Temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation.The nt-Ni exhibits enhanced...Temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation.The nt-Ni exhibits enhanced critical load and hardness compared to nc-Ni,where perfect,stair-rod and Shockley dislocations are activated at (111),(111) and (111) slip planes in nt-Ni compared to only SSockley dislocation nucleation at (111) and (111) slip planes of nc-Ni.The nt-Ni exhibits a less significant indentation size effect in comparison with nc-Ni due to the dislocation slips hindrance of the twin boundary.The atomic deformation associated with the indentation size effect is investigated during dislocation transmission.Different from the decreasing partial slips parallel to the indenter surface in nc-Ni with increasing temperature,the temperaturedependent atomic deformation of nt-Ni is closely related to the twin boundary:from the partial slips parallel to the twin boundary (~10 K),to increased confined layer slips and decreased twin migration(300 K–600 K),to decreased confined layer slips and increased dislocation interaction of dislocation pinning and dissociation (900 K–1200 K).Dislocation density and atomic structure types through quantitative analysis are implemented to further reveal the above-mentioned dislocation motion and atomic structure alteration.Our study is helpful for understanding the temperature-dependent plasticity of twin boundary in nanotwinned materials.展开更多
We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient, D, of a Lennard Jones fluid over a wide density and temperature range. The change in self-diffusion coefficient with t...We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient, D, of a Lennard Jones fluid over a wide density and temperature range. The change in self-diffusion coefficient with temperature decreases by increasing density. For density ρ＊ = ρσ3 = 0.84 we observe a peak at the value of the self-diffusion coefficient and the critical temperature T＊ = kT/ε = 1.25. The value of the self-diffusion coefficient strongly depends on system size. The data of the self-diffusion coefficient are fitted to a simple analytic relation based on hydrodynamic arguments. This correction scales as N-α, where α is an adjustable parameter and N is the number of particles. It is observed that the values of a 〈 1 provide quite a good correction to the simulation data. The system size dependence is very strong for lower densities, but it is not as strong for higher densities. The self-diffusion coefficient calculated with non-equilibrium molecular dynamic simulations at different temperatures and densities is in good agreement with other calculations fronl the literature.展开更多
Molecular dynamic simulations based on a coarse-gralned, bead-spring model are adopted to investigate the spreading of both nonfunctional and functional perfluoropolyether （PFPE） on solid substrates. For nonfunction...Molecular dynamic simulations based on a coarse-gralned, bead-spring model are adopted to investigate the spreading of both nonfunctional and functional perfluoropolyether （PFPE） on solid substrates. For nonfunctional PFPE, the spreading generally exhibits a smooth profile with a precursor film. The spreading profiles on different substrates are compared, which indicate that the bead-substrate interaction has a significant effect on the spreading behaviour, especially on the formation of the precursor film. For functional PFPE, the spreading generally exhibits a complicated terraced profile. The spreading profiles with different endbeads are compared, which indicate that the endbead-substrate interaction and the endbead-endbead interaction, especially the latter, have a significant effect on the spreading behaviour.展开更多
The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the...The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the framework of topological fluctuation theory, and the fluctuation of atomic hydrostatic stress gradually decreases upon cooling. The left sub peak of the second peak of Fe–B partial pair distribution functions（PDFs） becomes pronounced below the glass transition temperature, which may be the major reason why B promotes the glass formation ability significantly. The magnetization mainly originates from Fe 3d states, while small contribution results from metalloid elements P and B. This work may be helpful for developing Fe-based metallic glasses with both high saturation flux density and glass formation ability.展开更多
A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological funct...A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological functions of many RNA molecules. Due to the fast transition rate, it is difficult to directly observe opening and closing of single nucleic acid base pair in experiments. This review will provide a brief summary of the studies about the thermodynamic and kinetic properties of a base pair opening and closing by using molecular dynamic simulation methods.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
The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this wo...The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.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
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
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
