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A molecular device: A DNA molecular lock driven by the nicking enzymes

Computational and structural biotechnology journal 2020年 18卷 2107-2116页

作者： Xiaokang Zhang Qiang Zhang Yuan Liu Bin Wang Shihua Zhou Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China. School of Computer Science and Technology Dalian University of Technology Dalian 116024 China.

As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES-YES cascade circuit and a YES-AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.

关键词： DNA Information Security Molecular Lock Nicking Enzyme

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Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump

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BMC bioinformatics 2022年第SUPPL 12期22卷 437页

作者： Hao Fu Hui Lv Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China. Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China. lh8481@***. State Key Laboratory of Synthetical Automation for Process Industries Northeastern University Shenyang 110004 China. lh8481@***. Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China. zhangq@***. School of Computer Science and Technology Dalian University of Technology Dalian 116024 China. zhangq@***.

BACKGROUND:Bioinformatics is a subject produced by the combination of life science and computer science. It mainly uses computer technology to study the laws of biological systems. The design and realization of DNA circuit reaction is one of the important contents of bioinformatics. RESULTS:In this paper, nonlinear dynamic system model with Lévy jump based on entropy-driven amplifier (EDA) circuit response is studied. Firstly, nonlinear biochemical reaction system model is established based on EDA circuit response. Considering the influence of disturbance factors on the system, nonlinear biochemical reaction system with Lévy jump is built. Secondly, in order to prove that the constructed system conforms to the actual meaning, the existence and uniqueness of the system solution is analyzed. Next, the sufficient conditions for the end and continuation of EDA circuit reaction are certified. Finally, the correctness of the theoretical results is proved by numerical simulation, and the reactivity of THTSignal in EDA circuit under different noise intensity is verified. CONCLUSIONS:In EDA circuit reaction, the intensity of external noise has a significant impact on the system. The end of EDA circuit reaction is closely related to the intensity of Lévy noise, and Lévy jump has a significant impact on the nature of biochemical reaction system.

关键词： Entropy-driven amplifier Lyapunov function Lévy jump Nonlinear system model

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Dual-Domain deep prior guided sparse-view CT reconstruction with multi-scale fusion attention

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Scientific Reports 2025年第1期15卷 1-20页

作者： Wu, Jia Lin, Jinzhao Jiang, Xiaoming Zheng, Wei Zhong, Lisha Pang, Yu Meng, Hongying Li, Zhangyong School of Communications and Information Engineering Chongqing University of Posts and Telecommunications Chongqing 400065 China School of Medical Information and Engineering Southwest Medical University Luzhou 646000 China Chongqing Engineering Research Center of Medical Electronics and Information Technology Chongqing University of Posts and Telecommunications Chongqing 400065 China Key Laboratory of Intelligent Computing for Advanced Manufacturing Chongqing University of Posts and Telecommunications Chongqing 400065 China School of Optoelectronic Engineering Chongqing University of Posts and Telecommunications Chongqing China Department of Electronic and Electrical Engineering College of Engineering Design and Physical Sciences Brunel University London Uxbridge UB8 3PH United Kingdom

Sparse-view CT reconstruction is a challenging ill-posed inverse problem, where insufficient projection data leads to degraded image quality with increased noise and artifacts. Recent deep learning approaches have shown promising results in CT reconstruction. However, existing methods often neglect projection data constraints and rely heavily on convolutional neural networks, resulting in limited feature extraction capabilities and inadequate adaptability. To address these limitations, we propose a Dual-domain deep Prior-guided Multi-scale fusion Attention (DPMA) model for sparse-view CT reconstruction, aiming to enhance reconstruction accuracy while ensuring data consistency and stability. First, we establish a residual regularization strategy that applies constraints on the difference between the prior image and target image, effectively integrating deep learning-based priors with model-based optimization. Second, we develop a multi-scale fusion attention mechanism that employs parallel pathways to simultaneously model global context, regional dependencies, and local details in a unified framework. Third, we incorporate a physics-informed consistency module based on range-null space decomposition to ensure adherence to projection data constraints. Experimental results demonstrate that DPMA achieves improved reconstruction quality compared to existing approaches, particularly in noise suppression, artifact reduction, and fine detail preservation. © The Author(s) 2025.

