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An overview for monitoring and prediction of pathogenic microorganisms in the atmosphere

Fundamental Research 2024年第3期4卷 430-441页

作者： Jianping Huang Danfeng Wang Yongguan Zhu Zifeng Yang Maosheng Yao Xiaoming Shi Taicheng An Qiang Zhang Cunrui Huang Xinhui Bi Jiang Li Zifa Wang Yongqin Liu Guibing Zhu Siyu Chen Jian Hang Xinghua Qiu Weiwei Deng Huaiyu Tian Tengfei Zhang Tianmu Chen Sijin Liu Xinbo Lian Bin Chen Beidou Zhang Yingjie Zhao Rui Wang Han Li Collaborative Innovation Center for Western Ecological Safety College of Atmospheric SciencesLanzhou UniversityLanzhou 730000China Research Center for Eco-Environmental Sciences Chinese Academy of SciencesBeijing 100085China National Clinical Research Center for Respiratory Disease Guangzhou Institute of Respiratory HealthFirst Affiliated Hospital of Guangzhou Medical UniversityState Key Laboratory of Respiratory Disease(Guangzhou Medical University)Guangzhou 510230China College of Environmental Sciences and Engineering Peking UniversityBeijing 100871China China CDC Key Laboratory of Environment and Population Health National Institute of Environmental HealthChinese Center for Disease Control and PreventionBeijing 100021China Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health School of Environmental Science and EngineeringInstitute of Environmental Health and Pollution ControlGuangdong University of TechnologyGuangzhou 510006China Ministry of Education Key Laboratory for Earth System Modeling Department of Earth System ScienceTsinghua UniversityBeijing 100084China Vanke School of Public Health Tsinghua UniversityBeijing 100084China State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization Guangzhou Institute of GeochemistryChinese Academy of SciencesGuangzhou 510640China National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Center for Pan-third Pole Environment Lanzhou UniversityLanzhou 730000China College of Atmospheric Sciences Lanzhou UniversityLanzhou 730000China School of Atmospheric Sciences Sun Yat-sen Universityand Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Zhuhai 510640

Corona virus disease 2019(COVID-19)has exerted a profound adverse impact on human *** have demonstrated that aerosol transmission is one of the major transmission routes of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Pathogenic microorganisms such as SARS-CoV-2 can survive in the air and cause widespread infection among *** monitoring of pathogenic microorganism transmission in the atmosphere and accurate epidemic prediction are the frontier guarantee for preventing large-scale epidemic *** of pathogenic microorganisms in the air,especially in densely populated areas,may raise the possibility to detect viruses before people are widely infected and contain the epidemic at an earlier *** multi-scale coupled accurate epidemic prediction system can provide support for governments to analyze the epidemic situation,allocate health resources,and formulate epidemic response *** review first elaborates on the effects of the atmospheric environment on pathogenic microorganism transmission,which lays a theoretical foundation for the monitoring and prediction of epidemic ***,the monitoring technique development and the necessity of monitoring pathogenic microorganisms in the atmosphere are summarized and ***,this review introduces the major epidemic prediction methods and highlights the significance to realize a multi-scale coupled epidemic prediction system by strengthening the multidisciplinary cooperation of epidemiology,atmospheric sciences,environmental sciences,sociology,demography,*** summarizing the achievements and challenges in monitoring and prediction of pathogenic microorganism transmission in the atmosphere,this review proposes suggestions for epidemic response,namely,the establishment of an integrated monitoring and prediction platform for pathogenic microorganism transmission in the atmosphere.

