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  1. Article ; Online: A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems.

    Zou, Chengye

    Physical chemistry chemical physics : PCCP

    2024  Volume 26, Issue 15, Page(s) 11854–11866

    Abstract: With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due to ... ...

    Abstract With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due to its super-strong parallel computing capability and outstanding data storage capacity, DNA computing has become an important branch and hot research topic of new computer technology. DNA enzyme-free hybridization reaction technology is widely used in DNA computing, showing excellent performance in computing power and information processing. Studies have shown that DNA molecules not only have the computing function of electronic devices, but also exhibit certain human brain-like functions. In the field of artificial intelligence, activation functions play an important role as they enable artificial intelligence systems to fit and predict non-linear and complex variable relationships. Due to the difficulty of implementing activation functions in DNA computing, DNA circuits cannot easily achieve all the functions of artificial intelligence. DNA circuits need to rely on electronic computers to complete the training and learning process. Based on the parallel computing characteristics of DNA computing and the kinetic features of DNA molecule displacement reactions, this paper proposes a new activation function. This activation function can not only be easily implemented by DNA enzyme-free hybridization reaction reactions, but also has good nesting properties in DNA circuits, and can be cascaded with other DNA reactions to form a complete DNA circuit. This paper not only provides the mathematical analysis of the proposed activation function, but also provides a detailed analysis of its kinetic features. The activation function is then nested into a nonlinear neural network for DNA computing. This system is capable of fitting and predicting a certain nonlinear function.
    MeSH term(s) Humans ; Artificial Intelligence ; Computers, Molecular ; Computers ; Neural Networks, Computer ; DNA/genetics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2024-04-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp02811a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Research Progress in Construction and Application of Enzyme-Based DNA Logic Gates.

    Liu, Jia / Liu, Shuang / Zou, Chengye / Xu, Shujuan / Zhou, Changjun

    IEEE transactions on nanobioscience

    2023  Volume 22, Issue 2, Page(s) 245–258

    Abstract: As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide ... ...

    Abstract As a research hotspot in the field of information processing, DNA computing exhibits several important underlying characteristics-from parallel computing and low energy consumption to high-performance storage capabilities-thereby enabling its wide application in nanomachines, molecular encryption, biological detection, medical diagnosis, etc. Based on DNA computing, the most rapidly developed field focuses on DNA molecular logic-gates computing. In particular, the recent advances in enzyme-based DNA logic gates has emerged as ideal materials for constructing DNA logic gates. In this review, we explore protein enzymes that can manipulate DNA, especially, nicking enzymes and polymerases with high efficiency and specificity, which are widely used in constructing DNA logic gates, as well as ribozyme that can construct DNA logic gates following various mechanism with distinct biomaterials. Accordingly, the review highlights the characteristics and applications of various types of DNAzyme-based logic gates models, considering their future developments in information, biomedicine, chemistry, and computers.
    MeSH term(s) DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Logic ; Substrate Specificity ; Enzymes/metabolism ; Computer Simulation ; Humans ; Biosensing Techniques
    Chemical Substances DNA (9007-49-2) ; Enzymes
    Language English
    Publishing date 2023-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1558-2639
    ISSN (online) 1558-2639
    DOI 10.1109/TNB.2022.3181615
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: State estimation for delayed genetic regulatory networks with reaction diffusion terms and Markovian jump

    Chengye Zou / Changjun Zhou / Qiang Zhang / Xinyu He / Chun Huang

    Complex & Intelligent Systems, Vol 9, Iss 5, Pp 5297-

    2023  Volume 5311

    Abstract: Abstract Robust state estimation for delayed genetic regulatory networks with reaction–diffusion terms and uncertainties terms under Dirichlet boundary conditions is addressed in this article. The main purpose of the problem investigation is to design a ... ...

    Abstract Abstract Robust state estimation for delayed genetic regulatory networks with reaction–diffusion terms and uncertainties terms under Dirichlet boundary conditions is addressed in this article. The main purpose of the problem investigation is to design a novel state observer for estimate the true concentrations of mRNA and protein by available measurement outputs. Based on Lyapunov–Krasovskii functions and linear matrix inequalities (LMI), sufficient conditions are given to ensure the robust stability of the estimation error networks. Two examples are presented to illustrate the effectiveness of the proposed approach.
    Keywords Genetic regulatory networks ; Dirichlet boundary ; State estimation ; Reaction–diffusion ; Markov jumping ; Parameter uncertain ; Electronic computers. Computer science ; QA75.5-76.95 ; Information technology ; T58.5-58.64
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Springer
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: A nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit.

    Zou, Chengye / Zhang, Qiang / Zhou, Changjun / Cao, Wenyu

    Nanoscale

    2022  Volume 14, Issue 17, Page(s) 6585–6599

    Abstract: The DNA toehold mediated strand displacement reaction is one of the semi-synthetic biology technologies for next-generation computers. In this article, we present a framework for a novel nonlinear neural network based on an engineered biochemical circuit, ...

