering Huazhong University of Science and Technology Wuhan 430074 China Shaanxi university of technology Hanzhong 723000 China

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.

关键词： DNA computing 3-vertex-colorability problem.

The optimization of DNA encodings based on GA/SA algorithms

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Progress in Natural science:Materials International 2007年第6期17卷 739-744页

作者： Wang Wei1, Zheng Xuedong2, Zhang Qiang1 and Xu Jin2(1. Liaoning key laboratory of intelligent Information processing, Dalian university, Dalian 116622, china 2. department of control science and engineering, huazhong university of science and technology, wuhan 430074, china) Liaoning key laboratory of intelligent Information processing Dalian University Dalian 116622 China department of control science and engineering Huazhong University of Science and Technology Wuhan 430074 China

The design of DNA sequence plays an important role in improving the reliability of DNA computation. Proper constrained terms that DNA sequence should satisfy are selected, and then the evaluation formulas of each DNA individual corresponding to the selected constrained terms are proposed. The heuristic improved genetic algorithm (GA)/simulated annealing (SA) algorithm is presented to solve the multi-objective optimize problem, and the DNA sequence design system is developed. Furthermore, an example is illustrated to show the efficiency of our method given here.

关键词： DNA encoding multi-objective optimize GA/SA algorithms

The integration of methanogenesis with denitrification and anaerobic ammonium oxidation in an expanded granular sludge bed reactor

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Journal of Environmental sciences 2003年第3期15卷 423-432页

作者： ZHANG Dai-jun 1,2 (1. department of Environmental science, Chongqing university, Campus A, Chongqing 400044, china 2. key laboratory for the Southwest china Resources Exploitation and Environmental Disaster control engineering, ministry of education, china.) department of Environmental science Chongqing University China

The integration of methanogenesis with denitrification and anaerobic ammonium oxidation(ANAMMOX) was studied in an expanded granular sludge bed(EGSB) reactor in this work. Experimental results from the continuous treatment of wastewater with nitrite and ammonium, which lasted for 107 days, demonstrated that wastewater with high nitrite and ammonium could be anaerobically treated in an expanded granular sludge bed reactor. More than 91% to 97% of COD were removed at up to about 3.9 g COD/(L·d) of COD volumetric loading rate. More than 97% to 100% of nitrite was denitrified at up to about 0.8 g NO -_2-N/(L·d), which is 16 times higher than that in a conventional activated sludge system with nitrification/denitrification(0.05 gN/(L·d)). No dissimilatory reduction of nitrite to ammonium occurred in the process. However, maximum of about 40% ammonium was found to be lost. Batch tests of 15 days with sludge from the reactor showed that 100% of nitrite was denitrified completely, and about 3% of ammonium was removed when only ammonium (34.3 mg/L) and nitrite(34.3 mg/L) were added into the sludge suspension medium. Furthermore, about 15% of ammonium amounts were lost with organic COD addition. It suggested that the methanogenesis in the system could enhance ANAMMOX because of intermediate hydrogen produced during methanogenesis.

关键词： methanogenesis denitrification ANAMMOX EGSB reactor

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