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Q-BioLiP:A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 151-159页

作者： hong Wei Wenkai Wang Zhenling peng Jianyi Yang School of Mathematical Sciences Nankai UniversityTianjin 300071China MOE Frontiers Science Center for Nonlinear Expectations Research Center for Mathematics and Interdisciplinary SciencesShandong UniversityQingdao 266237China

Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand ***,several known issues occurred with it over the past *** example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand *** major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex *** these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://***/Q-BioLiP/.

关键词： Protein-ligand interaction Quaternary structure Protein-ligand binding site Protein-protein interaction Binding affinity

Atomistic study of inverse size effect induced by interfacial plasticity in pearlitic multi-principal element alloy

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Rare Metals 2024年第7期43卷 3341-3355页

作者： Chen Yang Qiao-Sheng Xia Cun-hong Yin Dong-peng Hua College of Mechanical Engineering Guizhou UniversityGuiyang 550025China Key Laboratory of Advanced Manufacturing Technology Ministry of EducationGuizhou UniversityGuiyang 550025China State Key Laboratory of Solidification Processing Center of Advanced Lubrication and Seal MaterialsNorthwestern Polytechnical UniversityXi'an 710072China

Owing to the fine nano-laminated structure,the pearlitic multi-principal element alloy(PMPEA) exhibits excellent mechanical and tribological ***,the incomplete understanding of the size effect of its lamella thickness and the unclear understanding of the plasticity-interface interaction mechanism limit further optimization of *** this study,the FeCoNi/Ni_3Ti interface-mediated plastic deformation behavior in PMPEA and the variation of mechanical and tribological properties with lamella thickness within the nanoscale range using molecular dynamics(MD) simulation were *** results indicate that the mechanical and tribological properties of the PMPEA with lamella thicknesses below 10 nm have a significant inverse size effect,i.e.,the smaller the lamella thickness,the weaker the *** is because the plastic carrier-interface interaction mechanism changes from a strengthening mechanism that hinders dislocations to a weakening mechanism that promotes dislocations with the decreases in the lamella thickness,and the weakening effect becomes more pronounced as the lamella thickness decreases and the number of interfaces *** particular,the deformation behavior of Ni_3Ti lamellae changes from crystal-like to amorphous-like with decreasing ***,in the sample with larger lamella thickness,the occurrence of hierarchical slips in the body-centered cubic(BCC) phase due to the multiprincipal elements effect can better alleviate the stress concentration caused by the dislocation accumulation at the interface,so that the phase interface exhibits outstanding load-bearing *** the dislocation pattern in BCC phase shows a firm high-density cell,which makes the substrate exhibit a stable tribological response.

关键词： Multi-principal element alloy Nano-laminated structure Molecular dynamics simulation Nanoindentation and nanoscratch

Improved Reall-Santos method for AdS black holes in general 4-derivative gravities

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Science China(Physics,Mechanics & Astronomy) 2024年第8期67卷 74-86页

作者： peng-Ju Hu Liang Ma hong Lü Yi Pang Center for Joint Quantum Studies and Department of Physics School of ScienceTianjin UniversityTianjin 300350China Joint School of National University of Singapore and Tianjin University International Campus of Tianjin UniversityFuzhou 350207China peng Huanwu Center for Fundamental Theory Hefei 230026China

For asymptotically flat black holes,Reall-Santos method is a convenient tool to compute leading higher derivative corrections to the thermodynamic quantities without actually solving the modified field ***,there are subtleties in its generalization to asymptotically AdS black holes with general higher derivative *** of all,it is necessary to know all the higher derivative holographic counterterms and the surface terms implementing the variational principle and subtracting the *** then needs to solve for the modified AdS radius and rescale the time coordinate in an appropriate way such that the induced metric on the conformal boundary of AdS black hole is not *** observe that Reall-Santos method can be directly applied to a particular 4-derivative gravity model,known as the Einstein-Weyl gravity,which does not modify the AdS radius and requires only the Gibbons-Hawking-York term and holographic counterterms for the 2-derivative *** thus suggest that to compute the thermodynamic quantities of AdS black holes in general 4-derivative theories of gravity,one simply needs to transform it to a Einstein-Weyl gravity with identical thermodynamic variables by appropriate field *** explicitly verify this proposal with spherically-symmetric and static charged black holes in Einstein-Maxwell theory extended with generic 4-derivative interactions.

