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A molecular dynamics study on mechanical performance and deformation mechanisms in nanotwinned NiCo-based alloys with nano-precipitates under high temperatures
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作者 Zihao Yu Hongyu Wang +2 位作者 Ligang Sun Zhihui Li Linli Zhu 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第11期349-355,共7页
Molecular dynamics simulations are performed to investigate the mechanical behavior of nanotwinned NiCo-based alloys containing coherent L12 nano-precipitates at different temperatures,as well as the interactions betw... Molecular dynamics simulations are performed to investigate the mechanical behavior of nanotwinned NiCo-based alloys containing coherent L12 nano-precipitates at different temperatures,as well as the interactions between the dislocations and nano-precipitates within the nanotwins.The simulation results demonstrate that both the yield stress and flow stress in the nanotwinned NiCo-based alloys with nano-precipitates decrease as the temperature rises,because the higher temperatures lead to the generation of more defects during yielding and lower dislocation density during plastic deformation.Moreover,the coherent L12 phase exhibits excellent thermal stability,which enables the hinderance of dislocation motion at elevated temperatures via the wrapping and cutting mechanisms of dislocations.The synergistic effect of nanotwins and nano-precipitates results in more significant strengthening behavior in the nanotwinned NiCo-based alloys under high temperatures.In addition,the high-temperature mechanical behavior of nanotwinned NiCo-based alloys with nano-precipitates is sensitive to the size and volume fraction of the microstructures.These findings could be helpful for the design of nanotwins and nano-precipitates to improve the high-temperature mechanical properties of NiCo-based alloys. 展开更多
关键词 NiCo-based alloys high temperature nano-precipitate NANOTWINS molecular dynamics simulation mechanical behavior deformation mechanism dislocations
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Unravelling biotoxicity of graphdiyne:Molecular dynamics simulation of the interaction between villin headpiece protein and graphdiyne
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作者 Bei-Wei Zhang Bing-Quan Zhang +1 位作者 Zhi-Gang Shao Xianqiu Wu 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第11期441-447,共7页
Recently,there has been a growing prevalence in the utilization of graphdiyne(GDY)in the field of biomedicine,attributed to its distinctive physical structure and chemical properties.Additionally,its biocompatibility ... Recently,there has been a growing prevalence in the utilization of graphdiyne(GDY)in the field of biomedicine,attributed to its distinctive physical structure and chemical properties.Additionally,its biocompatibility has garnered increasing attention.However,there is a lack of research on the biological effects and physical mechanisms of GDYprotein interactions at the molecular scale.In this study,the villin headpiece subdomain(HP35)served as a representative protein model.Molecular dynamics simulations were employed to investigate the interaction process between the HP35 protein and GDY,as well as the structural evolution of the protein.The data presented in our study demonstrate that GDY can rapidly adsorb HP35 protein and induce denaturation to one of the a-helix structures of HP35 protein.This implies a potential cytotoxicity concern of GDY for biological systems.Compared to graphene,GDY induced less disruption to HP35 protein.This can be attributed to the presence of natural triangular vacancies in GDY,which prevents p–p stacking action and the limited interaction of GDY with HP35 protein is not conducive to the expansion of protein structures.These findings unveil the biological effects of GDY at the molecular level and provide valuable insights for the application of GDY in biomedicine. 展开更多
关键词 graphdiyne villin headpiece molecular dynamics simulation biotoxicity
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Molecular dynamics simulation of the flow mechanism of shear-thinning fluids in a microchannel
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作者 杨刚 郑庭 +1 位作者 程启昊 张会臣 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第4期516-525,共10页
