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Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

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Chinese Physics B 2021年第10期30卷 665-672页

作者： Jun-Bao Ma Wei-Bu Wang ji-guo su Key Laboratory for Microstructural Material Physics of Hebei Province School of ScienceYanshan UniversityQinhuangdao 066004China

The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric *** the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of *** our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the *** protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our *** calculated results are in good agreement with the experimental *** location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

关键词： protein functional movements molecular dynamics simulations perturbation-response scanning method

Force-constant-decayed anisotropic network model:An improved method for predicting RNA flexibility

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Chinese Physics B 2022年第6期31卷 765-771页

作者： Wei-Bu Wang Xing-Yuan Li ji-guo su Key Laboratory for Microstructural Material Physics of Hebei Province School of ScienceYanshan UniversityQinhuangdao 066004China The Sixth Laboratory National Vaccine and Serum InstituteBeijing 101111China

RNA is an important biological macromolecule,which plays an irreplaceable role in many life *** functions are largely determined by its tertiary structure and the intrinsic dynamics encoded in the ***,how to effective extract structure-encoded dynamics is of great significance for understanding RNA *** network model(ANM)is an efficient method to investigate macromolecular dynamical properties,which has been widely used in protein ***,the performance of the conventional ANM in describing RNA flexibility is not as good as that on *** this study,we proposed a new approach,named force-constant-decayed anisotropic network model(fcdANM),to improve the performance in investigating the dynamical properties encoded in RNA *** fcd-ANM,nucleotide pairs in RNA structure were connected by springs and the force constant of springs was decayed exponentially based on the separation distance to describe the differences in the inter-nucleotide interaction *** performance of fcd-ANM in predicting RNA flexibility was evaluated using a non-redundant structure database composed of 51 *** results indicate that fcd-ANM significantly outperforms the conventional ANM in reproducing the experimental B-factors of nucleotides in RNA structures,and the Pearson correlation coefficient between the predicted and experimental nucleotide B-factors was distinctly improved by 21.05%compared to the conventional ***-ANM can serve as a more effective method for analysis of RNA dynamical properties.

关键词： anisotropic network model B-factor RNA

Dynamic characteristics of multi-span spinning beams with elastic constraints under an axial compressive force

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Applied Mathematics and Mechanics(English Edition) 2024年第2期45卷 295-310页

作者： Xiaodong guo Zhu su Lifeng WANG State Key Laboratory of Mechanics and Control for Aerospace Structures Nanjing University of Aeronautics and AstronauticsNanjing 210016China

A theoretical model for the multi-span spinning beams with elastic constraints under an axial compressive force is *** displacement and bending angle functions are represented through an improved Fourier series,which ensures the continuity of the derivative at the boundary and enhances the *** exact characteristic equations of the multi-span spinning beams with elastic constraints under an axial compressive force are derived by the Lagrange *** efficiency and accuracy of the present method are validated in comparison with the finite element method(FEM)and other *** effects of the boundary spring stiffness,the number of spans,the spinning velocity,and the axial compressive force on the dynamic characteristics of the multi-span spinning beams are *** results show that the present method can freely simulate any boundary constraints without modifying the solution *** elastic range of linear springs is larger than that of torsion springs,and it is not affected by the number of *** an increase in the axial compressive force,the attenuation rate of the natural frequency of a spinning beam with a large number of spans becomes larger,while the attenuation rate with an elastic boundary is lower than that under a classic simply supported boundary.

关键词： multi-span spinning beam elastic constraint improved Fourier series free vibration semi-analytical solution

Role of catalyst surface-active sites in the hydrogenation ofα,β-unsaturated aldehyde

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Frontiers of Chemical Science and Engineering 2024年第6期18卷 41-69页

作者： Haixiang Shi Tongming su Zuzeng Qin Hongbing ji School of Chemistry and Chemical Engineering Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification TechnologyGuangxi UniversityNanning 530004China Zhejiang Green Petrochemical and Light Hydrocarbon Transformation Research Institute Zhejiang University of TechnologyHangzhou 310014China

