Lattice dynamical simulation of methane hydrate

INS （Inelastic Neutron Scattering） spectrum of methane hydrate was measured on MARI （a direct-geometry chopper spectrometer） at Ruther-ford Appleton Laboratory, UK. Compared with ice Ih, it is found that the whole spectrum of methane hydrate moves toward high-energy by about 1.5 meV. Using lattice dynamical （LD） technique, computer simulations of methane hydrate were carried out. In the simulations, four potential models （BE TIP3P, TIP4P, MCY） were employed to calculate the phonon density of states （PDOS）. Comparing the calculated PDOS spectrum with the experimental spectrum, it is found that BF, TIP4P, and TIP3P potential lattices give out well-separated translational and librational bands while MCY potential lattice is unstable to do so and this model is not suitable to describe hydrate system.

Analysis of Micromechanical Properties at the Interface of Pre-wet SBS Modified Asphalt Mixture Based on Molecular Simulation Technology

The pre-wetting of aggregate surface is a means to improve the interface performance of SBS modified asphalt and aggregate.The effect of pre-wetting technology on the interaction between SBS modified asphalt and aggregate was analyzed by molecular dynamics simulation.The diffusion coefficient and concentration distribution of SBS modified asphalt on aggregate surface are included.The simulation results show that the diffusion coefficient of the aggregate surface of SBS modified asphalt is increased by 47.6%and 70.5%respectively after 110#asphalt and 130#asphalt are pre-wetted.The concentration distribution of SBS modified asphalt on the aggregate surface after pre-wetting is more uniform.According to the results of interface energy calculation,the interface energy of SBS modified bitumen and aggregate can be increased by about 5%after pre-wetting.According to the results of molecular dynamics simulation,the pre-wetting technology can effectively improve the interface workability of SBS modified bitumen and aggregate,so as to improve the interface performance.

Molecular simulation study of the microstructures and properties of pyridinium ionic liquid[HPy][BF_(4)]mixed with acetonitrile

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.

Plastic deformation mechanism of γ-phase U–Mo alloy studied by molecular dynamics simulations

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.

Dynamical Simulation of Cornea Deformation in Laser Surgery

A dynamical simulation method is presented to model the cornea deformation in surgery of laser thermokeratoplasty. The virtual cornea is constructed as a mass-spring system. The corneal surface tension is simulated by damping spring stretch between mass points on the cornea model. The aqueous humor in the eyeball is modeled as ideal gas, and the intraocular pressure is simulated by gas pressure. The coagulation force is exerted on each photocoagulation spot to demonstrate its collapse caused by the condensation of corneal soft tissue irradiated by laser. An extra viscous drag force is added to each mass point to weaken the mass point oscillation. The use of the effective time-corrected Verlet integral method brings about flowing and stable dynamic simulation procedures. The simulation results show that, comparing to the undeformed model, the curvature of the region between the optical center and photocoagulation spot increases obviously. Moreover, the shape of the deformed virtual cornea is much similar to that of the real cornea after surgery.

Development of new electromagnetic suspension-based high-speed Maglev vehicles in China:Historical and recent progress in the field of dynamical simulation

High-speed Maglev is a cutting-edge technology brought back into the focus of research by plans of the Chinese government for the development of a new 600 km/h Maglev train.A Chinese‐German cooperation with industrial and academic partners has been established to pursue this ambitious goal and bring together experts from multiple disciplines.This contribution presents the joint work and achievements of CRRC Qingdao Sifang,thyssenkrupp Transrapid,CDFEB,and the ITM of the University of Stuttgart,regarding research and development in the field of high‐speed Maglev systems.Furthermore,an overview is given of the historical development of the Transrapid in Germany,the associated development of dynamical simulation models,and recent developments regarding high-speed Maglev trains in China.

Application and dynamical performance simulation of tooth surface measured data of hypoid gear

The tooth surface shape of hypoid gear is very complicated, and tooth surface accuracy of hypoid gear can be measured by using the latticed measurement and scanning measurement. Advantages and disadvantages of the two measurement patterns are compared and application of their measurement data on hypoid gear＇s quality management is analyzed. How to use these measurement data to simulate the dynamical performance of hypoid gear is researched, and the intelligent predicton of the dynamical performance indexes of contact spot, root stress, vibration exciting forces and load distribution and hertz contact stress on the tooth surface are carried out. This research work has an important guiding sense to design and ma- chine hypoid gear with low vibration and noise.

Numerical Simulation and Dynamical Analysis for Low Salinity Water Lens in the Expansion Area of the Changjiang Diluted Water

The low salinity water lenses（LSWLes） in the expansion area of the Changjiang diluted water（CDW） exist in a certain period of time in some years. The impact of realistic river runoff, ocean currents and weather conditions need to be taken into account in the dynamical analysis of LSWL, which is in need of research. In this paper, the POM-σ-z model is used to set up the numerical model for the expansion of the CDW. Then LSWL in summer 1977 is simulated, and its dynamic mechanism driven by wind, tide, river runoff and the Taiwan Warm Current is also analyzed. The simulated results indicate that the isolated LSWL detaches itself from the CDW near the river mouth, and then moves towards the northeast region outside the Changjiang Estuary. Its maintaining period is from July 26 to August 11. Its formation and development is mainly driven by two factors. One is the strong southeasterly wind lasting for ten days. The other is the vertical tidal mixing during the transition from neap tide to spring tide.

