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Predicting the assembly/disassembly order of protein complexes via coarse-grained simulations
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作者 Yunxiao Lu Xin Liu Zhiyong Zhang 《中国科学技术大学学报》 CSCD 北大核心 2024年第12期7-15,I0002,I0008,共11页
The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many pro... The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data. 展开更多
关键词 protein complexes assembly/disassembly order coarse-grained simulations native contacts
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Coarse-grained Simulations of Chemical Oscillation in Lattice Brusselator System
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作者 饶汀 张珍 +1 位作者 侯中怀 辛厚文 《Chinese Journal of Chemical Physics》 SCIE CAS CSCD 2011年第4期425-433,I0003,I0004,共11页
The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo (CG-KMC) procedure, where m×m microscopic lattice sites are group... The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo (CG-KMC) procedure, where m×m microscopic lattice sites are grouped together to form a CG cell, upon which CG processes take place with well-defined CG rates. Such a CG approach almost fails if the CG rates are obtained by a simple local mean field (s-LMF) approximation, due to the ignorance of correlation among adjcent cells resulting fl'om the trimolecular reaction in this nonlinear system. By proper incorporating such boundary effects, thus introduce the so-cMled b-LMF CG approach. Extensive numerical simulations demonstrate that the b-LMF method can reproduce the oscillation behavior of the system quite well, given that the diffusion constant is not too small. In addition, the deviation from the KMC results reaches a nearly zero minimum level at an intermediate cell size, which lies in between the effective diffusion length and the minimal size required to sustain a well-defined temporal oscillation. 展开更多
关键词 Chemical oscillation coarse-grained Kinetic Monte Carlo
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Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers
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作者 Xuegui Lin Xiaojie Chen Qing Liang 《Chinese Physics B》 SCIE EI CAS CSCD 2021年第6期703-710,共8页
Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between sp... Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine(PE) lipids rather than with phosphatidylcholine(PC) lipids, and tend to contact with the liquid-disordered(Ld) domains enriched in unsaturated PE.Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases. 展开更多
关键词 PROTEIN lipid bilayer interaction molecular dynamics simulation
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Coarse-grained molecular dynamics simulations on self-assembly of polystyrene-block-poly(2-vinylpyridine)
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作者 Daiwen Li Shoutian Qiu +6 位作者 Gan Liu Ming Liu Mingjie Wei Shipeng Sun Weihong Xing Xiaohua Lu Yong Wang 《Chinese Journal of Chemical Engineering》 2025年第7期15-25,共11页
Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)mole... Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)molecular dynamics(MD)simulation offers a microscopic angle to view the self-assembly of BCPs.Although some molecular details are sacrificed during CG processes,this method exhibits remarkable computational efficiency.In this study,a comprehensive CG model for polystyrene-block-poly(2-vinylpyridine),PS-b-P2VP,one of the most extensively studied BCPs for its high Flory-Huggins interaction parameter,is constructed,with parameters optimized using target values derived from all-atom MD simulations.The CG model precisely coincides with various classical self-assembling morphologies observed in experimental studies,matching the theoretical phase diagrams.Moreover,the conformational asymmetry of the experimental phase diagram is also clearly revealed by our simulation results,and the phase boundaries obtained from simulations are highly consistent with experimental results.The CG model is expected to extend to simulate the self-assembly behaviors of other BCPs in addition to PS-b-P2VP,thus increasing understanding of the microphase separation of BCPs from the molecular level. 展开更多
关键词 Block copolymers SELF-ASSEMBLY Martini force field POLYMERS Computer simulation Molecular simulation
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Protein aging dynamics:A perspective from non-equilibrium coarse-grained models
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作者 Yue Shan Chun-Lai Ren Yu-Qiang Ma 《Chinese Physics B》 2025年第5期609-617,共9页
