Water is ubiquitous and so is its presence in the proximity of surfaces.To determine and control the properties of interfacial water molecules at nanoscale is essential for its successful applications in environmental...Water is ubiquitous and so is its presence in the proximity of surfaces.To determine and control the properties of interfacial water molecules at nanoscale is essential for its successful applications in environmental and energy-related fields.It is very challenging to explore the atomic structure and electronic properties of water under various conditions,especially at the surfaces.Here we review recent progress and open challenges in describing physicochemical properties of water on surfaces for solar water splitting,water corrosion,and desalination using first-principles approaches,and highlight the key role of these methods in understanding the complex electronic and dynamic interplay between water and surfaces.We aim at showing the importance of unraveling fundamental mechanisms and providing physical insights into the behavior of water on surfaces,in order to pave the way to water-related material design.展开更多
Molecular hydrogen(H_(2))may be an important form of water in nominally anhydrous minerals in the Earth’s mantle and plays a critical role in mantle water cycle,but the transport properties of H2 remain unclear.Here,...Molecular hydrogen(H_(2))may be an important form of water in nominally anhydrous minerals in the Earth’s mantle and plays a critical role in mantle water cycle,but the transport properties of H2 remain unclear.Here,the diffusion of H2 in Fe-free olivine lattice is investigated at pressures of 1-13 GPa and temperatures of 1300-1900 K by first-principles molecular dynamics.The activation energy and activation volume for H2 diffusion in Fe-free olivine are determined to be 55±8 kJ/mol and 3.6±0.2 cm3/mol,respectively.H2 diffusion in Fe-free olivine is faster than H+by 1-4 orders of magnitude and therefore it is more favorable for hydrogen transportation under upper mantle conditions.H2 can be carried to the mantle transition zone by subducting slabs without releasing to the surrounding mantle.The upper mantle may act as a lid,preventing the releasing of H2 produced in the deep mantle to the surface.展开更多
Objective To evaluate the antibacterial potential of bioactive compounds from Persicaria hydropiper(L.)(P.hydropiper)against bacterial virulence proteins through molecular docking(MD)and experimental validation.Method...Objective To evaluate the antibacterial potential of bioactive compounds from Persicaria hydropiper(L.)(P.hydropiper)against bacterial virulence proteins through molecular docking(MD)and experimental validation.Methods Six bioactive compounds from P.hydropiper were investigated:catechin(CAT1),hyperin(HYP1),ombuin(OMB1),pinosylvin(PSV1),quercetin 3-sulfate(QSF1),and scutellarein(SCR1).Their binding affinities and potential binding pockets were assessed through MD against four bacterial target proteins with Protein Data Bank identifiers(PDB IDs):topoisomerase IV from Escherichia coli(E.coli)(PDB ID:3FV5),Staphylococcus aureus(S.aureus)gyrase ATPase binding domain(PDB ID:3U2K),CviR from Chromobacterium violaceum(C.violaceum)(PDB ID:3QP1),and glycosyl hydrolase from Pseudomonas aeruginosa(P.aeruginosa)(PDB ID:5BX9).Molecular dynamics simulations(MDS)were performed on the most promising compound-protein complexes for 50 nanoseconds(ns).Drug-likeness was evaluated using Lipinski's Rule of Five(RO5),followed by absorption,distribution,metabolism,excretion,and toxicity(ADMET)analysis using SwissADME and pkCSM web servers.Antibacterial activity was evaluated through disc diffusion assays,testing both individual compounds and combinations with conventional antibiotics[cefotaxime(CTX1,30μg/disc),ceftazidime(CAZ1,30μg/disc),and piperacillin(PIP1,100μg/disc)].Results MD revealed strong binding affinity(ranging from-9.3 to-5.9 kcal/mol)for all compounds,with CAT1 showing exceptional binding to 3QP1(-9.3 kcal/mol)and 5BX9(-8.4 kcal/mol).MDS confirmed the stability of CAT1-protein complexes with binding free energies of-84.71 kJ/mol(5BX9-CAT1)and-95.59 kJ/mol(3QP1-CAT1).Five compounds(CAT1,SCR1,PSV1,OMB1,and QSF1)complied with Lipinski's RO5 and showed favorable ADMET profiles.All compounds were non-carcinogenic,with CAT1 classified in the lowest toxicity class(VI).In antibacterial assays,CAT1 demonstrated significant activity against both gram-positive bacteria[Streptococcus pneumoniae(S.pneumoniae),S.aureus,and Bacillus cereus(B.cereus)][zone diameter of inhibition(ZDI):10-22 mm]and gram-negative bacteria[Acinetobacter baumannii(A.baumannii),E.coli,and P.aeruginosa](ZDI:14-27 mm).Synergistic effects were observed when CAT1 was combined with antibiotics and the growth inhibitory indices(GII)was 0.69-1.00.Conclusion P.hydropiper bioactive compounds,particularly CAT1,show promising antibacterial potential through multiple mechanisms,including direct inhibition of bacterial virulence proteins and synergistic activity with conventional antibiotics.The favorable pharmacological properties and low toxicity profiles support their potential development as therapeutic agents against bacterial infections.展开更多
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
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
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