The effects of a twin boundary（TB） on the mechanical properties of two types of bicrystal Al thin films during the nanoimprint process are investigated by using molecular dynamics simulations.The results indicate th...The effects of a twin boundary（TB） on the mechanical properties of two types of bicrystal Al thin films during the nanoimprint process are investigated by using molecular dynamics simulations.The results indicate that for the TB direction parallel to the imprinting direction,the yield stress reaches the maximum for the initial dislocation nucleation when the mould directly imprints to the TB,and the yield stress first decreases with the increase of the marker interval and then increases.However,for the TB direction perpendicular to the imprinting direction,the effect of the TB location to the imprinting forces is very small,and the yield stress is greater than that with the TB direction parallel to the imprinting direction.The results also demonstrate that the direction of the slip dislocations and the deformation of the thin film caused by spring-back are different due to various positions and directions of the TB.展开更多
Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simul...Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simulated under the polymer consistent force field(PCFF).Three types of curing agents(rigidity1,3-phenylenediamine(1,3-P),4,4-diaminodiphenylmethane(DDM),and phenol-formaldehyde-ethylenediamine(PFE))with different numbers of active sites are selected in the simulations.We focus on the effects of the cross-linkers on thermo-mechanical properties such as density,glass transition temperature(T_(g)),elastic constants,and strength.Our simulations show a significant increase in the Tg,Young’s modulus and yield stress with the increase in the degree of conversion.The simulation results reveal that the mechanical properties of thermosetting polymers are strongly dependent on the molecular structures of the cross-linker and network topological properties,such as end-to-end distance,crosslinking density and degree of conversion.展开更多
In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules ca...In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.展开更多
Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of...Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of products.Besides the topology effect on reaction kinetics,the topology influences the diffusion of reactants and products in catalysts as well.In this work,by using COMPASS force-field molecular dynamics method,we investigated the intracrystalline diffusion of ethene and propene in four different zeolites,CHA,MFI,BEA and FAU,at different temperatures.The self-diffusion coefficients and diffusion activation barriers were calculated.A strong restriction on the diffusion of propene in CHA was observed because the self-diffusion coefficient ratio of ethene to propene is larger than 18 and the diffusion activation barrier of propene is more than 20 kJ/mol in CHA.This ratio decreases with the increase of temperature in the four investigated zeolites.The shape selectivity on products from diffusion perspective can provide some implications on the understanding of the selectivity difference between HSAPO-34 and HZSM-5 catalysts for the MTO conversion.展开更多
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
This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF for...This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduced the swelling pattern of these montmorillonites, suggesting a mechanism of their hydration different （K＋ 〈 Na＋ 〈 Ca2＋） from that of K＋-, Na＋-, and Ca2＋-montmorillonites. In particular, these results indicate that the valence of the cations has the larger impact on the behaviour of clay water systems. It also finds that the differences in size and hydration energy of K＋, Na＋ and Ca2＋ ions have strong implications for the structure of interlayer. This leads to the differences in the layer spacings of the simulated K＋-, Na＋-, and Ca2＋-montmorillonites. Furthermore, these simulations show that the K cations interact strongly with the clay sheets for the dehydrated clay sheets, but for the hydrated clays the Ca cations interact clearly strongly with the clay sheets.展开更多
Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results...Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.展开更多
The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an eg...The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an egg-white derived peptide,LAPYK,using the amino acids with different properties to produce the LAPYK-modified peptides.The ACE inhibitory activities of the modified peptides were determined to explore the structural requirements of ACE inhibitory peptides(ACEIPs).Molecular simulation and isothermal titration calorimetry analysis were used to investigate interactions between the peptides and ACE.We found that hydrophobicity and the amino acids with ring structures were benefi cial for the ACE inhibitory activities of the peptides.The results of the molecular mechanics poisson boltzmann surface area(MMPBSA)binding free energy calculations indicated that the polar solvation free energy(ΔG_(polar))of the charged peptides(LAPYK,LAPYE)were unfavorable for binding to ACE.On the other hand,the results of isothermal titration calorimetry analyses suggested that the enthalpy-driven ACE-peptide interactions were more favorable than the entropy-driven ACE-peptide interaction counterparts.展开更多
