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Analysis of CH_(4) and H_(2) Adsorption on Heterogeneous Shale Surfaces Using aMolecular Dynamics Approach 被引量:1
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作者 Surajudeen Sikiru Hassan Soleimani +2 位作者 Amir Rostami Mohammed Falalu Hamza Lukmon Owolabi Afolabi 《Fluid Dynamics & Materials Processing》 EI 2024年第1期31-44,共14页
Determining the adsorption of shale gas on complex surfaces remains a challenge in molecular simulation studies.Difficulties essentially stem from the need to create a realistic shale structure model in terms of miner... Determining the adsorption of shale gas on complex surfaces remains a challenge in molecular simulation studies.Difficulties essentially stem from the need to create a realistic shale structure model in terms of mineral heterogeneityand multiplicity.Moreover,precise characterization of the competitive adsorption of hydrogen andmethane in shale generally requires the experimental determination of the related adsorptive capacity.In thisstudy,the adsorption of adsorbates,methane(CH_(4)),and hydrogen(H_(2))on heterogeneous shale surface modelsof Kaolinite,Orthoclase,Muscovite,Mica,C_(60),and Butane has been simulated in the frame of a moleculardynamic’s numerical technique.The results show that these behaviors are influenced by pressure and potentialenergy.On increasing the pressure from 500 to 2000 psi,the sorption effect for CH_(4)significantly increasesbut shows a decline at a certain stage(if compared to H_(2)).The research findings also indicate that raw shalehas a higher capacity to adsorb CH_(4)compared to hydrogen.However,in shale,this difference is negligible. 展开更多
关键词 Shale gas ADSORPTION METHANE hydrogen molecular dynamic SORPTION
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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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Ab initio nonadiabatic molecular dynamics study on spin–orbit coupling induced spin dynamics in ferromagnetic metals
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作者 朱万松 郑镇法 +1 位作者 郑奇靖 赵瑾 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第1期156-163,共8页
Understanding the photoexcitation induced spin dynamics in ferromagnetic metals is important for the design of photo-controlled ultrafast spintronic device.In this work,by the ab initio nonadiabatic molecular dynamics... Understanding the photoexcitation induced spin dynamics in ferromagnetic metals is important for the design of photo-controlled ultrafast spintronic device.In this work,by the ab initio nonadiabatic molecular dynamics simulation,we have studied the spin dynamics induced by spin–orbit coupling(SOC)in Co and Fe using both spin-diabatic and spin-adiabatic representations.In Co system,it is found that the Fermi surface(E_(F))is predominantly contributed by the spin-minority states.The SOC induced spin flip will occur for the photo-excited spin-majority electrons as they relax to the E_(F),and the spin-minority electrons tend to relax to the EFwith the same spin through the electron–phonon coupling(EPC).The reduction of spin-majority electrons and the increase of spin-minority electrons lead to demagnetization of Co within100 fs.By contrast,in Fe system,the E_(F) is dominated by the spin-majority states.In this case,the SOC induced spin flip occurs for the photo-excited spin-minority electrons,which leads to a magnetization enhancement.If we move the E_(F) of Fe to higher energy by 0.6eV,the E_(F) will be contributed by the spin-minority states and the demagnetization will be observed again.This work provides a new perspective for understanding the SOC induced spin dynamics mechanism in magnetic metal systems. 展开更多
关键词 nonadiabatic molecular dynamics spin dynamics spin–orbit coupling ferromagnetic metal
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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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Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer
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作者 徐耀 黄舒伟 +1 位作者 丁泓铭 马余强 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第2期512-521,共10页
Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,... Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers. 展开更多
关键词 RNA DNA lipid bilayer molecular dynamics interface interaction divalent cation
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The chemical environment and structural ordering in liquid Mg-Y-Zn system:An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure
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作者 Tangpeng Ma Jin Wang +5 位作者 Kaiming Cheng Chengwei Zhan Jixue Zhou Jingyu Qin Guochen Zhao Xinfang Zhang 《Journal of Magnesium and Alloys》 SCIE EI CAS CSCD 2024年第2期815-824,共10页
In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular... In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation.In liquid Mg-rich Mg-Y alloys,the strong Mg-Y interaction is determined,which promotes the formation of fivefold symmetric local structure.For Mg-Zn alloys,the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure.Due to the coexistence of Y and Zn,the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy,and contributes to the clustering of Mg,Y,Zn launched from Zn.What is more,the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys.These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure,which provides a new insight into the formation mechanism of LPSO structure at atomic level. 展开更多
关键词 Mg-Y-Zn Chemical environment Structural ordering ab-initio molecular dynamics
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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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Machine learning molecular dynamics simulations of liquid methanol
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作者 Jie Qian Junfan Xia Bin Jiang 《中国科学技术大学学报》 CAS CSCD 北大核心 2024年第6期12-21,I0009,I0010,共12页