关键词： Aerosol transmission Epidemic monitoring methods Epidemic prediction modelsEpidemic response Multidisciplinary cooperation

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Crystalline order and disorder in dusty plasmas investigated by nonequilibrium molecular dynamics simulations

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Chinese Physics B 2019年第5期28卷 181-188页

作者： Aamir Shahzad Maogang He Sheeba Ghani Muhammad Kashif Tariq Munir Fang Yang Molecular Modeling and Simulation Laboratory Department of Physics Government College University Faisalabad (GCUF) Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education Xi’an Jiaotong University Department of Physics University of Engineering and Technology (UET) Lahore College of Physics Civil Aviation University of China

The particle structure of a complex system has been explored through a unique Evans' s homogenous nonequilibrium molecular dynamics(HNEMD) simulation technique. The crystalline order–disorder structures(OD-structures) and the corresponding energies of three-dimensional(3 D) nonideal complex systems(NICSs) have been measured over a wide range of plasma states(■, κ) for a body-centered cubic(BCC) structure. The projected technique provides accurate ODstructures with fast convergence and applicable to very small size effect for different temperatures(≡ 1/■) and constant force field(F~*) values. The OD-structure obtained through HNEMD approach is found to be reasonable agreement and more reliable than those earlier identified by simulation approaches and experimental data of NICSs. New simulations of OD-structures show that dusty plasma remains in crystalline(strongly coupled) state at lower temperature and constant F*values, for the whole simulation runs. Our investigations show that the crystalline structure is changed and the particle structure switches from intermediate to disorder(nonideal gaseous) state with an increase of the system's temperature. It has been shown that the long range order shifts toward lower temperature with increasing κ. The presented technique exhibits that the potential energy has a maximum value when the dusty plasma remains in crystalline states(low temperatures),which confirms earlier 3 D simulation results.

关键词： nonequilibrium molecular dynamics crystalline structures nonideal complex systems dusty plasmas strongly coupled regime

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Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide

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Immunoinformatics (Amsterdam, Netherlands) 2022年 7卷 100015页

作者： Leonardo Pereira de Araújo Maria Eduarda Carvalho Dias Gislaine Cristina Scodeler Ana de Souza Santos Letícia Martins Soares Patrícia Paiva Corsetti Ana Carolina Barbosa Padovan Nelson José de Freitas Silveira Leonardo Augusto de Almeida Laboratory of Molecular Biology of Microorganisms Federal University of Alfenas Alfenas Minas Gerais Brazil. Laboratory of Molecular Modeling and Computer Simulation Federal University of Alfenas Alfenas Minas Gerais Brazil.

The short time between the first cases of COVID-19 and the declaration of a pandemic initiated the search for ways to stop the spread of SARS-CoV-2. There are great expectations regarding the development of effective vaccines that protect against all variants, and in the search for it, we hypothesized the obtention of a predicted rational immunogenic peptide from structural components of SARS-CoV-2 might help the vaccine research direction. In the search for a candidate of an immunogenic peptide of the SARS-CoV-2 envelope (E), membrane (M), nucleocapsid (N), or spike (S) proteins, we access the predicted sequences of each protein after the genome sequenced worldwide. We obtained the consensus amino acid sequences of about 14,441 sequences of each protein of each continent and the worldwide consensus sequence. For epitope identification and characterization from each consensus structural protein related to MHC-I or MHC-II interaction and B-cell receptor recognition, we used the IEDB reaching 68 epitopes to E, 174 to M, 245 to N, and 833 to S proteins. To select an epitope with the highest probability of binding to the MHC or BCR, all epitopes of each consensus sequence were aligned. The curation indicated 1, 4, 8, and 21 selected epitopes for E, M, N, and S proteins, respectively. Those epitopes were tested in silico for antigenicity obtaining 16 antigenic epitopes. Physicochemical properties and allergenicity evaluation of the obtained epitopes were done. Ranking the results, we obtained one epitope of each protein except for the S protein that presented two epitopes after the selection. To check the 3D position of each selected epitope in the protein structure, we used molecular homology modeling. Afterward, each selected epitope was evaluated by molecular docking to reference MHC-I or MHC-II allelic protein sequences. Taken together, the results obtained in this study showed a rational search for a putative immunogenic peptide of SARS-CoV-2 structural proteins tha