In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of in...In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of interbubble interaction,this study employs molecular dynamics simulation combined with a coarse-grained force field.By focusing on collapsemorphology,local density,and pressure,it elucidates how the number and arrangement of bubbles influence the collapse process.The mechanisms behind inter-bubble interactions are also considered.The findings indicate that the collapse speed of unbounded bubbles located in lateral regions is greater than that of the bubbles in the center.Moreover,it is shown that asymmetrical bubble distributions lead to a shorter collapse time overall.展开更多
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
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
The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope ...The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope and image processing technology were employed to achieve a quantitative grain size distribution of NiTi alloys so as to provide experimental data for molecular dynamics modeling at the atomic scale.Considering the size effect of molecular dynamics model on material properties,a reasonable modeling size was provided by taking into account three characteristic dimensions from the perspective of macro,meso,and micro scales according to the Buckinghamπtheorem.Then,the corresponding MD simulation on deformation and fracture behavior was investigated to derive a parameterized traction-separation(T-S)law,and then it was embedded into cohesive elements of finite element software.Thus,the crack propagation behavior in NiTi alloys was reproduced by the finite element method(FEM).The experimental results show that the predicted initiation fracture toughness is in good agreement with experimental data.In addition,it is found that the dynamics initiation fracture toughness increases with decreasing grain size and increasing loading velocity.展开更多
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
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
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
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
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
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
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
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
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
This study explores the mechanical behavior of single-crystal copper with silver inclusions,focusing on the effects of dendritic and spherical geometries using molecular dynamics simulations.Uniaxial tensile tests rev...This study explores the mechanical behavior of single-crystal copper with silver inclusions,focusing on the effects of dendritic and spherical geometries using molecular dynamics simulations.Uniaxial tensile tests reveal that dendritic inclusions lead to an earlier onset of plasticity due to the presence of high-strain regions at the complex inclusion/matrix interfaces,whereas spherical inclusions exhibit delayed plasticity associated with their symmetric geometry and homogeneous strain distribution.During the plastic regime,the dislocation density is primarily influenced by the volume fraction of silver inclusions rather than their shape,with spherical inclusions showing the highest densities due to their larger volume and higher silver content.Stacking faults,quantified via hexagonal closed-packed atom populations,are strongly correlated with dislocation activity but exhibit transient behavior,indicating that many faults are swept out or transformed during deformation.This transfient effect is observed in all cases,independently of the inclusion size.These findings highlight the complex interplay between inclusion geometry,dislocation activity,and stacking fault evolution in shaping the mechanical properties of copper.The study underscores the need to account for inclusion morphology and defect dynamics when designing advanced copper-based materials and suggests further investigations into the role of dendrite orientation and distribution to enhance material performance in engineering applications.展开更多
基金Project supported by the National Key Basic Research Program of China(Grant Nos.2016YFA0300902 and 2015CB921001),the National Natural Science Foundation of China(Grant Nos.11974400,91850120,and 11774396)Strategic Priority Research Program B of the Chinese Academy of Sciences(Grant No.XDB070301).
文摘Water is ubiquitous and so is its presence in the proximity of surfaces.To determine and control the properties of interfacial water molecules at nanoscale is essential for its successful applications in environmental and energy-related fields.It is very challenging to explore the atomic structure and electronic properties of water under various conditions,especially at the surfaces.Here we review recent progress and open challenges in describing physicochemical properties of water on surfaces for solar water splitting,water corrosion,and desalination using first-principles approaches,and highlight the key role of these methods in understanding the complex electronic and dynamic interplay between water and surfaces.We aim at showing the importance of unraveling fundamental mechanisms and providing physical insights into the behavior of water on surfaces,in order to pave the way to water-related material design.
基金supported by the National Natural Science Foundation of China for Distinguished Young Scholars(42325203).
