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Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations 被引量:1
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作者 Song Hu C Y Zhao Xiaokun Gu 《Chinese Physics B》 SCIE EI CAS CSCD 2022年第5期561-568,共8页
The knowledge of interfacial thermal conductance(ITC)is key to understand thermal transport in nanostructures.The non-equilibrium molecular dynamics(NEMD)simulation is a useful tool to calculate the ITC.In this study,... The knowledge of interfacial thermal conductance(ITC)is key to understand thermal transport in nanostructures.The non-equilibrium molecular dynamics(NEMD)simulation is a useful tool to calculate the ITC.In this study,we investigate the impact of thermostat on the prediction of the ITC.The Langevin thermostat is found to result in larger ITC than the Nose-Hoover thermostat.In addition,the results from NEMD simulations with the Nose-Hoover thermostat exhibit strong size effect of thermal reservoirs.Detailed spectral heat flux decomposition and modal temperature calculation reveal that the acoustic phonons in hot and cold thermal reservoirs are of smaller temperature difference than optical phonons when using the Nose-Hoover thermostat,while phonons in the Langevin thermostat are of identical temperatures.Such a nonequilibrium state of phonons in the case of the Nose-Hoover thermostat reduces the heat flux of low-to-middle-frequency phonons.We also discuss how enlarging the reservoirs or adding an epitaxial rough wall to the reservoirs affects the predicted ITC,and find that these attempts could help to thermalize the phonons,but still underestimate the heat flux from low-frequency phonons. 展开更多
关键词 interfacial thermal conductance phonon transport molecular dynamics
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A non-equilibrium molecular dynamics study of the thermal conductivity of uranium dioxide
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作者 WANG Zenghui HUANG Xiaofeng 《Nuclear Science and Techniques》 SCIE CAS CSCD 2010年第1期39-43,共5页
The thermal conductivity of uranium dioxide in the temperature range of 300–2400 K was estimated by non-equilibrium molecular dynamics calculation using Fourier law.The Kawamura function was adopted as the interatomi... The thermal conductivity of uranium dioxide in the temperature range of 300–2400 K was estimated by non-equilibrium molecular dynamics calculation using Fourier law.The Kawamura function was adopted as the interatomic potential function.The calculated thermal conductivities are found to be strongly dependent on the temperature of the simulation cube.The thermal conductivity simulation results are compared with the experiment results and agreed well with the experimental results when the temperature is above 600 K.The thermal conductivities scale effects are found to be existed in uranium dioxide nanometer thin film.The approximate mean free paths of phonons in different temperatures can be examined. 展开更多
关键词 非平衡分子动力学 二氧化铀 热导率 模拟计算 温度范围 温度依赖性 傅里叶法 仿真结果
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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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Elastic-plastic behavior of nickel-based single crystal superalloys with γ-γ′phases based on molecular dynamics simulations
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作者 Jing-Zhao Cao Yun-Guang Zhang +3 位作者 Zhong-Kui Zhang Jiang-Peng Fan Qi Dong Ying-Ying Fang 《Chinese Physics B》 2025年第4期510-521,共12页
The effects of temperature and Re content on the mechanical properties,dislocation morphology,and deformation mechanism of γ-γ′phases nickel-based single crystal superalloys are investigated by using the molecular ... The effects of temperature and Re content on the mechanical properties,dislocation morphology,and deformation mechanism of γ-γ′phases nickel-based single crystal superalloys are investigated by using the molecular dynamics method through the model of γ-γ′phases containing hole defect.The addition of Re makes the dislocation distribution tend towards the γ phase.The higher the Re content,the earlier theγphase yields,while the γ′phase yields later.Dislocation bends under the combined action of the applied force and the resistance of the Re atoms to form a bend point.The Re atoms are located at the bend points and strengthen the alloy by fixing the dislocation and preventing it from cutting the γ′phase.Dislocations nucleate first in the γ phase,causing theγphase to deform plastically before the γ′phase.As the strain increases,the dislocation length first remains unchanged,then increases rapidly,and finally fluctuates and changes.The dislocation lengths in the γ phase are larger than those in the γ′phase at different temperatures.The dislocation length shows a decreasing tendency with the increase of the temperature.Temperature can affect movement of the dislocation,and superalloys have different plastic deformation mechanisms at low,medium and high temperatures. 展开更多
关键词 nickel-based single crystal superalloys elastic-plastic behavior dislocations molecular dynamics simulation
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Plastic deformation mechanism of γ-phase U–Mo alloy studied by molecular dynamics simulations
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作者 Chang Wang Peng Peng Wen-Sheng Lai 《Chinese Physics B》 2025年第1期468-475,共8页
Uranium–molybdenum(U–Mo) alloys are critical for nuclear power generation and propulsion because of their superior thermal conductivity, irradiation stability, and anti-swelling properties. This study explores the p... Uranium–molybdenum(U–Mo) alloys are critical for nuclear power generation and propulsion because of their superior thermal conductivity, irradiation stability, and anti-swelling properties. This study explores the plastic deformation mechanisms of γ-phase U–Mo alloys using molecular dynamics(MD) simulations. In the slip model, the generalized stacking fault energy(GSFE) and the modified Peierls–Nabarro(P–N) model are used to determine the competitive relationships among different slip systems. In the twinning model, the generalized plane fault energy(GPFE) is assessed to evaluate the competition between slip and twinning. The findings reveal that among the three slip systems, the {110}<111>slip system is preferentially activated, while in the {112}<111> system, twinning is favored over slip, as confirmed by MD tensile simulations conducted in various directions. Additionally, the impact of Mo content on deformation behavior is emphasized. Insights are provided for optimizing process conditions to avoid γ → α′′ transitions, thereby maintaining a higher proportion of γ-phase U–Mo alloys for practical applications. 展开更多