As an important technology in fine chemical production,the selective hydrogenation ofα,β-unsaturated aldehydes has attracted much attention in recent *** the process ofα,β-unsaturated aldehyde hydrogenation,a conjugated system is formed between>C=CC=O,leading to hydrogenation at both ends of the conjugated system,which competes with each other and results in more complex ***,improving the reaction selectivity is also difficult in industrial ***,many researchers have reported that surface-active sites on catalysts play a crucial role inα,β-unsaturated aldehyde *** review attempts to summarize recent advances in understanding the effects of surface-active sites(SASs)over metal catalysts for enhancing the process of *** construction strategies and roles of SASs for hydrogenation catalysts are *** attention has been given to the adsorption configuration and transformation mechanism ofα,β-unsaturated aldehydes on catalysts,which contributes to understanding the relationship between SASs and hydrogenation *** addition,recent advances in metal-supported catalysts for the selective hydrogenation ofα,β-unsaturated aldehydes to understand the role of SASs in hydrogenation are briefly ***,the opportunities and challenges will be highlighted for the future development of the precise construction of SASs.

关键词： α,β-unsaturatedd aldehydes hydrogenation active site cinnamaldehyde

Performance evaluation for multi-target tracking with temporal dimension specifics

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Chinese Journal of Aeronautics 2024年第2期37卷 446-458页

作者： Zhenzhen su Hongbing ji Cong TIAN Yongquan ZHANG School of Computer Science and Technology Xidian UniversityXi’an 710071China School of Electronic Engineering Xidian UniversityXi’an 710071China

With the great development of Multi-Target Tracking(MTT)technologies,many MTT algorithms have been proposed with their own advantages and *** to the fact that requirements to MTT algorithms vary from the application scenarios,performance evaluation is significant to select an appropriate MTT algorithm for the specific application *** this paper,we propose a performance evaluation method on the sets of trajectories with temporal dimension specifics to compare the estimated trajectories with the true *** proposed method evaluates the estimate results of an MTT algorithm in terms of tracking accuracy,continuity and ***,its computation is based on a multi-dimensional assignment problem,which is formulated as a computable form using linear *** enhance the influence of recent estimated states of the trajectories in the evaluation,an attention function is used to reweight the trajectory errors at different time ***,simulation results show that the proposed performance evaluation method is able to evaluate many aspects of the MTT *** evaluations are worthy for selecting suitable MTT algorithms in different application scenarios.

关键词： Multi-target tracking Temporal dimension specifics Performance evaluation Random finite sets Linear programming

Multiple exciton generation effect in photocatalytic overall water splitting

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Science China Chemistry 2024年第2期67卷 424-425页

作者： Xiaolei guo ji-Jun Zou Key Laboratory for Green Chemical Technology of Ministry of Education School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China

This highlight is based on recent research published in Nature Energy by Li and co-workers [1] from Northwestern Polytechnology University, reporting an exceeding 100% internal quantum efficiency(IQE) in photocatalytic overall water splitting. This breakthrough promises a bright future for efficient photocatalyst design by utilizing the multiple exciton effect(MEG).

关键词： splitting effect utilizing

Numerical study of the influence of the atmospheric pressure on the thermal environment in the passenger cabin

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Building Simulation 2024年第2期17卷 253-265页

作者： Xin su Yu guo Zhengwei Long Yi Cao Tianjin Key Lab.of Indoor Air Environmental Quality Control School of Environmental Science and EngineeringTianjin UniversityTianjin300072China Shanghai Aircraft Design and Research Institute Jinke RoadPudong DistrictShanghai201210China