文摘Molecular hydrogen(H_(2))may be an important form of water in nominally anhydrous minerals in the Earth’s mantle and plays a critical role in mantle water cycle,but the transport properties of H2 remain unclear.Here,the diffusion of H2 in Fe-free olivine lattice is investigated at pressures of 1-13 GPa and temperatures of 1300-1900 K by first-principles molecular dynamics.The activation energy and activation volume for H2 diffusion in Fe-free olivine are determined to be 55±8 kJ/mol and 3.6±0.2 cm3/mol,respectively.H2 diffusion in Fe-free olivine is faster than H+by 1-4 orders of magnitude and therefore it is more favorable for hydrogen transportation under upper mantle conditions.H2 can be carried to the mantle transition zone by subducting slabs without releasing to the surrounding mantle.The upper mantle may act as a lid,preventing the releasing of H2 produced in the deep mantle to the surface.
基金Research Grants of Senior Research Fellowship in favor of first author(Gloak Majumdar)from Council of Scientific and Industrial Research(CSIR,New Delhi,Government of India)(CSIR-SRF)with Award No.09/1151/(0008)2020-EMR-I.
文摘Objective To evaluate the antibacterial potential of bioactive compounds from Persicaria hydropiper(L.)(P.hydropiper)against bacterial virulence proteins through molecular docking(MD)and experimental validation.Methods Six bioactive compounds from P.hydropiper were investigated:catechin(CAT1),hyperin(HYP1),ombuin(OMB1),pinosylvin(PSV1),quercetin 3-sulfate(QSF1),and scutellarein(SCR1).Their binding affinities and potential binding pockets were assessed through MD against four bacterial target proteins with Protein Data Bank identifiers(PDB IDs):topoisomerase IV from Escherichia coli(E.coli)(PDB ID:3FV5),Staphylococcus aureus(S.aureus)gyrase ATPase binding domain(PDB ID:3U2K),CviR from Chromobacterium violaceum(C.violaceum)(PDB ID:3QP1),and glycosyl hydrolase from Pseudomonas aeruginosa(P.aeruginosa)(PDB ID:5BX9).Molecular dynamics simulations(MDS)were performed on the most promising compound-protein complexes for 50 nanoseconds(ns).Drug-likeness was evaluated using Lipinski's Rule of Five(RO5),followed by absorption,distribution,metabolism,excretion,and toxicity(ADMET)analysis using SwissADME and pkCSM web servers.Antibacterial activity was evaluated through disc diffusion assays,testing both individual compounds and combinations with conventional antibiotics[cefotaxime(CTX1,30μg/disc),ceftazidime(CAZ1,30μg/disc),and piperacillin(PIP1,100μg/disc)].Results MD revealed strong binding affinity(ranging from-9.3 to-5.9 kcal/mol)for all compounds,with CAT1 showing exceptional binding to 3QP1(-9.3 kcal/mol)and 5BX9(-8.4 kcal/mol).MDS confirmed the stability of CAT1-protein complexes with binding free energies of-84.71 kJ/mol(5BX9-CAT1)and-95.59 kJ/mol(3QP1-CAT1).Five compounds(CAT1,SCR1,PSV1,OMB1,and QSF1)complied with Lipinski's RO5 and showed favorable ADMET profiles.All compounds were non-carcinogenic,with CAT1 classified in the lowest toxicity class(VI).In antibacterial assays,CAT1 demonstrated significant activity against both gram-positive bacteria[Streptococcus pneumoniae(S.pneumoniae),S.aureus,and Bacillus cereus(B.cereus)][zone diameter of inhibition(ZDI):10-22 mm]and gram-negative bacteria[Acinetobacter baumannii(A.baumannii),E.coli,and P.aeruginosa](ZDI:14-27 mm).Synergistic effects were observed when CAT1 was combined with antibiotics and the growth inhibitory indices(GII)was 0.69-1.00.Conclusion P.hydropiper bioactive compounds,particularly CAT1,show promising antibacterial potential through multiple mechanisms,including direct inhibition of bacterial virulence proteins and synergistic activity with conventional antibiotics.The favorable pharmacological properties and low toxicity profiles support their potential development as therapeutic agents against bacterial infections.
基金Project supported by the National MCF Energy Research and Development Program of China(Grant No.2018YFE0308101)the National Key Research and Development Program of China(Grant No.2018YFB0704000)+1 种基金the Suqian Science and Technology Program(Grant No.K202337)the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(Grant No.23KJD490001).
文摘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.
基金supported by the Science and Technology Project of State Grid Corporation of China(5419-202199552A-0-5-ZN).
文摘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.
基金Project supported by the Xi’an Science and Technology Plan Project of Shaanxi Province of China(Grant No.23GXFW0086).
文摘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.
基金funded by the Natural Science Foundation of China[U20A20292]Shandong Province Science andTechnology SMES InnovationAbility Improvement Project[2023TSGC0005]China Postdoctoral Science Foundation[2024M752697].
