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designing logic gates based on 3-way DNAzyme complex

Analytical Methods 2019年第5期12卷 693-700页

作者： Donglin Liu Yuan Liu Bin Wang Qiang Zhang 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 China

In recent years, DNA has been regarded as a reliable raw material for building biological computers and biochips due to its nanoscale size, ultralow energy consumption, and high-performance computing potential. As the basis of building a biological computer, the research on the construction of nanoscale logic arithmetic and nanoscale biochemical logic circuits based on DNA molecules as carriers has attracted increasing attention. Although researchers use DNA strand replacement systems to achieve it this requires adjustment and careful design of the toehold, making sequence selection more difficult. To reduce dependence on the toehold, we propose a 3-way DNAzyme complex composed of three E6 DNAzymes assembled using the biological characteristics of E6 DNAzyme. This complex enriched the recognition vector of E6 DNAzyme, which can be used for multiple substrates, thus improving the reusability and efficiency of DNA molecules. At the same time, based on the 3-way DNAzyme complex and without the involvement of the toehold, we designed logic gates such as the OR gate, the AND gate, and the INHIBIT gate, and realized the construction of a new half subtractor and nanoscale biochemical logic circuit. These explorations and attempts extended the practicality of the 3-way DNAzyme complex. We believe that these logic elements will have a wide range of applications in DNA nanoscale programming, biological computing, and nanoscale medicine.

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Predicting the Legal Risk of "Section 337 Investigations" by Elastic Time Predictor

Predicting the Legal Risk of "Section 337 Investigations" by...

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IEEE International Symposium on Parallel and Distributed Processing with Applications and IEEE International Conference on Ubiquitous computing and Communications (ISPA/IUCC)

作者： Xing Gao Chao Che Lasheng Zhao Jianxin Zhang Key Lab of Advanced Design and Intelligent Computing (Ministry of Education) Dalian University Dalian China

ISBN: (纸本)9781728152103

In recent years, more and more patent lawsuits have been filed by Chinese enterprises, represented by the "Section 337 investigations" of the United States. In order to help Chinese enterprises cope with the challenges of patent litigation, a matrix factorization based recommendation system are used to predict the legal risk of 337 investigation. However, the results predicted by the model are prone to over-fitting. In order to solve this problem, this paper proposes a new recommendation framework, namely elastic time predictor. The model is a hybrid model combining matrix factorization and truncation function. We encode the information of the prosecution case of major companies and decompose it into two sub-matrices, and then combine the decomposed matrix with the segmentation of the truncation function to maintain the entire recommended frame flexible. In the recommended approach, we consider the risk of litigation that a company may experience when entering a new market, for example the risk that a potential competitor will file a lawsuit against a new entrant. We use actual data to conduct experiments, and the experimental results show that the proposed method is superior to the baseline method and has significant advantages.

关键词： matrix decomposition organisational aspects patents risk management matrix decomposition Organizational aspects Patents patenting Risk Management baseline method Litigation Cutoffs Companies Recommender systems

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A Novel Solution of Underdetermined Equations for DGTD based on Prior knowledge

A Novel Solution of Underdetermined Equations for DGTD based...

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International Conference on Microwave and Millimeter Wave Technology Proceedings

作者： Qi Qi Xinyuan Cao Mingsheng Chen Zhixiang Huang Yi Liu Xianliang Wu Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei Anhui Province Key Laboratory of Simulation and Design for Electronic Information System Hefei Normal University Hefei China School of Electronic Engineering Huainan Normal University Huainan China

ISBN: (数字)9781728157337

ISBN: (纸本)9781728157344

To accelerate solving transient electromagnetic problems by discontinuous Galerkin time domain (DGTD) method, a solution of underdetermined equations is established based on prior knowledge. In the proposed method, nodal basis function and a leapfrog scheme are used to Maxwell curl equations for spatial and time discretization. Electromagnetic fields in each element of computation domain are updated individually by applying conventional DGTD in initial time. When the electromagnetic wave covers the domain, the fields of all elements are updated as a whole. The underdetermined equations are established by randomly extracting rows from global mass matrix. Taking the results of a few previous time steps as the prior knowledge, a sparse transform is constructed. Then the underdetermined system of equations can be solved by recovery algorithms. Meanwhile,in order to maintain the advantage of low computational complexity, a restart mechanism is presented. The validity of the proposed method is verified by numerical experiments.