关键词： black holes thermodynamics higher-derivative corrections effective theories higher dimensional black holes quantum gravity

A disk I/O optimized system for concurrent graph processing jobs

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Frontiers of Computer Science 2024年第3期18卷 13-29页

作者： Xianghao XU Fang WANG hong JIANG Yongli CHENG Dan FENG peng FANG School of Computer Science and Engineering Nanjing University of Science and TechnologyNanjing 210094China Wuhan National Laboratory for Optoelectronics Huazhong University of Science and TechnologyWuhan 430074China Department of Computer Science&Engineering University of Texas at ArlingtonArlingtonTX 76019USA College of Computer and Data Science Fuzhou UniversityFuzhou 350108China Zhejiang Lab Hangzhou 311121China

In order to analyze and process the large graphs with high cost efficiency,researchers have developed a number of out-of-core graph processing systems in recent years based on just one commodity *** the other hand,with the rapidly growing need of analyzing graphs in the real-world,graph processing systems have to efficiently handle massive concurrent graph processing(CGP)***,due to the inherent design for single graph processing job,existing out-of-core graph processing systems usually incur unnecessary data accesses and severe competition of I/O bandwidth when handling the CGP *** this paper,we propose GraphCP,a disk I/O optimized out-of-core graph processing system that efficiently supports the processing of CGP *** proposes a benefit-aware sharing execution model to share the I/O access and processing of graph data among the CGP jobs and adaptively schedule the graph data loading based on the states of vertices,which efficiently overcomes above challenges faced by existing out-of-core graph processing ***,GraphCP adopts a dependency-based future-vertex updating model so as to reduce disk I/Os in the future *** addition,GraphCP organizes the graph data with a Source-Sorted Sub-Block graph representation for better processing capacity and I/O access *** evaluation results show that GraphCP is 20.5×and 8.9×faster than two out-of-core graph processing systems GridGraph and GraphZ,and 3.5×and 1.7×faster than two state-of-art concurrent graph processing systems Seraph and GraphSO.

关键词： graph processing disk I/O concurrent jobs

Vertically grown MoS_(2)nanosheets on graphene with defect-rich structure for efficient sodium storage

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Rare Metals 2024年第3期43卷 1062-1071页

作者： Ying Wang Jia-peng He Han-Qing Pan Qing-peng Wang Lei Zhang Yong-Chang Liu Qing-hong Wang School of Chemistry&Materials Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional MaterialsJiangsu Normal UniversityXuzhou221116China Institute of Biopharmaceutical Research Liaocheng UniversityLiaocheng252059China Beijing Advanced Innovation Center for Materials Genome Engineering Institute for Advanced Materials and TechnologyState Key Laboratory for Advanced Metals and MaterialsUniversity of Science and Technology BeijingBeijing100083China Centre for Catalysis and Clean Energy Gold Coast CampusGriffith UniversityGold CoastQLD4222Australia