关键词： Deep prior Model-based optimization Multi-scale fusion attention Physics-informed consistency Sparse-view CT reconstruction

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Humanoid Robot Control Based on Deep Learning 12th

Humanoid Robot Control Based on Deep Learning

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12th International Conference on e-Learning and Games, Edutainment 2018

作者： Guo, Bin Yi, Pengfei Zhou, Dongsheng Wei, Xiaopeng Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China College of Computer Science and Technology Dalian University of Technology Dalian1160243 China

ISBN: (纸本)9783030237110

The direct control of humanoid robot by human motion is an important aspect of current research. Most of these methods are based on additional equipments, such as Kinect, which are usually not equipped on robot. In order to avoid using these external equipments, we explored a robot controlling method only using the low-resolution camera on robot. Firstly, a stacked hourglass network is employed to obtain the accurate 2D heatmap containing positions of human joints from RGB image captured by camera on robot. Then, 3D human poses including coordinates of human body joints are estimated from 2D heatmaps by a method aiming to reconstruct 3D human poses from 2D poses. Finally, the rotation angles of robot are computed according to these 3D coordinates and are transmitted to the robot to reconstruct the original human pose. Using the NAO robot as an example, the experimental results show that the humanoid robot can imitate motions of different human actors in different scenes well while applying our method. © 2019, Springer Nature Switzerland AG.

关键词： Anthropomorphic robots

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Missing Data Recovery for Human Mocap Data Based on A-LSTM and LS Constraint

Missing Data Recovery for Human Mocap Data Based on A-LSTM a...

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IEEE International Conference on Signal and Image Processing (ICSIP)

作者： Lu Ji Rui Liu Dongsheng Zhou Qiang Zhang Xiaopeng Wei Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian China School of Computer Science and Technology Dalian University of Technology Dalian China

ISBN: (数字)9781728168968

ISBN: (纸本)9781728168975

Human mocap (motion capture) data has been widely used in many fields. However, influenced by the occlusion and falling, missing of markers is inevitable in optical motion capture system. According to the temporal and spatial characteristics of mocap data, a missing data recovery method based on attention-based LSTM network (A-LSTM) and least-squares (LS) constraint is proposed in this paper. First, the LSTM is chosen as the basic network to estimate the position of the missing markers, in which an attention mechanism is introduced to learn the temporal continuity of human mocap data. Then, a space affine transformation based on least-squares fitting is adopted as the spatial constraint to refine the estimated positions, after which the restored error can be reduced significantly. Experiments show that the proposed A-LSTM+LS method is robust to the length of missing gap and the number of missing markers. Under the same conditions, our method achieves smaller restore error than the state of the art.

关键词： Legged locomotion Deep learning Image recognition Correlation Fitting Neural networks Image restoration

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A real-time one-time pad DNA-chaos image encryption algorithm based on multiple keys

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Optics & Laser Technology 2021年 143卷

作者： Shihua Zhou Key laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian China

Image encryption is an important necessity when sharing data over public networks, and many image encryption algorithms have been proposed for the task. However, most of these algorithms are complex and slow. We propose a real-time one-time pad DNA-chaos image encryption algorithm using multiple keys. The proposed encryption algorithm uses a greatly simplified mechanism and a large, unpredictable sequence to encrypt the image. Our algorithm has three main advantages. First, its reliance on the original image for four of the keys makes it sensitive to changes in the original image. Small changes in the image produce large changes in the keys, making the algorithm resistant to differential attacks. Second, we integrate the natural DNA sequence into the process of generating the key, and the algorithm uses the massive DNA sequences stored in the DNA gene bank to solve the problem that it is difficult to store one-time pad. The keys have the property of one-time pad, and the key space is considerablely large. Finally, our algorithm encrypts quickly enough to make it suitable for real-time applications. On the premise of ensuring that the results of this paper are not worse than those of the comparison literature in other performance indicators, in terms of encryption time, even if we use a computing environment that is worse than all the comparison literature computer configurations, the algorithm of this paper can still save at least 14%–86%. As the picture size becomes larger, the advantages of the algorithm in this paper are more obvious.

关键词： Image encryption Multiple keys DNA coding Chaos 00-01 99-00

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DNA logic circuits based on FokI enzyme regulation

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New Journal of Chemistry 2020年第5期44卷 1931-1941页

作者： Sue Zhao Yuan Liu Bin Wang Changjun Zhou Qiang Zhang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China School of Computer Science and Technology Dalian University of Technology Dalian 116024 China College of Computer Science and Engineering Dalian Minzu University Dalian China

In biomolecular programming, researchers have attempted to use DNA molecules as a new kind of highly reliable raw material, due to the high predictability and good programmability of DNA molecules, and construct DNA circuits that can realize logical calculation. In DNA circuits with a multi-step cascade, autonomy, and complex behavior, it is very important to be able to controllably activate and regulate toeholds. Therefore, we propose a strategy using an enzyme-assisted cleavage regulation system to solve the above problems. In this strategy, the DNA input strand regulates the recognition domain of FokI and initiates the activity of FokI due to the reconfiguration of programmable information. In addition, FokI induced conformational changes regulate the toehold-mediated strand displacement reaction, which optimizes the complex function and the signal transmission of logic circuits. In order to prove the feasibility of this strategy, we constructed a series of logic gates (YES, AND, and INHIBIT), and on this basis, we successfully implemented both a demultiplexer circuit and a multiplexer cascade circuit. The proposed enzyme-assisted cleavage regulation strategy provides a new approach for constructing more complex molecular computing systems, with applications in biosensors and medical detection systems.