As the simplest hydrogen-bonded alcohol,liquid methanol has attracted intensive experimental and theoretical interest.However,theoretical investigations on this system have primarily relied on empirical intermolecular... As the simplest hydrogen-bonded alcohol,liquid methanol has attracted intensive experimental and theoretical interest.However,theoretical investigations on this system have primarily relied on empirical intermolecular force fields or ab initio molecular dynamics with semilocal density functionals.Inspired by recent studies on bulk water using increasingly accurate machine learning force fields,we report a new machine learning force field for liquid methanol with a hybrid functional revPBE0 plus dispersion correction.Molecular dynamics simulations on this machine learning force field are orders of magnitude faster than ab initio molecular dynamics simulations,yielding the radial distribution functions,selfdiffusion coefficients,and hydrogen bond network properties with very small statistical errors.The resulting structural and dynamical properties are compared well with the experimental data,demonstrating the superior accuracy of this machine learning force field.This work represents a successful step toward a first-principles description of this benchmark system and showcases the general applicability of the machine learning force field in studying liquid systems. 展开更多
关键词 liquid methanol molecular dynamics machine learning hydrogen bond force field
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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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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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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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Probing the electric double layer structure at nitrogen-doped graphite electrodes by constant-potential molecular dynamics simulations
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作者 Legeng Yu Nan Yao +5 位作者 Yu-Chen Gao Zhong-Heng Fu Bo Jiang Ruiping Li Cheng Tang Xiang Chen 《Journal of Energy Chemistry》 SCIE EI CAS CSCD 2024年第6期299-305,I0008,共8页
Electric double layer(EDL)is a critical topic in electrochemistry and largely determines the working performance of lithium batteries.However,atomic insights into the EDL structures on heteroatom-modified graphite ano... Electric double layer(EDL)is a critical topic in electrochemistry and largely determines the working performance of lithium batteries.However,atomic insights into the EDL structures on heteroatom-modified graphite anodes and EDL evolution with electrode potential are very lacking.Herein,a constant-potential molecular dynamics(CPMD)method is proposed to probe the EDL structure under working conditions,taking N-doped graphite electrodes and carbonate electrolytes as an example.An interface model was developed,incorporating the electrode potential and atom electronegativities.As a result,an insightful atomic scenario for the EDL structure under varied electrode potentials has been established,which unveils the important role of doping sites in regulating both the EDL structures and the following electrochemical reactions at the atomic level.Specifically,the negatively charged N atoms repel the anions and adsorb Li~+at high and low potentials,respectively.Such preferential adsorption suggests that Ndoped graphite can promote Li~+desolvation and regulate the location of Li~+deposition.This CPMD method not only unveils the mysterious function of N-doping from the viewpoint of EDL at the atomic level but also applies to probe the interfacial structure on other complicated electrodes. 展开更多
关键词 Lithium batteries Graphite N-DOPING Electric double layer molecular dynamics Constant potential method Electrode potential
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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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Improvement Mechanism of Adhesion Performance of Anti-stripping Agents and Coupling Agents on Asphalt-Aggregate Interface Based on Molecular Dynamics
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作者 SONG Jing XIE Jianguang DAI Zexinyu 《Transactions of Nanjing University of Aeronautics and Astronautics》 EI CSCD 2024年第S01期111-120,共10页
This study examined the mechanisms for improving the adhesion performance of the asphalt-aggregate interface with two anti-stripping agents and two coupling agents.The investigation of contact behavior between various... This study examined the mechanisms for improving the adhesion performance of the asphalt-aggregate interface with two anti-stripping agents and two coupling agents.The investigation of contact behavior between various asphalt-aggregate surfaces was conducted using molecular dynamics(MD)simulations.The interaction energy and the relative concentration distribution were employed as the parameters to analyze the enhancement mechanisms of anti-stripping agents and coupling agents on the asphalt-aggregate interface.Results indicated that the adhesion at the asphalt-aggregate interface could be strengthened by both anti-stripping agents and coupling agents.Anti-stripping agents primarily improve adhesion through the reinforcement of electrostatic attraction,while coupling agents primarily upgrade adhesion by strengthening the van der Waals.Hence,the molecular dynamics modeling and calculation techniques presented in this study can be utilized to elucidate the development mechanism of the asphalt-aggregate interface through the use of anti-stripping agents and coupling agents. 展开更多
关键词 asphalt-aggregate interface adhesion performance anti-stripping agents coupling agents molecular dynamics
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Comparative study of nudged elastic band and molecular dynamics methods for diffusion kinetics in solid-state electrolytes
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作者 林啊鸣 石晶 +1 位作者 魏苏淮 孙宜阳 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第8期96-100,共5页