The synthesis of a perpendicular growth structure of MoS_(2)nanosheets on graphene for efficient sodium storage is challenging yet ideal due to the benefits of open ion diffusion channels and high electronic *** this study,we have successfully fabricated a novel structure of vertical MoS_(2)nanosheets on graphene,with ZnS nanoparticles serving as bonding points(MoS_(2)/ZnS/G),through a facile hydrothermal *** the synthesis process,Zn^(2+)not only acts as a landing site for the vertical growth of MoS_(2)nanosheets but also triggers the formation of a defect-rich structure in the final *** unique architecture of MoS_(2)/ZnS/G effectively combines the advantages of a vertically aligned geometry and a defectrich structure for energy *** resulting structure displays shortened transport paths for electrons/ions,enhanced conductivity,improved structural integrity,and an increased number of active sites for promising electrochemical *** expected,when used as anode for sodium-ion batteries,the as-synthesize d MoS_(2)/ZnS/G exhibits excellent rate capability(high capacity of 298 mAh·g^(-1)at 5 A·g^(-1))and good cycling stability(a capacity decay of 0.056%per cycle after 500 cycles at 1 A·g^(-1)).According to the kinetic investigations,the electrochemical process of the MoS_(2)/ZnS/G sample is primarily governe d by a pseudocapacitive behavior,which enhances the charge/discharge kinetics and allows the MoS_(2)/ZnS/G structure to remain intact during cycling.

关键词： MoS_(2) Perpendicular growth Graphene Sodium storage Electrochemical performance

CD209 signaling pathway as a biomarker for cisplatin chemotherapy response in small cell lung cancer

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Genes & Diseases 2024年第3期11卷 11-14页

作者： Anqi Lin hong Yang Jian Zhang peng Luo Department of Oncology Zhujiang HospitalSouthern Medical UniversityGuangzhouGuangdong 510282China The First Clinical Medical School Southern Medical UniversityGuangzhouGuangdong 510515China

One of the bottlenecks in the clinical treatment of small cell lung cancer(SCLC)is its susceptibility to multidrug *** SCLC is sensitive to platinum-based chemotherapy at the initial stage of treatment,it can rapidly become drug-resistant,allowing tumor growth to accelerate.A significant decrease in drug sensitivity after recurrence and multidrug resistance can seriously interfere with the effectiveness of treatment,making sensitivity maintenance one of the urgent challenges to be ***,discovering prognostic markers for cisplatin chemotherapy and understanding the mechanisms of cisplatin resistance have great practical significance for improving the outcomes of sCLC patients.

关键词： cisplatin chemotherapy lung

Enhanced Grain Refining Effect of Mg–Zr Master Alloy on Magnesium Alloys via a Synergistic Strategy Involving Heterogeneous Nucleation and Solute‑Driven Growth Restriction

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Acta Metallurgica Sinica(English Letters) 2024年第8期37卷 1354-1366页

作者： Gang Zeng hong Liu Jing‑peng Xiong Jian‑Long Li Yong Liu Key Laboratory of Lightweight and High Strength Structural Materials of Jiangxi Province School of Advanced ManufacturingNanchang UniversityNanchang 330031China

Zirconium(Zr)emerges as the most effective grain refiner for magnesium(Mg)alloys incorporating ***,Zr is introduced in the form of an Mg–Zr master ***,within Mg–Zr master alloys,Zr predominantly exists in a particle form,which tends to aggregate due to attractive van der Waals *** clustered Zr is prone to settling,thereby reducing its refining impact on Mg *** this work,a combined pretreatment process for Mg–Zr master alloys was proposed,encompassing the introduction of a physical field to intervene the agglomeration of particle Zr and the employ of high-temperature dissolution and peritectic reactions to promote the solid solution of *** results demonstrate that the particle Zr within the pretreated Mg–Zr master alloy is effectively dispersed and refined,and greater solute Zr levels can be *** subsequent grain refinement ability was studied on a typical Mg–6Zn–0.6Zr(wt%)*** outcome highlights that an improvement in the grain refinement efficacy(32.4%)of Mg–Zr master alloys was obtained with a holding time of 60 *** pretreated Mg–Zr master alloy significantly augments the efficiency of grain refinement for Mg alloys through a synergistic strategy involving heterogeneous nucleation and solute-driven growth *** crucial factor in achieving effective grain refinement of Zr in Mg alloys lies in regulating the presence and morphology of Zr in the Mg–Zr master alloy,distinguishing between particle Zr and solute *** study introduces a novel method for developing more efficient Mg–Zr refiners.