关键词： COVID-19 New coronavirus Reverse vaccinology SARS-CoV-2

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AllohubPy: Detecting Allosteric Signals Through An Information-theoretic Approach

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Journal of molecular Biology 2025年 168969页

作者： Carmona, Oriol Gracia Kleinjung, Jens Anastasiou, Dimitrios Oostenbrink, Chris Fraternali, Franca Department of Structural and Molecular Biology Division of Biosciences and Institute of Structural and Molecular Biology University College London London WC1E 6BT United Kingdom Department of Biological Sciences Birkbeck University of London London WC1E 7HX United Kingdom Randall Centre for Cell & Molecular Biosciences King's College London London SE1 1UL United Kingdom Institute for Molecular Modeling and Simulation Department of Material Sciences and Process Engineering BOKU University Vienna 1190 Australia Nxera Pharma Steinmetz & Cori Buildings Granta Park Great Abington Cambridge CB21 6DG United Kingdom Cancer Metabolism Laboratory The Francis Crick Institute 1 Midland Road London NW1 1AT United Kingdom

Allosteric regulation is crucial for biological processes like signal transduction, transcriptional regulation, and metabolism, yet the mechanisms and macromolecular properties that govern it are still not well understood. Several methods have been developed over the years to study allosterism through different angles. Among the possible ways to study allosterism, information-theoretic approaches, like AlloHubMat or GSAtools, can be particularly effective due to their use of robust statistics and the possibility to be combined with graph analysis. These methods capture local conformational changes associated with global motions from molecular dynamics simulations through the use of a Structural Alphabet, which simplifies the complexity of the Cartesian space by reducing the dimensionality down to a string of encoded fragments, representing sets of internal coordinates that still capture the overall conformation changes. In this work, we present “AllohubPy,” an improved and standardized methodology of AlloHubMat and GSAtools coded in Python. We analyse the performance, limitations and sampling requirements of AllohubPy by using extensive molecular dynamics simulations of model allosteric systems and apply convergence analysis techniques to estimate result reliability. Additionally, we expand the methodology to use different dimensionality reduction Structural Alphabets, such as the 3DI alphabet, and integrate Protein Language Models (PLMs) to refine allosteric hub communication detection by monitoring the detected evolutionary constraints. Overall, AllohubPy expands its preceding methods and simplifies the use and reliability of the method to effectively capture dynamic allosteric motions and residue pathways. AllohubPy is freely available on GitHub (https://***/Fraternalilab/AlloHubPy) as a package and as a Jupyter Notebook. © 2025 The Author(s)

关键词： allosteric hubs allostery information theory molecular dynamics mutual information

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Wave analysis of Yukawa liquids and solids using molecular dynamics simulations

Wave analysis of Yukawa liquids and solids using molecular d...

引用

International Bhurban Conference on Applied Sciences & Technology, IBCAST

作者： A. Shahzad M. Kashif A. Fatima M-G. He Molecular Modeling and Simulation Laboratory Government College University Faisalabad (GCUF) Faisalabad Pakistan Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education (MOE) Xi'an Jiaotong University Xi'an P. R. China

ISBN: (数字)9781728146768

ISBN: (纸本)9781728146775

The wave properties for two-dimensional (2D) Yukawa liquids and solids have been investigated using Equilibrium molecular dynamics (EMD) technique for the first time. In present work, the longitudinal current correlation (LCC) CL(k, t) and the transverse current correlation (TCC) CT(k, t) functions have been computed for plasma parameters of Debye screening strength κ and the Coulomb coupling parameter Γ and explain the oscillation, frequency and damping behavior of the waves. New simulations provide the modes of wave propagation in 2D Yukawa liquids and solids with series of increasing frequency ( ω) and decreasing frequency ( ω) at different combinations of plasmas parameters ( κ, Γ). The obtained results from present simulations for 2D dusty plasma liquids and solids have been compared and discussed with previous known results from simulation and theoretical calculations, by using different numerical methods.