Shear-thinning fluids have been widely used in microfluidic systems,but their internal flow mechanism is still unclear.Therefore,in this paper,molecular dynamics simulations are used to study the laminar flow of shear... Shear-thinning fluids have been widely used in microfluidic systems,but their internal flow mechanism is still unclear.Therefore,in this paper,molecular dynamics simulations are used to study the laminar flow of shear-thinning fluid in a microchannel.We validated the feasibility of our simulation method by evaluating the mean square displacement and Reynolds number of the solution layers.The results show that the change rule of the fluid system's velocity profile and interaction energy can reflect the shear-thinning characteristics of the fluids.The velocity profile resembles a top-hat shape,intensifying as the fluid's power law index decreases.The interaction energy between the wall and the fluid decreases gradually with increasing velocity,and a high concentration of non-Newtonian fluid reaches a plateau sooner.Moreover,the velocity profile of the fluid is related to the molecule number density distribution and their values are inversely proportional.By analyzing the radial distribution function,we found that the hydrogen bonds between solute and water molecules weaken with the increase in velocity.This observation offers an explanation for the shear-thinning phenomenon of the non-Newtonian flow from a micro perspective. 展开更多
关键词 molecular dynamics simulation non-Newtonian fluid MICROCHANNEL SHEAR-THINNING
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Electronic effects on radiation damage inα-iron:A molecular dynamics study
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作者 江林 李敏 +2 位作者 付宝勤 崔节超 侯氢 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期521-529,共9页
Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation dur... Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation during operation,thus,the problems associated with the safe operation of nuclear reactors have been put forward naturally.In this work,a molecular dynamics simulation approach combined with electronic effects is developed for investigating the primary radiation damage process inα-Fe.Specifically,the influence of electronic effects on the collision cascade in Fe is systematically evaluated based on two commonly used interatomic potentials for Fe.The simulation results reveal that both electronic stopping(ES)and electron-phonon coupling(EPC)can contribute to the decrease of the number of defects in the thermal spike phase.The application of ES reduces the number of residual defects after the cascade evolution,whereas EPC has a reverse effect.The introduction of electronic effects promotes the formation of the dispersive subcascade:ES significantly changes the geometry of the damaged region in the thermal spike phase,whereas EPC mainly reduces the extent of the damaged region.Furthermore,the incorporation of electronic effects effectively mitigates discrepancies in simulation outcomes when using different interatomic potentials. 展开更多
关键词 radiation damage electronic effects molecular dynamics simulation α-iron
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Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation
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作者 SUN Wenting HU Yangdong +5 位作者 ZHENG Jiahuan SUN Qichao Chen Xia DING Jiakun ZHANG Weitao WU Lianying 《Journal of Ocean University of China》 CAS CSCD 2024年第2期467-476,共10页
Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is... Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is proposed by using molecular dynamics simulation,and the relationship between ion-to-ion interaction and salt solubility in a simulated seawater water-salt system is investigated.By analyzing the variation of distance and contact time between ions in an electrolyte solution,from both spatial and temporal perspectives,new parameters were proposed to describe the interaction between ions:interaction distance(ID),and interaction time ratio(ITR).The best correlation between characteristic time ratio and solubility was found for a molar ratio of salt-to-water of 10:100 with a correlation coefficient of 0.96.For the same salt,a positive correlation was found between CTR and the molar ratio of salt and water.For type 1-1,type 2-1,type 1-2,and type 2-2 salts,the correlation coefficients between CTR and solubility were 0.93,0.96,0.92,and 0.98 for a salt-to-water molar ratio of 10:100,respectively.The solubility of multiple salts was predicted by simulations and compared with experimental values,yielding an average relative deviation of 12.4%.The new ion-interaction parameters offer significant advantages in describing strongly correlated and strongly hydrated electrolyte solutions. 展开更多
关键词 molecular dynamics simulation interaction distance interaction time rate electrolyte aqueous solutions SOLUBILITY