    Abstract The DNA toehold mediated strand displacement reaction is one of the semi-synthetic biology technologies for next-generation computers. In this article, we present a framework for a novel nonlinear neural network based on an engineered biochemical circuit, which is constructed by several reaction modules including catalysis, degradation and adjustment reaction modules. The proposed neural network possesses an architecture that is similar to that of an error back propagation neural network, and is built of an input layer, hidden layer and output layer. As a proof of concept, we utilize this nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit to learn the standard quadratic form function and analyze the robustness of the nonlinear neural network toward DNA strand concentration detection, DNA strand displacement reaction rate and noise. Unlike in error back propagation neural networks, the adaptive behavior of this DNA molecular neural network system endows it with supervised learning capability. This investigation will highlight the potential of analog DNA displacement reaction circuits for implementing artificial intelligence.
    MeSH term(s) Artificial Intelligence ; Catalysis ; DNA/chemistry ; Neural Networks, Computer ; Synthetic Biology
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-05-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/d1nr06861j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Synchronization of Hyper-Lorenz System Based on DNA Strand Displacement.

    Zou, Chengye / Zhang, Qiang / Wei, Xiaopeng

    IEEE/ACM transactions on computational biology and bioinformatics

    2022  Volume 19, Issue 3, Page(s) 1897–1908

    Abstract: Lorenz system is depicted by chemical reaction equations of an ideal formal chemical reaction network, and a series of reversible reactions are added into chemical reaction network in order to construct a cluster of hyper-Lorenz system. DNA as a ... ...

    Abstract Lorenz system is depicted by chemical reaction equations of an ideal formal chemical reaction network, and a series of reversible reactions are added into chemical reaction network in order to construct a cluster of hyper-Lorenz system. DNA as a universal substrate for chemical dynamics can approximate arbitrary dynamical characteristics of ideal formal chemical reaction network through auxiliary DNA strands and displacement reactions. Based on Lyapunov's stableness theory, a novel synchronization strategy is proposed. A 6-dimensional hyper-Lorenz system is taken as examples for simulation and shows that DNA strands displacement reactions can implement the synchronization of ideal formal chemical reaction networks. Numerical simulations indicate that synchronization based on DNA strand displacement is robust to the detection of DNA strand concentration, control of reaction rate, and noise.
    MeSH term(s) Computer Simulation ; DNA/genetics ; Recombination, Genetic
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-06-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2020.3048753
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Novel Adaptive Linear Neuron Based on DNA Strand Displacement Reaction Network.

    Zou, Chengye / Wei, Xiaopeng / Zhang, Qiang / Zhou, Changjun

    IEEE/ACM transactions on computational biology and bioinformatics

    2022  Volume 19, Issue 3, Page(s) 1424–1434

    Abstract: Analog DNA strand displacement circuits can be used to build artificial neural network due to the continuity of dynamic behavior. In this study, DNA implementations of novel catalysis, novel degradation and adjustment reaction modules are designed and ... ...

    Abstract Analog DNA strand displacement circuits can be used to build artificial neural network due to the continuity of dynamic behavior. In this study, DNA implementations of novel catalysis, novel degradation and adjustment reaction modules are designed and used to build an analog DNA strand displacement reaction network. A novel adaptive linear neuron (ADALINE) is constructed by the ordinary differential equations of an ideal formal chemical reaction network, which is built by reaction modules. When reaction network approaches equilibrium, the weights of the ADALINE are updated without learning algorithm. Simulation results indicate that, ADALINE based on the analog DNA strand displacement circuit has ability to implement the learning function of the ADALINE based on the ideal formal chemical reaction networks, and fit a class of linear function.
    MeSH term(s) Algorithms ; Computer Simulation ; DNA/genetics ; DNA/metabolism ; Neural Networks, Computer ; Neurons/metabolism
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-06-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2020.3045567
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Rheo-Fermentation Dough Properties, Bread-Making Quality and Aroma Characteristics of Red Bean (

    Huang, Chengye / Huang, Jing / Zhang, Binle / Omedi, Jacob Ojobi / Chen, Cheng / Zhou, Liyuan / Liang, Li / Zou, Qibo / Zheng, Jianxian / Zeng, Yongqing / Huang, Weining

    Foods (Basel, Switzerland)

    2023  Volume 12, Issue 3

    Abstract: This study investigated the impact of in situ-formed exopolysaccharides (EPS) in red bean ( ...

    Abstract This study investigated the impact of in situ-formed exopolysaccharides (EPS) in red bean (
    Language English
    Publishing date 2023-02-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods12030605
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Encryption Algorithm Based on DNA Strand Displacement and DNA Sequence Operation.

