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Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles

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Molecular phylogenetics and evolution 2015年 89卷 37-45页

作者： Xian-Hua Xie Zu-Guo Yu Guo-Sheng Han Wei-Feng Yang Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China School of Mathematics and Computer Science Gannan Normal University Jiangxi 341000 PR China. Electronic address: xxianhua@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: yuzuguo@***. Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China. Electronic address: korea10282003@***. Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China. Electronic address: yangweifeng09@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: v.anh@qut.edu.au.

There has been a growing interest in alignment-free methods for whole genome comparison and phylogenomic studies. In this study, we propose an alignment-free method for phylogenetic tree construction using whole-proteome sequences. Based on the inter-amino-acid distances, we first convert the whole-proteome sequences into inter-amino-acid distance vectors, which are called observed inter-amino-acid distance profiles. Then, we propose to use conditional geometric distribution profiles (the distributions of sequences where the amino acids are placed randomly and independently) as the reference distribution profiles. Last the relative deviation between the observed and reference distribution profiles is used to define a simple metric that reflects the phylogenetic relationships between whole-proteome sequences of different organisms. We name our method inter-amino-acid distances and conditional geometric distribution profiles (IAGDP). We evaluate our method on two data sets: the benchmark dataset including 29 genomes used in previous published papers, and another one including 67 mammal genomes. Our results demonstrate that the new method is useful and efficient.

关键词： Alignment-free whole-proteome comparison Conditional geometric distribution profile Inter-amino-acid distances Phylogenetic tree

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Randomness expansion with a one-sided trusted device

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Physical Review A 2015年第5期91卷 052308-052308页

作者： Hong Wang Kai Chen Ming Gao Zhi Ma Weilong Wang Chaobo Li Chuangui Ma State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou 450002 China Zhengzhou Information Science and Technology Institute Zhengzhou 450002 China National Laboratory for Physical Sciences at Microscale and Department of Modern Physics University of Science and Technology of China Hefei 230026 P.R. China CAS Excellence Innovation Center Synergetic Innovation Center of Quantum Information and Quantum Physics University of Science and Technology of China Hefei Anhui 230026 China

We study a semi-device-independent (SDI) randomness expansion protocol with a trusted source or detector. It is not difficult to characterize the source or the detector when their dimensions are limited in the SDI scenario. By adding the reasonable assumption, our protocol offers higher min-entropy and, thus, can be used to certify more randomness than the standard SDI protocol of H.-W. Li et al. [Phys. Rev. A 84, 034301 (2011)]. Moreover, randomness expansion can be realized with a lower detection efficiency (about 85.4%) in the trusted source case than the standard one (about 93.4%). Meanwhile, this advantage is robust against parameter deviations of the source. But on the other hand, the sharp measurement cannot improve the performance much in this case. So, there is no need to characterize the measurement accurately. Furthermore, an analytical formula describing the relationship between the dimension witness value and the min-entropy of the output string is derived directly.

关键词： Expansion

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Research on General Permutation Encryption Module based on Chaos Theory

Research on General Permutation Encryption Module based on C...

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2014 5th International Conference on Information Technology for Manufacturing Systems(ITMS 2014)

作者： Wenjie Sun State Key Laboratory of Mathematical Engineering and Advanced Computing

Replacement and substitution encryption are two basic types of encryption historically. The classical encryption algorithm has been compromised now, but they still can play special role for modern cryptology. For example, in digital image encryption system, substitution can disrupt the original order of the images and eliminate the correlation of image information which not only can realize security of images, but also can resist intentional attack and destruction of clipping and noise. And transposition transformation is introduced into the design of block ciphers. The substitution has the feature of high efficiency and resistance, which makes it meet the specific requirements of encryption. So substitution cypher can be applied to modern encryption system.

关键词： Chaos theory General substitution Encryption

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Register one-to-one mapping strategy in Dynamic Binary Translation

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2014 International Conference on Network Security and Communication engineering(NSCE 2014)

作者： Y.N.Cui J.M.Pang Z.Shan F.Yue State Key Laboratory of Mathematical Engineering and Advanced Computing

Dynamic Binary Translation（DBT） is an important technology to cross-platform software transplantation such as enhancing the compatibility of ***,there exist some factors that impede its performance:high translation overhead and translated code of low *** this work,we take advantage of host registers,using register mapping strategy to promote the performance of *** mapping registers from guest Instruction-Set Architectures（ISA） to host machines,it could off-load the overhead caused by load and store operations of *** simplifying the rules of the intermediate code generated,it could lower the number of intermediate code and improve the quality of translated *** X86 to ALPHA on SPEC 2006,the code expansion reduces 32.86%and the performance of the optimized translator is improved by 7.55%.