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Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects
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作者 Changlin Li Wei Yang +5 位作者 Qiang Gan Yajun Wang Lin Liang Wenbo Zhang Shuangfei Zhu Changgen Feng 《Defence Technology(防务技术)》 SCIE EI CAS CSCD 2024年第1期364-374,共11页
To investigate the effect of void defects on the shock response of hexanitrohexaazaisowurtzitane(CL-20)co-crystals,shock responses of CL-20 co-crystals with energetic materials ligands trinitrotoluene(TNT),1,3-dinitro... To investigate the effect of void defects on the shock response of hexanitrohexaazaisowurtzitane(CL-20)co-crystals,shock responses of CL-20 co-crystals with energetic materials ligands trinitrotoluene(TNT),1,3-dinitrobenzene(DNB),solvents ligands dimethyl carbonate(DMC) and gamma-butyrolactone(GBL)with void were simulated,using molecular dynamics method and reactive force field.It is found that the CL-20 co-crystals with void defects will form hot spots when impacted,significantly affecting the decomposition of molecules around the void.The degree of molecular fragmentation is relatively low under the reflection velocity of 2 km/s,and the main reactions are the formation of dimer and the shedding of nitro groups.The existence of voids reduces the safety of CL-20 co-crystals,which induced the sensitivity of energetic co-crystals CL-20/TNT and CL-20/DNB to increase more significantly.Detonation has occurred under the reflection velocity of 4 km/s,energetic co-crystals are easier to polymerize than solvent co-crystals,and are not obviously affected by voids.The results show that the energy of the wave decreases after sweeping over the void,which reduces the chemical reaction frequency downstream of the void and affects the detonation performance,especially the solvent co-crystals. 展开更多
关键词 CL-20 co-crystals Molecular dynamics simulation Reactive forcefield Impact response Hot spot Void defect
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Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation
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作者 LIU Ji ZHANG Shiyu +1 位作者 ZENG Yu DENG Yi 《食品科学》 EI CAS CSCD 北大核心 2024年第18期55-76,共22页
In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the re... In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes. 展开更多
关键词 staphylococcal enterotoxin B circular dichroism molecular dynamics simulations temperature-induced unfolding
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Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations
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作者 Xinyu Zhang Wenjie Xia +2 位作者 Yang Wang Liang Wang Xiaofeng Liu 《Computer Modeling in Engineering & Sciences》 SCIE EI 2024年第6期3047-3061,共15页
Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectil... Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectile impacts is thoroughly investigated using full-atomic molecular dynamics(MD)simulations.The study results show that the porous structure and density are key factors determining the mechanical response of GA under impact loading.Specifically,the impact-induced penetration of the projectile leads to the collapse of the pore structure,causing stretching and subsequent rupture of covalent bonds in graphene sheets.Moreover,the effects of temperature on the mechanical performance of GA have been proven to be minimal,thereby highlighting the mechanical stability of GA over a wide range of temperatures.Finally,the energy absorption density(EAD)and energy absorption efficiency(EAE)metrics are adopted to assess the energy absorption capacity of GA during projectile penetration.The research findings of this work demonstrate the significant potential of GA for energy absorption applications. 展开更多
关键词 Graphene aerogel molecular dynamics simulation impact response energy absorption
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Ab initio molecular dynamics simulation reveals the influence of entropy effect on Co@BEA zeolite-catalyzed dehydrogenation of ethane
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作者 Yumeng Fo Shaojia Song +8 位作者 Kun Yang Xiangyang Ji Luyuan Yang Liusai Huang Xinyu Chen Xueqiu Wu Jian Liu Zhen Zhao Weiyu Song 《Chinese Journal of Catalysis》 SCIE CAS CSCD 2024年第10期195-205,共11页
The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulati... The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures.AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased.Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction.The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels.We provided explanations consistent with the principles of thermodynamics and statistical physics.The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments. 展开更多