关键词： Magnesium alloy Mg-Zr master alloy Grain refinement Heterogeneous nucleation Solute-driven growth restriction Synergistic strategy

Data-driven discovery of formation ability descriptors for high-entropy rare-earth monosilicates

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Journal of Materiomics 2024年第3期10卷 738-747页

作者： hong Meng peng Wei Zhongyu Tang Hulei Yu Yanhui Chu School of Materials Science and Engineering South China University of TechnologyGuangzhou510641China

Herein we establish formation ability descriptors of high-entropy rare-earth monosilicates(HEREMs)via the data-driven discovery based on the high-throughput solid-state reaction and machine learning(ML)***,adequate high-quality data are generated with 132 samples synthesized by the self-developed high-throughput solid-state reaction apparatuses,and 30 potential descriptors are considered in ML *** classifications are proposed to study the phase formation of HEREMs via the ML approach combined with the genetic algorithm:(Ⅰ)to distinguish pure HEREMs(X)from other phases and(Ⅱ)to categorize the detail phases of HEREMs(X2,X1,or X2+X1).Four formation ability descriptors(r_(Me),EF,d_(Eg),and d_(Z*))with a high validation accuracy(96.2%)are proposed as the optimal combination for Classification I,where a smaller r_(Me)is determined to have the most significant influence on the formation of *** ClassificationⅡ,a 100%validation accuracy is achieved by using only two formation ability descriptors(rion and d_(Z*)),where the rion is analyzed to be the dominant feature and a lower rion is beneficial to the formation of *** on our established formation ability descriptors,6,045 unreported multicomponent silicates are explored,and 3,478 new HEREMs with 2,700 X2-and 423 X1-HEREMs are predicted.

关键词： High-entropy rare-earth monosilicates Formation ability descriptors High-throughput experiments Machine learning

Fast charge transfer kinetics in Sv-ZnIn_(2)S_(4)/Sb_(2)S_(3)S-scheme heterojunction photocatalyst for enhanced photocatalytic hydrogen evolution

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Rare Metals 2024年第2期43卷 533-542页

作者： Wei Li Jia-Jun Li Zhi-Fei Liu hong-Yu Ma peng-Fei Fang Rui Xiong Jian-hong Wei Key Laboratory of Artificial Micro-and Nano-Structures of Ministry of Education School of Physics and TechnologyWuhan UniversityWuhan430072China

Constructing a S-scheme heterojunction with tight interface contact and fast charge transfer is beneficial to improving the photocatalytic hydrogen evolution ***,a unique one-dimensional(1D)/two-dimensional(2D)S-scheme heterojunction containing 1D Sb_(2)S_(3) nanorods and 2D ZnIn_(2)S_(4) with affluent sulfur vacancies(denoted as Sv-ZnIn_(2)S_(4)@Sb_(2)S_(3)) was *** introduced sulfur vacancy can promote the effective adsorption of H+for the following interfacial hydrogen-evolution ***,the larger contact area and stronger electron interaction between Sb_(2)S_(3) and ZnIn_(2)S_(4) effectively inhibits the recombination of photo-generated electron–hole pairs and abridges the migration distance of *** a result,the optimal Sv-ZnIn_(2)S_(4)@Sb_(2)S_(3) sample achieves H_(2) evolution activity of 2741.3 mol·h^(−1)·g^(−1),which is 8.6 times that of pristine ZnIn_(2)S_(4) and 3.0 times that of the Sv-ZnIn_(2)S_(4) *** on the experimental result,the photo-reactivity S-scheme mechanism of hydrogen evolution from water splitting with Sv-ZnIn_(2)S_(4)@Sb_(2)S_(3) is *** work provides an effective method for developing S-scheme heterojunction composites of transition metal sulfide with high hydrogen evolution performance.

关键词： ZnIn_(2)S_(4) nanosheets S-scheme heterojunction Sulfur vacancy Charge transfer and separation Photocatalytic H_(2)evolution