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Protein–protein docking with interface residue restraints

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Chinese Physics B 2021年第1期30卷 19-26页

作者： Hao Li sheng-You huang School of Physics Huazhong University of Science and TechnologyWuhan 430074China

The prediction of protein–protein complex structures is crucial for fundamental understanding of celluar processes and drug design. Despite significant progresses in the field, the accuracy of ab initio docking without using any experimental restraints remains relatively low. With the rapid advancement of structural biology, more and more information about binding can be derived from experimental data such as NMR experiments or chemical cross-linking. In addition, information about the residue contacts between proteins may also be derived from their sequences by using evolutionary analysis or deep learning. Here, we propose an efficient approach to incorporate interface residue restraints into protein–protein docking, which is named as HDOCKsite. Extensive evaluations on the protein–protein docking benchmark 4.0 showed that HDOCKsite significantly improved the docking performance and obtained a much higher success rate in binding mode predictions than original ab initio docking.

关键词： protein-protein interaction scoring function residue restraint molecular docking

Design of a personnel safety interlock system for proton therapy

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Nuclear Science and Techniques 2021年第4期32卷 49-59页

作者： Shou-Yuan Wang yun-Tao Song Han-sheng Feng Shi Li Hai-Lin Cao Jing Zhang Ou-Wen huang Zhu Li Institute of Plasma Physics Chinese Academy of SciencesHefei 230031China University of Science and Technology of China Hefei 230026China Hefei CAS Ion Medical and Technical Devices Co.Ltd Hefei 230088China

Proton therapy is the most advanced radiotherapy approach in the world,and causes less damage to normal human tissue than traditional *** the treatment process produces a high-energy proton beam,the personnel safety interlock system mainly considers measures to protect personnel from radiation hazards during beam preparation and the beam release *** other safety interlock systems,the personnel safety interlock system designed in this study focuses on the safety and stability of the system *** hardware and software of important interlock control loops are designed and developed according to the requirements of Safety Integrity Level 3 specified by IEC61508.A set of redundant ring networks was developed to ensure that damage to a certain network line does not affect the normal operation of the system.A set of friendly operation interfaces and data storage systems were developed to ensure that the operator can monitor the data in real time and trace the *** personnel safety interlock system mainly includes a beam enabling function,clearance function,and emergency stop *** system was put into actual use and successfully ensured personnel safety.

关键词： Personnel safety Radiation protection Interlock system Safety integrity levels

SARS-CoV-2 membrane glycoprotein M antagonizes the MAVS-mediated innate antiviral response

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Cellular & Molecular Immunology 2021年第3期18卷 613-620页

作者： Yu-Zhi Fu Su-yun Wang Zhou-Qin Zheng Yi huang Wei-Wei Li Zhi-sheng Xu Yan-Yi Wang Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega-ScienceWuhan Institute of VirologyChinese Academy of Sciences430071 WuhanChina University of Chinese Academy of Sciences 100049 BdjingChina

A novel SARS-related coronavirus(SARS-CoV-2)has recently emerged as a serious pathogen that causes high morbidity and substantial ***,the mechanisms by which SARS-CoV-2 evades host immunity remain poorly ***,we identified SARS-CoV-2 membrane glycoprotein M as a negative regulator of the innate immune *** found that the M protein interacted with the central adaptor protein MAVS in the innate immune response *** interaction impaired MAVS aggregation and its recruitment of downstream TRAF3,TBK1,and IRF3,leading to attenuation of the innate antiviral *** findings reveal a mechanism by which SARS-CoV-2 evades the innate immune response and suggest that the M protein of SARSCoV-2 is a potential target for the development of SARS-CoV-2 interventions.