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Half adder and half subtractor logic gates based on nicking enzymes

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Molecular Systems design and Engineering 2019年第6期4卷 1103-1113页

作者： Zhao, Yunbin Liu, Yuan Zheng, Xuedong Wang, Bin Lv, Hui Zhou, Shihua Zhang, Qiang Wei, Xiaopeng Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian 116622 China School of Computer Science and Technology Dalian University of Technology Dalian 116024 China College of Computer Science Shenyang Aerospace University Shenyang 110136 China

The excellent specificity and predictability of DNA pairing and its natural ability to interact with other biomolecules make DNA an ideal material for building molecular logic devices (MLDs). However, there are still many challenges in the process of building such devices, including their complex structures, potentially harsh reaction conditions, long reaction times and so on. Thus, the parallel nature of DNA and other biomolecules needs to be developed before MLDs based on DNA can be exploited to a greater extent. In order to solve this problem, herein, we carefully selected two enzymes, *** and ***, that were both persistent and compatible, and used them to build a nicking enzyme platform. Based on this enzyme platform, we constructed a novel XOR logic gate with flexible internal signaling. Furthermore, AND and INHIBIT logic gates were also modified to use the same enzymes as the XOR logic gate as their inputs. As a result, the algorithm process of half adder and half subtractor was realized by this work. This study provides a new approach for typical DNA-based arithmetic operations and promotes the development of advanced MLDs. © 2019 The Royal Society of Chemistry.

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A hybrid algorithm based on artificial bee colony and pigeon inspired optimization for 3D protein structure prediction

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Journal of Bionanoscience 2018年第1期12卷 100-108页

作者： Li, Ting Zhou, Changjun Wang, Bin Xiao, Boxiang Zheng, Xuedong Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China Beijing Key Laboratory of Digital Plant Beijing100097 China

With the accomplishment of the Human Genome Project, the significance of protein structure research becomes more outstanding. The prediction of protein structure is aimed at the study of amino acid molecules, and belongs to the field of Bio-Nano research. There are two kinds of methods to study protein structure: Experiment and theory. This paper adopts ab-initio prediction method which is one of theoretical methods. Based on the "thermodynamic hypothesis," there are many different models applied to the field. This paper selects 3D AB off-lattice model to solve this problem. ABC-PIO combines the characteristics of the diversity generated by artificial bee colony algorithm and the fast convergence speed of pigeon inspired optimization. At the end of this algorithm, Cauchy perturbation strategy is added to optimize the local optimum. Two functions are introduced to dynamically control two operators of the hybrid algorithm. In order to test the quality of ABC-PIO, ten real protein sequences from the Protein Data Bank have been selected. Compared with other four algorithms, the algorithm gets better result. To calculate the error between the predicted and the true protein structure RMSD is set. Comparisons are made not only in the convergence curves but also in the backbone drawings. © 2018 American Scientific Publishers.

关键词： Optimization

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DNA circuits driven by conformational changes in DNAzyme recognition arms

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RSC advances 2020年第13期10卷 7956-7966页

作者： Xinyi Sun Xuedong Zheng Sue Zhao Yuan Liu Bin Wang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian 116622 China wangbinpaper@***. College of Computer Science Shenyang Aerospace University Shenyang 110136 China xuedongzheng@***. School of Computer Scicence and Technology Dalian University of Technology Dalian 116024 China Liuyuan.dlut@***.

DNA computing plays an important role in nanotechnology due to the unique programmability and parallelism of DNA molecules. As an important tool to realize DNA computation, various logic computing devices have great application potential. The application of DNAzyme makes the achievements in the field of logical computing more diverse. In order to improve the efficiency of the logical units run by DNAzyme, we proposed a strategy to regulate the DNA circuit by the conformational change of the E6-type DNAzyme recognition arms driven by Mg. This strategy changes the single mode of DNAzyme signal transmission, extends the functions of E6-type DNAzyme, and saves the time of signal transmission in the molecular scale. To verify the feasibility of this strategy, first, we constructed DNA logic gates (YES, OR, and AND). Second, we cascade different logic gates (YES-YES, YES-AND) to prove the scalability. Finally, a self-catalytic DNA circuit is established. Through the experimental results, we verified that this DNAzyme regulation strategy relatively reduces the cost of logic circuits to some extent and significantly increases the reaction rate, and can also be used to indicate the range of Mg concentrations. This research strategy provides new thinking for logical computing and explores new directions for detection and biosensors.

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