关键词： Microwave technology Millimeter wave technology Transforms Sparse matrices Electromagnetic fields Transient analysis Time-domain analysis

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The microstructure and mechanical properties analysis of H13/Ni60 functionally gradient coating fabricated by laser cladding method

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Optics and Laser Technology 2025年 190卷

作者： Wang, Zixuan Fu, Bowen Chen, Tianhang Chen, Liaoyuan Yu, Tianbiao Zhao, Jun School of Mechanical Engineering and Automation Northeastern University Shenyang110819 China Liaoning Provincial Key Laboratory of High-end Equipment Intelligent Design and Manufacturing Technology Shenyang110819 China School of Mechatronics Engineering Henan University of Science and Technology Luoyang471000 China School of Advanced Manufacturing Sun Yat-sen University Shenzhen518107 China

H13 mold steel has excellent hardenability, wear resistance, and thermal fatigue resistance. However, long-term high-temperature thermal load and friction loss will seriously affect the service life of the mold. Surface modification treatment can be used to repair the worn parts. In this study, the surface treatment of H13 mold steel was carried out by laser cladding method to improve its hardness and wear resistance. The H13/Ni60 functionally gradient coating was designed and obtained, and its structure and performance variation with composition were investigated. The optimal processing parameter combinations, including laser power of 400 W, powder feeding rate of 1.2 r/min, scanning speed of 4 mm/s, overlap rate of 23 %, and lifting amount of 0.42 mm, were obtained through orthogonal experiments and the equal area method. The microstructure and physical phase analysis were conducted, and the growth direction of the grains is along the normal direction to the melt pool boundary. With the gradual increase of Ni60 content, the grain structure becomes finer. The [Fe, Ni] and Cr7C3 are produced and reach their maximum contents in the top surface of functionally gradient coating with 100 % Ni60. The average microhardness of the surface is 797.8 HV, which is 3.4 times higher than that of the substrate. Its average friction coefficient is 0.465, which is only 73 % of that of the substrate. The obtained functionally gradient coating has significantly improved the hardness and wear resistance of the H13 mold steel surface. The metallurgical bonds were formed between the different gradient layers and the substrate. © 2025 Elsevier Ltd

关键词： Microhardness

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Loop Quantum Photonic Chip for Coherent Multi-Time-Step Evolution

arXiv

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arXiv 2024年

作者： Zhan, Yuancheng Zhang, Hui Erbanni, Rebecca Burger, Andreas Wan, Lingxiao Jiang, Xudong Chae, Sanghoon Liu, Aiqun Poletti, Dario Kwek, Leong Chuan Nanyang Technological University Singapore Nanyang Technological University Singapore Institute of Precision Optical Engineering School of Physics Science and Engineering Tongji University Shanghai200092 China MOE Key Laboratory of Advanced Micro-Structured Materials Shanghai Institute of Intelligent Science and Technology Shanghai Frontiers Science Center of Digital Optics Tongji University Shanghai200092 China Science Mathematics and Technology Cluster Singapore University of Technology and Design 8 Somapah Road 487372 Singapore Department of Computer Science University of Toronto Canada The Hong Kong Polytechnic University Hong Kong Engineering Product Development Pillar Singapore University of Technology and Design 8 Somapah Road 487372 Singapore Centre for Quantum Technologies National University of Singapore 117543 Singapore MajuLab CNRS-UNS-NUS-NTU International Joint Research Unit UMI 3654 Singapore National Institute of Education Nanyang Technological University Singapore

Quantum evolution is crucial for the understanding of complex quantum systems. However, current implementations of time evolution on quantum photonic platforms face challenges of limited light source efficiency due to propagation loss and merely single-layer complexity. In this work, we present a loop quantum photonic chip (Loop-QPC) designed to efficiently simulate quantum dynamics over multiple time steps in a single chip. Our approach employs a recirculating loop structure to reuse computational resources and eliminate the need for multiple quantum tomography steps or chip reconfigurations. We experimentally demonstrate the dynamics of the spin-boson model on a low-loss Silicon Nitride (SiN) integrated photonic chip. The Loop-QPC achieves a three-step unitary evolution closely matching the theoretical predictions. These results establish the Loop-QPC as a promising method for efficient and scalable quantum simulation, advancing the development of quantum simulation on programmable photonic circuits. Copyright © 2024, The Authors. All rights reserved.