The aging of biomolecular condensates has been implicated in the pathogenesis of various neurodegenerative diseases,characterized by a transition from a physiologically liquid-like state to a pathologically ordered st... The aging of biomolecular condensates has been implicated in the pathogenesis of various neurodegenerative diseases,characterized by a transition from a physiologically liquid-like state to a pathologically ordered structure.However,the mechanisms governing the formation of these pathological aggregates remain poorly understood.To address this,the present study utilizes coarse-grained molecular dynamics simulations based on Langevin dynamics to explore the structural,dynamical,and material property changes of protein condensates during the aging process.Here,we further develop a nonequilibrium simulation algorithm that not only captures the characteristics of time-dependent amount of aging beads but also reflects the structural information of chain-like connections between aging beads.Our findings reveal that aging induces compaction of the condensates,accompanied by a decrease in diffusion rates and an increase in viscosity.Further analysis suggests that the heterogeneous diffusivity within the condensates may drive the aging process to initiate preferentially at the condensate surface.Our simulation results align with the experimental phenomena and provide a clear physical picture of the aging dynamics. 展开更多
关键词 protein condensates aging coarse-grained simulation liquid-to-solid transition
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Multidisciplinary and multi-fidelity coupling methods in aircraft engine simulations
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作者 YANG Xin XIE Pengfu +2 位作者 DONG Xuezhi HE Ai TAN Chunqing 《推进技术》 北大核心 2025年第5期1-12,共12页
To address the limitations of existing coupling methods in aero-engine system simulation,which fail to adaptively adjust iterative parameters and coupling relationships,which can result in low efficiency and in⁃stabil... To address the limitations of existing coupling methods in aero-engine system simulation,which fail to adaptively adjust iterative parameters and coupling relationships,which can result in low efficiency and in⁃stability,this study introduces a‘Dynamic Event-Driven Co-Simulation’algorithm integrated with decision tree algorithms.This algorithm separates the overall coupling relationships and the main solver from the primary mod⁃el,utilizing a dynamic event monitoring module to adaptively adjust simulation strategies,including iteration pa⁃rameters,coupling relationships,and convergence criteria.This facilitates efficient adaptive simulations of dy⁃namic events while balancing solution accuracy and computational efficiency.The research focuses on a twinshaft turbofan engine,establishing six system-level models that encompass overall performance and various sub⁃systems based on three coupling methods,along with a multidisciplinary multi-fidelity simulation framework in⁃corporating a 3D CFD nozzle model.The study tests both model exchange and coupled simulation methods under a 14 s transient acceleration and deceleration scenario.In a 100%throttle condition,a high-fidelity nozzle model is used to analyze the sensitivity of different convergence criteria on computational efficiency and accuracy.Re⁃sults indicate that the accuracy and efficiency achieved with this method are comparable to those of PROOSIS soft⁃ware(18 s and 35 s,respectively),while being 71%more efficient than Simulink software(62 s and 120 s,re⁃spectively).Furthermore,appropriately relaxing the convergence criteria for the 0D model(from 10-6 to 10-4)while enhancing those for the 3D model(from 3000 steps to 6000 steps)can effectively balance computational accuracy and efficiency. 展开更多
关键词 AERO-ENGINE Multi-fidelity simulation Overall performance CO-simulATION Integrated model Zooming strategy
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Darcy to non-Darcy seepage transition in heterogeneous coarse-grained soil:Seepage characteristics and critical threshold prediction
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作者 Xin Zhang Yufeng Wei +3 位作者 Guoxiang Tu Hao Yang Shixin Zhang Peng Liang 《Journal of Rock Mechanics and Geotechnical Engineering》 2025年第4期2526-2538,共13页