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Theoretical insights into the chemical bonding, electronic structure, and spectroscopic properties of the lanarkite Pb2SO5 structure

arXiv

引用

arXiv 2023年

作者： Fabris, Guilherme S.L. Ferrer, Mateus M. Sambrano, Julio R. Almeida, Cláudio R.R. Paskocimas, Carlos A. La Porta, Felipe A. Graduate Program in Materials Science and Engineering Technological Development Center Universidade Federal de Pelotas RS Pelotas96010-610 Brazil Modeling and Molecular Simulation Group São Paulo State University Bauru São Paulo17033-360 Brazil Department of Materials Engineering Federal University of Rio Grande do Norte RN Natal59078-970 Brazil Postgraduate Program in Science and Engineering of Materials Federal University of Rio Grande do Norte RN Natal59078-970 Brazil Federal University of Technology - Paraná Nanotechnology and Computational Chemistry Laboratory Avenida dos Pioneiros 3131 CEP PR Londrina86036-370 Brazil State University of Londrina Post-Graduation Program in Chemistry Rodovia Celso Garcia Cid 445 km 380 CEP PR Londrina86057-970 Brazil

Lanarkite is a mineral formed by a combination of lead, sulphur, and oxygen atoms arranged in the general chemical formula Pb2SO5 (PSO) that crystallises with monoclinic symmetry (belonging to the C2/m space group, No. 12). This mineral was first discovered in Lanarkshire, Scotland and was named after its location. PSO has a unique structure comprising alternating penta-coordinated lead [PbO5] and tetra-coordinated sulphur [SO4] clusters. This lanarkite-type structure has recently attracted significant scientific interest and has been the focus of the superconducting material research community. However, its chemistry needs to be explored further. This article presents a comprehensive investigation on the chemical bonding, electronic structure, and spectroscopic properties of the lanarkite-type PSO structure from a computational perspective. Thus, different functionals in the DFT (e.g., PBE, PBE0, PBESOL, PBESOL0, BLYP, WC1LYP37, and B3LYP) were assessed to accurately predict their fundamental properties. All the DFT calculations were performed using a triple-zeta valence plus polarisation basis set. Among all the DFT functionals tested in this study, PBE showed the best agreement with the experimental data available in the literature. Our results also reveal that the [PbO5] clusters are formed with three Pb–O bond lengths, with values of about 2.32, 2.59, and 2.84 Å, respectively, while the [SO4] clusters have the same S–O bond length of 1.57 Å. We performed a complete topological analysis of this system to comprehend these structural differences. Additionally, the PSO structure has an indirect band gap energy of 2.9 eV and an effective mass ratio (mℎ∗ /me∗) of about 0.415 (using PBE calculations) which may, in principle, indicate a low recombination of electron-hole pairs in the lanarkite structure. Therefore, we believe that a detailed understanding of their electronic structures, spectroscopic properties as well as their chemical bonding is critically important

关键词： Lead compounds

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Thermal Conductivity of Complex Plasmas Using Novel Evan-Gillan Approach

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Communications in Theoretical Physics 2018年第6期69卷 704-710页

作者： Aamir Shahzad Syed Irfan Haider Muhammad Kashif Muhammad Shahzad Shifa Tariq Munir Mao-Gang He Molecular Modeling and Simulation Laboratory Department of PhysicsGovernment College University Faisalabad(GCUF)Allama Iqbal RoadFaisalabad 38040Pakistan Key Laboratory of Thermo-Fluid Science and Engineering Ministry of Education(MOE)Xi'an Jiaotong UniversityXi'an 710049China

