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The optimization of DNA encoding based on chaotic optimization particle swarm algorithm

Journal of Computational and Theoretical Nanoscience 2016年第1期13卷 443-449页

作者： Liu, Yuanyuan Zheng, Xuedong Wang, Bin Zhou, Shihua Zhou, Changjun Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China

DNA sequence encoding is significant for the improvement of reliability and validity of DNA computing. The hybridization reaction between DNA molecules is the most important and core reaction in the field of DNA computing, because its efficiency and accuracy directly affect the result of DNA computing. In view of the disadvantages of precocious phenomena and local optimum of particle swarm optimization (PSO), chaotic mapping is integrated into the traditional particle swarm optimization, namely chaotic optimization particle swarm algorithm (CPSO). The algorithm not only has the property of chaotic with ergodic, randomness and the sensitivity to the initial value, but also has the fast convergence of the PSO. Thus, we use the chaotic optimization particle swarm algorithm to design the DNA sequences. Compared with other algorithms, the simulation results and security analysis of our DNA sequences are more reliable and stable. At same time, our DNA sequences have low similarity and stable melting temperature. Therefore, it is proved that this method is feasible and has better optimization effect. © 2016 American Scientific Publishers All rights reserved.

关键词： DNA sequences

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Construction and validation analysis of the transcriptional regulatory network based on the gibbs sampler strategy and cytoscape software

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Journal of Computational and Theoretical Nanoscience 2014年第2期11卷 504-510页

作者： Zhang, Qiang Zheng, Xuedong Zhou, Changjun Zhang, Qian Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China

To reveal the inner control mechanism of organism is an important content in the research of bioinformatics. The proliferation of a variety of high-throughput biological data for the reconstruction of gene regulatory networks from genome scale may be provided. Because the single data source only can provide about regulation relationship one-sided information and contain noise, so a variety of biological data integration method is expected to be of high reliability control network. We use Gibbs sampling method to integrate the SGD in gene expression data with YEASTRACT in mutual regulation data to infer the transcription regulatory networks. Firstly, based on the sampling distribution method for the given transcription factor to identify their target gene set;then, combining the Outlier sum t-statistical tests calculate the polymerization evidence for given transcription factor regulation of their target gene;finally, we exploit the two step existing results identify transcription factor regulation module. The key is that we utilize the Cytoscape Software reconstructing the transcriptional regulatory networks, and the transcription regulation is found by the Gibbs sampling method, which are consistent with utilizing the Cytoscape Software reconstruct the transcriptional regulatory networks. It verifies the feasibility and accuracy of the Gibbs sampling method. At the same time, we analyze the characteristic of the biological networks. © 2014 American Scientific Publishers.

关键词： Transcription

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A novel DWT-based watermarking for image with the SIFT

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Telkomnika 2013年第1期11卷 191-198页

作者： Xu, Yuan Zhang, Qiang Zhou, Changjun Key Laboratory of Advanced Design and Intelligent Computing Dalian university Ministry of Education Dalian 116622 China

A kind of scale invariant features transformation (SIFT for short) operators on DWT domain are proposed for watermarking algorithm. Firstly, the low frequency of the image is obtained by DWT. And then the SIFT transformation is used to calculate the key feature points for the low frequency sub-image. Based on the chosen space's key points with moderate scale, a circular area as watermark embedding area is constructed. According to the research and final results, the novel digital watermark algorithm is proposed benefiting from the characteristics of SIFT's key points and local time-frequency of DWT. The algorithm not only has good robustness to resist on such operations as compression, shearing, noise addition, median filtering and scaling, but also has good inhibition to possible watermark fake verification.

关键词： Median filters

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A novel image fusion encryption algorithm based on DNA sequence operation and hyper-chaotic system

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Optik 2013年第18期124卷 3596-3600页

作者： Qiang Zhang Ling Guo Xiaopeng Wei Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian 116622 China

A new image fusion encryption algorithm based on image fusion and DNA sequence operation and hyper-chaotic system is presented. Firstly, two DNA sequences matrices are obtained by encoding the original image and the key image. Secondly, using the chaotic sequences generated by Chen's hyper-chaotic maps to scramble the locations of elements from the DNA sequence matrix which generated form original image. Thirdly, XOR the scrambled DNA matrix and the random DNA matrix by using DNA sequence addition operation. At last, decoding the DNA sequence matrix, we will get the encrypted image. The simulation experimental results and security analysis show that our algorithm not only has good encryption effect, but also has the ability of resisting exhaustive attack and statistical attack.

关键词： Image encryption DNA sequence XOR operation Chen's hyper-chaotic Security

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An Image Encryption Algorithm Based on Chaos System and DNA Strand Displacement Model

An Image Encryption Algorithm Based on Chaos System and DNA ...

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2017 2nd International Conference on Artificial Intelligence: Techniques and Applications (AITA 2017)

作者： Ze-jun ZHANG Bo-xiang XIAO Xue-dong ZHENG Chang-jun ZHOU Key Laboratory of Advanced Design and Intelligent Computing(Dalian University) Ministry of Education

In this paper,we proposed a novel algorithm for image *** the scheme,three chaotic sequences are generated by Lorenz chaos *** chaotic sequences are used to permutation and diffusion the digital ***,the algorithm introduce the DNA strand displacement reaction model to extract the secret key and then encrypt the image with a combination of XOR *** simulation results and security analysis show that our algorithm can successfully encrypts and decrypts the input image and gets a better encryption ***,the method also has a good ability of resisting attacks.