关键词： SARS-CoV-2 Membrane glycoprotein M MAVS TypeⅠinterferon Innate immunity

Experimental investigation of vortex generator influences on propeller cavitation and hull pressure fluctuations

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Journal of Hydrodynamics 2020年第1期32卷 82-92页

作者： Hong-bo huang yun Long Bin Ji National Key Laboratory on Ship Vibration and Noise China Ship Scientific Research CenterWiuxi 214082China State Key Laboratory of Water Resources and Hydropower Engineering Science Wuhan UniversityWuhan 430072China

In this paper,the transient turbulent cavitating flow around a marine propeller behind a ship was investigated experimentally with emphasis on how vortex generator(VG)influences propeller cavitation and hull pressure *** experiments were carried out in China Large Cavitation Channel with the closed test section covering 10.5 m in length and cross-section of 2.2 m^2×2.0m^*** experiment recorded instantaneous cavitation photos of the propeller and pressure fluctuations on the hull *** results demonstrate that without vortex generator,the sheet cavitation inception begins at-50°(310°),and then from-50°(310°)to 30°,the extent and area of sheet cavitation *** vortex generator installed on the hull,the sheet cavitation inception occurs in advance at-60°(300°),and the sheet cavitation expands to larger rotation range due to the vortex *** is shown that the vortex generator with proper geometry and installed location may contribute the highly nonuniform wake to be more uniform,and can make the change of propeller cavitation to be milder,which decrease the pressure fluctuations in this *** analysis indicates that the vortex generator may promote the energy distribution to be more uniform in physical and spectral space in some degree.

关键词： Cavitating flow pressure fluctuations propeller and ship hull vortex generator

Dynamical Analysis and Exact Solutions of a New(2+1)-Dimensional Generalized Boussinesq Model Equation for Nonlinear Rossby Waves

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Communications in Theoretical Physics 2019年第9期71卷 1054-1062页

作者： Quan-sheng Liu Zai-yun Zhang Rui-Gang Zhang Chuang-Xia huang School of Mathematical Sciences Inner Mongolia UniversityHohhot010021China School of Aeronautics Science and Engineering Beihang UniversityBeijing100191China School of Mathematics Hunan Institute of Science and TechnologyYueyang414006China Hunan Provincial Key Laboratory of Mathematical Modeling and Analysis in Engineering Changsha University of Scienceand Technology Changsha410014China School of Mathematics and Statistics Changsha University of Science and TechnologyChangsha410014China

In this paper, we study the higher dimensional nonlinear Rossby waves under the generalized beta *** methods of the multiple scales and weak nonlinear perturbation expansions [Q. S. Liu, et al., Phys. Lett. A383(2019) 514], we derive a new(2 + 1)-dimensional generalized Boussinesq equation from the barotropic potential vorticity equation. Based on bifurcation theory of planar dynamical systems and the qualitative theory of ordinary differential equations, the dynamical analysis and exact traveling wave solutions of the new generalized Boussinesq equation are obtained. Moreover, we provide the numerical simulations of these exact solutions under some conditions of all parameters. The numerical results show that these traveling wave solutions are all the Rossby solitary waves.

关键词： generalized Boussinesq model equation nonlinear Rossby waves dynamical analysis traveling wave solutions nonlinear perturbation expansions bifurcation theory of planar dynamical systems

Spatial distribution and formation mechanism of aeolian sand in the middle reaches of the Yarlung Zangbo River

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Journal of Mountain Science 2019年第9期16卷 1987-2000页

作者： LIU Yong WANG yun-sheng SHEN Tong State Key Lab. of Geo-Hazard Prevention and Geo-Environment Protection Chengdu University of Technology Chengdu China Institute of Exploration Technology Chinese Academy of Geological Sciences Chengdu China

Aeolian sand landforms in the Yarlung Zangbo River(YZR) valley are a special type of aeolian landform that has attracted the attention of many scholars. However, the spatial distribution as well as the formation mechanism of aeolian sand has rarely been reported with integrated studies. In this paper, for remote sensing interpretation, scanning electron microscopy(SEM), X-ray diffraction(XRD) and particle size distribution(PSD) methods were used to analyze the spatial distribution and the deposition characteristics of aeolian sand. Combined with wind data and topography, the main driving factors and the formation mechanism of aeolian sand landforms were also examined. In the middle reaches of the YZR valley, there is a total of 2324.43 km^2 of aeolian sand, especially on the north bank of the wide valleys. In different wide valleys, the aeolian sand landforms exhibit a decreasing trend from the upstream to the downstream regions in both the area and expansion rate of aeolian sand. The cyclonic vortexes generated by the westerly winds and glacial winds are the main driving factors for transporting alluvial sand to the riverbank areas to form aeolian dunes. There are three main types of sand dunes in the river valley: climbing dunes, lee dunes and circumfluent dunes. Climbing dunes and lee dunes are mostly located west of the Jiacha Gorge, and the circumfluent dunes are mostly located east of the Jiacha Gorge.