关键词 Ethane dehydrogenation C-H bond activation Ab initio molecular dynamics simulation ENTROPY Heterogeneous catalysis
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Micropillar compression using discrete dislocation dynamics and machine learning
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作者 Jin Tao Dean Wei +3 位作者 Junshi Yu Qianhua Kan Guozheng Kang Xu Zhang 《Theoretical & Applied Mechanics Letters》 CAS CSCD 2024年第1期39-47,共9页
Discrete dislocation dynamics(DDD)simulations reveal the evolution of dislocation structures and the interaction of dislocations.This study investigated the compression behavior of single-crystal copper micropillars u... Discrete dislocation dynamics(DDD)simulations reveal the evolution of dislocation structures and the interaction of dislocations.This study investigated the compression behavior of single-crystal copper micropillars using fewshot machine learning with data provided by DDD simulations.Two types of features are considered:external features comprising specimen size and loading orientation and internal features involving dislocation source length,Schmid factor,the orientation of the most easily activated dislocations and their distance from the free boundary.The yielding stress and stress-strain curves of single-crystal copper micropillar are predicted well by incorporating both external and internal features of the sample as separate or combined inputs.It is found that the machine learning accuracy predictions for single-crystal micropillar compression can be improved by incorporating easily activated dislocation features with external features.However,the effect of easily activated dislocation on yielding is less important compared to the effects of specimen size and Schmid factor which includes information of orientation but becomes more evident in small-sized micropillars.Overall,incorporating internal features,especially the information of most easily activated dislocations,improves predictive capabilities across diverse sample sizes and orientations. 展开更多
关键词 Discrete dislocation dynamics simulations Machine learning Size effects Orientation effects Microstructural features
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Molecular dynamics study of primary radiation damage in TiVTa concentrated solid-solution alloy
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作者 赵永鹏 豆艳坤 +4 位作者 贺新福 曹晗 王林枫 邓辉球 杨文 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期530-535,共6页
The primary radiation damage in pure V and TiVTa concentrated solid-solution alloy(CSA)was studied using a molecular dynamics method.We have performed displacement cascade simulations to explore the generation and evo... The primary radiation damage in pure V and TiVTa concentrated solid-solution alloy(CSA)was studied using a molecular dynamics method.We have performed displacement cascade simulations to explore the generation and evolution behavior of irradiation defects.The results demonstrate that the defect accumulation and agglomeration in TiVTa CSA are significantly suppressed compared to pure V.The peak value of Frenkel pairs during cascade collisions in TiVTa CSA is much higher than that in pure V due to the lower formation energy of point defects.Meanwhile,the longer lifetime of the thermal spike relaxation and slow energy dissipation capability of TiVTa CSA can facilitate the recombination of point defects.The defect agglomeration rate in TiVTa CSA is much lower due to the lower binding energy of interstitial clusters and reduced interstitial diffusivity.Furthermore,the occurrence probability of dislocation loops in TiVTa CSA is lower than that in pure V.The reduction in primary radiation damage may enhance the radiation resistance of TiVTa CSA,and the improved radiation tolerance is primarily attributed to the relaxation stage and long-term defect evolution rather than the ballistic stage.These results can provide fundamental insights into irradiation-induced defects evolution in refractory CSAs. 展开更多
关键词 concentrated solid-solution alloy primary radiation damage molecular dynamics simulation
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Molecular Dynamics Numerical Simulation of Adsorption Characteristics and Exploitation Limits in Shale Oil Microscopic Pore Spaces
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作者 Guochen Xu 《Fluid Dynamics & Materials Processing》 EI 2024年第8期1915-1924,共10页