Seepage in coarse-grained soil exhibits distinct non-Darcy characteristics,and the transition from linear to nonlinear seepage significantly affects the hydraulic characteristics and geotechnical applications.Due to t... Seepage in coarse-grained soil exhibits distinct non-Darcy characteristics,and the transition from linear to nonlinear seepage significantly affects the hydraulic characteristics and geotechnical applications.Due to the complexity of pore structure in heterogeneous coarse-grained soil,identifying the critical threshold for the transition from Darcy to non-Darcy seepage is challenging.This paper introduces equivalent particle size(dep)and relative roughness(λt)as indirect indicators reflecting the pore characteristics,quantifying the complex pore structure of heterogeneous coarse-grained soil.The formulae for the derivation of Reynolds number and resistance coefficient for heterogeneous coarse-grained soil are presented.By conducting permeability tests on coarse-grained soils with different pore structures,the effect of particle composition heterogeneity on seepage characteristics was analyzed.The flow regime of heterogeneous coarse-grained soil is divided into laminar,transitional,and turbulent stages based on the relationship between Reynolds number and resistance coefficient.The energy loss patterns in each stage are closely related to pore structure.By setting the permeability ratio k∗=0.95 as the critical threshold for the transition from Darcy to non-Darcy seepage,a method for calculating the critical Reynolds number(Recr)for heterogeneous coarse-grained soil is proposed.Furthermore,we applied this method to other published laboratory data,analyzing the differences in the critical threshold for seepage transition between homogeneous and heterogeneous coarse-grained soil.This study aims to propose a more accurate and general criterion for the transition from Darcy to non-Darcy seepage in heterogeneous coarse-grained soil. 展开更多
关键词 coarse-grained soil Porous media Seepage characteristics Non-Darcy seepage Pore characteristics
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Microscopic swelling behaviors and structural responses of aggregate system: A coarse-grained molecular dynamics study
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作者 Kaiwen Tong Jean-Michel Pereira +4 位作者 Fei Yu Jianhua Guo Zihang Liu Zhangjun Dai Shanxiong Chen 《Journal of Rock Mechanics and Geotechnical Engineering》 2025年第6期3833-3844,共12页
To overcome the limitations of microscale experimental techniques and molecular dynamics(MD)simulations,a coarse-grained molecular dynamics(CGMD)method was used to simulate the wetting processes of clay aggregates.Bas... To overcome the limitations of microscale experimental techniques and molecular dynamics(MD)simulations,a coarse-grained molecular dynamics(CGMD)method was used to simulate the wetting processes of clay aggregates.Based on the evolution of swelling stress,final dry density,water distribution,and clay arrangements under different target water contents and dry densities,a relationship between the swelling behaviors and microstructures was established.The simulated results showed that when the clay-water well depth was 300 kcal/mol,the basal spacing from CGMD was consistent with the X-ray diffraction(XRD)data.The effect of initial dry density on swelling stress was more pronounced than that of water content.The anisotropic swelling characteristics of the aggregates are related to the proportion of horizontally oriented clay mineral layers.The swelling stress was found to depend on the distribution of tactoids at the microscopic level.At lower initial dry density,the distribution of tactoids was mainly controlled by water distribution.With increase in the bound water content,the basal spacing expanded,and the swelling stresses increased.Free water dominated at higher water contents,and the particles were easily rotated,leading to a decrease in the number of large tactoids.At higher dry densities,the distances between the clay mineral layers decreased,and the movement was limited.When bound water enters the interlayers,there is a significant increase in interparticle repulsive forces,resulting in a greater number of small-sized tactoids.Eventually,a well-defined logarithmic relationship was observed between the swelling stress and the total number of tactoids.These findings contribute to a better understanding of coupled macro-micro swelling behaviors of montmorillonite-based materials,filling a study gap in clay-water interactions on a micro scale. 展开更多
关键词 coarse-grained molecular dynamics (CGMD) Clay aggregates Swelling stress Water distribution Distribution of tactoids
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Effect of Al content on nanoprecipitates, austenite grain growth and toughness in coarse-grained heat-affected zones of Al–Ti–Ca deoxidized shipbuilding steels
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作者 Tingting Li Jian Yang +3 位作者 Yinhui Zhang Han Sun Yanli Chen Yuqi Zhang 《International Journal of Minerals,Metallurgy and Materials》 2025年第4期879-891,共13页