关键词： Aeolian processes Remote sensing interpretation Scanning electron microscopy X-ray diffraction Particle size distribution Glacial winds Cyclonic vortexes

Fe/MCM-41 as a promising heterogeneous catalyst for ozonation of p-chlorobenzoic acid in aqueous solution

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Chinese Chemical Letters 2011年第6期22卷 683-686页

作者： Rui Huan huang Jie Liu Lai sheng Li Qiu yun Zhang Li Xuan Zeng Ping Lu School of Chemistry & Environment South China Normal University Guangzhou 510006 China

Mesoporous MCM-41 and Fe loaded MCM-41（Fe/MCM-41）,which were successfully prepared by a hydrothermal method and a dipping method respectively,were applied as heterogeneous catalysts for ozonation of p-chlorobenzoic acid（p-CBA） in aqueous ***-41 and Fe/MCM-41 were characterized by XRD,FT-IR and diffuse reflectance UV-vis（DR-UV-vis） techniques. The presence of either MCM-41 or Fe/MCM-41 improves p-CBA and total organic carbon（TOC） removal efficiency compared to ozonation *** the experimental condition,TOC removal rate of Fe/MCM-41/O_3 process is over 63.5%at 60 min oxidation time,44.5%using MCM-41 as catalyst,only 37.7%with ozonation *** presence of tert-butanol（TBA） in the Fe/MCM-41/ O_3 process indicated that the oxidation mechanism of p-CBA occurs via OH in the liquid *** Fe/MCM-41 is a promising catalyst.

关键词： Fe/MCM-41 Catalytic ozonation p-Chlorobenzoic acid TOC

Effect of damage on gas seepage behavior of sandstone specimens

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Journal of Rock Mechanics and Geotechnical Engineering 2020年第4期12卷 866-876页

作者： sheng-Qi Yang Yan-Hua huang State Key Laboratory for Geomechanics and Deep Underground Engineering School of Mechanics and Civil EngineeringChina University of Mining and TechnologyXuzhou221116China

In underground engineering,such as geological CO2 sequestration,unconventional oil and gas exploration,and radioactive waste storage,permeability of rock is important to evaluate the potential CO2 storage capacity,improve oil and gas production,and prevent leakage of radioactive *** this study,hydrostatic stress tests and triaxial compression tests with gas permeability measurements were carried out on intact and damaged sandstone *** series of experiment were designed to evaluate the permeability evolution laws of sandstone under different testing *** included triaxial seepage tests on intact specimens under different confining pressures,triaxial seepage tests on damaged specimens with different extents of damage,and hydrostatic seepage tests on damaged specimens under increasing and decreasing gas *** on the experimental results,the effects of effective confining pressure,extent of damage and increasing and decreasing gas pressure on permeability of sandstone were *** shows that the permeability of the intact sandstone specimens first decreased and then increased,followed by a constant value with increase in axial *** permeability of the sandstone specimens was observed to decrease with increase in effective confining *** extent of damage affects the permeability evolution,but does not influence the failure patterns of damaged *** the gas pressure increased,the permeability of the damaged sandstone specimen *** the same gas pressure condition,the permeability during the decreasing process is generally higher than that during the increasing *** experiments are expected to enhance our understanding of seepage behavior in underground rock masses.

关键词： Experimental study Sandstone Gas seepage Rock damage Loading and unloading

Lower Bounds for Moments of Quadratic Twisted Self-dual GL(3)Central L-values

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Acta Mathematica Sinica,English Series 2023年第11期39卷 2139-2148页

作者： sheng Hao HUA Bing Rong huang Data Science Institute and School of Mathematics Shandong UniversityJi’nan 250100P.R.China

In this paper,we prove the conjectured order lower bound for the k-th moment of central values of quadratic twisted self-dual GL(3)L-functions for all k≥1,based on our recent work on the twisted first moment of centr... 详细信息

关键词： GL(3)cusp form lower bound quadratic twist central value L-function