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.

Molecular Dynamic Simulation on the Absorbing Process of Isolating and Coating of α-olefin Drag Reducing Polymer

The absorbing process in isolating and coating process of α-olefin drag reducing polymer was studied by molecular dynamic simulation method, on basis of coating theory of α-olefin drag reducing polymer particles with polyurethane as coating material. The distributions of sodium laurate, sodium dodeeyl sulfate, and sodium dodeeyl benzene sulfonate on the surface of α-olefin drag reducing polymer particles were almost the same, but the bending degrees of them were obviously different. The bending degree of SLA molecules was greater than those of the other two surfactant molecules. Simulation results of absorbing and accumulating structure showed that, though hydrophobie properties of surfactant molecules were almost the same, water density around long chain sulfonate sodium was bigger than that around alkyl sulfate sodium. This property goes against useful absorbing and accumulating on the surface of α-olefin drag reducing polymer particles; simulation results of interactions of different surfactant and multiple hydroxyl compounds on surface of particles showed that, interactions of different surfaetant and one kind of multiple hydroxyl compound were similar to those of one kind of surfaetant and different multiple hydroxyl compounds. These two contrast types of interactions also exhibited the differences of absorbing distribution and closing degrees to surface of particles. The sequence of closing degrees was derived from simulation; control step of addition polymerization interaction in coating process was absorbing mass transfer process, so the more closed to surface of particle the multiple hydroxyl compounds were, the easier interactions With isoeyanate were. Simulation results represented the compatibility relationship between surfactant and multiple hydroxyl compounds. The isolating and coating processes of α-olefin drag reducing polymer were further understood on molecule and atom level through above simulation research, and based on the simulation, a referenced theoretical basis was provided for practical optimal selection and experimental preparation of α-olefin drag reducing polymer particles suspension isolation agent.

Molecular Dynamic Simulation of Melting Points of Trans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD） with Some Propellants

Molecular dynamic simulation was employed to predict the melting points Tm of TNAD/HMX, TNAD/RDX, TNAD/DINA, and TNAD/DNP systems （tans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD）, dinitropiperazine （DNP）, cyclotetramethylenetetranitroamine （HMX）, cyclotrimethylenetrinitramine （RDX）, and N-nitrodihydroxyethylaminedinitrate （DINA））. Tm was determined from the inflexion point on the curve of mean specific volume vs. temperature. The result shows that the Tm values of TNAD/HMX, TNAD/RDX, and TNAD/DINA systems are 500, 536, and 488 K, respectively. The TNAD/DNP system has no obvious Tm value, which shows the system is insoluble. Using Tm, the solubility of the four systems was analyzed. The radial distribution functions of the four systems were analyzed and the main intermolecular forces between TNAD and other energetic components are short-range interactions. The better the solubility is, the stronger the intermoleenlar interaction is. In addition, the force field energy at different temperature was also analyzed to predict Tm of the four systems.

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.

Molecular dynamic simulation of lubricant spreading： effect from the substrate and endbead

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.

Study of structural and magnetic properties of Fe(80)P-9B(11) amorphous alloy by ab initio molecular dynamic simulation

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.

Molecular Dynamic Simulation of Lattice Distortion Region Produced by Rounded Grain Boundary in Nanocrystalline Materials

The distortion structure in nanocrystalline NiAl is studied using molecular dynamics simulation. The rounded grain boundaries in these nanograins are a direct source for the observed lattice distortion. The change of grain size affects directly the volume fraction of the distorted lattice in the nanograin.

Molecular dynamic simulation of the thermodynamic and kinetic properties of nucleotide base pair

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.

Atomic scale imaging of monocrystalline Si (001) surface by molecular dynamic simulation

Non-contact atomic force microscopy（nc-AFM） atomic-scale imaging process of monocrystalline silicon surface using capped single-wall carbon nanotube tip is simulated by molecular dynamic method. The simulation resuhs show that the nc-AFM imaging force mainly comes from the C-Si and C-C chemical covalent bonding forces, especially the former, the nonbonding Van der Waals force change is small during the range of stable imaging height. When the tip-surface distance is smaller than the stable imaging height, several neighboring carbon atoms at the tip apex are attracted, and some of them jump onto the sample surface. Finally the tip apex configuration is destroyed with the tip indenting further.

Studies on sensitivity to tension and gating pathway of MscL by molecular dynamic simulation

Mechanosensitive（MS） ion channels play an important role in various physiological processes.Although the determination of the structure of mechanosensitive channel of large conductance（MscL） makes the simulation study possible,it has not so far been possible to directly simulate the gating mechanism of MscL in atomic detail.In this article,MscL has been studied via molecular dynamic（MD） simulations to gain a detailed description of the sensitivity to lateral tension and the gating pathway.MscL undergoes conformational rearrangement in sustaining lateral tension,and the open state is obtained when 2.0 MPa lateral tension is directly applied on the pure protein.During the opening process,Loop region responds to tension first,and the mechanical sensitivity is followed by S1 domain.Transmembrane（TM） bundle is the key position for channel opening,and the motion of TM1 helices finally realizes the significant expansion of the constricted gating pore.C-terminus domain presents expansion later during the TM opening.In our study,return of the whole protein to the initial closed state is achieved only in the early opening stage.During the relaxation from the open state,the TM helices are the most mobile domain,which is different from the opening process.

Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.

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.

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-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%.

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.

Exploring the molecular mechanism of action of curcumin for the treatment of diabetic retinopathy,using network pharmacology,molecular docking,and molecular dynamics simulation

Background:Based on network pharmacology and molecular docking,the present study investigated the mechanism of curcumin(CUR)in diabetic retinopathy treatment.Methods:Based on the DisGeNET,Swiss TargetPrediction,GeneCards,Online Mendelian Inheritance in Man,Gene Expression Omnibus,and Comparative Toxicogenomics Database,the intersection core targets of CUR and diabetic retinopathy were identified.The intersection target was imported into the STRING database to obtain the protein-protein interaction map.According to the Database for Annotation,Visualization and Integrated Discovery database,the intersected targets were enriched in Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes pathways.Then Cytoscape 3.9.1 is used to make the drug-target-disease-pathway network.The mechanism of CUR and diabetic retinopathy was further verified by molecular docking and molecular dynamics simulation.Results:There were 203 intersecting targets of CUR and diabetic retinopathy identified.1320 GO entries were enriched for GO functions,which were primarily involved in the composition of cells such as identical protein binding,protein binding,enzyme binding,etc.It was found that 175 pathways were enriched using Kyoto Encyclopedia of Genes and Genomes pathway enrichment methods,which were mainly included in the lipid and atherosclerosis,AGE-RAGE signaling pathway in diabetic complications,pathways in cancer,etc.In the molecular docking analysis,CUR was found to have a good ability to bind to the core targets of albumin,IL-1B,and IL-6.The binding of albumin to CUR was further verified by molecular dynamics simulation.Conclusion:As a result of this study,CUR may exert a role in the treatment of diabetic retinopathy through multi-target and multi-pathway regulation,which indicates a possible direction of future research.

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.