Critical anomaly and finite size scaling of the self-diffusion coefficient for Lennard Jones fluids by non-equilibrium molecular dynamic simulation

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.

Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations

The knowledge of interfacial thermal conductance(ITC)is key to understand thermal transport in nanostructures.The non-equilibrium molecular dynamics(NEMD)simulation is a useful tool to calculate the ITC.In this study,we investigate the impact of thermostat on the prediction of the ITC.The Langevin thermostat is found to result in larger ITC than the Nose-Hoover thermostat.In addition,the results from NEMD simulations with the Nose-Hoover thermostat exhibit strong size effect of thermal reservoirs.Detailed spectral heat flux decomposition and modal temperature calculation reveal that the acoustic phonons in hot and cold thermal reservoirs are of smaller temperature difference than optical phonons when using the Nose-Hoover thermostat,while phonons in the Langevin thermostat are of identical temperatures.Such a nonequilibrium state of phonons in the case of the Nose-Hoover thermostat reduces the heat flux of low-to-middle-frequency phonons.We also discuss how enlarging the reservoirs or adding an epitaxial rough wall to the reservoirs affects the predicted ITC,and find that these attempts could help to thermalize the phonons,but still underestimate the heat flux from low-frequency phonons.

A non-equilibrium molecular dynamics study of the thermal conductivity of uranium dioxide

The thermal conductivity of uranium dioxide in the temperature range of 300–2400 K was estimated by non-equilibrium molecular dynamics calculation using Fourier law.The Kawamura function was adopted as the interatomic potential function.The calculated thermal conductivities are found to be strongly dependent on the temperature of the simulation cube.The thermal conductivity simulation results are compared with the experiment results and agreed well with the experimental results when the temperature is above 600 K.The thermal conductivities scale effects are found to be existed in uranium dioxide nanometer thin film.The approximate mean free paths of phonons in different temperatures can be examined.

Emerging structures and dynamic mechanisms ofγ-secretase for Alzheimer’s disease

γ-Secretase,called“the proteasome of the membrane,”is a membrane-embedded protease complex that cleaves 150+peptide substrates with central roles in biology and medicine,including amyloid precursor protein and the Notch family of cell-surface receptors.Mutations inγ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer’s disease.γ-Secretase has thus served as a critical drug target for treating familial Alzheimer’s disease and the more common late-onset Alzheimer’s disease as well.However,critical gaps remain in understanding the mechanisms of processive proteolysis of substrates,the effects of familial Alzheimer’s disease mutations,and allosteric modulation of substrate cleavage byγ-secretase.In this review,we focus on recent studies of structural dynamic mechanisms ofγ-secretase.Different mechanisms,including the“Fit-Stay-Trim,”“Sliding-Unwinding,”and“Tilting-Unwinding,”have been proposed for substrate proteolysis of amyloid precursor protein byγ-secretase based on all-atom molecular dynamics simulations.While an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-boundγ-secretase,molecular dynamics simulations on a resolved model of Notch1-boundγ-secretase that was reconstructed using the amyloid precursor protein-boundγ-secretase as a template successfully capturedγ-secretase activation for proper cleavages of both wildtype and mutant Notch,being consistent with biochemical experimental findings.The approach could be potentially applied to decipher the processing mechanisms of various substrates byγ-secretase.In addition,controversy over the effects of familial Alzheimer’s disease mutations,particularly the issue of whether they stabilize or destabilizeγ-secretase-substrate complexes,is discussed.Finally,an outlook is provided for future studies ofγ-secretase,including pathways of substrate binding and product release,effects of modulators on familial Alzheimer’s disease mutations of theγ-secretase-substrate complexes.Comprehensive understanding of the functional mechanisms ofγ-secretase will greatly facilitate the rational design of effective drug molecules for treating familial Alzheimer’s disease and perhaps Alzheimer’s disease in general.

Thermal conductivity prediction of MgAl2O4:a non-equilibrium molecular dynamics calculation

Magnesium aluminate spinel(MgAl2O4)is widely used in steel metallurgy industry.Thermal conductivity at high temperature signifcantly infuences the cooling process of blast furnace and the heat preservation of steel converter.The efect of external(temperature)and internal(antisite defect and grain boundary)factors on the thermal conductivity of MgAl2O4 was studied with non-equilibrium molecular dynamics.The main factors afecting the thermal conductivity of MgAl2O4 were summarized.In the temperature range of 100-2000 K,the results showed that the thermal conductivity of MgAl2O4 changed from 11.54 to 4.95 W/(m K)with the increase in temperature and was relatively stable at the temperature above 1000 K.The thermal conductivity of MgAl2O4 declined frst and then rose with the increase in the antisite defects,and the minimum value was 6.95 W/(m K)at the inversion parameter i=0.35.In addition,grain boundaries reduced the thermal conductivity of MgAl2O4 by 20%-30%at temperature below 1000 K comparing with the non-grain boundary system.The grain boundary rotation angle at temperature above 1000 K had less efect on the thermal conductivity than that below 1000 K.Present simulation scheme for thermal conductivity of MgAl2O4 can also be applied to the study of other nonmetallic ceramics.

Analysis of CH_(4) and H_(2) Adsorption on Heterogeneous Shale Surfaces Using aMolecular Dynamics Approach

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.

Probing the interaction between asphaltene-wax and its effects on the crystallization behavior of waxes in heavy oil via molecular dynamics simulation

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.

Ab initio nonadiabatic molecular dynamics study on spin–orbit coupling induced spin dynamics in ferromagnetic metals

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.