    Zou, Chengye / Wei, Xiaopeng / Zhang, Qiang / Zhou, Changjun / Zhou, Shuang

    IEEE transactions on nanobioscience

    2021  Volume 20, Issue 2, Page(s) 223–234

    Abstract: DNA strand displacement is introduced in this study and used to construct an analog DNA strand displacement chaotic system based on six reaction modules in nanoscale size. The DNA strand displacement circuit is employed in encryption as a chaotic ... ...

    Abstract DNA strand displacement is introduced in this study and used to construct an analog DNA strand displacement chaotic system based on six reaction modules in nanoscale size. The DNA strand displacement circuit is employed in encryption as a chaotic generator to produce chaotic sequences. In the encryption algorithm, we convert chaotic sequences to binary ones by comparing the concentration of signal DNA strand. Simulation results show that the encryption scheme is sensitive to the keys, and key space is large enough to resist the brute-force attacks, furthermore algorithm has a high capacity to resist statistic attack. Based on robustness analysis, our proposed encryption scheme is robust to the DNA strand displacement reaction rate control, noise and concentration detection to a certain extent.
    MeSH term(s) Algorithms ; Base Sequence ; Computer Simulation ; DNA/genetics ; Image Processing, Computer-Assisted
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1558-2639
    ISSN (online) 1558-2639
    DOI 10.1109/TNB.2021.3058399
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Compilation of a Coupled Hyper-Chaotic Lorenz System Based on DNA Strand Displacement Reaction Network.

    Zou, Chengye / Zhang, Qiang / Wei, Xiaopeng

    IEEE transactions on nanobioscience

    2020  Volume 20, Issue 1, Page(s) 92–104

    Abstract: Ideal formal chemical reaction network is an effective programming language to design complex system dynamical behavior. In this article, a coupled hyper-chaotic Lorenz system can be described by the ordinary differential equations of an ideal formal ... ...

    Abstract Ideal formal chemical reaction network is an effective programming language to design complex system dynamical behavior. In this article, a coupled hyper-chaotic Lorenz system can be described by the ordinary differential equations of an ideal formal reaction network, which is constructed by catalysis, annihilation and adjust reaction modules, where the variables of system are represented by the difference in concentration of two chemical species. The ideal formal reaction network can be implemented by DNA strand displacement reaction network. Through Lyapunov exponent, we have analyzed hyper-chaotic dynamical behavior of coupled Lorenz system. In discussion and analysis, we have analyzed effect of noise, reaction rate control error and concentration detection error to DNA strand displacement reaction network.
    MeSH term(s) Catalysis ; Computer Simulation ; DNA
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2020-12-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1558-2639
    ISSN (online) 1558-2639
    DOI 10.1109/TNB.2020.3031360
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Ground Deformation and Permafrost Degradation in the Source Region of the Yellow River, in the Northeast of the Qinghai-Tibet Plateau

    Chengye Li / Lin Zhao / Lingxiao Wang / Shibo Liu / Huayun Zhou / Zhibin Li / Guangyue Liu / Erji Du / Defu Zou / Yingxu Hou

    Remote Sensing, Vol 15, Iss 3153, p

    2023  Volume 3153

    Abstract: The source region of the Yellow River (SRYR) is situated on the permafrost boundary in the northeast of the Qinghai-Tibet Plateau (QTP), which is an area highly sensitive to climate change. As a result of increasing global temperatures, the permafrost in ...

    Abstract The source region of the Yellow River (SRYR) is situated on the permafrost boundary in the northeast of the Qinghai-Tibet Plateau (QTP), which is an area highly sensitive to climate change. As a result of increasing global temperatures, the permafrost in this region has undergone significant degradation. In this study, we utilized Sentinel-1 to obtain ground surface deformation data in the SRYR from June 2017 to January 2022. We then analyzed the differences in terrain deformation under various environmental conditions. Our findings indicated an overall subsidence trend in the SRYR, with a long-term deformation velocity of −4.2 mm/a and seasonal deformation of 8.85 mm. Furthermore, the results showed that terrain deformation varied considerably from region to region, and that the Huanghe’ yan sub-basin with the highest permafrost coverage among all sub-basins significantly higher subsidence rates than other regions. Topography strongly influenced ground surface deformation, with flat slopes exhibiting much higher subsidence rates and seasonal deformation. Moreover, the ground temperature and ground ice richness played a certain role in the deformation pattern. This study also analyzed regional deformation details from eight boreholes and one profile line covering different surface conditions, revealing the potential for refining the permafrost boundary. Overall, the results of this study provide valuable insights into the evolution of permafrost in the SRYR region.
    Keywords permafrost ; ground surface deformation ; SBAS-InSAR ; source region of the Yellow River (SRYR) ; Science ; Q
    Subject code 550
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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