关键词 U-Mo alloy molecular dynamics simulation plastic deformation mechanism dislocation slip twin formation
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Molecular dynamics evaluation of self-diffusion coefficients in two-dimensional dusty plasmas
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作者 Muhammad Asif Shakoori Misbah Khan +3 位作者 Haipeng Li Aamir Shahzad Maogang He Syed Ali Raza 《Chinese Physics B》 2025年第4期457-466,共10页
We employ the Green–Kubo(G-K)and Einstein relations to estimate the self-diffusion coefficients(denoted as D_(G)and D_(E),respectively)in two-dimensional(2D)strongly coupled dusty plasmas(SC-DPs)via equilibrium molec... We employ the Green–Kubo(G-K)and Einstein relations to estimate the self-diffusion coefficients(denoted as D_(G)and D_(E),respectively)in two-dimensional(2D)strongly coupled dusty plasmas(SC-DPs)via equilibrium molecular dynamics(EMD)simulations.D_(G)and D_(E)are computed for a broad domain of screening length(κ)and coupling parameters(Г)along with different system sizes.It is observed that both D_(G)and D_(E)decrease linearly with increasing G in warm liquid states and increase with increasingκ.In cold liquid states,the Einstein relation accurately predicts D_(E)in 2D SC-DPs because diffusion motion is close to normal diffusion,but the G-K relation provides overestimations of D_(G),because VACF indicates anomalous diffusion;thus,D_(G)is not accurate.Our new simulation outcomes reveal that D_(G)and D_(E)remain independent of system sizes.Furthermore,our investigations demonstrate that at higher temperatures,D_(G)and D_(E)converge,suggesting diffusion motion close to normal diffusion,while at lower temperatures,these two values diverge.We find reasonable agreement by comparing current and existing numerical,theoretical and experimental data.Moreover,when normalizing diffusion coefficients by the Einstein frequency and testing against the universal temperature scaling law,D_(G)deviates from theoretical curves at low temperatures and k,whereas D_(E)only disagrees with theory at very smallκ(■0.10).These findings provide valuable insight into diagnosing dust component parameters within 2D DP systems and contribute to the broader understanding of diffusion processes in DP environments. 展开更多
关键词 dusty(complex)plasmas self-diffusion coefficients molecular dynamics simulation Green-Kubo and Einstein relations
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Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation 被引量:1
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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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Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects 被引量:1
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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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Effect of TiB_(2) Nanoparticles on Microstructure and Mechanical Properties of Ni_(60)Cr_(21)Fe_(19) Alloy in Rapid Directional Solidification Process:Molecular Dynamics Study 被引量:1
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作者 WANG Jin JIANG Wugui HU Chenxi 《Transactions of Nanjing University of Aeronautics and Astronautics》 EI CSCD 2024年第5期575-588,共14页
Molecular dynamics(MD)simulations are employed to delve into the multifaceted effects of TiB_(2) nanoparticles on the intricate grain refinement mechanism,microstructural evolution,and tensile performance of Inconel 7... Molecular dynamics(MD)simulations are employed to delve into the multifaceted effects of TiB_(2) nanoparticles on the intricate grain refinement mechanism,microstructural evolution,and tensile performance of Inconel 718 superalloys during the rapid directional solidification.Specifically,the study focuses on elucidating the role of TiB2 nanoparticles in augmenting the nucleation rate during the rapid directional solidification process of Ni_(60)Cr_(21)Fe_(19) alloy system.Furthermore,subsequent tensile simulations are conducted to comprehensively evaluate the anisotropic behavior of tensile properties within the solidified microstructures.The MD results reveal that the incorporation of TiB₂nanoparticles during the rapid directional solidification of the Ni_(60)Cr_(21)Fe_(19) significantly enhances the average nucleation rate,escalating it from 1.27×10^(34)m^(-3)·s^(-1)to 2.55×10^(34)m^(-3)·s^(-1).Notably,within the face centered cube(FCC)structure,Ni atoms exhibit pronounced compositional segregation,and the solidified alloy maintains an exceptionally high dislocation density reaching up to 10^(16)m^(-2).Crucially,the rapid directional solidification process imparts a distinct microstructural anisotropy,leading to a notable disparity in tensile strength.Specifically,the tensile strength along the solidification direction is markedly superior to that perpendicular to it.This disparity arises from different deformation mechanisms under varying loading orientations.Tensile stress perpendicular to the solidification direction encourages the formation of smooth and organized mechanical twins.These twins act as slip planes,enhancing dislocation mobility and thereby improving stress relaxation and dispersion.Moreover,the results underscore the profound strengthening effect of TiB_(2) nanoparticles,particularly in enhancing the tensile strength along the rapid directional solidification direction. 展开更多