This work focuses on the influence of Al content on the precipitation of nanoprecipitates,growth of prior austenite grains(PAGs),and impact toughness in simulated coarse-grained heat-affected zones (CGHAZs) of two exp... This work focuses on the influence of Al content on the precipitation of nanoprecipitates,growth of prior austenite grains(PAGs),and impact toughness in simulated coarse-grained heat-affected zones (CGHAZs) of two experimental shipbuilding steels after being subjected to high-heat input welding at 400 kJ·cm^(-1).The base metals (BMs) of both steels contained three types of precipitates Type Ⅰ:cubic (Ti,Nb)(C,N),Type Ⅱ:precipitate with cubic (Ti,Nb)(C,N) core and Nb-rich cap,and Type Ⅲ:ellipsoidal Nb-rich precipitate.In the BM of 60Al and 160Al steels,the number densities of the precipitates were 11.37×10^(5) and 13.88×10^(5) mm^(-2),respectively The 60Al and 160Al steel contained 38.12% and 6.39% Type Ⅲ precipitates,respectively.The difference in the content of Type Ⅲ precipitates in the 60Al steel reduced the pinning effect at the elevated temperature of the CGHAZ,which facilitated the growth of PAGs The average PAG sizes in the CGHAZ of the 60Al and 160Al steels were 189.73 and 174.7μm,respectively.In the 60Al steel,the low lattice mismatch among Cu_(2)S,TiN,and γ-Al_(2)O_(3)facilitated the precipitation of Cu_(2)S and TiN onto γ-Al_(2)O_(3)during welding,which decreased the number density of independently precipitated (Ti,Nb)(C,N) particles but increased that of γ-Al_(2)O_(3)–Ti N–Cu_(2)S particles.Thus abnormally large PAGs formed in the CGHAZ of the 60Al steel,and they reached a maximum size of 1 mm.These PAGs greatly reduced the microstructural homogeneity and consequently decreased the impact toughness from 134 (0.016wt%Al) to 54 J (0.006wt%Al)at-40℃. 展开更多
关键词 oxide metallurgy Al–Ti–Ca deoxidization Al content PRECIPITATES coarse-grained heat-affected zone
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Characterization of unsaturated coarse-grained railway embankment fill:Water retention and dilatancy
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作者 Yuanjie Xiao Wenqi Li +4 位作者 Liuxin Chen Xiaoming Wang Yunbo Li Pan Tan Jiapei Du 《Journal of Rock Mechanics and Geotechnical Engineering》 2025年第5期3125-3145,共21页
This study investigated the hydraulic and mechanical behaviors of unsaturated coarse-grained railway embankment fill materials(CREFMs)using a novel unsaturated large-scale triaxial apparatus equipped with the axis tra... This study investigated the hydraulic and mechanical behaviors of unsaturated coarse-grained railway embankment fill materials(CREFMs)using a novel unsaturated large-scale triaxial apparatus equipped with the axis translation technique(ATT).Comprehensive soil-water retention and constant-suction triaxial compression tests were conducted to evaluate the effects of initial void ratio,matric suction,and confining pressure on the properties of CREFMs.Key findings reveal a primary suction range of 0 e100 kPa characterized by hysteresis,which intensifies with decreasing density.Notably,the air entry value and residual suction are influenced by void ratio,with higher void ratios leading to decreased air entry values and residual suctions,underscoring the critical role of void ratio in hydraulic behavior.Additionally,the critical state line(CSL)in the bi-logarithmic space of void ratio and mean effective stress shifts towards higher void ratios with increasing matric suction,significantly affecting dilatancy and critical states.Furthermore,the study demonstrated that the mobilized friction angle and modulus properties depend on confining pressure and matric suction.A novel modified dilatancy equation was proposed,which enhances the predictability of CREFMs'responses under variable loading,particularly at high stress ratios defined by the deviatoric stress over the mean effective stress.This research advances the understanding of CREFMs'performance,especially under fluctuating environmental conditions that alter suction levels. 展开更多
关键词 coarse-grained railway embankment fill materials(CREFMs) Soil-water retention curve(SWRC) Constant-suction triaxial compression test Critical state Dilatancy equation Unsaturated soil
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Multi-scale Numerical Simulations for Crack Propagation in NiTi Shape Memory Alloys by Molecular Dynamics-based Cohesive Zone Model
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作者 LI Yunfei WANG Yuancen HE Qinshu 《Journal of Wuhan University of Technology(Materials Science)》 2025年第2期599-609,共11页