Microscopic pore structure in continental shale oil reservoirs is characterized by small pore throats and complex micro-structures.The adsorption behavior of hydrocarbons on the pore walls exhibits unique physical and... Microscopic pore structure in continental shale oil reservoirs is characterized by small pore throats and complex micro-structures.The adsorption behavior of hydrocarbons on the pore walls exhibits unique physical and chemical properties.Therefore,studying the adsorption morphology of hydrocarbon components in nanometer-sized pores and clarifying the exploitation limits of shale oil at the microscopic level are of great practical significance for the efficient development of continental shale oil.In this study,molecular dynamics simulations were employed to investigate the adsorption characteristics of various single-component shale oils in inorganic quartz fissures,and the influence of pore size and shale oil hydrocarbon composition on the adsorption properties in the pores was analyzed.The results show that different molecules have different adsorption capacities in shale oil pores,with lighter hydrocarbon components(C6H14)exhibiting stronger adsorption abilities.For the same adsorbed molecule,the adsorption amount linearly increases with the increase in pore diameter,but larger pores contribute more to shale oil adsorption.In shale pores,the thickness of the adsorption layer formed by shale oil molecules ranges from 0.4 to 0.5 nm,which is similar to the width of alkane molecules.Shale oil in the adsorbed state that is difficult to be exploited is mainly concentrated in the first adsorption layer.Among them,the volume fraction of adsorbed shale oil in 6 nm shale pores is 40.8%,while the volume fraction of shale oil that is difficult to be exploited is 16.2%. 展开更多
关键词 Shale oil utilization limit micro adsorption molecular dynamics simulation
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Network pharmacology and molecular dynamics study of the effect of the Astragalus-Coptis drug pair on diabetic kidney disease
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作者 Mo-Yan Zhang Shu-Qin Zheng 《World Journal of Diabetes》 SCIE 2024年第7期1562-1588,共27页
BACKGROUND Diabetic kidney disease(DKD)is the primary cause of end-stage renal disease.The Astragalus-Coptis drug pair is frequently employed in the management of DKD.However,the precise molecular mechanism underlying... BACKGROUND Diabetic kidney disease(DKD)is the primary cause of end-stage renal disease.The Astragalus-Coptis drug pair is frequently employed in the management of DKD.However,the precise molecular mechanism underlying its therapeutic effect remains elusive.AIM To investigate the synergistic effects of multiple active ingredients in the Astragalus-Coptis drug pair on DKD through multiple targets and pathways.METHODS The ingredients of the Astragalus-Coptis drug pair were collected and screened using the TCMSP database and the SwissADME platform.The targets were predicted using the SwissTargetPrediction database,while the DKD differential gene expression analysis was obtained from the Gene Expression Omnibus database.DKD targets were acquired from the GeneCards,Online Mendelian Inheritance in Man database,and DisGeNET databases,with common targets identified through the Venny platform.The protein-protein interaction network and the“disease-active ingredient-target”network of the common targets were constructed utilizing the STRING database and Cytoscape software,followed by the analysis of the interaction relationships and further screening of key targets and core active ingredients.Gene Ontology(GO)function and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichments were performed using the DAVID database.The tissue and organ distributions of key targets were evaluated.PyMOL and AutoDock software validate the molecular docking between the core ingredients and key targets.Finally,molecular dynamics(MD)simulations were conducted to simulate the optimal complex formed by interactions between core ingredients and key target proteins.RESULTS A total of 27 active ingredients and 512 potential targets of the Astragalus-Coptis drug pair were identified.There were 273 common targets between DKD and the Astragalus-Coptis drug pair.Through protein-protein interaction network topology analysis,we identified 9 core active ingredients and 10 key targets.GO and KEGG pathway enrichment analyses revealed that Astragalus-Coptis drug pair treatment for DKD involves various biological processes,including protein phosphorylation,negative regulation of apoptosis,inflammatory response,and endoplasmic reticulum unfolded protein response.These pathways are mainly associated with the advanced