关键词 TiB_(2) nanoparticle rapid directional solidification microstructure evolution molecular dynamics
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Exploring superconductivity in dynamically stable carbon-boron clathrates trapping molecular hydrogen
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作者 Akinwumi Akinpelu Mangladeep Bhullar +1 位作者 Timothy A.Strobel Yansun Yao 《Chinese Physics B》 2025年第3期131-140,共10页
The recent discovery of type-Ⅶboron-carbon clathrates with calculated superconducting transition temperatures approaching~100 K has sparked interest in exploring new conventional superconductors that may be stabilize... The recent discovery of type-Ⅶboron-carbon clathrates with calculated superconducting transition temperatures approaching~100 K has sparked interest in exploring new conventional superconductors that may be stabilized at ambient pressure.The electronic structure of the clathrate is highly tunable based on the ability to substitute different metal atoms within the cages,which may also be large enough to host small molecules.Here we introduce molecular hydrogen(H_(2))within the clathrate cages and investigate its impact on electron-phonon coupling interactions and the superconducting transition temperature(T_(c)).Our approach involves combining molecular hydrogen with the new diamond-like covalent framework,resulting in a hydrogen-encapsulated clathrate,(H_(2))B_(3)C_(3).A notable characteristic of(H_(2))B_(3)C_(3)is the dynamic behavior of the H_(2)molecules,which exhibit nearly free rotations within the B-C cages,resulting in a dynamic structure that remains cubic on average.The static structure of(H_(2))B_(3)C_(3)(a snapshot in its dynamic trajectory)is calculated to be dynamically stable at ambient and low pressures.Topological analysis of the electron density reveals weak van der Waals interactions between molecular hydrogen and the B-C cages,marginally influencing the electronic structure of the material.The electron count and electronic structure calculations indicate that(H_(2))B_(3)C_(3)is a hole conductor,in which H_(2)molecules donate a portion of their valence electron density to the metallic cage framework.Electron-phonon coupling calculation using the Migdal-Eliashberg theory predicts that(H_(2))B_(3)C_(3)possesses a T_(c) of 46 K under ambient pressure.These results indicate potential for additional light-element substitutions within the type-Ⅶclathrate framework and suggest the possibility of molecular hydrogen as a new approach to optimizing the electronic structures of this new class of superconducting materials. 展开更多
关键词 SUPERCONDUCTIVITY electronic structure density functional theory molecular dynamics
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Probing the interaction between asphaltene-wax and its effects on the crystallization behavior of waxes in heavy oil via molecular dynamics simulation
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作者 Yong Hu Xi Lu +3 位作者 Hai-Bo Wang Ji-Chao Fang Yi-Ning Wu JianFang Sun 《Petroleum Science》 SCIE EI CAS CSCD 2024年第4期2839-2848,共10页
High content of asphaltenes and waxes leads to the high pour point and the poor flowability of heavy oil,which is adverse to its efficient development and its transportation in pipe.Understanding the interaction mecha... High content of asphaltenes and waxes leads to the high pour point and the poor flowability of heavy oil,which is adverse to its efficient development and its transportation in pipe.Understanding the interaction mechanism between asphaltene-wax is crucial to solve these problems,but it is still unclear.In this paper,molecular dynamics simulation was used to investigate the interaction between asphaltenewax and its effects on the crystallization behavior of waxes in heavy oil.Results show that molecules in pure wax are arranged in a paralleled geometry.But wax molecules in heavy oil,which are close to the surface of asphaltene aggregates,are bent and arranged irregularly.When the mass fraction of asphaltenes in asphaltene-wax system(ω_(asp))is 0-25 wt%,the attraction among wax molecules decreases and the bend degree of wax molecules increases with the increase ofω_(asp).Theω_(asp)increases from 0 to 25 wt%,and the attraction between asphaltene-wax is stronger than that among waxes.This causes that the wax precipitation point changes from 353 to 333 K.While theω_(asp)increases to 50 wt%,wax molecules are more dispersed owing to the steric hindrance of asphaltene aggregates,and the interaction among wax molecules transforms from attraction to repulsion.It causes that the ordered crystal structure of waxes can't be formed at normal temperature.Simultaneously,the asphaltene,with the higher molecular weight or the more hetero atoms,has more obvious inhibition to the formation of wax crystals.Besides,resins also have an obvious inhibition on the wax crystal due to the formation of asphalteneresin aggregates with a larger radius.Our results reveal the interaction mechanism between asphaltene-wax,and provide useful guidelines for the development of heavy oil. 展开更多
关键词 Heavy oil Interaction mechanism ASPHALTENES Waxes molecular dynamics
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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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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 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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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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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 L1_(2) nano-precipitates at different temperatures,as well as the interactions b... Molecular dynamics simulations are performed to investigate the mechanical behavior of nanotwinned NiCo-based alloys containing coherent L1_(2) 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 L1_(2) 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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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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