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Tissue P systems with cell separation: attacking the partition problem

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science china(Information sciences) 2011年第2期54卷 293-304页

作者： ZHANG XingYi1, WANG Shuo2, NIU YunYun2 & PAN LinQiang2 1key Lab of intelligent Computing and Signal processing of ministry of education, School of Computer science and technology, Anhui university, Hefei 230039, china 2image processing and intelligent control key laboratory of education ministry of china, department of control science and engineering, huazhong university of science and technology, wuhan 430074, china 1. key Lab of intelligent Computing and Signal processing of ministry of education School of Computer Science and Technology Anhui University Hefei 230039 China2. Image Processing and Intelligent Control Key Laboratory of Education Ministry of China Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China

Tissue P systems are distributed parallel and non-deterministic computing models in the framework of membrane computing, which are inspired by intercellular communication and cooperation between neurons. Recently, cell separation is introduced into tissue P systems, which enables systems to generate an exponential workspace in a polynomial time. In this work, the computational power of tissue P systems with cell separation is investigated. Specifically, a uniform family of tissue P systems with cell separation is constructed for effciently solving a well-known NP-complete problem, the partition problem.

关键词： membrane computing tissue P system cell separation partition problem

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) [a]The key laboratory of image processing and intelligent control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan China

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.

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 [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

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) [a]The key laboratory of image processing and intelligent control Department of Control Science & Engineering Huazhong University of Science and Technology Wuhan China [b]Shaanxi university of technology Hanzhong 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) [a]Liaoning key laboratory of intelligent Information processing Dalian University Dalian China [b]department of control science and engineering Huazhong Univerisity of Science and Technology Wuhn 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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V_2O_5/C catalyst for liquid phase oxidation of glyoxal to glyoxylic acid

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science china Chemistry 2009年第7期52卷 1057-1062页

作者： NIU YuLan1,2 & LI RuiFeng1 1 key laboratory of Coal science and technology, ministry of education, Institute of Special Chemicals, Taiyuan university of technology, Taiyuan 030024, china 2 department of Chemical engineering, Taiyuan Institute of technology, Taiyuan 030008, china key laboratory of Coal science and technology Ministry of Education Institute of Special Chemicals Taiyuan University of Technology Taiyuan 030024 China department of Chemical engineering Taiyuan Institute of Technology Taiyuan 030008 China

A study of the catalytic activity of V2O5/C catalyst for the oxygen oxidation of glyoxal has been made, showing that glyoxylic acid can be formed without control of pH value and there is little oxalic acid from the excessive oxidation of glyoxylic acid. The studies of XRD and TEM have shown that V2O5 diffraction peaks gradually strengthen with the increase of the content of V2O5. With the content of 3% V2O5 and the calcination temperature of 573 K, V2O5/C catalyst displayed the best activity and selectivity. The conversion of glyoxal and the selectivity of glyoxylic acid reached 18.76% and 77.70% after 5 h, respectively. Moreover, V2O5/C catalyst showed small deactivation after recycling three times, which indicates that V2O5/C has a higher stability than noble metal catalysts in the reaction medium.

关键词： glyoxal glyoxylic acid V2O5/C catalyst

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