Shale oil formations contain both inorganic and organic media.The organic matter holds both free oil in the pores and dissolved oil within the kerogen molecules.The free oil flow in organic pores and the dissolved oil...Shale oil formations contain both inorganic and organic media.The organic matter holds both free oil in the pores and dissolved oil within the kerogen molecules.The free oil flow in organic pores and the dissolved oil diffusion in kerogen molecules are coupled together.The molecular flow of free n-alkanes is an important process of shale oil accumulation and production.To study the dynamics of imbibition process of n-alkane molecules into kerogen slits,molecular dynamics(MD)simulations are conducted.Effects of slit width,temperature,and n-alkane types on the penetration speed,dynamic contact angle,and molecular conformations were analyzed.Results showed that molecular transportation of n-alkanes is dominated by molecular structure and molecular motion at this scale.The space-confinement conformational changes of molecules slow down the filling speeds in the narrow slits.The n-alkane molecules with long carbon chains require more time to undergo conformational changes.The high content of short-chain alkanes and high temperature facilitate the flow of alkane mixtures in kerogen slits.Results obtained from this study are useful for understanding the underlying nanoscale flow mechanism in shale formations.展开更多
基金supported by the National Natural Science Foundation of China (Grant No.11572090)。
文摘Temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation.The nt-Ni exhibits enhanced critical load and hardness compared to nc-Ni,where perfect,stair-rod and Shockley dislocations are activated at (111),(111) and (111) slip planes in nt-Ni compared to only SSockley dislocation nucleation at (111) and (111) slip planes of nc-Ni.The nt-Ni exhibits a less significant indentation size effect in comparison with nc-Ni due to the dislocation slips hindrance of the twin boundary.The atomic deformation associated with the indentation size effect is investigated during dislocation transmission.Different from the decreasing partial slips parallel to the indenter surface in nc-Ni with increasing temperature,the temperaturedependent atomic deformation of nt-Ni is closely related to the twin boundary:from the partial slips parallel to the twin boundary (~10 K),to increased confined layer slips and decreased twin migration(300 K–600 K),to decreased confined layer slips and increased dislocation interaction of dislocation pinning and dissociation (900 K–1200 K).Dislocation density and atomic structure types through quantitative analysis are implemented to further reveal the above-mentioned dislocation motion and atomic structure alteration.Our study is helpful for understanding the temperature-dependent plasticity of twin boundary in nanotwinned materials.
基金supported by the National Natural Science Foundation of China (Grant No. 51076128)the National High Technology Research and Development Program of China (Grant No. 2009AA05Z107)
文摘We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient, D, of a Lennard Jones fluid over a wide density and temperature range. The change in self-diffusion coefficient with temperature decreases by increasing density. For density ρ＊ = ρσ3 = 0.84 we observe a peak at the value of the self-diffusion coefficient and the critical temperature T＊ = kT/ε = 1.25. The value of the self-diffusion coefficient strongly depends on system size. The data of the self-diffusion coefficient are fitted to a simple analytic relation based on hydrodynamic arguments. This correction scales as N-α, where α is an adjustable parameter and N is the number of particles. It is observed that the values of a 〈 1 provide quite a good correction to the simulation data. The system size dependence is very strong for lower densities, but it is not as strong for higher densities. The self-diffusion coefficient calculated with non-equilibrium molecular dynamic simulations at different temperatures and densities is in good agreement with other calculations fronl the literature.
基金Project supported by the National Natural Science Foundation of China （Grant No 50390060） and the State Key Development Program for Basic Research of China （Grant No 2003CB716201）.
文摘Molecular dynamic simulations based on a coarse-gralned, bead-spring model are adopted to investigate the spreading of both nonfunctional and functional perfluoropolyether （PFPE） on solid substrates. For nonfunctional PFPE, the spreading generally exhibits a smooth profile with a precursor film. The spreading profiles on different substrates are compared, which indicate that the bead-substrate interaction has a significant effect on the spreading behaviour, especially on the formation of the precursor film. For functional PFPE, the spreading generally exhibits a complicated terraced profile. The spreading profiles with different endbeads are compared, which indicate that the endbead-substrate interaction and the endbead-endbead interaction, especially the latter, have a significant effect on the spreading behaviour.