glycation end products(AGE)-receptor for AGE products signaling pathway in diabetic complications,as well as the Lipid and atherosclerosis.Molecular docking and MD simulations demonstrated high affinity and stability between the core active ingredients and key targets.Notably,the quercetin-AKT serine/threonine kinase 1(AKT1)and quercetin-tumor necrosis factor(TNF)protein complexes exhibited exceptional stability.CONCLUSION This study demonstrated that DKD treatment with the Astragalus-Coptis drug pair involves multiple ingredients,targets,and signaling pathways.We propose a novel approach for investigating the molecular mechanism underlying the therapeutic effects of the Astragalus-Coptis drug pair on DKD.Furthermore,we suggest that quercetin is the most potent active ingredient and specifically targets AKT1 and TNF,providing a theoretical foundation for further exploration of pharmacologically active ingredients and elucidating their molecular mechanisms in DKD treatment. 展开更多
关键词 Astragalus membranaceus Coptis chinensis Franch Diabetic kidney disease Network pharmacology Molecular docking Molecular dynamics simulation
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Subpicosecond laser ablation behavior of a magnesium target and crater evolution:Molecular dynamics study and experimental validation
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作者 江国龙 周霞 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第7期613-622,共10页
The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.... The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly. 展开更多
关键词 laser-material interaction molecular dynamics(MD)simulation ablation crater morphology MAGNESIUM
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Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond
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作者 Wei Zhao Zongwei Xu +1 位作者 Pengfei Wang Hanyi Chen 《Nanotechnology and Precision Engineering》 EI CAS CSCD 2024年第3期71-78,共8页
Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition... Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition.However,there is a lack of studies of the yield of NV color centers at the atomic scale.In the molecular dynamics simulations described in this paper,NV color centers are pre-pared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing.The differences between the yields of NV color centers produced by implantation of carbon(C)and nitrogen(N)ions,respectively,are investigated.It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy.The effects of different pre-doping concentrations(400–1500 ppm)and implantation energies(1.0–3.0 keV)on the NV color center yield are analyzed,and it is shown that a pre-doping concentra-tion of 1000 ppm with 2 keV C-ion implantation can produce a 13%yield of NV color centers after 1600 K annealing for 7.4 ns.Finally,a brief comparison of the NV color center identification methods is presented,and it is found that the error rate of an analysis utiliz-ing the identify diamond structure coordination analysis method is reduced by about 7%compared with conventional identification+methods. 展开更多
关键词 NV color center Ion implantation Molecular dynamics(MD)simulation Yield enhancement
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Exploring the molecular mechanism of action of curcumin for the treatment of diabetic retinopathy,using network pharmacology,molecular docking,and molecular dynamics simulation
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作者 Yuan-Yuan Gan Yan-Mei Xu +4 位作者 Quan Shu Qi-Zhi Huang Tian-Long Zhou Ju-Fang Liu Wei Yu 《Integrative Medicine Discovery》 2024年第8期1-10,共10页
Background:Based on network pharmacology and molecular docking,the present study investigated the mechanism of curcumin(CUR)in diabetic retinopathy treatment.Methods:Based on the DisGeNET,Swiss TargetPrediction,GeneCa... Background:Based on network pharmacology and molecular docking,the present study investigated the mechanism of curcumin(CUR)in diabetic retinopathy treatment.Methods:Based on the DisGeNET,Swiss TargetPrediction,GeneCards,Online Mendelian Inheritance in Man,Gene Expression Omnibus,and Comparative Toxicogenomics Database,the intersection core targets of CUR and diabetic retinopathy were identified.The intersection target was imported into the STRING database to obtain the protein-protein interaction map.According to the Database for Annotation,Visualization and Integrated Discovery database,the intersected targets were enriched in Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes pathways.Then Cytoscape 3.9.1 is used to make the drug-target-disease-pathway network.The mechanism