The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope ... The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope and image processing technology were employed to achieve a quantitative grain size distribution of NiTi alloys so as to provide experimental data for molecular dynamics modeling at the atomic scale.Considering the size effect of molecular dynamics model on material properties,a reasonable modeling size was provided by taking into account three characteristic dimensions from the perspective of macro,meso,and micro scales according to the Buckinghamπtheorem.Then,the corresponding MD simulation on deformation and fracture behavior was investigated to derive a parameterized traction-separation(T-S)law,and then it was embedded into cohesive elements of finite element software.Thus,the crack propagation behavior in NiTi alloys was reproduced by the finite element method(FEM).The experimental results show that the predicted initiation fracture toughness is in good agreement with experimental data.In addition,it is found that the dynamics initiation fracture toughness increases with decreasing grain size and increasing loading velocity. 展开更多
关键词 NiTi shape memory alloys multi-scale numerical simulation crack propagation the cohesive zone model molecular dynamics simulation
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Land use/cover change and ecological network in Gansu Province,China during 2000-2020 and their simulations in 2050 被引量:1
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作者 MA Xinshu XIN Cunlin +6 位作者 CHEN Ning XIN Shunjie CHEN Hongxiang ZHANG Bo KANG Ligang WANG Yu JIAO Jirong 《Journal of Arid Land》 2025年第1期43-57,共15页
Land use/cover change(LUCC)constitutes the spatial and temporal patterns of ecological security,and the construction of ecological networks is an effective way to ensure ecological security.Exploring the spatial and t... Land use/cover change(LUCC)constitutes the spatial and temporal patterns of ecological security,and the construction of ecological networks is an effective way to ensure ecological security.Exploring the spatial and temporal change characteristics of ecological network and analyzing the integrated relationship between LUCC and ecological security are crucial for ensuring regional ecological security.Gansu is one of the provinces with fragile ecological environment in China,and rapid changes in land use patterns in recent decades have threatened ecological security.Therefore,taking Gansu Province as the study area,this study simulated its land use pattern in 2050 using patch-generating land use simulation(PLUS)model based on the LUCC trend from 2000 to 2020 and integrated the LUCC into morphological spatial pattern analysis(MSPA)to identify ecological sources and extract the ecological corridors to construct ecological network using circuit theory.The results revealed that,according to the prediction results in 2050,the areas of cultivated land,forest land,grassland,water body,construction land,and unused land would be 63,447.52,39,510.80,148,115.18,4605.21,8368.89,and 161,752.40 km^(2),respectively.The number of ecological sources in Gansu Province would increase to 80,with a total area of 99,927.18 km^(2).The number of ecological corridors would increase to 191,with an estimated total length of 6120.66 km.Both ecological sources and ecological corridors showed a sparse distribution in the northwest and dense distribution in the southeast of the province at the spatial scale.The number of ecological pinch points would reach 312 and the total area would expect to increase to 842.84 km^(2),with the most pronounced increase in the Longdong region.Compared with 2020,the number and area of ecological barriers in 2050 would decrease significantly by 63 and 370.71 km^(2),respectively.In general,based on the prediction results,the connectivity of ecological network of Gansu Province would increase in 2050.To achieve the predicted ecological network in 2050,emphasis should be placed on the protection of cultivated land and ecological land,the establishment of ecological sources in desert areas,the reinforcement of the protection for existing ecological sources,and the construction of ecological corridors to enhance the stability of ecological network.This study provides valuable theoretical support and references for the future construction of ecological networks and regional land resource management decision-making. 展开更多
关键词 patch-generating land use simulation(PLUS)model morphological spatial pattern analysis(MSPA) circuit theory ecological source ecological resistance surface ecological corridor ecological pinch point
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Molecular dynamics simulations of collision cascades in polycrystalline tungsten
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作者 Lixia Liu Mingxuan Jiang +3 位作者 Ning Gao Yangchun Chen Wangyu Hu Hiuqiu Deng 《Chinese Physics B》 2025年第4期468-476,共9页