关键词： Dynamic binary translation Overhead Registers mapping Performance optimization

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Results on constructions of rotation symmetric bent and semi-bent functions

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2014年 8865卷 21-33页

作者： Carlet, Claude Gao, Guangpu Liu, Wenfen University of Paris 8 and University of Paris 13 CNRS 2 Rue de la Liberté Saint-Denis Cedex93526 France State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou China State Key Laboratory of Networking and Switching Technology Beijing University of Posts and Telecommunications Beijing China

In this paper, we introduce a class of cubic rotation symmetric (RotS) functions and prove that it can yield bent and semi-bent functions. To the best of our knowledge, this is the second primary construction of an infinite class of nonquadratic RotS bent functions which could be found and the first class of nonquadratic RotS semi-bent functions. We also study a class of idempotents (giving RotS functions through the choice of a normal basis of GF(2n) over GF(2)). We derive a characterization of the bent functions among these idempotents and we relate their precise determination to a problem studied in the framework of APN functions. Incidentally, the proofs of bentness given here are useful for a paper studying a construction of idempotents from RotS functions, entitled "A secondary construction and a transformation on rotation symmetric functions, and their action on bent and semi-bent functions" by the same authors, to appear in the journal JCT series A. © Springer International Publishing Switzerland 2014.

关键词： Boolean functions

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Coexistence of Midgap Antiferromagnetic and Mott States in Undoped, Hole- and Electron-Doped Ambipolar Cuprates

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Physical Review Letters 2016年第19期116卷 197002-197002页

作者： Xinmao Yin Shengwei Zeng Tanmoy Das G. Baskaran Teguh Citra Asmara Iman Santoso Xiaojiang Yu Caozheng Diao Ping Yang Mark B. H. Breese T. Venkatesan Hsin Lin Ariando Andrivo Rusydi Singapore Synchrotron Light Source National University of Singapore 5 Research Link Singapore 117603 Singapore NUSSNI-NanoCore National University of Singapore Singapore 117576 Singapore Department of Physics National University of Singapore Singapore 117542 Singapore SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Optoelectronic Engineering Shenzhen University Shenzhen 518060 China Centre for Advanced 2D Materials and Graphene Research Centre National University of Singapore Singapore 117546 Singapore Department of Physics Indian Institute of Science Bangalore 560012 India The Institute of Mathematical Sciences Chennai 600041 India Perimeter Institute for Theoretical Physics Waterloo Ontario N2L 2Y5 Canada Department of Electrical and Computer Engineering National University of Singapore Singapore 117583 Singapore

We report the first observation of the coexistence of a distinct midgap state and a Mott state in undoped and their evolution in electron and hole-doped ambipolar Y0.38La0.62(Ba0.82La0.18)2Cu3Oy films using spectroscopic ellipsometry and x-ray absorption spectroscopies at the O K and Cu L3,2 edges. Supported by theoretical calculations, the midgap state is shown to originate from antiferromagnetic correlation. Surprisingly, while the magnetic state collapses and its correlation strength weakens with dopings, the Mott state in contrast moves toward a higher energy and its correlation strength increases. Our result provides important clues to the mechanism of electronic correlation strengths and superconductivity in cuprates.

关键词： Impurities in superconductors Antiferromagnets Cuprates High-temperature superconductors Mott insulators Ellipsometry X-ray absorption near-edge spectroscopy

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Research on General Permutation Encryption Module Based on Chaos Theory

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International Journal of Technology Management 2014年第7期 58-61页

作者： Sun Wenjie State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou Henan 102206

Replacement and substitution encryption are two basic types of encryption historically. The classical encryption algorithm has been compromised now, but they still can play special role for modem cryptnlogy. For example, in digital image encryption system, substitution can disrupt the original order of the images and eliminate the correlation of image information which not only can realize security of images, but also can resist intentional attack and destruction of clipping and noise. And transposition transformation is introduced into the design of block ciphers. The substitution has the feature of high efficiency and resistance, which makes it meet the specific requirements of encryption. So substitution cypher can be applied to modern encryption system.

关键词： chaos theory general substitution encryption.

