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Statistical potentials for 3D structure evaluation:From proteins to RNAs

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Chinese Physics B 2021年第2期30卷 103-115页

作者： Ya-Lan tan Chen-jie Feng Xunxun Wang Wenbing Zhang zhi-jie tan Department of Physics and Key Laboratory of Artificial Micro&Nano-structures of Education School of Physics and TechnologyWuhan UniversityWuhan 430072China

Structure evaluation is critical to in silico 3-dimensional structure predictions for biomacromolecules such as proteins and *** proteins,structure evaluation has been paid attention over three decades along with protein folding problem,and statistical potentials have been shown to be effective and efficient in protein structure prediction and *** recent two decades,RNA folding problem has attracted much attention and several statistical potentials have been developed for RNA structure evaluation,partially with the aid of the progress in protein structure *** this review,we will firstly give a brief overview on the existing statistical potentials for protein structure ***,we will introduce the recently developed statistical potentials for RNA structure ***,we will emphasize the perspective on developing new statistical potentials for RNAs in the near future.

关键词： statistical potential 3-dimensional structure evaluation RNA protein

Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

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Communications in Theoretical Physics 2021年第7期73卷 127-135页

作者： Xiao-Wei Qiang Hai-Long Dong Kai-Xin Xiong Wenbing Zhang zhi-jie tan Department of Physics and Key Laboratory of Artificial Micro&Nano-Structures of Ministry of Education School of Physics and TechnologyWuhan UniversityWuhan 430072China

Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein *** all-atom molecular dynamics simulations,we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T)(AA-TT),poly(AT)-poly(TA)(AT-TA),and a generic sequence(GENE).Our calculations indicate that,AA-TT has an apparently larger bending persistence length(P~63 nm)than GENE(P~49 nm)and AT-TA(P~48 nm)while the persistence length of AT-TA is only very slightly smaller than that of GENE,which agrees well with those from existing ***,through extensive electrostatic calculations,we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT,AT-TA and GENE,which is coupled to their backbone ***,the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor ***,for the three DNAs,we predicted the non-electrostatic persistence length of~17 nm,thus electrostatic interaction makes the major contribution to DNA bending *** mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.

关键词： DNA elasticity molecular dynamic simulation persistence length electrostatic interaction

Coarse-grained modeling for RNA 3D structure,stability and salt effect

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Coarse-grained modeling for RNA 3D structure,stability and s...

Electro-optic tuning in ferroelectric capacitor with photonic crystal nanobeam cavity

中国化学会2016年软物质理论计算与模拟会议

作者： zhi-jie tan School of Physics ＆ Technology Wuhan University

＜正＞RNA 3D structure and stability is essential for the biological functions of RNAs,and the ion condition is critical for RNA 3D structure and stability due to the polyanionic ***,there is still lack of a unified model for predicting RNA3D structure,stability and salt *** the work,we proposed a coarse-grained model for predicting 3D structure and stability of small RNAs,including RNA

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来源： cnki会议评论

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Science China(Information Sciences) 2025年

作者： Tongtong WANG Yong ZHANG Danyang YAO zhi JIANG Dongxin tan jie WEN Qiyu YANG Xuetao GAN Yan LIU Yue HAO Genquan HAN State Key Discipline Laboratory of Wide Band Gap Semiconductor Technology School of MicroelectronicsXidian University Key Laboratory of Light Field Manipulation and Information Acquisition Ministry of Industry and Information TechnologyShaanxi Key Laboratory of Optical Information Technology School of Physical Science and TechnologyNorthwestern Polytechnical University Hangzhou Institute of Technology Xidian University

Silicon photonics has provided a platform for the convergency of photonic devices and electronic circuits, facilitating the development of optical telecommunications and optical interconnects on chip[1]. As the basic building block of optical communication systems, electro-optic tuning is expected to be more compact, high bandwidth, energy efficient, and allow for CMOS-compatible fabrication in the future[2]. Resonator-based electro-optic tuning has attracted more and more interest due to the small footprint, enhanced light-matter interactions and high energy efficiency. Compared with microring and microdisk resonators, photonic crystal nanobeam cavities （PCNBCs） realize higher quality factors, stronger light-matter interactions, ultrasmall mode volume and a much larger free spectral range （FSR）[3].

