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A Sensitive Nanothermometer Based on DNA Triplex Structure 1

17th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2022

作者： Chen, Zhekun Hu, Yingxin Xie, Chun Chen, Kuiting Pan, Linqiang Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China College of Information Science and Technology Shijiazhuang Tiedao University Shijiazhuang050043 China

ISBN: (数字)9789819915491

ISBN: (纸本)9789819915484

DNA has been used to construct a variety of nanoscale thermometers due to its unique thermodynamic properties. It has proven to be one of the most promising, yet challenging aspects of DNA-based thermometers, to obtain significant signal changes when the temperature changes slightly. Here, we propose a strategy to construct nanoscale thermometers with sensitive temperature responses based on DNA triplex. The thermometers consist of a CT-rich DNA strand and stabilizing strands, whose conformations vary with temperature. By adjusting the sequence design or introducing mismatch bases in stabilizing strands, the temperature response interval of the thermometer can be reduced to 7 ∘C, which lead to higher sensitivity compared to the interval of 12–15 ∘C for conventional designs. The temperature responses of the thermometer are characterized by fluorescence experiments. The fluorescence kinetics experiments demonstrate the good repeatability. The design of the nanothermometer will be helpful for constructing advanced nanosystem with sensitive temperature responses as well as long service times. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Thermometers

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Tuning Geometric Conformations of Curved DNA Structures by controlling Positions of Nicks 1

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17th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2022

作者： Xie, Chun Hu, Yingxin Chen, Kuiting Chen, Zhekun Pan, Linqiang Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China College of Information Science and Technology Shijiazhuang Tiedao University Shijiazhuang050043 China

ISBN: (数字)9789819915491

ISBN: (纸本)9789819915484

DNA origami is one of the powerful techniques that utilize DNA as building blocks to synthesize nanostructures. Traditionally, through introducing different numbers of insertions and deletions of base pairs in DNA helices, the in-plane bending angle of curved DNA structures could be roughly tuned. Here, we explored a strategy that used the position patterns of nicks in staple strands to tune the geometric conformation of curved DNA origami structures, including in-plane bending, out-of-plane bending, and twisting angles. When the structure adopted different patterns of nicks positions, great difference appeared in the geometric properties. Further, by combining subunits of different nicks position patterns, the bending and twisting of the combined structure was effectively tuned. The strategy increases the design accuracy of curved DNA origami structures and expands the toolbox for designing DNA structures. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Molecular dynamics

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Cluster Consensus Problem on Time-varying Higher-Order Interaction Networks

Cluster Consensus Problem on Time-varying Higher-Order Inter...

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IEEE Conference on Decision and control

作者： Haoyu Wei Lulu Pan Haibin Shao Dewei Li Wenbin Yu Department of Automation Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China and Shanghai Engineering Research Center of Intelligent Control and Management Shanghai China

ISBN: (数字)9798350316339

ISBN: (纸本)9798350316346

This paper examines the cluster consensus problem of higher-order interaction networks on switching networks. The matrix-valued inter-agent coupling mechanism is employed to capture the higher-order interactions amongst neighboring agents. Specifically, for a higher-order interaction network with both positive definite and positive semi-definite coupling matrices, we examine the scenario in which the nullspace of positive semi-definite coupling matrices is constructed by a set of orthogonal basis vectors. From the perspective of the lower-order component graph -the projection of network structure onto the direction of each orthogonal basis–results on the explicit characterization of cluster consensus of higher-order interaction networks are provided. Moreover, for time-varying higher-order interaction networks, necessary and sufficient conditions are provided to ensure that a time-varying network shares the same steady-state values as the integral time-invariant network. Simulation results are provided to demonstrate the theory.

关键词： Couplings Sufficient conditions Network topology Simulation Switches Vectors Topology Steady-state Matrix decomposition Convergence

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End-to-end Automatic Targetless Calibration between Low-resolution LiDARs and Cameras based on Cross-modal Attention

End-to-end Automatic Targetless Calibration between Low-reso...

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Chinese control and Decision Conference, CCDC

作者： Tianyang Huang Jun-Guo Lu Ming Wei Qing-Hao Zhang Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Engineering Research Center of Intelligent Control and Management Shanghai China

ISBN: (数字)9798350387780

ISBN: (纸本)9798350387797

LiDARs and cameras, commonly used sensors on autonomous vehicles and robots, require precise calibration for accurate joint environmental perception. Current calibration methods, capable of adjusting both intrinsic and extrinsic parameters, often depend on physical targets or human intervention, making them unsuitable for automatic online calibration. Moreover, these methods are primarily optimized for dense point clouds, as they are often tuned on open datasets featuring high-quality point cloud data. However, low-resolution LiDARs, preferred for their cost-effectiveness, are prevalent in practical applications. To automate the calibration process while maintaining high precision on sparse point clouds, multi-modal image registration techniques are leveraged to develop an end-to-end, cross-attention-based neural network for automatic calibration of low-resolution LiDARs and Cameras. Specifically, given an initial perturbation on point clouds, our network is capable of recovering the true extrinsic parameters without manual intervention. Additionally, specialized input preprocessing and training strategies are incorporated to enhance performance with sparse point clouds. Promising results are achieved on both open datasets and custom sensor acquisitions, highlighting the effectiveness and adaptability of our network to diverse scenarios.