Using molecular dynamics methods,simulations of collision cascades in polycrystalline tungsten(W)have been conducted in this study,including different primary-knock-on atom(PKA)directions,grain sizes,and PKA energies ... Using molecular dynamics methods,simulations of collision cascades in polycrystalline tungsten(W)have been conducted in this study,including different primary-knock-on atom(PKA)directions,grain sizes,and PKA energies between 1 keV and 150 keV.The results indicate that a smaller grain size leads to more defects forming in grain boundary regions during cascade processes.The impact of high-energy PKA may cause a certain degree of distortion of the grain boundaries,which has a higher probability in systems with smaller grain sizes and becomes more pronounced as the PKA energy increases.The direction of PKA can affect the formation and diffusion pathways of defects.When the PKA direction is perpendicular to the grain boundary,defects preferentially form near the grain boundary regions;by contrast,defects are more inclined to form in the interior of the grains.These results are of great significance for comprehending the changes in the performance of polycrystalline W under the high-energy fusion environments and can provide theoretical guidance for further optimization and application of W-based plasma materials. 展开更多
关键词 collision cascades molecular dynamics simulations TUNGSTEN POLYCRYSTALLINE
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Improving the reliability of classical molecular dynamics simulations in battery electrolyte design
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作者 Xin He Yujie Zhang +5 位作者 Haomiao Li Min Zhou Wei Wang Ruxing Wang Kai Jiang Kangli Wang 《Journal of Energy Chemistry》 2025年第2期34-41,I0002,共9页
Explorations into new electrolytes have highlighted the critical impact of solvation structure on battery performance,Classical molecular dynamics(CMD)using semi-empirical force fields has become an essential tool for... Explorations into new electrolytes have highlighted the critical impact of solvation structure on battery performance,Classical molecular dynamics(CMD)using semi-empirical force fields has become an essential tool for simulating solvation structures.However,mainstream force fields often lack accuracy in describing strong ion-solvent interactions,causing disparities between CMD simulations and experimental observations.Although some empirical methods have been employed in some of the studies to address this issue,their effectiveness has been limited.Our CMD research,supported by quantum chemical calculations and experimental data,reveals that the solvation structure is influenced not only by the charge model but also by the polarization description.Previous empirical approaches that focused solely on adjusting ion-solvent interaction strengths overlooked the importance of polarization effects.Building on this insight,we propose integrating the Drude polarization model into mainstream force fields and verify its feasibility in carbonate,ether,and nitrile electrolytes.Our experimental results demonstrate that this approach significantly enhances the accuracy of CMD-simulated solvation structures.This work is expected to provide a more reliable CMD method for electrolyte design,shielding researchers from the pitfalls of erroneous simulation outcomes. 展开更多
关键词 ELECTROLYTE Classical molecular dynamics Solvation structure simulations
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Research Progress and Applications of Carbon Nanotubes,Black Phosphorus,and Graphene-Based Nanomaterials:Insights from Computational Simulations
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作者 Qinghua Qin 《Computers, Materials & Continua》 2025年第10期1-39,共39页
Carbon nanotubes(CNTs),black phosphorus nanotubes(BPNTs),and graphene derivatives exhibit significant promise for applications in nano-electromechanical systems(NEMS),energy storage,and sensing technologies due to the... Carbon nanotubes(CNTs),black phosphorus nanotubes(BPNTs),and graphene derivatives exhibit significant promise for applications in nano-electromechanical systems(NEMS),energy storage,and sensing technologies due to their exceptional mechanical,electrical,and thermal properties.This review summarizes recent advances in understanding the dynamic behaviors of these nanomaterials,with a particular focus on insights gained from molecular dynamics(MD)simulations.Key areas discussed include the oscillatory and rotational dynamics of double-walled CNTs,fabrication and stability challenges associated with BPNTs,and the emerging potential of graphyne nanotubes(GNTs).The review also outlines design strategies for enhancing nanodevice performance and underscores the importance of future efforts in experimental validation,multi-scale coupling analyses,and the development of novel nanocomposites to accelerate practical deployment. 展开更多