Considerable efforts are being made to transition current lithium-ion and sodium-ion batteries towards the use of solid-state electrolytes.Computational methods,specifically nudged elastic band(NEB)and molecular dynam... Considerable efforts are being made to transition current lithium-ion and sodium-ion batteries towards the use of solid-state electrolytes.Computational methods,specifically nudged elastic band(NEB)and molecular dynamics(MD)methods,provide powerful tools for the design of solid-state electrolytes.The MD method is usually the choice for studying the materials involving complex multiple diffusion paths or having disordered structures.However,it relies on simulations at temperatures much higher than working temperature.This paper studies the reliability of the MD method using the system of Na diffusion in MgO as a benchmark.We carefully study the convergence behavior of the MD method and demonstrate that total effective simulation time of 12 ns can converge the calculated diffusion barrier to about 0.01 eV.The calculated diffusion barrier is 0.31 eV from both methods.The diffusion coefficients at room temperature are 4.3×10^(-9) cm^(2)⋅s^(−1) and 2.2×10^(-9) cm^(2)⋅s^(−1),respectively,from the NEB and MD methods.Our results justify the reliability of the MD method,even though high temperature simulations have to be employed to overcome the limitation on simulation time. 展开更多
关键词 nudged elastic band method molecular dynamics solid electrolyte ion transport density func-tional theory
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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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Revealing Al-O/Al-F reaction dynamic effects on the combustion of aluminum nanoparticles in oxygen/fluorine containing environments:A reactive molecular dynamics study meshing together experimental validation
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作者 Gang Li Chuande Zhao +2 位作者 Qian Yu Fang Yang Jie Chen 《Defence Technology(防务技术)》 SCIE EI CAS CSCD 2024年第4期313-327,共15页
Improving the energy conversion efficiency in metallic fuel(e.g.,Al)combustion is always desirable but challenging,which often involves redox reactions of aluminum(Al)with various mixed oxidizing environments.For inst... Improving the energy conversion efficiency in metallic fuel(e.g.,Al)combustion is always desirable but challenging,which often involves redox reactions of aluminum(Al)with various mixed oxidizing environments.For instance,Al-O reaction is the most common pathway to release limited energy while Al-F reaction has received much attentions to enhance Al combustion efficiency.However,microscopic understanding of the Al-O/Al-F reaction dynamics remains unsolved,which is fundamentally necessary to further improve Al combustion efficiency.In this work,for the first time,Al-O/Al-F reaction dynamic effects on the combustion of aluminum nanoparticles(n-Al)in oxygen/fluorine containing environments have been revealed via reactive molecular dynamics(RMD)simulations meshing together combustion experiments.Three RMD simulation systems of Al core/O_(2)/HF,n-Al/O_(2)/HF,and n-Al/O_(2)/CF4 with oxygen percentage ranging from 0%to 100%have been performed.The n-Al combustion in mixed O_(2)/CF_4 environments have been conducted by constant volume combustion experiments.RMD results show that Al-O reaction exhibits kinetic benefits while Al-F reaction owns thermodynamic benefits for n-Al combustion.In n-Al/O_(2)/HF,Al-O reaction gives faster energy release rate than Al-F reaction(1.1 times).The optimal energy release efficiency can be achieved with suitable oxygen percentage of 10%and 50%for n-Al/O_(2)/HF and n-Al/O_(2)/CF_4,respectively.In combustion experiments,90%of oxygen percentage can optimally enhance the peak pressure,pressurization rate and combustion heat.Importantly,Al-O reaction prefers to occur on the surface regions while Al-F reaction prefers to proceed in the interior regions of n-Al,confirming the kinetic/thermodynamic benefits of Al-O/Al-F reactions.The synergistic effect of Al-O/Al-F reaction for greatly enhancing n-Al combustion efficiency is demonstrated at atomicscale,which is beneficial for optimizing the combustion performance of metallic fuel. 展开更多
关键词 Al-O/Al—F reaction Kinetic benefits Thermodynamic benefits molecular dynamics COMBUSTION
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Study on the Mechanism of Nanopatterning in Printed Electronics Based on Molecular Dynamics Simulation
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作者 HUANG Hai-yang LI Yan ZHANG Run-liang 《印刷与数字媒体技术研究》 CAS 北大核心 2024年第4期237-244,共8页
In order to research the feasibility of using the selective adsorption principle to achieve automatic shaping of nano patterns,in this study,using the liquid gallium as the conductive ink and graphene as the printing ... In order to research the feasibility of using the selective adsorption principle to achieve automatic shaping of nano patterns,in this study,using the liquid gallium as the conductive ink and graphene as the printing plate surface,by changing the surface wettability of patterned areas on the nanoscale of graphene printed boards,the automatic formation of liquid gallium patterns on the graphene printed plate surface was simulated.The results indicated that liquid gallium can achieve automatic patterning on the surface of graphene patterned areas;the greater the interaction energy between gallium and carbon atoms,the clearer the pattern;gallium liquid is prone to remain in complex local positions of the pattern,making it difficult to shape the pattern;if the spacing between adjacent pattern lines is too large or too small,it will result in residual gallium liquid between the lines;increasing the thickness of the gallium film will cause the pattern to expand beyond the boundary,but increasing the thickness of the gallium film can also enhance the thickness and uniformity of the pattern lines.In summary,the principle of selective adsorption can be used to achieve the automatic formation of nano patterns,and the pattern formation effect is influenced by factors such as atomic interaction energy and pattern configuration. 展开更多
关键词 molecular dynamics Liquid gallium GRAPHENE Pattern forming
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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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