Dynamic simulation of double-cased perforation in deepwater high temperature and high-pressure oil and gas wells

In order to ensure the penetrability of double-cased perforation in offshore oil and gas fields and to maximize the capacity of perforation completion, This study establishes a dynamic model of double-cased perforation using ANSYS/LS-DYNA simulation technology. The combination of critical perforation parameters for double casing is obtained by studying the influencing factors of the jet-forming process,perforation depth, diameter, and stress changes of the inner and outer casing. The single-target perforation experiments under high-temperature and high-pressure(HTHP) conditions and ground full-scale ring target perforation tests are designed to verify the accuracy of numerical simulation results. The reduced factor is adopted as the quantitative measure of perforation depth and diameter for different types of perforation charge under different conditions. The results show that the perforation depth reduction increases with temperature and pressure, and the reduced factor is between 0.67 and 0.87 under HTHP conditions of 130℃/44 MPa and 137℃/60 MPa. Comparing the results of the numerical simulation and the full-scale test correction, the maximum error is less than 8.91%, and this numerical simulation has strong reliability. This research provides a basis for a reasonable range of double-cased perforation parameters and their optimal selection.

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.

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.

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 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.

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.

Ab initio molecular dynamics simulation reveals the influence of entropy effect on Co@BEA zeolite-catalyzed dehydrogenation of ethane

The C–H bond activation in alkane dehydrogenation reactions is a key step in determining the reaction rate.To understand the impact of entropy,we performed ab initio static and molecular dynamics free energy simulations of ethane dehydrogenation over Co@BEA zeolite at different temperatures.AIMD simulations showed that a sharp decrease in free energy barrier as temperature increased.Our analysis of the temperature dependence of activation free energies uncovered an unusual entropic effect accompanying the reaction.The unique spatial structures around the Co active site at different temperatures influenced both the extent of charge transfer in the transition state and the arrangement of 3d orbital energy levels.We provided explanations consistent with the principles of thermodynamics and statistical physics.The insights gained at the atomic level have offered a fresh interpretation of the intricate long-range interplay between local chemical reactions and extensive chemical environments.

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.

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.

Molecular Dynamics Numerical Simulation of Adsorption Characteristics and Exploitation Limits in Shale Oil Microscopic Pore Spaces

Microscopic pore structure in continental shale oil reservoirs is characterized by small pore throats and complex micro-structures.The adsorption behavior of hydrocarbons on the pore walls exhibits unique physical and chemical properties.Therefore,studying the adsorption morphology of hydrocarbon components in nanometer-sized pores and clarifying the exploitation limits of shale oil at the microscopic level are of great practical significance for the efficient development of continental shale oil.In this study,molecular dynamics simulations were employed to investigate the adsorption characteristics of various single-component shale oils in inorganic quartz fissures,and the influence of pore size and shale oil hydrocarbon composition on the adsorption properties in the pores was analyzed.The results show that different molecules have different adsorption capacities in shale oil pores,with lighter hydrocarbon components(C6H14)exhibiting stronger adsorption abilities.For the same adsorbed molecule,the adsorption amount linearly increases with the increase in pore diameter,but larger pores contribute more to shale oil adsorption.In shale pores,the thickness of the adsorption layer formed by shale oil molecules ranges from 0.4 to 0.5 nm,which is similar to the width of alkane molecules.Shale oil in the adsorbed state that is difficult to be exploited is mainly concentrated in the first adsorption layer.Among them,the volume fraction of adsorbed shale oil in 6 nm shale pores is 40.8%,while the volume fraction of shale oil that is difficult to be exploited is 16.2%.

Dynamic simulation of differential accumulation history of deep marine oil and gas in superimposed basin:A case study of Lower Paleozoic petroleum system of Tahe Oilfield,Tarim Basin,NW China

According to the complex differential accumulation history of deep marine oil and gas in superimposed basins,the Lower Paleozoic petroleum system in Tahe Oilfield of Tarim Basin is selected as a typical case,and the process of hydrocarbon generation and expulsion,migration and accumulation,adjustment and transformation of deep oil and gas is restored by means of reservoine-forming dynamics simulation.The thermal evolution history of the Lower Cambrian source rocks in Tahe Oilfield reflects the obvious differences in hydrocarbon generation and expulsion process and intensity in different tectonic zones,which is the main reason controlling the differences in deep oil and gas phases.The complex transport system composed of strike-slip fault and unconformity,etc.controlled early migration and accumulation and late adjustment of deep oil and gas,while the Middle Cambrian gypsum-salt rock in inner carbonate platform prevented vertical migration and accumulation of deep oil and gas,resulting in an obvious"fault-controlled"feature of deep oil and gas,in which the low potential area superimposed by the NE-strike-slip fault zone and deep oil and gas migration was conducive to accumulation,and it is mainly beaded along the strike-slip fault zone in the northeast direction.The dynamic simulation of reservoir formation reveals that the spatio-temporal configuration of"source-fault-fracture-gypsum-preservation"controls the differential accumulation of deep oil and gas in Tahe Oilfield.The Ordovician has experienced the accumulation history of multiple periods of charging,vertical migration and accumulation,and lateral adjustment and transformation,and deep oil and gas have always been in the dynamic equilibrium of migration,accumulation and escape.The statistics of residual oil and gas show that the deep stratum of Tahe Oilfield still has exploration and development potential in the Ordovician Yingshan Formation and Penglaiba Formation,and the Middle and Upper Cambrian ultra-deep stratum has a certain oil and gas resource prospect.This study provides a reference for the dynamic quantitative evaluation of deep oil and gas in the Tarim Basin,and also provides a reference for the study of reservoir formation and evolution in carbonate reservoir of paleo-craton basin.

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.