文摘In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of interbubble interaction,this study employs molecular dynamics simulation combined with a coarse-grained force field.By focusing on collapsemorphology,local density,and pressure,it elucidates how the number and arrangement of bubbles influence the collapse process.The mechanisms behind inter-bubble interactions are also considered.The findings indicate that the collapse speed of unbounded bubbles located in lateral regions is greater than that of the bubbles in the center.Moreover,it is shown that asymmetrical bubble distributions lead to a shorter collapse time overall.
基金Project supported by the National Natural Science Foundation of China (Grant No. 52271105)。
文摘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.
基金support of the Fundamental Research Funds for the Central Universities of China(Grant No.2019ZDPY16).
文摘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.
基金Funded by the National Natural Science Foundation of China Academy of Engineering Physics and Jointly Setup"NSAF"Joint Fund(No.U1430119)。
文摘The multi-scale modeling combined with the cohesive zone model(CZM)and the molecular dynamics(MD)method were preformed to simulate the crack propagation in NiTi shape memory alloys(SMAs).The metallographic microscope and image processing technology were employed to achieve a quantitative grain size distribution of NiTi alloys so as to provide experimental data for molecular dynamics modeling at the atomic scale.Considering the size effect of molecular dynamics model on material properties,a reasonable modeling size was provided by taking into account three characteristic dimensions from the perspective of macro,meso,and micro scales according to the Buckinghamπtheorem.Then,the corresponding MD simulation on deformation and fracture behavior was investigated to derive a parameterized traction-separation(T-S)law,and then it was embedded into cohesive elements of finite element software.Thus,the crack propagation behavior in NiTi alloys was reproduced by the finite element method(FEM).The experimental results show that the predicted initiation fracture toughness is in good agreement with experimental data.In addition,it is found that the dynamics initiation fracture toughness increases with decreasing grain size and increasing loading velocity.
基金PETRONAS Research fund(PRF)under PETRONAS Teknologi Transfer(PTT)Pre-Commercialization—External:YUTP-PRG Cycle 2022(015PBC-020).
文摘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.
文摘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.
基金supported by the National Natural Science Foundation of China (22275018)the Project of State Key Laboratory of Explosion Science and Technology (Beijing Institute of Technology)(Grant No.QNKT20-04)。
文摘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.
基金supported by the Na⁃tional Natural Science Foundation of China(Nos.12462006,12062016)the high-performance computing services of⁃fered by the Information Center of Nanchang Hangkong Uni⁃versity.
文摘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.
基金supported by Carnegie Canada and Natural Sciences and Engineering Research Council of Canada(NSERC)support from the U.S.Department of Energy(DOE),Office of Science,Basic Energy Sciences,under Award No.DESC0020683。
文摘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.
基金financially supported by the Project funded by China Postdoctoral Science Foundation (NO.2022M723500)the National Natural Science Foundation of China (NO.52204069)the Sinopec Science and Technology Project of China (NO.P22015)。
文摘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.
基金support of Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB0450101)the National Natural Science Foundation of China(Grant Nos.12125408 and 11974322)+1 种基金the Informatization Plan of Chinese Academy of Sciences(Grant No.CAS-WX2021SF-0105)the support of the National Natural Science Foundation of China(Grant No.12174363)。
文摘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.
基金Project supported by the National Natural Science Foundation of China (Grant Nos.51775077 and 51909023)。
文摘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.
基金Project supported by the National Natural Science Foundation of China(Grant No.52072132).
文摘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.
基金Project supported by the Competition for Research Regular Projects,year 2023,code LPR23-05,Universidad Tecnológica Metropolitana(NA).
文摘This study explores the mechanical behavior of single-crystal copper with silver inclusions,focusing on the effects of dendritic and spherical geometries using molecular dynamics simulations.Uniaxial tensile tests reveal that dendritic inclusions lead to an earlier onset of plasticity due to the presence of high-strain regions at the complex inclusion/matrix interfaces,whereas spherical inclusions exhibit delayed plasticity associated with their symmetric geometry and homogeneous strain distribution.During the plastic regime,the dislocation density is primarily influenced by the volume fraction of silver inclusions rather than their shape,with spherical inclusions showing the highest densities due to their larger volume and higher silver content.Stacking faults,quantified via hexagonal closed-packed atom populations,are strongly correlated with dislocation activity but exhibit transient behavior,indicating that many faults are swept out or transformed during deformation.This transfient effect is observed in all cases,independently of the inclusion size.These findings highlight the complex interplay between inclusion geometry,dislocation activity,and stacking fault evolution in shaping the mechanical properties of copper.The study underscores the need to account for inclusion morphology and defect dynamics when designing advanced copper-based materials and suggests further investigations into the role of dendrite orientation and distribution to enhance material performance in engineering applications.