The thermal conductivity of complex fluid materials （dusty plasmas） has been explored through novel Evan-Gillan homogeneous non-equilibrium molecular dynamic （HNEMD） algorithm. The thermal conductivity coefficient obtained from HNEMD is dependent on various plasma parameters （T,k）. The proposed algorithm gives accurate results with fast convergence and small size effect over a wide range of plasma parameters. The cross microscopic heat energy current is discussed in association with variation of temperature （1/Г） and external perturbations （Pz）. The thermal conductivity obtained from HNEMD simulations is found to be very good agreement and more reliable than previously known numerical techniques of equilibrium molecular dynarnic, nonequilibrium molecular dynamic simulations. Our new investigations point to an effective conclusion that the thermal conductivity of complex dusty plasmas is dependent on an extensive range of plasma coupling （P） and screening parameter （k） and it varies by the alteration in these parameters. It is also shown that a different approach is used for computations of thermal conductivity in 2D complex plasmas and can be appropriate method for behaviors of complex systems.

关键词： complex dusty plasma homogenous nonequilibrium molecular dynamics canonical ensemble scaling law thermal conductivity Yukawa liquids

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Structure-Based Experimental Datasets for Benchmarking of Protein simulation Force Fields

arXiv

引用

arXiv 2023年

作者： Cavender, Chapin E. Case, David A. Chen, Julian C.-H. Chong, Lillian T. Keedy, Daniel A. Lindorff-Larsen, Kresten Mobley, David L. Ollila, O.H. Samuli Oostenbrink, Chris Robustelli, Paul Voelz, Vincent A. Wall, Michael E. Wych, David C. Gilson, Michael K. Skaggs School of Pharmacy and Pharmaceutical Sciences UC San Diego 9500 Gilman Drive La Jolla CA92093 United States Dept. of Chemistry & Chemical Biology Rutgers University PiscatawayNJ08854 United States Bioscience Division Los Alamos National Laboratory Los Alamos NM87545 United States Department of Chemistry and Biochemistry The University of Toledo ToledoOH43606 United States University of Pittsburgh 219 Parkman Avenue PittsburghPA15260 United States Structural Biology Initiative CUNY Advanced Science Research Center New YorkNY10031 United States Department of Chemistry and Biochemistry City College of New York New YorkNY10031 United States PhD Programs in Biochemistry Biology and Chemistry CUNY Graduate Center New YorkNY10016 United States Linderstrøm-Lang Centre for Protein Science Department of Biology University of Copenhagen Copenhagen NDK-2200 Denmark Pharmaceutical Sciences Department University of California Irvine IrvineCA United States University of Helsinki Institute of Biotechnology Helsinki Finland Institute for Molecular Modeling and Simulation University of Natural Resources and Life Sciences Muthgasse 11 Vienna1190 Austria Dartmouth College Department of Chemistry HanoverNH03755 United States Department of Chemistry Temple University PhiladelphiaPA United States Computer Computational and Statistical Sciences Division Los Alamos National Laboratory Los AlamosNM87545 United States The Center for Nonlinear Studies Los Alamos National Laboratory Los AlamosNM87545 United States

This review article provides an overview of structurally oriented, experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography. We discuss why these observables are useful for assessing force field accuracy, how they can be calculated from simulation trajectories, and statistical issues that arise when comparing simulations with experiment. The target audience for this article is computational researchers and trainees who develop, benchmark, or use protein force fields for molecular simulations. © 2023, CC BY.

关键词： Proteins

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

引用

arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： molecular dynamics

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Front Cover: Internal Redox Polarity of an IndividualG. sulfurreducensBacterial Cell Attached to an Inorganic Substrate (ChemPhysChem 15/2018)

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ChemPhysChem 2018年第15期19卷 1797-1797页

作者： Dr. Nikolai Lebedev Dr. Matthew D. Yates Prof. Igor Griva Dr. Leonard M. Tender Center for Bio/Molecular Science and Engineering US Naval Research Laboratory Washington DC 20375 USA Department of Mathematical Sciences and Center of Simulation and Modeling George Mason University Fairfax VA 22030 USA

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