关键词： Silicon nitride

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Surface state induced velocity transition for layered carbon nanotube films under transverse penetration loading

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Composite Structures 2025年 369卷

作者： Pengfei Wang Wenshuai Wang Jie Tian Zhenhua Song Songlin Xu CAS Key Laboratory of Mechanical Behavior and Design of Materials Department of Modern Mechanics University of Science and Technology of China Hefei 230027 China Engineering and Materials Science Experiment Center University of Science and Technology of China Hefei 230027 China Department of Aeronautics and Astronautics College of Intelligent Robotics and Advanced Manufacturing Fudan University Shanghai 200433 China

Carbon nanotube (CNT) films, consisting of entangled two-dimensional networks, exhibit prominent surface-dependent characteristics. Lubricants have been recognized as an effective strategy for reducing interfacial friction. However, experimental evidence indicates that lubricants unexpectedly increased the interfacial friction, demonstrating a counterintuitive velocity-dependent behavior. To elucidate the anomalous interfacial dynamics, experimental and computational methodologies were employed to systematically investigate the transverse penetrating behaviors of CNT films with different interface states and loading velocities. Experimental results indicate that the lubricant exhibits a decreasing trend at lower relative velocities, but transitions from decreasing to strengthening behavior as penetration velocity increases. The proposed equation reveals that the strengthening mechanism is not solely velocity-dependent but is jointly governed by the load magnitude and surface conditions. The high specific surface area of CNT films induces enhanced interface states and pronounced velocity-dependent characteristics, which collectively govern the fracture pattern observed in films subjected to distinct surface stress conditions. Deciphering the lubricant-induced velocity-transition mechanisms in CNT films yields new theoretical insights into interface-governed penetration behavior, while establishing material design principles for engineering impact-resistant membranes with tunable energy dissipation pathways.

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VarBen

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The Journal of Molecular Diagnostics 2021年第3期23卷 285-299页

作者： Ziyang Li Shuangsang Fang Rui Zhang Lijia Yu Jiawei Zhang Dechao Bu Liang Sun Yi Zhao Jinming Li National Center for Clinical Laboratories Beijing Hospital National Center of Gerontology Beijing People's Republic of China Graduate School Peking Union Medical College Chinese Academy of Medical Sciences Beijing People's Republic of China Key Laboratory of Intelligent Information Processing Advanced Computer Research Center Institute of Computing Technology Chinese Academy of Medical Sciences Beijing People's Republic of China Beijing Engineering Research Center of Laboratory Medicine Beijing Hospital Beijing People's Republic of China

Next-generation sequencing is increasingly being adopted as a valuable method for the detection of somatic variants in clinical oncology. However, it is still challenging to reach a satisfactory level of robustness and standardization in clinical practice when using the currently available bioinformatics pipelines to detect variants from raw sequencing data. Moreover, appropriate reference data sets are lacking for clinical bioinformatics pipeline development, validation, and proficiency testing. Herein, we developed the Variant Benchmark tool (VarBen), an open-source software for variant simulation to generate customized reference data sets by directly editing the original sequencing reads. VarBen can introduce a variety of variants, including single-nucleotide variants, small insertions and deletions, and large structural variants, into targeted, exome, or whole-genome sequencing data, and can handle sequencing data from both the Illumina and Ion Torrent sequencing platforms. To demonstrate the feasibility and robustness of VarBen, we performed variant simulation on different sequencing data sets and compared the simulated variants with real-world data. The validation study showed that the simulated data are highly comparable to real-world data and that VarBen is a reliable tool for variant simulation. In addition, our collaborative study of somatic variant calling in 20 laboratories emphasizes the need for laboratories to evaluate their bioinformatics pipelines with customized reference data sets. VarBen may help users develop and validate their bioinformatics pipelines using locally generated sequencing data.

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Graph classification based on skeleton and component features

arXiv

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arXiv 2021年

作者： Liu, Xue Wei, Wei Feng, Xiangnan Cao, Xiaobo Sun, Dan Beijing System Design Institute of Electro-Mechanic Engineering Beijing100854 China School of Mathematical Sciences Beihang University Beijing100191 China Key Laboratory of Mathematics Informatics and Behavioral Semantics Ministry of Education 100191 China Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing100191 China Peng Cheng Laboratory Shenzhen Guangdong518066 China

Most existing popular methods for learning graph embedding only consider fixed-order global structural features and lack structures hierarchical representation. To address this weakness, we propose a novel graph embedding algorithm named GraphCSC that realizes classification based on skeleton information using fixed-order structures learned in anonymous random walks manner, and component information using different size subgraphs. Two graphs are similar if their skeletons and components are both similar, thus in our model, we integrate both of them together into embeddings as graph homogeneity characterization. We demonstrate our model on different datasets in comparison with a comprehensive list of up-to-date state-of-the-art baselines, and experiments show that our work is superior in real-world graph classification tasks. © 2021, CC BY.