The cabin air pressure remains lower than the horizontal atmospheric pressure when the airplane is in *** pressure is one of the parameters that must be taken into consideration while studying the thermal environment of an airplane *** are still no reference values for aircraft cabins despite the fact that numerous studies on low pressure heat transfer have demonstrated the connection between convective heat transfer coefficient(CHTC)and air *** this paper,a correction method for CHTC under low pressure conditions was established by using the dummy heat dissipation in the low-pressure cabin *** this basis,a thermal environment simulation model was developed,then was applied to the simulation of a seven-row aircraft cabin containing 42 passengers,and the CHTC and heat loss of dummy surface in the cabin were ***,the results of PMV calculated by using heat dissipation and air parameters at sampling points were *** results show that the modified CHTC can accurately reflect the cabin thermal environment under low pressure conditions,and the correction of CHTC can be realized by adjusting the turbulent Prandtl number,which is nonlinear correlated with the *** simulation results of the thermal environment in the seven-row cabin show that the CHTC changes by about 42%before and after *** air pressure decreases during take-off,which reduces the average CHTC of the crew surface from 5.09 W/(m^(2)·K)to 4.56 W/(m^(2)·K),but the air temperature rises by about 0.2°C as a *** deviation of PMV results calculated by using simulated heat loss data and using air parameters of measuring points in space is up to 0.5,but the latter is representative for calculating the thermal comfort level of the whole cabin.

关键词： low pressure aircraft cabin simulation heat dissipation convective heat transfer coefficient

Novel data-driven sparse polynomial chaos and analysis of covariance for aerodynamics of compressor cascades with dependent geometric uncertainties

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Chinese Journal of Aeronautics 2024年第6期37卷 89-108页

作者： Zhengtao guo Wuli CHU Haoguang ZHANG Tianyuan ji School of Power and Energy Northwestern Polytechnical UniversityXi’an 710072China

Polynomial Chaos Expansion(PCE)has gained significant popularity among engineers across various engineering disciplines for uncertainty ***,traditional PCE suffers from two major ***,the orthogonality of polynomial basis functions holds only for independent input variables,limiting the model’s ability to propagate uncertainty in dependent ***,PCE encounters the"curse of dimensionality"due to the high computational cost of training the model with numerous polynomial *** practical manufacturing,compressor blades are subject to machining precision limitations,leading to deviations from their ideal geometric *** deviations require a large number of geometric parameters to describe,and exhibit significant *** efficiently quantify the impact of high-dimensional dependent geometric deviations on the aerodynamic performance of compressor blades,this paper firstly introduces a novel approach called Data-driven Sparse PCE(DSPCE).The proposed method addresses the aforementioned challenges by employing a decorrelation algorithm to directly create multivariate basis functions,accommodating both independent and dependent random ***,the method utilizes an iterative Diffeomorphic Modulation under Observable Response Preserving Homotopy regression algorithm to solve the unknown coefficients,achieving model sparsity while maintaining fitting ***,the study investigates the simultaneous effects of seven dependent geometric deviations on the aerodynamics of a high subsonic compressor cascade by using the DSPCE method proposed and sensitivity analysis of *** joint distribution of the dependent geometric deviations is determined using Quantile-Quantile plots and normal copula functions based on finite measurement *** results demonstrate that the correlations between geometric deviations significantly impact the variance of aerodynamic performance and the flow ***,

关键词： Data-driven sparse polyno-mial chaos Analysis of covariance Dependent uncertainty Aerodynamic performance Compressor cascade

A molecular insight into coke formation process of vacuum residue in thermal cracking reaction

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Petroleum Science 2024年第3期21卷 2130-2138页

作者： ji-Guang Li Xin guo Huan-Di Hou Heavy Oil Processing Department Sinopec Research Institute of Petroleum Processing Co.LtdBeijing100083China

Understanding the coking behaviors has been considered to be really essential for developing better vacuum residue processing technologies.A battery of thermal cracking tests of typical vacuum residue at 410℃ with various reaction time were performed to evaluate the coke formation *** total yields of ideal components including naphtha,atmospheric gas oil(AGO)and vacuum gas oil(VGO)of thermal cracking reactions increased from 10.89%to 40.81%,and the conversion ratios increased from8.05%to 43.33%with increasing the reaction time from 10 to 70 *** asphaltene content increased from 12.14%to a maximum of 22.39%and then decreased,and this maximum of asphaltene content occurred at the end of the coking induction *** asphaltenes during the coking induction period,at the end and after coking induction period of those tested thermal cracking reactions were characterized to disclose the structure changing rules for coke formation process,and the coke formation pathways were discussed to reveal the coke formation process at molecular level.

关键词： Vacuum residue Thermal cracking Asphaltene Coking induction period sulfur Nitrogen