of CUR and diabetic retinopathy was further verified by molecular docking and molecular dynamics simulation.Results:There were 203 intersecting targets of CUR and diabetic retinopathy identified.1320 GO entries were enriched for GO functions,which were primarily involved in the composition of cells such as identical protein binding,protein binding,enzyme binding,etc.It was found that 175 pathways were enriched using Kyoto Encyclopedia of Genes and Genomes pathway enrichment methods,which were mainly included in the lipid and atherosclerosis,AGE-RAGE signaling pathway in diabetic complications,pathways in cancer,etc.In the molecular docking analysis,CUR was found to have a good ability to bind to the core targets of albumin,IL-1B,and IL-6.The binding of albumin to CUR was further verified by molecular dynamics simulation.Conclusion:As a result of this study,CUR may exert a role in the treatment of diabetic retinopathy through multi-target and multi-pathway regulation,which indicates a possible direction of future research. 展开更多
关键词 CURCUMIN diabetic retinopathy network pharmacology molecular docking molecular dynamics simulation
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Droplet Condensation and Transport Properties on Multiple Composite Surface:A Molecular Dynamics Study
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作者 Haowei Hu Qi Wang +3 位作者 Xinnuo Chen Qin Li Mu Du Dong Niu 《Frontiers in Heat and Mass Transfer》 EI 2024年第4期1245-1259,共15页
To investigate the microscopicmechanism underlying the influence of surface-chemical gradient on heat andmass recovery,a molecular dynamicsmodel including droplet condensation and transport process has been developed ... To investigate the microscopicmechanism underlying the influence of surface-chemical gradient on heat andmass recovery,a molecular dynamicsmodel including droplet condensation and transport process has been developed to examine heat and mass recovery performance.This work aimed at identify optimal conditions for enhancing heat and mass recovery through the combination of wettability gradient and nanopore transport.For comprehensive analysis,the structure in the simulation was categorized into three distinct groups:a homogeneous structure,a small wettability gradient,and a large wettability gradient.The homogeneous surface demonstrated low efficiency in heat and mass transfer,as evidenced by filmwise condensation.In contrast,the surface with a small wettability gradient experienced a transition from dropwise condensation to filmwise condensation,resulting in a gradual decrease in the efficiency of vapor heat and mass transfer.Only a large wettability gradient could achieve periodic and efficient dropwise condensation heat and mass transfer which was attributed to the rapid droplet coalescence and transport to the nanopore after condensing on the cold surface. 展开更多
关键词 Wettability gradients NANOPORE surface tension molecular dynamics simulation
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Insight of Natural Compounds Halimane Diterpenoids against Mycobacterium tuberculosis: Virtual Screening, DFT, Drug-Likeness, and Molecular Dynamics Approach
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作者 Laurent Gael Eyia Andiga Boris Davy Bekono +3 位作者 Désiré Mama Bikele Pie Pascal Onguéné Amoa Luc Calvin Owono Owono Luc Léonard Mbaze Meva’a 《Computational Molecular Bioscience》 2024年第2期35-58,共24页
In the purpose to design novel antituberculosis (anti-TB) drugs agents against Mycobacterium tuberculosis (Mtb), we have built a molecular library around 42 Halimane Diterpenoids isolated from natural sources. Two Mtb... In the purpose to design novel antituberculosis (anti-TB) drugs agents against Mycobacterium tuberculosis (Mtb), we have built a molecular library around 42 Halimane Diterpenoids isolated from natural sources. Two Mtb enzymes drug targets (Mtb Mycothiol S-transferase and Mtb Homoserine transacetylase) have been adopted. The pharmacological potential was investigated through molecular docking, molecular dynamics simulation, density functional theory (gas phase and water) and ADMET analysis. Our results indicate that (2R,5R,6S)-1,2,3,4,5,6,7,8-octahydro-5-((E)-5-hydroxy-3-methylpent-3-enyl)-1,1,5,6-tetramethylnaphtha-lene-2-ol (compound 20) has displays higher docking score with each of the selected drug targets. In addition, this molecule exhibits a satisfactory drug potential activity and a good chemical reactivity. Its improved kinetic stability in the Mtb Mycothiol S-transferase enzyme reflects its suitability as a novel inhibitor of Mtb growth. This molecule has displayed a good absorption potential. Our results also show that its passive passage of the intestinal permeability barrier is more effective than that of first-line treatments (ethambutol, isoniazid). In the same way, this anti-TB druglikeness has shown to be able to cross the blood brain barrier. 展开更多