基金supported by the National Natural Science Foundation of China(Grant No.51571115)a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions
文摘The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the framework of topological fluctuation theory, and the fluctuation of atomic hydrostatic stress gradually decreases upon cooling. The left sub peak of the second peak of Fe–B partial pair distribution functions（PDFs） becomes pronounced below the glass transition temperature, which may be the major reason why B promotes the glass formation ability significantly. The magnetization mainly originates from Fe 3d states, while small contribution results from metalloid elements P and B. This work may be helpful for developing Fe-based metallic glasses with both high saturation flux density and glass formation ability.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11574234 and 31270761)
文摘A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological functions of many RNA molecules. Due to the fast transition rate, it is difficult to directly observe opening and closing of single nucleic acid base pair in experiments. This review will provide a brief summary of the studies about the thermodynamic and kinetic properties of a base pair opening and closing by using molecular dynamic simulation methods.
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.
文摘The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.
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 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supported by the National Natural Science Foundation of China(Grant No.10902083)the Program for New Century Excellent Talent in University of Ministry of Education of China(Grant No.NCET-12-1046)+1 种基金the Program for New Scientific and Technological Star of Shaanxi Province,China(Grant No.2012KJXX-39)the Program for Natural Science Basic Research Plan in Shaanxi Province,China(Grant No.2014JQ1036)
文摘The effects of a twin boundary（TB） on the mechanical properties of two types of bicrystal Al thin films during the nanoimprint process are investigated by using molecular dynamics simulations.The results indicate that for the TB direction parallel to the imprinting direction,the yield stress reaches the maximum for the initial dislocation nucleation when the mould directly imprints to the TB,and the yield stress first decreases with the increase of the marker interval and then increases.However,for the TB direction perpendicular to the imprinting direction,the effect of the TB location to the imprinting forces is very small,and the yield stress is greater than that with the TB direction parallel to the imprinting direction.The results also demonstrate that the direction of the slip dislocations and the deformation of the thin film caused by spring-back are different due to various positions and directions of the TB.
基金supported by the National Natural Science Foundation of China(Grant No.11772043)。
文摘Molecular dynamics(MD)simulations are conducted to study the thermo-mechanical properties of a family of thermosetting epoxy-amines.The crosslinked epoxy resin EPON862 with a series of cross-linkers is built and simulated under the polymer consistent force field(PCFF).Three types of curing agents(rigidity1,3-phenylenediamine(1,3-P),4,4-diaminodiphenylmethane(DDM),and phenol-formaldehyde-ethylenediamine(PFE))with different numbers of active sites are selected in the simulations.We focus on the effects of the cross-linkers on thermo-mechanical properties such as density,glass transition temperature(T_(g)),elastic constants,and strength.Our simulations show a significant increase in the Tg,Young’s modulus and yield stress with the increase in the degree of conversion.The simulation results reveal that the mechanical properties of thermosetting polymers are strongly dependent on the molecular structures of the cross-linker and network topological properties,such as end-to-end distance,crosslinking density and degree of conversion.
基金supported in part by National Natural Science Foundation of China (Grant Nos 10474109 and 10674146)supported is part by the Shanghai Supercomputer Center of China
文摘In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.
基金supported by the National Basic Research Program of China (2009CB623504)the National Science Foundation of China (21103231)Shanghai Science Foundation (11ZR1449700)
文摘Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of products.Besides the topology effect on reaction kinetics,the topology influences the diffusion of reactants and products in catalysts as well.In this work,by using COMPASS force-field molecular dynamics method,we investigated the intracrystalline diffusion of ethene and propene in four different zeolites,CHA,MFI,BEA and FAU,at different temperatures.The self-diffusion coefficients and diffusion activation barriers were calculated.A strong restriction on the diffusion of propene in CHA was observed because the self-diffusion coefficient ratio of ethene to propene is larger than 18 and the diffusion activation barrier of propene is more than 20 kJ/mol in CHA.This ratio decreases with the increase of temperature in the four investigated zeolites.The shape selectivity on products from diffusion perspective can provide some implications on the understanding of the selectivity difference between HSAPO-34 and HZSM-5 catalysts for the MTO conversion.