Balanced Fracturing and Cold-welding of Magnesium during Ball Milling Assisted by Carbon Coating:Experimental and Molecular Dynamic Simulation

The lignite-derived carbon from self-protection pyrolysis was employed to balance the fracturing and cold-welding of magnesium during ball milling.Particle size analysis indicates that the introduction of lignite-derived carbon can effectively reduce the particle size of Mg while the introduction of graphite does no help.Besides,the effect of lignite-derived carbon on crystallite size reduction of Mg is also better than graphite.A moderate cold-welding phenomenon was observed after ball-milling Mg with the lignite-derived carbon,suggesting less Mg is wasted on the milling vials and balls.Molecular dynamic simulations reveal that the balanced fracturing and cold-welding of magnesium during ball milling is mainly attributed to the special structure of the lignite-derived carbon:graphitized short-range ordered stacking function as dry lubricant and irregular shape/sharp edge function as milling aid.The preliminary findings in current study are expected to offer implications for designing efficient Mg-based hydrogen storage materials.

Molecular dynamics simulation of the flow mechanism of shear-thinning fluids in a microchannel

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.

Unravelling biotoxicity of graphdiyne:Molecular dynamics simulation of the interaction between villin headpiece protein and graphdiyne

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.

Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

Temperature effect on nanotwinned Ni under nanoindentation using molecular dynamic simulation

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.

The chemical environment and structural ordering in liquid Mg-Y-Zn system:An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure

In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation.In liquid Mg-rich Mg-Y alloys,the strong Mg-Y interaction is determined,which promotes the formation of fivefold symmetric local structure.For Mg-Zn alloys,the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure.Due to the coexistence of Y and Zn,the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy,and contributes to the clustering of Mg,Y,Zn launched from Zn.What is more,the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys.These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure,which provides a new insight into the formation mechanism of LPSO structure at atomic level.

Electronic effects on radiation damage inα-iron:A molecular dynamics study

Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation during operation,thus,the problems associated with the safe operation of nuclear reactors have been put forward naturally.In this work,a molecular dynamics simulation approach combined with electronic effects is developed for investigating the primary radiation damage process inα-Fe.Specifically,the influence of electronic effects on the collision cascade in Fe is systematically evaluated based on two commonly used interatomic potentials for Fe.The simulation results reveal that both electronic stopping(ES)and electron-phonon coupling(EPC)can contribute to the decrease of the number of defects in the thermal spike phase.The application of ES reduces the number of residual defects after the cascade evolution,whereas EPC has a reverse effect.The introduction of electronic effects promotes the formation of the dispersive subcascade:ES significantly changes the geometry of the damaged region in the thermal spike phase,whereas EPC mainly reduces the extent of the damaged region.Furthermore,the incorporation of electronic effects effectively mitigates discrepancies in simulation outcomes when using different interatomic potentials.

Machine learning molecular dynamics simulations of liquid methanol

As the simplest hydrogen-bonded alcohol,liquid methanol has attracted intensive experimental and theoretical interest.However,theoretical investigations on this system have primarily relied on empirical intermolecular force fields or ab initio molecular dynamics with semilocal density functionals.Inspired by recent studies on bulk water using increasingly accurate machine learning force fields,we report a new machine learning force field for liquid methanol with a hybrid functional revPBE0 plus dispersion correction.Molecular dynamics simulations on this machine learning force field are orders of magnitude faster than ab initio molecular dynamics simulations,yielding the radial distribution functions,selfdiffusion coefficients,and hydrogen bond network properties with very small statistical errors.The resulting structural and dynamical properties are compared well with the experimental data,demonstrating the superior accuracy of this machine learning force field.This work represents a successful step toward a first-principles description of this benchmark system and showcases the general applicability of the machine learning force field in studying liquid systems.

Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations

Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectile impacts is thoroughly investigated using full-atomic molecular dynamics(MD)simulations.The study results show that the porous structure and density are key factors determining the mechanical response of GA under impact loading.Specifically,the impact-induced penetration of the projectile leads to the collapse of the pore structure,causing stretching and subsequent rupture of covalent bonds in graphene sheets.Moreover,the effects of temperature on the mechanical performance of GA have been proven to be minimal,thereby highlighting the mechanical stability of GA over a wide range of temperatures.Finally,the energy absorption density(EAD)and energy absorption efficiency(EAE)metrics are adopted to assess the energy absorption capacity of GA during projectile penetration.The research findings of this work demonstrate the significant potential of GA for energy absorption applications.

Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation

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.

A molecular dynamics study on mechanical performance and deformation mechanisms in nanotwinned NiCo-based alloys with nano-precipitates under high temperatures

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.

Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation

Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is proposed by using molecular dynamics simulation,and the relationship between ion-to-ion interaction and salt solubility in a simulated seawater water-salt system is investigated.By analyzing the variation of distance and contact time between ions in an electrolyte solution,from both spatial and temporal perspectives,new parameters were proposed to describe the interaction between ions:interaction distance(ID),and interaction time ratio(ITR).The best correlation between characteristic time ratio and solubility was found for a molar ratio of salt-to-water of 10:100 with a correlation coefficient of 0.96.For the same salt,a positive correlation was found between CTR and the molar ratio of salt and water.For type 1-1,type 2-1,type 1-2,and type 2-2 salts,the correlation coefficients between CTR and solubility were 0.93,0.96,0.92,and 0.98 for a salt-to-water molar ratio of 10:100,respectively.The solubility of multiple salts was predicted by simulations and compared with experimental values,yielding an average relative deviation of 12.4%.The new ion-interaction parameters offer significant advantages in describing strongly correlated and strongly hydrated electrolyte solutions.