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.

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.

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.

Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants

The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

The Effect of Interatomic Potentials on the Molecular Dynamics Simulation of Nanometric Machining

One of the major tasks in a molecular dynamics （MD） simulation is the selection of adequate potential functions, from which forces are derived. If the potentials do not model the behaviour of the atoms correctly, the results produced from the simulation would be useless. Three popular potentials, namely, Lennard-Jones （L J）, Morse, and embedded-atom method （EAM） potentials, were employed to model copper workpiece and diamond tool in nanometric machining. From the simulation results and further analysis, the EAM potential was found to be the most suitable of the three potentials. This is because it best describes the metallic bonding of the copper atoms; it demonstrated the lowest cutting force variation, and the potential energy is most stable for the EAM.

基于MVVM的ReaxFF MD模拟的化学反应数据系统的建立

基于反应力场(reactive force field,ReaxFF)的反应分子动力学模拟的结果分析具有挑战性。国际首个ReaxFF MD化学反应分析及可视化工具VARxMD(visulization and analysis of ReaxFF molecular dynamics)可自动生成不同时刻之间完整的化学反应列表,通过物种检索进一步对反应路径进行分类。但VARxMD目前的反应分析针对的是某一确定条件下单一的ReaxFF MD模拟轨迹,利用VARxMD分析获得一次模拟的完整反应列表需要消耗大量计算资源和时间。本文提出基于数据库来储存VARxMD反应分析结果数据,基于数据库检索进一步分析反应的思路,并采用MVVM(model-view-view model)的系统设计模式、结合渐进式框架Vue.js建立了ReaxFF MD模拟的化学反应数据系统ReaxMDDB(reaction database of ReaxFF MD simulation)。系统应用于多个RP-3模型热解和氧化模拟反应数据的结果表明:该系统不仅实现了多个ReaxFF MD模拟的详细反应的统一分析和化学反应的2D分子结构显示,而且可永久保存模拟获得的反应数据集以备后续进一步分析反应机理。ReaxMDDB具有很好的通用性,为认识不同反应模拟所揭示的共性化学反应机理提供了方便的平台。

COMPUTERIZED SIMULATION OF MOLTEN SALT SOLUTION OF Li,KF,Cl SYSTEM BY MOLECULAR DYNAMIC METHOD

The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusion coeffients of Li^+,K^+,F^- and Cl^- have been calculated. The results are in agreement with the experimental values.The regularities of the distribution of ions and mieroscopic holes are discussed based on the results of computerized simulation.

Molecular dynamics simulation on thermodynamic properties of Pb-Ag alloys

Molecular dynamics simulation was used to simulate the thermodynamic properties of three binary alloys,Pb-Ag （1：1）,Pb-Ag （4：1）,and Pb-Ag （9：1）.The energy functions,such as excess free energy,cohesive energy,and formation energy,were calculated.The calculated values agree well with the experimental ones.The atomic interactions were analyzed in macroscopic and microcosmic views and both are consistent well.

Solid−solid phase transition of tungsten induced by high pressure:A molecular dynamics simulation

The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster analysis(LSCA).It is found that under 40−100 GPa at a cooling rate of 0.1 K/ps a pure W melt first crystallizes into the body-centred cubic(BCC)crystal,and then transfers into the hexagonal close-packed(HCP)crystal through a series of BCC−HCP coexisting states.The dynamic factors may induce intermediate stages during the liquid−solid transition and the criss-cross grain boundaries cause lots of indistinguishable intermediate states,making the first-order BCC−HCP transition appear to be continuous.Furthermore,LSCA is shown to be a parameter-free method that can effectively analyze both ordered and disordered structures.Therefore,LSCA can detect more details about the evolution of the structure in such structure transition processes with rich intermediate structures.