关键词 Carbon nanotubes black phosphorus GRAPHENE NANOMATERIALS molecular dynamics simulations
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Rockburst tendency prediction in a deeply buried tunnel based on numerical simulations
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作者 HUO Yuxiang HUANG Jian +3 位作者 JU Nengpan ZHANG Min WANG Qingwu HU Yong 《Journal of Mountain Science》 2025年第4期1261-1273,共13页
Deeply buried mountain tunnels are often exposed to the risk of rock bursts,which always cause serious damage to the supporting structures and threaten the safety of the engineers.Due to the limited data available,a s... Deeply buried mountain tunnels are often exposed to the risk of rock bursts,which always cause serious damage to the supporting structures and threaten the safety of the engineers.Due to the limited data available,a suitable approach to predict the rockburst tendency at the preliminary stage becomes very important.In this study,an integrated methodology combining 3D initial stress inversion and rockburst tendency prediction was developed and subsequently applied to a case study of the Sangzhuling Tunnel on the Sichuan–Tibet Railway.The numerical modelling involved inverting the initial stress field using a multiple linear regression method.The tunnel excavation was simulated separately by FDM and DEM,based on a stress boundary condition from the inverted stress field.The comparative analysis demonstrates that the rockburst ratio calculated using DEM(76.70%)exhibits a slight increase compared to FDM(75.38%),and the rockburst location is consistent with the actual situation.This suggests that DEM is more suitable for simulating the stress redistribution during excavation in a jointed rock mass.The numerical simulation combined with the deviatoric stress approach effectively predicts rockburst tendency,meeting the engineering requirements.Despite its limitations,numerical simulation remains a reliable method for predicting rock bursts. 展开更多
关键词 Geostress inversion Rockburst tendency Numerical simulation Deeply buried tunnel
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Unraveling the formation and stabilization of vesicle penetration pore by molecular dynamics simulations
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作者 Zhi Zheng Mingkun Zhang +2 位作者 Qing Yang Mian Long Shouqin Lü 《Acta Mechanica Sinica》 2025年第7期357-376,共20页
The formation of donut-shaped penetration pore upon membrane fusion in a closed lipid membrane system is of biological significance,since such the structures extensively exist in living body with various functions.How... The formation of donut-shaped penetration pore upon membrane fusion in a closed lipid membrane system is of biological significance,since such the structures extensively exist in living body with various functions.However,the related formation dynamics is unclear because of the limitation of experimental techniques.This work developed a new model of intra-vesicular fusion to elaborate the formation and stabilization of penetration pores by employing molecular dynamics simulations,based on simplified spherical lipid vesicle system,and investigated the regulation of membrane lipid composition.Results showed that penetration pore could be successfully formed based on the strategy of membrane fusion.The ease of intra-vesicular fusion and penetration pore formation was closely correlated with the lipid curvature properties,where negative spontaneous curvature of lipids seemed to be unfavorable for intra-vesicle fusion.Furthermore,the inner membrane tension around the pore was much larger than other regions,which governed the penetration pore size and stability.This work provided basic understanding for vesicle penetration pore formation and stabilization mechanisms. 展开更多
关键词 Penetration pore Membrane fusion Membrane tension Molecular dynamics simulation
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Tropical Cyclone Simulations:The Impact of Model Top/Damping Layer and the Role of Stratospheric Gravity Waves
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作者 Xu WANG Yuan WANG +2 位作者 Lifeng ZHANG Yun ZHANG Jiping GUAN 《Advances in Atmospheric Sciences》 2025年第11期2290-2304,共15页
