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Molecular dynamics simulations of helium transport through inorganic mineral nanopores

Science China Earth Sciences 2025年第1期68卷 237-252页

作者： dandan song Ping GUAN Chi ZHANG Jiahao REN School of Earth and Space Sciences Peking University

Helium transport through nanoscale inorganic mineral pores and pore throats is essential for its overall migration. To elucidate helium's transport dynamics within nanopores, we employed equilibrium and non-equilibrium molecular dynamics simulations to investigate helium's static self-diffusion and pressure-driven flow in quartz slit-shaped nanopores. We also introduced water and various gases, including hydrogen, methane, ethane, nitrogen, and carbon dioxide, into the nanopores to assess their influence on helium transport. Our findings indicate minimal helium adsorption on quartz pore surfaces. Under conditions where the pore size is less than 5 nm and the pressure under 10 MPa, environmental factors markedly influence helium diffusion. Large pore sizes, high temperatures, and low gas pressures enhance helium desorption and facilitate faster diffusion. We observed a positive correlation between helium flow velocity and factors such as pore size, pressure gradient, and surface smoothness of the pores. Notably, the presence of pore water and carrier gases in quartz nanopores, which diffuse more slowly than helium, tends to reduce helium surface adsorption and slow its diffusion. Among the carrier gases studied, nitrogen showed similar adsorption capacity, diffusivity, and stability to helium, while carbon dioxide displayed the highest adsorption capacity and the slowest diffusion rate, markedly differing from helium. Based on the simulation results, we concluded that water and carrier gases primarily function as transport mediums in helium migration, moving together with helium. Nitrogen, which shares similar properties with helium, effectively assists in this co-migration process. Conversely, carbon dioxide, due to its high adsorption capacity and slow diffusion, tends to be lost during co-migration. As a result, gas reservoirs with high nitrogen levels and low carbon dioxide levels are more likely to have higher helium concentrations. Additionally, the smaller por

关键词： Helium transport Slit nanopores Molecular dynamics simulations Diffusion Flow carriers

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A fuzzy model of predicting RNA secondary structure

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Science in China(Series F) 2007年第6期50卷 846-866页

作者： song dandan DENG ZhiDong Department of Computer Science National Laboratory of Information Science and TechnologyTsinghua University Beijing 100084 China

We propose a novel model to predict RNA secondary structure based on the fuzzy sets theory. Through the fuzzy partition of state spaces and the incorporation of fuzzy goals, we can find the optimal fuzzy policy of the model using fuzzy dynamic programming algorithm effectively, and then determine optimal and suboptimal RNA secondary structures. Compared to the existing sophisticated prediction models, such as Zuker＇s method and the SCFG model, our fuzzy model based approach has many advantages： 1） computational complexity can be reduced by the fuzzy partition; 2） the optimal secondary structure and several suboptimal ones can be generated simultaneously; and 3） subjective prior knowledge can readily be incorporated. This paper presents a complete description of our fuzzy model and gives the implementation of the proposed method. We also apply the BJK fuzzy model structure to secondary structure predictions based on datasets of tRNA and tmRNA sequences. By the comparison of our fuzzy method with both the minimum free energy based mfold tool and the BJK grammar model of SCFG, our experimental results validate the effectiveness of the proposed method and the prediction accuracy is shown to be further improved.

关键词： RNA secondary structure fuzzy model fuzzy dynamic programming

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PSVM: a preference-enhanced SVM model using preference data for classification

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Science China(Information Sciences) 2017年第12期60卷 165-178页

作者： Lerong MA dandan song Lejian LIAO Jingang WANG Engineering Research Center of High Volume Language Information Processing and Cloud Computing Applications School of Computer Science and Technology Beijing Institute of Technology College of Mathematics and Computer Science Yan'an University Search Business Department Alibaba Group