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Efficient Electrocatalytic Reduction of CO2by Nitrogen‐Doped Nanoporous Carbon/Carbon Nanotube Membranes: A Step Towards the Electrochemical CO2Refinery

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Angewandte Chemie 2017年第27期129卷

作者： Hong Wang Jia Jia Pengfei Song Qiang Wang Debao Li Shixiong Min Chenxi Qian Lu Wang Young Feng Li Chun Ma Tom Wu Jiayin Yuan Markus Antonietti Geoffrey A. Ozin Materials Chemistry and Nanochemistry Research Group Solar Fuels Cluster Centre for Inorganic and Polymeric Nanomaterials Departments of Chemistry Chemical Engineering and Applied Chemistry and Electrical and Computing Engineering University of Toronto 80 St. George Street Toronto Ontario M5S3H6 Canada College of Chemistry and Chemical Engineering Northwest Normal University Lanzhou 730070 China State Key Laboratory of Coal Conversion Institute of Coal Chemistry the Chinese Academy of Sciences Taiyuan 030001 China School of Chemistry and Chemical Engineering Beifang University of Nationalities Yinchuan Ningxia China Physical Science and Engineering Division King Abdullah University of Science & Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Department of colloidal chemistry Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany Department of Chemistry and Biomolecular Science and Center for Advanced Materials Processing Clarkson University Potsdam NY 13699 USA

Herein we introduce a straightforward, low cost, scalable, and technologically relevant method to manufacture an all‐carbon, electroactive, nitrogen‐doped nanoporous‐carbon/carbon‐nanotube composite membrane, dubbed “HNCM/CNT”. The membrane is demonstrated to function as a binder‐free, high‐performance gas diffusion electrode for the electrocatalytic reduction of CO 2 to formate. The Faradaic efficiency (FE) for the production of formate is 81 %. Furthermore, the robust structural and electrochemical properties of the membrane endow it with excellent long‐term stability.

关键词： CO2-Reduktion Hierarchischer Kohlenstoff Kohlenstoff-Nanoröhren Membranen Stickstoffdotierung

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Design of TPM chip based on signal integrity analysis

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Ruan Jian Xue Bao/Journal of Software 2014年 25卷 44-52页

作者： Li, Yan-Bing Ye, Jian Zhu, Zhen-Min PLA Information Engineering University Zhengzhou450001 China State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou450001 China

It is important for personalized social services to calculate the relationship strength between users in a social network. Meanwhile, the psychological studies has shown that the personality traits is one of the key factors affecting the user's relationship strength. Based on the relationship generation principle in the social psychology, this paper proposes a personality embedded social relationship strength hierarchical model and algorithm. With the analysis of a user's behavior in social network, this paper predicts the Big Five personality traits of the user to calculate the propensity of personality. The propensity of personality is combined with the similarity of preference and the familiarity of interaction to formalize the personality embedded user relationship strength calculation. At the end of this paper, the proposed algorithm is demonstrated to be reasonable and effective in a simulation experiment of RENREN social network. ©2014 ISCAS.

关键词： Hierarchical systems

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A novel and fast chaotic cryptosystem for image encryption

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Journal of Computational and Theoretical Nanoscience 2014年第3期11卷 731-738页

作者： Wang, Bin Wei, Xiaopeng Zhang, Qiang School of Mechanical and Engineering Dalian University of Technology Dalian 116024 China Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China

In recent years, there has been growing interesting in image encryption based on chaotic systems. In order to improve the effect of encryption, a large amount of operations are implemented in the most chaos-based cryptosystems. However, the runtime of chaos-based cryptosystems would be increased with the rise of operations. In this paper, a novel algorithm is proposed to generate cipher key for the permutation-diffusion architecture. The cipher key not only relates to the plain-image, but also the generated time of cipher key is shorter than the conventional method. On the premise of security, a novel and fast permutation-diffusion architecture based on chaotic systems and variable control conditions is proposed. For the sake of increasing the key space and enhancing the security of proposed architecture, variable control conditions used in this cryptosystem as the parameter and initial value of same chaotic system are generated from the cipher key related to the plain-image. So the proposed algorithm can effectively resist the most attacks against permutation-diffusion architectures. Finally, theoretical analyses and numerical experimental results show that the proposed chaos-based cryptosystem possesses high security and sound time of image encryption, which is suitable for protecting the image information Copyright © 2014 American Scientific Publishers.

关键词： Chaotic systems

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