关键词： Point cloud compression Training Image registration Visualization Laser radar Perturbation methods Neural networks

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Evolutionary Dynamics of Cooperation on Coupled Networks

Evolutionary Dynamics of Cooperation on Coupled Networks

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control Theory and Applications (ICoCTA), International Conference on

作者： Zhenyu Shi Qi Su Department of Automation Ministry of Education of China Key Laboratory of System Control and Information Processing Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai China

ISBN: (数字)9798331506155

ISBN: (纸本)9798331506162

Network reciprocity has been recognized as a crucial mechanism for promoting the evolution of cooperation. However, prior studies on network reciprocity have predominantly focused on isolated networks, neglecting the interconnected nature of real-world systems. In reality, many large-scale systems are closely coupled, where the interaction patterns between systems differ significantly from those within individual networks. Motivated by this observation, we construct a strategy evolution model on coupled networks to explore the effects of such interconnections. Our findings reveal that coupled networks foster cooperation more effectively than isolated networks. This advantage persists across various network structures, suggesting the universality of this phenomenon. Interestingly, we discover that the strength of the coupling plays a pivotal role: weaker coupling between networks is more conducive to the emergence and stability of cooperation compared to stronger coupling. These results high-light the importance of considering cross-system interactions in understanding and designing mechanisms to enhance cooperative behavior.

关键词： Couplings Stability analysis Large-scale systems control theory Game theory

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Two-Stage Robust Optimization Under Decision Dependent Uncertainty

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IEEE/CAA Journal of Automatica Sinica 2022年第7期9卷 1295-1306页

作者： Yunfan Zhang Feng Liu Yifan Su Yue Chen Zhaojian Wang João P.S.Catalão State Key Laboratory of Power System and Generation Equipment the Department of Electrical EngineeringTsinghua UniversityBeijing 100084China Department of Mechanical and Automation Engineering the Chinese University of Hong KongHong Kong SARChina Ministry of Education Key Laboratory of System Control and Information Processing the Department of AutomationShanghai Jiao Tong Universityand also with Shanghai Engineering Research Center of Intelligent Control and ManagementShanghai 200240China Faculty of Engineering of the University of Porto and Institute for Systems and Computer Engineering Technology and Science(INESC TEC)Porto 4200-465Portugal IEEE

In the conventional robust optimization(RO)context,the uncertainty is regarded as residing in a predetermined and fixed uncertainty *** many applications,however,uncertainties are affected by decisions,making the current RO framework *** paper investigates a class of two-stage RO problems that involve decision-dependent *** introduce a class of polyhedral uncertainty sets whose right-hand-side vector has a dependency on the here-and-now decisions and seek to derive the exact optimal wait-and-see decisions for the second-stage problem.A novel iterative algorithm based on the Benders dual decomposition is proposed where advanced optimality cuts and feasibility cuts are designed to incorporate the uncertainty-decision *** computational tractability,robust feasibility and optimality,and convergence performance of the proposed algorithm are guaranteed with theoretical *** motivating application examples that feature the decision-dependent uncertainties are ***,the proposed solution methodology is verified by conducting case studies on the pre-disaster highway investment problem.

关键词： Benders decomposition decision-dependent uncertainty endogenous uncertainty robust optimization(RO)

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DELFlow: Dense Efficient Learning of Scene Flow for Large-Scale Point Clouds

DELFlow: Dense Efficient Learning of Scene Flow for Large-Sc...

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International Conference on Computer Vision (ICCV)

作者： Chensheng Peng Guangming Wang Xian Wan Lo Xinrui Wu Chenfeng Xu Masayoshi Tomizuka Wei Zhan Hesheng Wang Department of Automation Key Laboratory of System Control and Information Processing of Ministry of Education Shanghai Jiao Tong University Mechanical Systems Control Laboratory University of California Berkeley

Point clouds are naturally sparse, while image pixels are dense. The inconsistency limits feature fusion from both modalities for point-wise scene flow estimation. Previous methods rarely predict scene flow from the entire point clouds of the scene with one-time inference due to the memory inefficiency and heavy overhead from distance calculation and sorting involved in commonly used farthest point sampling, KNN, and ball query algorithms for local feature aggregation. To mitigate these issues in scene flow learning, we regularize raw points to a dense format by storing 3D coordinates in 2D grids. Unlike the sampling operation commonly used in existing works, the dense 2D representation 1) preserves most points in the given scene, 2) brings in a significant boost of efficiency, and 3) eliminates the density gap between points and pixels, allowing us to perform effective feature fusion. We also present a novel warping projection technique to alleviate the information loss problem resulting from the fact that multiple points could be mapped into one grid during projection when computing cost volume. Sufficient experiments demonstrate the efficiency and effectiveness of our method, outperforming the prior-arts on the FlyingThings3D and KITTI dataset. Our source codes will be released on https://***/IRMVLab/DELFlow.