Classification is an essential task in data mining, machine learning and pattern recognition *** classification models focus on distinctive samples from different categories. There are fine-grained differences between data instances within a particular category. These differences form the preference information that is essential for human learning, and, in our view, could also be helpful for classification models. In this paper, we propose a preference-enhanced support vector machine(PSVM), that incorporates preference-pair data as a specific type of supplementary information into SVM. Additionally, we propose a two-layer heuristic sampling method to obtain effective preference-pairs, and an extended sequential minimal optimization(SMO)algorithm to fit PSVM. To evaluate our model, we use the task of knowledge base acceleration-cumulative citation recommendation(KBA-CCR) on the TREC-KBA-2012 dataset and seven other datasets from UCI,Stat Lib and ***. The experimental results show that our proposed PSVM exhibits high performance with official evaluation metrics.

关键词： preference SVM classification sampling sequential minimal optimization(SMO)

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A Bayesian Recommender Model for User Rating and Review Profiling

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Tsinghua Science and Technology 2015年第6期20卷 634-643页

作者： Mingming Jiang dandan song Lejian Liao Feida Zhu School of Computer Science and Technology Beijing Institute of Technology School of Information Systems Singapore Management University

Intuitively, not only do ratings include abundant information for learning user preferences, but also reviews accompanied by ratings. However, most existing recommender systems take rating scores for granted and discard the wealth of information in accompanying reviews. In this paper, in order to exploit user profiles’ information embedded in both ratings and reviews exhaustively, we propose a Bayesian model that links a traditional Collaborative Filtering(CF) technique with a topic model seamlessly. By employing a topic model with the review text and aligning user review topics with 'user attitudes'(i.e., abstract rating patterns) over the same distribution, our method achieves greater accuracy than the traditional approach on the rating prediction task. Moreover, with review text information involved, latent user rating attitudes are interpretable and 'cold-start' problem can be *** property qualifies our method for serving as a 'recommender' task with very sparse datasets. Furthermore,unlike most related works, we treat each review as a document, not all reviews of each user or item together as one document, to fully exploit the reviews’ information. Experimental results on 25 real-world datasets demonstrate the superiority of our model over state-of-the-art methods.

关键词： collaborative filtering topic model recommender sy

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A Latent Entity-Document Class Mixture of Experts Model for Cumulative Citation Recommendation

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Tsinghua Science and Technology 2018年第6期23卷 660-670页

作者： Lerong Ma Lejian Liao dandan song Jingang Wang Engineering Research Center of High Volume Language Information Processing and Cloud Computing Applications Beijing Institute of Technology College of Mathematics and Computer Science Yan'an University

Knowledge Bases （KBs） are valuable resources of human knowledge which contribute to many applications. However, since they are manually maintained, there is a big lag between their contents and the upto-date information of entities. Considering a target entity in KBs, this paper investigates how Cumulative Citation Recommendation （CCR） can be used to effectively detect its worthy-citation documents in large volumes of stream data. Most global relevant models only consider semantic and temporat features of entity-document instances, which does not sufficiently exploit prior knowledge underlying entity-document instances. To tackle this problem, we present a Mixture of Experts （ME） model by introducing a latent layer to capture relationships between the entity-document instances and their latent class information. An extensive set of experiments was conducted on TREC-KBA-2013 dataset. The results show that the model can significantly achieve a better performance gain compared to state-of-the-art models in CCR.

关键词： knowledge base acceleration cumulative citation recommendation Mixture of Experts (ME) LatentEntity-Document Classes (LEDCs)

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The Multi-Objective Optimization of AFPM Generators with Double-Sided Internal Stator Structures for Vertical Axis Wind Turbines

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Energy Engineering 2021年第5期118卷 1439-1452页

作者： dandan song Lianjun Zhou Ziqi Peng Senhua Luo Jun Zhu Jiangsu Jinfeng Technology Co. Ltd.Yancheng224100China School of Automation Nanjing University of Science and TechnologyNanjing210094China School of Electrical Engineering and Automation Henan Polytechnic UniversityJiaozuo454000China