关键词 Antituberculosis Druglikeness Density Functional Theory Halimane Diterpenoids Molecular Docking Molecular dynamics Simulation
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Anti-sintering behavior and combustion process of aluminum nano particles coated with PTFE:A molecular dynamics study 被引量:4
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作者 Jun-peng Liu Hao-rui Zhang Qi-Long Yan 《Defence Technology(防务技术)》 SCIE EI CAS CSCD 2023年第6期46-57,共12页
The characteristic of easy sintering of aluminum nanoparticle(ANP)limits its application in solid propellants.Coating ANP with fluoropolymer could effectively improve its combustion performance.To find out how the coa... The characteristic of easy sintering of aluminum nanoparticle(ANP)limits its application in solid propellants.Coating ANP with fluoropolymer could effectively improve its combustion performance.To find out how the coating layer inhibits sintering and promotes complete combustion of particles from an atomic view,a comparative study has been done for bare ANP and PTFE coated ANP by using reactive molecular dynamics simulations.The sintering process is quantified by shrinkage ratio and gyration radius.Our results show that,at the same heating rate and combustion temperatures,bare ANPs are sintered together after the temperature exceeds the melting point of aluminum but the decomposition of PTFE coating layer pushes particles away and increases reaction surface area by producing small Al-F clusters.The sintering of ANPs which are heated in PTFE is alleviated compared with particles heated in oxygen,but particles still sinter together due to the lack of intimate contact between PTFE and alumina surface.The effect of temperature on the combustion of PTFE coated ANPs is also studied from 1000 to3500 K.The number density analysis shows the particles will not be sintered at any temperature.Aluminum fluoride prefers diffusing to the external space and the remained particles are mainly composed of Al,C and O.Fast ignition simulations are performed by adopting micro canonical ensemble.With the expansion of aluminum core and the melting of alumina shell,bare ANPs are sintered into a liquid particle directly.For PTFE coated ANPs,the volatilization of gaseous aluminum fluoride products continually endows particles opposite momentum. 展开更多
关键词 Aluminum nanoparticle SINTERING Combustion Molecular dynamics simulation
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Molecular dynamics study of interactions between edge dislocation and irradiation-induced defects in Fe–10Ni–20Cr alloy 被引量:1
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作者 熊涛文 陈小平 +5 位作者 林也平 贺新福 杨文 胡望宇 高飞 邓辉球 《Chinese Physics B》 SCIE EI CAS CSCD 2023年第2期80-86,共7页
Irradiation-induced defects frequently impede the slip of dislocations, resulting in a sharp decline in the performance of nuclear reactor structural materials, particularly core structural materials. In the present w... Irradiation-induced defects frequently impede the slip of dislocations, resulting in a sharp decline in the performance of nuclear reactor structural materials, particularly core structural materials. In the present work, molecular dynamics method is used to investigate the interactions between edge dislocations and three typical irradiation-induced defects(void,Frank loop, and stacking fault tetrahedron) with the sizes of 3 nm, 5 nm, and 7 nm at different temperatures in Fe–10Ni–20Cr alloy. The critical resolved shear stresses(CRSSs) are compared among different defect types after interacting with edge dislocations. The results show that the CRSS decreases with temperature increasing and defect size decreasing for each defect type during the interaction with edge dislocations, except for the case of 3-nm Frank loops at 900 K. According to a comparison, the CRSS in Frank loop is significantly higher than that of others of the same size, which is due to the occurrence of unfaulting and formation of superjog or stacking-fault complex during the interaction. The atomic evolution of irradiation-induced defects after interacting with dislocations can provide a novel insight into the design of new structural materials. 展开更多
关键词 molecular dynamics simulation edge dislocation irradiation-induced defects austenitic stainless steel
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