This paper investigates the impact of the model top and damping layer on the numerical simulation of tropical cyclones(TCs)and reveals the significant role of stratospheric gravity waves(SGWs).TCs can generate SGWs,wh... This paper investigates the impact of the model top and damping layer on the numerical simulation of tropical cyclones(TCs)and reveals the significant role of stratospheric gravity waves(SGWs).TCs can generate SGWs,which propagate upward and outward into the stratosphere.These SGWs can reach the damping layer,which is a consequence of the numerical scheme employed,where they can affect the tangential circulation through the dragging and forcing processes.In models with a higher top boundary,this tangential circulation develops far from the TC and has minimal direct impact on TC intensity.By comparison,in models with a lower top(e.g.,20 km),the damping layer is located just above the top of the TC.The SGW dragging in the damping layer and the consequent tangential force can thus induce ascent outside the eyewall,promote latent heat release,tilt the eyewall,and enlarge the inner-core radius.This process will reduce inner-core vorticity advection within the boundary layer,and eventually inhibits the intensification of the TC.This suggests that when the thickness of the damping layer is 5 km,the TC numerical model top height should be at least higher than 20 km to generate more accurate simulations. 展开更多
关键词 gravity waves STRATOSPHERE tropical cyclones numerical simulations damping layer model top
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Influence ofγʹvolume fraction on creep of Ni-based superalloy through phase-field simulations
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作者 Min YANG Fan YANG +3 位作者 Jia CHEN Min GUO Hai-jun SU Jun ZHANG 《Transactions of Nonferrous Metals Society of China》 2025年第4期1168-1181,共14页
γʹvolume fraction(fv)plays a critical role in the mechanical properties of Ni-based single-crystal superalloys.A creep phase-field model is utilized to simulate the microstructure evolution and creep performance duri... γʹvolume fraction(fv)plays a critical role in the mechanical properties of Ni-based single-crystal superalloys.A creep phase-field model is utilized to simulate the microstructure evolution and creep performance during creep under different fv conditions.The influence mechanism of fv on creep properties is investigated based on the analysis of evolutions of internal stress and strain fields.As fv increases,the morphology ofγʹrafts changes from discontinuous to continuous,while the morphological change ofγchannels is opposite,the inclination ofγchannels from the[010]direction to(011)directions during tertiary creep first decreases and then increases,the creep life first increases and then decreases,and the main distribution of creep damage shifts fromγʹtoγʹ/γinterfaces andγchannels.The longest creep life under fv of 0.65 can be attributed to the stableγʹraft structure,the lowest stress and strain inγchannels,and the slowest damage accumulation. 展开更多
关键词 phase-field simulation internal stress internal strain creep behavior single-crystal superalloys
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Surface Wear Behavior of Nanograined NbMoTaW Refractory High‑Entropy Alloys via Nano‑scratching Simulations
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作者 Meisa Zhou Kun‑Ming Pan +3 位作者 Xiao‑Ye Zhou Shulong Ye Shaojie Du Hong‑Hui Wu 《Acta Metallurgica Sinica(English Letters)》 2025年第6期946-960,共15页
Surface nanocrystallization is a practical approach to enhance surface wear resistance,whereas the specific mechanism of how surface nanocrystallization affects the wear resistance of NbMoTaW refractory high-entropy a... Surface nanocrystallization is a practical approach to enhance surface wear resistance,whereas the specific mechanism of how surface nanocrystallization affects the wear resistance of NbMoTaW refractory high-entropy alloys(RHEAs)remains unclear.Herein,we performed molecular dynamics simulations to explore the wear behaviors of nanograined NbMoTaW RHEA during surface scratching.The wear resistance of nanograined models was significantly enhanced compared to the single-crystalline counterpart.As the grain size increases,the dominant plastic deformation mechanism switches from grain boundary deformation to dislocation movement.Notably,the model with a grain size of 20 nm exhibits the highest dislocation density,local stress,and degree of work hardening.At elevated temperatures,the dynamic recrystallization becomes a crucial plastic deformation mechanism and hinders the formation of dislocations,resulting in a decrease in dislocation density and consequently a decline in the wear resistance of NbMoTaW RHEAs.The current study provides insight into the mechanism underlying the enhanced wear resistance of NbMoTaW RHEAs. 展开更多
关键词 Refractory high-entropy alloys Surface nanocrystallization Molecular dynamics simulations Wear resistance
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