The axial flux permanent magnet(AFPM)generator with double-sided internal stator structure is highly suitable for vertical axis wind turbines due to its high power *** performance of the AFPM generator with double-sided internal stator structure can be improved by the reasonable design of electromagnetic *** further improve the overall performance of the AFPM generator with double-sided internal stator structure,multivariable(coil widthω_(c),permanent magnet thickness h,pole arc coefficient α_(p) and working air gap l_(g))and multi-objective(generator efficiencyη,total harmonic distortion of the voltage THD and induced electromotive force amplitude EMF)functional relationships are innovatively *** analysis,mean analysis and variance analysis are performed on the influence parameters by combining the Taguchi method and response surface methodology to study the influence degrees of each influence parameter on the optimization objectives to determine the most appropriate electromagnetic *** optimization results are verified by 3D finite element *** optimized APFM generator with double-sided internal stator structure exhibits superior economy,stronger magnetic density,higher efficiency and improved power quality.

关键词： Wind turbine double-sided internal stator structure multi-objective optimization axial flux permanent magnet generator

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Microplastic and Heavy Metals Distributions in Urban Rivers Sediments,China

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Journal of Ocean University of China 2024年第4期23卷 1015-1025页

作者： song dandan SHANG Yujun WANG Xiuli ZHUANG Yuwei GUO Hui BI Shuping HU Jianjun High and New Technology Research Center of Henan Academy of Sciences Zhengzhou 450002China Henan Provincial Cartographic Institute Zhengzhou 450008China

This study investigated the distribution of microplastics and heavy metals,along with the interaction between the two in the sediments of urban rivers in *** showed that the abundance of microplastics ranged from 2412±187.5 to 7638±1312items kg^(-1)dry sediment across different survey stations,with an average abundance at(4388±713)items kg^(-1)dry *** further categorization,it was found that transparent fragments were the primary color and type of microplastics *** potential ecological risk index(RI)of heavy metals in sediments suggested a low level of ecological risk within a majority of the urban rivers *** was identified as the main potential ecological risk factor in the sediments of the studied *** was a relatively good significant linear relationship between the RI of heavy metals and the abundance of microplastics,bolstering the linkage between these two environmental ***,the concentrations of heavy metals in microplastics were not dependent on their corresponding contents in *** fact,the concentration of Cu,Cd,and As in microplastics were higher than those in the *** finding confirmed that microplastics could serve as carriers of heavy metals and introduce potential risks to aquatic wildlife and human through the food chain.

关键词： microplastic heavy metals risk assessment river sediments

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Single-Molecule Measurement of Carbonic Anhydrase in Cation Coordinated Environment Using MspA Nanopore

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Chinese Journal of Chemistry 2023年第11期41卷 1341-1347页

作者： dandan song Yunjiao Wang Shaoxia Zhang Lingyu Zhao Linyu Gong Liyuan Liang Liang Wang School of Optoelectronic Engineering Chongqing University of Posts and TelecommunicationsChongqing400065 China Chongqing Institute of Green and Intelligent Technology Chinese Academy of Sciences & Chongqing SchoolUniversity of Chinese Academy of SciencesChongqing400714 China

Carbonic anhydrase accounts for catalytic reaction of CO_(2)/HCO_(3)^(–) transformation, thus resulting in neutralization and acidification of the cellular environment, thereby favoring tumor development. Hence, it is a classical protein model of greatly biocatalytic significance as well as a highly expressed biomarker with renal tumor. We herein proposed a single-molecule measurement on carbonic anhydrase using MspA nanopore, in [BMIM+] and asymmetric K^(+)/Ca^(2+) cationic coordinated environment, instead of usual symmetric KCl/NaCl electrolyte. Significantly, our empirical analysis showed that asymmetric K^(+)/Ca^(2+) cationic environment contributes to distinguishable current modulations, thus yielding better resolution for carbonic anhydrase measurement, which is independent of applied voltage and more importantly, is stable enough at varied pH conditions and for very low concentration test in urine sample. Our results provide a classical model for nanopore protein analysis, and may also permit biocatalytic measurement at single-molecule level.