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A low redox potential and long life organic anode material for sodium-ion batteries

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Journal of Energy Chemistry 2025年第1期100卷 557-564页

作者： zhi Li Yang Wei Kang Zhou Xin Huang Xing Zhou jie Xu Taoyi Kong Junwei Lucas Bao Xiaoli Dong Yonggang Wang Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Institute of New Energy Collaborative Innovation Center of Chemistry for Energy Materials (iChEM) Fudan University Department of Chemistry Boston College School of Materials Science and Engineering Anhui University of Technology

Sodium-ion batteries （SIBs） with organic electrodes are an emerging research direction due to the sustainability of organic materials based on elements like C,H,O,and sodium ***,organic electrode materials for SIBs are mainly used as cathodes because of their relatively high redox potentials（>1 V）.Organic electrodes with low redox potential that can be used as anode are ***,a novel organic anode material （tetrasodium 1,4,5,8-naphthalenetetracarboxylate,Na4TDC） has been developed with low redox potential （<0.7 V） and excellent cyclic *** three-sodium storage mechanism was demonstrated with various in-situ/ex-situ spectroscopy and theoretical calculations,showing a high capacity of 208 mAh/g and an average decay rate of merely 0.022%per ***,the Na4TDC-hard carbon composite can further acquire improved capacity and cycling stability for 1200 cycles even with a high mass loading of up to 20 mg *** pairing with a thick Na3V2（PO4）3cathode (20.6 mg cm-2),the as-fabricated full cell exhibited high operating voltage （2.8 V）,excellent rate performance and cycling stability with a high capacity retention of 88.7% after 200 cycles,well highlighting the Na4TDC anode material for SIBs.

关键词： Organic anode material Low redox potential Composite anode Sodium-ion batteries

Hydration, Microstructure, and Properties of Sulphoaluminate Cement in Pure Water and Simulated Seawater

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Journal of Wuhan University of Technology(Materials Science) 2025年第1期40卷 187-193页

作者： MA jie China Railway Design Corporation Tianjin 300250China

Paste and mortar specimens were prepared with sulfoaluminate cement(SAC),P⋅O 42.5 ordinary Portland cement(OPC),and standard sand,and mixed and cured with pure water and artificial seawater,*** mechanical properties of mortar specimens were *** and microstructure of paste specimens were also investigated using X-ray diffraction(XRD),scanning electron microscope(SEM),and 27Al nuclear magnetic resonance(NMR),*** results indicate that SAC mortar samples mixed and cured by seawater have faster strength growth before 28 d and higher compressive strength than OPC mortar *** to curing in deionized water,the hydration products of SAC are somewhat coarser when cured in simulated *** evolution of aluminum phase hydration products during the hydration process of SAC mixed and cured in simulated seawater is quite different from that of *** 3 to 28 d,the content of each aluminum phase hydration product in SAC paste cured in simulated seawater changed little,while that in OPC paste changed significantly;for example,from 7 to 28 d,the content of ettringite(AFt)in OPC paste increased *** type of AFt formed loosely,harming the mortar's microstructure.

关键词： sulfoaluminate cement seawater mixing and curing 27Al NMR AFt

Induced pluripotent stem cell-related approaches to generate dopaminergic neurons for Parkinson's disease

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Neural Regeneration Research 2025年第11期20卷 3193-3206页

作者： Ling-Xiao Yi Hui Ren Woon Genevieve Saw Li Zeng Eng King tan zhi Dong Zhou National Neuroscience Institute Singapore Nanyang Technology University Singapore Department of Neurology Singapore General HospitalSingapore Signature Research Program in Neuroscience and Behavioral Disorders Duke-NUS Medical SchoolSingapore