基金Project supported by the National Natural Science Foundation of China(Grant No.12072317)the Natural Science Foundation of Zhejiang Province(Grant No.LZ21A020002)+2 种基金Ligang Sun gratefully acknowledges the support received from the Guangdong Basic and Applied Basic Research Foundation(Grant No.22022A1515011402)the Science,Technology and Innovation Commission of Shenzhen Municipality(Grant No.GXWD20231130102735001)Development and Reform Commission of Shenzhen(Grant No.XMHT20220103004).
文摘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.
基金Project supported by the Key Laboratory of Mountain Hazards and Earth Surface Processes, the Chinese Academy of Sciences
文摘This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduced the swelling pattern of these montmorillonites, suggesting a mechanism of their hydration different （K＋ 〈 Na＋ 〈 Ca2＋） from that of K＋-, Na＋-, and Ca2＋-montmorillonites. In particular, these results indicate that the valence of the cations has the larger impact on the behaviour of clay water systems. It also finds that the differences in size and hydration energy of K＋, Na＋ and Ca2＋ ions have strong implications for the structure of interlayer. This leads to the differences in the layer spacings of the simulated K＋-, Na＋-, and Ca2＋-montmorillonites. Furthermore, these simulations show that the K cations interact strongly with the clay sheets for the dehydrated clay sheets, but for the hydrated clays the Ca cations interact clearly strongly with the clay sheets.
基金supported by the National Natural Science Foundation of China(No.51176192)CAS Program(KGZD-EW-301)NOG Program(GHZ2012006003)
文摘Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.
基金funded by the National Natural Science Foundation of China(31972096)Jilin Province Science and Technology Youth Talent Support Project(QT202021)Interdisciplinary Integration and Innovation Project of JLU(JLUXKJC2021QZ11)。
文摘The understanding of the structural requirements and the intermolecular-interaction mechanism are important for discovering potent angiotensin-converting enzyme(ACE)inhibitory peptides.In this study,we modifi ed an egg-white derived peptide,LAPYK,using the amino acids with different properties to produce the LAPYK-modified peptides.The ACE inhibitory activities of the modified peptides were determined to explore the structural requirements of ACE inhibitory peptides(ACEIPs).Molecular simulation and isothermal titration calorimetry analysis were used to investigate interactions between the peptides and ACE.We found that hydrophobicity and the amino acids with ring structures were benefi cial for the ACE inhibitory activities of the peptides.The results of the molecular mechanics poisson boltzmann surface area(MMPBSA)binding free energy calculations indicated that the polar solvation free energy(ΔG_(polar))of the charged peptides(LAPYK,LAPYE)were unfavorable for binding to ACE.On the other hand,the results of isothermal titration calorimetry analyses suggested that the enthalpy-driven ACE-peptide interactions were more favorable than the entropy-driven ACE-peptide interaction counterparts.
基金financially supported by the National Natural Science Foundation of China(Grant No.52004317,42090024)the Natural Science Foundation of Shandong Province of China(No.ZR2020ME091)+1 种基金the Fundamental Research Funds for the Central Universities(20CX06016A)the National Science and Technology Major Project(2017ZX05049-004)
文摘Shale oil formations contain both inorganic and organic media.The organic matter holds both free oil in the pores and dissolved oil within the kerogen molecules.The free oil flow in organic pores and the dissolved oil diffusion in kerogen molecules are coupled together.The molecular flow of free n-alkanes is an important process of shale oil accumulation and production.To study the dynamics of imbibition process of n-alkane molecules into kerogen slits,molecular dynamics(MD)simulations are conducted.Effects of slit width,temperature,and n-alkane types on the penetration speed,dynamic contact angle,and molecular conformations were analyzed.Results showed that molecular transportation of n-alkanes is dominated by molecular structure and molecular motion at this scale.The space-confinement conformational changes of molecules slow down the filling speeds in the narrow slits.The n-alkane molecules with long carbon chains require more time to undergo conformational changes.The high content of short-chain alkanes and high temperature facilitate the flow of alkane mixtures in kerogen slits.Results obtained from this study are useful for understanding the underlying nanoscale flow mechanism in shale formations.