关键词： Carbonic anhydrase Nanopore biosensing Biocatalytic biophysical analysis Cation coordinated environment Renal tumorbiomarker Proteinmodel lonicchannel

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Designing novel thin film polycrystalline solar cells for high efficiency:sandwich CIGS and heterojunction perovskite

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Journal of Semiconductors 2017年第1期38卷 71-76页

作者： Tianyue Wang Jiewei Chen Gaoxiang Wu dandan song Meicheng Li State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources North China Electric Power UniversityBeijing 102206China Chongqing Materials Research Institute Chongqing 400707China

Heterojunction and sandwich architectures are two new-type structures with great potential for solar ***,the heterojunction structure possesses the advantages of efficient charge separation but suffers from band offset and large interface recombination;the sandwich configuration is favorable for transferring carriers but requires complex fabrication ***,we have designed two thin-film polycrystalline solar cells with novel structures：sandwich CIGS and heterojunction perovskite,referring to the advantages of the architectures of sandwich perovskite（standard）and heterojunction CIGS（standard）solar cells,respectively.A reliable simulation software wxAMPS is used to investigate their inherent characteristics with variation of the thickness and doping density of absorber *** results reveal that sandwich CIGS solar cell is able to exhibit an optimized efficiency of 20.7%,which is much higher than the standard heterojunction CIGS structure（18.48%）.The heterojunction perovskite solar cell can be more efficient employing thick and doped perovskite films（16.9%）than these typically utilizing thin and weak-doping/intrinsic perovskite films（9.6%）.This concept of structure modulation proves to be useful and can be applicable for other solar cells.

关键词： sandwich CIGS solar cell heterojunction perovskite solar cell simulation wxAMPS

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Enhanced peroxidase-like activity of hierarchical MoS2-decorated N-doped carbon nanotubes with synergetic effect for colorimetric detection of H2O2 and ascorbic acid

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Chinese Chemical Letters 2020年第5期31卷 1109-1113页

作者： Jing Zheng dandan song Hong Chen Jingli Xu Njud SAlharbi Tasawar Hayat Min Zhang College of Chemistry and Chemical Engineering Shanghai University of Engineering ScienceShanghai 201620China Shanghai Key laboratory of Crime Scene Evidence Shanghai Research Institute of Criminal Science and TechnologyShanghai 200083China Biotechnology Research Group Department of Biological SciencesFaculty of ScienceKing Abdulaziz UniversityJeddah 21589Saudi Arabia Department of Mathematics Quaid-I-Azam UniversityIslamabad 44000Pakistan

The exploitation of multifunctional nanocomposites is highly desired in environmental monitoring,biosensors,and medical *** this paper,a simple approach has been proposed to fabricate MoS2 decorated N-doped carbon nanotubes(NCNTs@MoS2)hybrid composites as efficient peroxidase-like *** combination of the MoS2 and N-doped carbon nanotubes(NCNTs)brings about an enhanced synergistic effect,leading to remarkably decent intrinsic peroxidase-mimic activities than that of the single *** to the high catalytic efficiency of the resultant NCNTs@MoS2 hybrid nanotubes as peroxidase-like mimics,a co nvenient colorimetric approach for the sensitive determination of H2 O2 and ascorbic acid have been developed with a detection limit of about 0.14μmol/L and 0.12μmol/L,*** work offers a new strategy for the fabrication of peroxidase-like nanomaterials with excellent catalytic activity,which indicates great promising applications in sensitive detections in real samples.

关键词： MoS2 N-doped carbon nanotubes Peroxidase-1 ike Colorimetric detection Ascorbic acid

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