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.

Subpicosecond laser ablation behavior of a magnesium target and crater evolution:Molecular dynamics study and experimental validation

The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly.

Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond

Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition.However,there is a lack of studies of the yield of NV color centers at the atomic scale.In the molecular dynamics simulations described in this paper,NV color centers are pre-pared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing.The differences between the yields of NV color centers produced by implantation of carbon(C)and nitrogen(N)ions,respectively,are investigated.It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy.The effects of different pre-doping concentrations(400–1500 ppm)and implantation energies(1.0–3.0 keV)on the NV color center yield are analyzed,and it is shown that a pre-doping concentra-tion of 1000 ppm with 2 keV C-ion implantation can produce a 13%yield of NV color centers after 1600 K annealing for 7.4 ns.Finally,a brief comparison of the NV color center identification methods is presented,and it is found that the error rate of an analysis utiliz-ing the identify diamond structure coordination analysis method is reduced by about 7%compared with conventional identification+methods.

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.

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.

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 L12 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 L12 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.

Probing the electric double layer structure at nitrogen-doped graphite electrodes by constant-potential molecular dynamics simulations

Electric double layer(EDL)is a critical topic in electrochemistry and largely determines the working performance of lithium batteries.However,atomic insights into the EDL structures on heteroatom-modified graphite anodes and EDL evolution with electrode potential are very lacking.Herein,a constant-potential molecular dynamics(CPMD)method is proposed to probe the EDL structure under working conditions,taking N-doped graphite electrodes and carbonate electrolytes as an example.An interface model was developed,incorporating the electrode potential and atom electronegativities.As a result,an insightful atomic scenario for the EDL structure under varied electrode potentials has been established,which unveils the important role of doping sites in regulating both the EDL structures and the following electrochemical reactions at the atomic level.Specifically,the negatively charged N atoms repel the anions and adsorb Li~+at high and low potentials,respectively.Such preferential adsorption suggests that Ndoped graphite can promote Li~+desolvation and regulate the location of Li~+deposition.This CPMD method not only unveils the mysterious function of N-doping from the viewpoint of EDL at the atomic level but also applies to probe the interfacial structure on other complicated electrodes.

Molecular dynamics study of primary radiation damage in TiVTa concentrated solid-solution alloy

The primary radiation damage in pure V and TiVTa concentrated solid-solution alloy(CSA)was studied using a molecular dynamics method.We have performed displacement cascade simulations to explore the generation and evolution behavior of irradiation defects.The results demonstrate that the defect accumulation and agglomeration in TiVTa CSA are significantly suppressed compared to pure V.The peak value of Frenkel pairs during cascade collisions in TiVTa CSA is much higher than that in pure V due to the lower formation energy of point defects.Meanwhile,the longer lifetime of the thermal spike relaxation and slow energy dissipation capability of TiVTa CSA can facilitate the recombination of point defects.The defect agglomeration rate in TiVTa CSA is much lower due to the lower binding energy of interstitial clusters and reduced interstitial diffusivity.Furthermore,the occurrence probability of dislocation loops in TiVTa CSA is lower than that in pure V.The reduction in primary radiation damage may enhance the radiation resistance of TiVTa CSA,and the improved radiation tolerance is primarily attributed to the relaxation stage and long-term defect evolution rather than the ballistic stage.These results can provide fundamental insights into irradiation-induced defects evolution in refractory CSAs.

Improvement Mechanism of Adhesion Performance of Anti-stripping Agents and Coupling Agents on Asphalt-Aggregate Interface Based on Molecular Dynamics

This study examined the mechanisms for improving the adhesion performance of the asphalt-aggregate interface with two anti-stripping agents and two coupling agents.The investigation of contact behavior between various asphalt-aggregate surfaces was conducted using molecular dynamics(MD)simulations.The interaction energy and the relative concentration distribution were employed as the parameters to analyze the enhancement mechanisms of anti-stripping agents and coupling agents on the asphalt-aggregate interface.Results indicated that the adhesion at the asphalt-aggregate interface could be strengthened by both anti-stripping agents and coupling agents.Anti-stripping agents primarily improve adhesion through the reinforcement of electrostatic attraction,while coupling agents primarily upgrade adhesion by strengthening the van der Waals.Hence,the molecular dynamics modeling and calculation techniques presented in this study can be utilized to elucidate the development mechanism of the asphalt-aggregate interface through the use of anti-stripping agents and coupling agents.

Comparative study of nudged elastic band and molecular dynamics methods for diffusion kinetics in solid-state electrolytes

Considerable efforts are being made to transition current lithium-ion and sodium-ion batteries towards the use of solid-state electrolytes.Computational methods,specifically nudged elastic band(NEB)and molecular dynamics(MD)methods,provide powerful tools for the design of solid-state electrolytes.The MD method is usually the choice for studying the materials involving complex multiple diffusion paths or having disordered structures.However,it relies on simulations at temperatures much higher than working temperature.This paper studies the reliability of the MD method using the system of Na diffusion in MgO as a benchmark.We carefully study the convergence behavior of the MD method and demonstrate that total effective simulation time of 12 ns can converge the calculated diffusion barrier to about 0.01 eV.The calculated diffusion barrier is 0.31 eV from both methods.The diffusion coefficients at room temperature are 4.3×10^(-9) cm^(2)⋅s^(−1) and 2.2×10^(-9) cm^(2)⋅s^(−1),respectively,from the NEB and MD methods.Our results justify the reliability of the MD method,even though high temperature simulations have to be employed to overcome the limitation on simulation time.

Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects

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.