关键词： Musculoskeletal system

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Exploring Multi-level Mutual Information for Drug-target Interaction Prediction

Exploring Multi-level Mutual Information for Drug-target Int...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jiatao Chen Liang Zhang Ke Cheng Bo Jin Xinjiang Lu Chao Che Yiwei Liu Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian China International Business College Dongbei University of Finance and Economics Dalian China School of Computer Science and Technology Dalian University of Technology Dalian China Business Intelligence Lab Baidu Research

ISBN: (数字)9781728162157

ISBN: (纸本)9781728162164

Recent advances in graph representation learning provide new opportunities for computational drug-target interaction (DTI) prediction. Inspired by the emerging graph mutual information-based algorithms, we propose MMIDTI, a multi-level mutual information-aware DTI prediction framework based on a heterogeneous network (i.e., drug-protein, drug-drug and protein-protein interaction network; drug-disease, drug-side-effect, and protein-disease association network; drug-structure and protein-sequence similarity network). More specifically, MMIDTI leverages an encoder-decoder framework that can learn the type-aware and meta-path augmented node representations by following a contrastive learning paradigm. The encoder part is a Graph Convolutional Network (GCN) and the decoder is an inner product of the learned representations to recover the original heterogeneous network. Meanwhile, MMIDTI exploits two levels of mutual information: (1) maximizing local mutual information, to obtain node representations that capture the global information content of the entire heterogeneous graph. (2) maximizing the global mutual information, to constrain the node representation to have desired statistical characteristics. Experimental results show that our model can achieve better prediction performance than state-of-the-art methods.

关键词： Mutual information Proteins Drugs Predictive models Diffusion tensor imaging Heterogeneous networks Task analysis

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Observation of Electric Hysteresis, Polarization Oscillation, and Pyroelectricity in Nonferroelectric p−n Heterojunctions

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Physical Review Letters 2023年第19期130卷 196801-196801页

作者： Yucheng Jiang Xinglong Ma Lin Wang Jinlei Zhang Zhichao Wang Run Zhao Guozhen Liu Yang Li Cheng Zhang Chunlan Ma Yaping Qi Lin Wu Ju Gao Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application School of Physical Science and Technology Suzhou University of Science and Technology Suzhou 215009 China School of Physics Nanjing University Nanjing 210093 China School of Materials Science and Engineering Shanghai University Shanghai 200444 China Macau Institute of Systems Engineering Macau University of Science and Technology Macau 999078 China Advanced Institute for Materials Research Tohoku University Sendai 980-8577 Japan Science Mathematics and Technology Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore Institute of High Performance Computing Agency for Science Technology and Research 1 Fusionopolis Way #16-16 Connexis Singapore 138632 Singapore School for Optoelectronic Engineering Zaozhuang University Shandong 277160 China

The switchable electric polarization is usually achieved in ferroelectric materials with noncentrosymmetric structures, which opens exciting opportunities for information storage and neuromorphic computing. In another polar system of p−n junction, there exists the electric polarization at the interface due to the Fermi level misalignment. However, the resultant built-in electric field is unavailable to manipulate, thus attracting less attention for memory devices. Here, we report the interfacial polarization hysteresis (IPH) in the vertical sidewall van der Waals heterojunctions of black phosphorus and quasi-two-dimensional electron gas on SrTiO3. A nonvolatile switching of electric polarization can be achieved by reconstructing the space charge region (SCR) with long-lifetime nonequilibrium carriers. The resulting electric-field controllable IPH is experimentally verified by electric hysteresis, polarization oscillation, and pyroelectric effect. Further studies confirm the transition temperature of 340 K, beyond which the IPH vanishes. The second transition is revealed with the temperature dropping below 230 K, corresponding to the sharp improvement of IPH and the freezing of SCR reconstruction. This work offers new possibilities for exploring the memory phenomena in nonferroelectric p−n heterojunctions.

关键词： Electric polarization Electroresistance Pyroelectricity

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