关键词： Image encryption Chaos system DNA strand displacement XOR operation

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Research of DNA sequences sets based on the improved genetic algorithm

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Journal of Computational and Theoretical Nanoscience 2012年第7期9卷 969-973页

作者： Xia, Xue Zhang, Qiang Wang, Bin Zhao, Yuxia Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China

With the continuous development of biotechnology, DNA computing will bring rapid development to the mathematics, computer science and other fields. As the foundation and the core issue of DNA computing, DNA encoding can be divided into two aspects, one is the quality optimization and the other is set design. The main research methods are theoretical analysis and algorithm design. In this paper, the traditional genetic algorithm is improved in the initialization, selection and mutation operations. We use fixed probability selection and adaptive multi-bits mutation operations in the improved genetic algorithm (IGA). The IGA is used in the DNA code set design under the combinatorial constraints satisfied the Hamming distance and Reverse Hamming distance constraint. The experimental shows our results are better than the earlier results in the literature. © 2012 American Scientific Publishers All rights reserved.

关键词： Hamming distance

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DNA coding and chaos-based image encryption algorithm

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Journal of Computational and Theoretical Nanoscience 2013年第2期10卷 341-346页

作者： Zhang, Qiang Liu, Lili Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China

In this paper, an image encryption algorithm based on combination of DNA coding with chaotic map is proposed. The proposed algorithm uses chaotic sequence generated by Logistic system to scramble the image pixels which is encoded through the DNA encoding;then makes use of DNA addition operation for the rows of DNA sequence matrix and implements image encryption at last. The algorithm is simple and can resist a variety of attacks. Copyright © 2013 American Scientific Publishers.

关键词： DNA

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DNA sequence set design by improved genetic algorithm

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Journal of Computational and Theoretical Nanoscience 2014年第3期11卷 739-743页

作者： Zhang, Qiang Zhao, Yuxia Wang, Bin Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China

It has been proved that information encoding and processing in DNA is an important problem for biomolecular computing, including the encoding design problem. In recent years, there has been growing interest in the applications of DNA encoding theory in genetics and bioengineering, especially in the construction of synthetic DNA strands. In the paper, we use the improved genetic algorithm to design DNA sequences with combinational constraints including h-distance (H), hamming distance (HD) and GC-content. Furthermore, we improve the theoretical lower bounds of DNA encoding satisfying the above combinational constraints by using improved genetic algorithm, comparing our experimental results with the previous work. From the results, we can see that we succeed in obtaining more DNA sequences and give practical values satisfying h-distance, hamming distance (HD) and GC-content, and shorten the range of DNA encoding bounds. As far as we know, these results we obtain are the first time, and provide the direction for the future work such as the research of theoretical bounds of DNA encoding and algorithms Copyright © 2014 American Scientific Publishers.

关键词： Genetic algorithms

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Performance Verification of Smith Predictor Control Using IMC Scheme via Chemical Reaction Networks and DNA Strand Displacement Reaction 9

Performance Verification of Smith Predictor Control Using IM...

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9th IEEE Smart World Congress, SWC 2023

作者： Yao, Jingwang Lv, Hui Xiao, Yijun Dalian University Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian116622 China Northeastern University State Key Laboratory of Synthetical Automation for Process Industries Shenyang110004 China

ISBN: (纸本)9798350319804

Biochemical process control is often achieved through feedback control strategies for theoretical analysis and optimization of biochemical reaction processes. Here, the design improves the robustness of the biochemical process by taking advantage of the Smith prediction structure and internal mode control within the chemical reaction network theory framework to intervene against the time delays and perturbations present in the biochemical process. First, an IMC representation of Smith prediction is constructed using the presence of parameter rectification of the control method, and then an IMC-MSP control scheme is proposed. A first-order time-lag controlled object is established in the construction of the IMC-MSP control scheme. Besides, CRNs and kinetic representations are established based on the control structure to facilitate the evaluation of the control system performance. In this paper, CRNs representations of parabolic functions as signal inputs are defined for the first time and optimized for stepping signals to facilitate the design and study of biomolecular circuits. Notably, for the CRNs-based IMC-MSP control scheme, on the one hand, numerical simulation experiments are designed to verify the effectiveness of the whole scheme from multiple perspectives of time delays, external perturbations, and filter tuning parameters;on the other hand, using DNA strand displacement is reflected to verify the feasibility of the whole scheme. © 2023 IEEE.

关键词： Chemical reaction networks (CRNs) DNA strand displacement (DSD) Internal model control (IMC control) Smith predictor

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Obstacle Avoidance Path Planning of Space Manipulator Based on Improved Artificial Potential Field Method

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Journal of The Institution of Engineers (India): Series C 2014年第1期95卷 31-39页

作者： S. Liu Q. Zhang D. Zhou Key Laboratory of Advanced Design and Intelligent Computing (Dalian University) Ministry of Education Dalian People’s Republic of China

This paper proposes an approach about obstacle collision-free motion planning of space manipulator by utilizing a Configuration-Oriented Artificial Potential Field method in 3-D space environment. Firstly, the artificial potential field method, which is usually used in 2-D space, is extended to 3-D space. Secondly, improving the artificial potential field method enables to carry out obstacle avoidance planning for the configuration of entire space manipulator (including the end-effector and links). Finally, the approach is combined with the inverse kinematics calculation which is based on the Generalized Jacobian Matrix for planning a collision-free motion of space manipulator. At the end of the article, by simulating the method mentioned above, the validity of the proposed method is verified.

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