关键词：

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LHMap-loc: Cross-Modal Monocular Localization Using LiDAR Point Cloud Heat Map

LHMap-loc: Cross-Modal Monocular Localization Using LiDAR Po...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Xinrui Wu Jianbo Xu Puyuan Hu Guangming Wang Hesheng Wang Department of Automation Key Laboratory of System Control and Information Processing of Ministry of Education Key Laboratory of Marine Intelligent Equipment and System of Ministry of Education Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai China Department of Engineering University of Cambridge Cambridge U.K

ISBN: (数字)9798350384574

ISBN: (纸本)9798350384581

Localization using a monocular camera in the pre-built LiDAR point cloud map has drawn increasing attention in the field of autonomous driving and mobile robotics. However, there are still many challenges (e.g. difficulties of map storage, poor localization robustness in large scenes) in accurately and efficiently implementing cross-modal localization. To solve these problems, a novel pipeline termed LHMap-loc is proposed, which achieves accurate and efficient monocular localization in LiDAR maps. Firstly, feature encoding is carried out on the original LiDAR point cloud map by generating offline heat point clouds, by which the size of the original LiDAR map is compressed. Then, an end-to-end online pose regression network is designed based on optical flow estimation and spatial attention to achieve real-time monocular visual localization in a pre-built map. In addition, a series of experiments have been conducted to prove the effectiveness of the proposed method. Our code is available at: https://***/IRMVLab/LHMap-loc.

关键词： Location awareness Point cloud compression Visualization Laser radar Accuracy Robot vision systems Real-time systems

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Two-Stage OD Flow Prediction for Emergency in Urban Rail Transit

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IEEE Transactions on Intelligent Transportation systems 2024年第1期25卷 920-928页

作者： Zhu, Guangyu Ding, Jiacun Wei, Yun Yi, Yang Xu, Sendren Sheng-Dong Wu, Edmond Q. Beijing Jiaotong University Key Lab. of Transport Industry of Big Data Application Technologies for Comprehensive Transport The Beijing Research Center of Urban Traffic Information Sensing and Service Technologies Beijing100044 China Beijing Mass Transit Railway Operation Corporation Ltd. Beijing100014 China Yangzhou University College of Information Engineering Yangzhou225127 China National Taiwan University of Science and Technology Automation and Control Center The Graduate Institute of Automation and Control Taipei106335 Taiwan Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China The Shanghai Engineering Research Center of Intelligent Control and Management Department of Automation Shanghai200240 China

Urban rail transit (URT) is vulnerable to natural disasters and social emergencies including fire, storm and epidemic (such as COVID-19), and real-time origin-destination (OD) flow prediction provides URT operators with important information to ensure the safety of URT system. However, hindered by the high dimensionality of OD flow and the lack of supportive information reflecting the real-time passenger flow changes, study in this area is at the beginning stage. A novel model consisting of two stages is proposed for OD flow prediction. The first stage predicts the inflows of all stations by Long Short-Term Memory (LSTM) in real time, where the dimension is reduced compared with predicting OD flows directly. In the second stage, the notion of separation rate, namely, the proportion of inbound passengers bounding for another station, is estimated. Finally, The OD flow is predicted by multiplying the inflow and separation rate. Experiments based on Hangzhou Metro dataset show the proposed model outperforms the contrast model in weighted mean average error (WMAE) and weighted mean square error (WMSE). Results also suggest that the proposed prediction model performs better on weekdays than on weekends, and with greater accuracy on larger OD flows. © 2000-2011 IEEE.

关键词： Forecasting

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FoldExplorer: Fast and Accurate Protein Structure Search with Sequence-Enhanced Graph Embedding

arXiv

引用

arXiv 2023年

作者： Liu, Yuan Shen, Hong-Bin Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional alignment-based methods are dedicated to precise comparisons between pairs, exhibiting high accuracy. However, their sluggish processing speed is no longer adequate for managing the current massive volume of data. In response to this challenge, we propose a novel deep-learning approach FoldExplorer. It harnesses the powerful capabilities of graph attention neural networks and protein large language models for protein structures and sequences data processing to generate embeddings for protein structures. The structural embeddings can be used for fast and accurate protein search. And the embeddings also provide insights into the protein space. FoldExplorer demonstrates a substantial performance improvement of 5% to 8% over the current state-of-the-art algorithm on the benchmark datasets. Meanwhile, FoldExplorer does not compromise on search speed and excels particularly in searching on a large-scale dataset. Copyright © 2023, The Authors. All rights reserved.

关键词： Embeddings

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