The progressive loss of dopaminergic neurons in affected patient brains is one of the pathological features of Parkinson's disease,the second most common human neurodegenerative *** the detailed pathogenesis accounting for dopaminergic neuron degeneration in Parkinson's disease is still unclear,the advancement of stem cell approaches has shown promise for Parkinson's disease research and *** induced pluripotent stem cells have been commonly used to generate dopaminergic neurons,which has provided valuable insights to improve our understanding of Parkinson's disease pathogenesis and contributed to anti-Parkinson's disease *** current review discusses the practical approaches and potential applications of induced pluripotent stem cell techniques for generating and differentiating dopaminergic neurons from induced pluripotent stem *** benefits of induced pluripotent stem cell-based research are *** dopaminergic neuron differentiation protocols from induced pluripotent stem cells are *** emerging three-dimension-based brain organoid models compared with conventional two-dimensional cell culture are ***,limitations,challenges,and future directions of induced pluripotent stem cell–based approaches are analyzed and proposed,which will be significant to the future application of induced pluripotent stem cell-related techniques for Parkinson's disease.

关键词： dopaminergic neurons induced pluripotent stem cells Parkinson's disease stem cell approaches

Prospects on mangrove knowledge services in the smart era: From plant atlas to knowledge graphs

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Science China Earth Sciences 2025年第1期68卷 111-127页

作者： zhi-Wei HOU Wenlong JING Cheng-zhi QIN Ji YANG Qing XIA Xiaoling YIN Key Laboratory of Guangdong for Utilization of Remote Sensing and Geographical Information System Guangdong Open Laboratory of Geospatial Information Technology and Application Guangzhou Institute of Geography Guangdong Academy of Sciences Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) State Key Laboratory of Resources and Environmental Information System Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences College of Resources and Environment University of Chinese Academy of Sciences School of Traffic & Transportation Engineering Changsha University of Science and Technology

Mangroves are crucial to the ecological security of the Earth and human well-being. Their management, conservation, and restoration are of great importance and necessitate the support of spatio-temporal information and multidisciplinary knowledge such as biology and ecology. Traditional knowledge services such as plant atlas provide illustrated textual knowledge of mangroves. However, this kind of service is oriented to information retrieval and is incapable of effectively mining and utilizing fragmented knowledge from multi-source heterogeneous data, facing the problem of “massive data, rare knowledge”. Knowledge graphs are capable of extracting, organizing, and fusing the knowledge contained in massive data into semantic networks that can be understood and computed by computers. They provide a solution for the realization of intelligent knowledge services. Focusing on the urgent need for mangrove knowledge acquisition, formal representation, and intelligent services, this paper proposes a research prospect on mangrove knowledge graphs and knowledge services. We first analyze the similarities and differences between various domain-specific concepts of Tupu. On this basis, we define the mangrove knowledge graph as a large-scale knowledge base that integrates multi-disciplinary knowledge and spatio-temporal information with mangrove ecosystems as the core. Then, we propose a research framework for mangrove knowledge services that can realize the transformation from multi-modal data to intelligent knowledge services, including multiple research levels such as ubiquitous data sensing and aggregation, knowledge organization and graph construction, and intelligent mangrove knowledge services. Subsequently, the methods and workflow for constructing mangrove knowledge graphs are introduced. Finally, we discuss the challenges and possible future directions of mangrove knowledge services in the smart era, including the construction of a mangrove knowledge system that integra

关键词： Mangrove Tupu Knowledge graph Multi-modal Knowledge service

Apolipoprotein E elicits targetdirected miRNA degradation to maintain neuronal integrity

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Neural Regeneration Research 2025年第9期20卷 2577-2578页

作者： Jiazi tan Chin-Tong Ong Temasek Life Sciences Laboratory National University of SingaporeSingapore Department of Biological Sciences National University of SingaporeSingapore

Apolipoprotein E has diverse functions in neurons:Apolipoprotein E(ApoE)is a glycoprotein that primarily regulates lipid metabolism and transport in the central nervous *** are three predominant human ApoE protein isoforms with cysteine and arginine substitutions at amino acid positions 112 and 158 that impact their lipidation and related functions(Flowers and Rebeck,2020).ApoE2 is characterized by Cys112 and Cys158,ApoE3 by Cys112 and Arg158,whereas ApoE4 contains Arg112 and Arg158.

关键词： metabolism glycoprotein maintain