Sorption and permeation of gaseous molecules in amorphous and crystalline PPX C membranes: molecular dynamics and grand canonical Monte Carlo simulation studies

Amorphous and crystalline poly （chloro-p-xytylene） （PPX C） membranes are constructed by using a novel com- putational technique, that is, a combined method of NVT＋NPT-molecular dynamics （MD） and gradually reducing the size （GRS） methods. The related free volumes are defined as homology clusters. Then the sorption and the permeation of gases in PPX C polymers are studied using grand canonical Monte Carlo （GCMC） and NVT-MD methods. The results show that the crystalline PPX C membranes provide smaller free volumes for absorbing or transferring gases relative to the amorphous PPX C area. The gas sorption in PPX C membranes mainly belongs to the physical one, and H bonds can appear obviously in the amorphous area. By cluster analyzing on the mean square displacement of gases, we find that gases walk along the x axis in the crystalline area and walk randomly in the amorphous area. The calculated permeability coefficients are close to the experimental data.

Microstructural evolution and mechanical properties of FeCoCrNiCu high entropy alloys:a microstructure-based constitutive model and a molecular dynamics simulation study

High entropy alloys(HEAs)attract remarkable attention due to the excellent mechanical performance.However,the origins of their high strength and toughness compared with those of the traditional alloys are still hardly revealed.Here,using a microstructure-based constitutive model and molecular dynamics(MD)simulation,we investigate the unique mechanical behavior and microstructure evolution of FeCoCrNiCu HEAs during the indentation.Due to the interaction between the dislocation and solution,the high dislocation density in FeCoCrNiCu leads to strong work hardening.Plentiful slip systems are stimulated,leading to the good plasticity of FeCoCrNiCu.The plastic deformation of FeCoCrNiCu is basically affected by the motion of dislocation loops.The prismatic dislocation loops inside FeCoCrNiCu are formed by the dislocations with the Burgers vectors of a/6[112]and a/6[112],which interact with each other,and then emit along the<111>slip direction.In addition,the mechanical properties of FeCoCrNiCu HEA can be predicted by constructing the microstructure-based constitutive model,which is identified according to the evolution of the dislocation density and the stress-strain curve.Strong dislocation strengthening and remarkable lattice distortion strengthening occur in the deformation process of FeCoCrNiCu,and improve the strength.Therefore,the origins of high strength and high toughness in FeCoCrNiCu HEAs come from lattice distortion strengthening and the more activable slip systems compared with Cu.These results accelerate the discovery of HEAs with excellent mechanical properties,and provide a valuable reference for the industrial application of HEAs.

The role of fluid polarity in the swelling of sodium-montmorillonite clay:A molecular dynamics and Fourier transform infrared spectroscopy study

Swelling clays are found extensively in various parts of the world, and sodium-montmorillonite(NaMMT) is the main constituent of an expansive clay mineral. In this work, the swelling behavior of NaMMT clay with a wide range of organic fluids, high polar through low polar fluids, is studied using a combination of Fourier transform infrared(FTIR) technique and molecular dynamics(MD) simulations.The construction of the representative clayefluid models is carried out, and the nature of nonbonded interactions between clay and fluids is studied using MD. Our FTIR and MD simulations results suggest the significant nonbonded interactions between Na-MMT clay and polar fluids, such as formamide and water. The nonbonded interactions of Na-MMT with methanol and acetone are significantly less than those in Na-MMT with polar fluids. The interactions of the fluids with various entities of the clay such as Sie O, Fee OH, Mge OH, and Ale OH captured via the spectroscopy experiments and modeling provide a finer understanding of the interactions and their contributions to swelling. The MD simulations are able to capture the band shifts observed in the spectra obtained in the spectroscopy experiments. This work also captures the conformations of interlayer sodium ions with formamide, water, methanol, and acetone during swelling. These nonbonded interactions provide insight into the molecular mechanism that the polarity of fluids plays an important role in the initiation of interlayer swelling, alteration in the orientations, and evolution of microstructure of swelling clays at the molecular scale.

Molecular dynamics simulation on generalized stacking fault energies of FCC metals under preloading stress

Molecular dynamics(MD) simulations are performed to investigate the effects of stress on generalized stacking fault(GSF) energy of three fcc metals(Cu, Al, and Ni). The simulation model is deformed by uniaxial tension or compression in each of [111], [11-2], and [1-10] directions, respectively, before shifting the lattice to calculate the GSF curve. Simulation results show that the values of unstable stacking fault energy(γusf), stable stacking fault energy(γsf), and unstable twin fault energy(γutf) of the three elements can change with the preloaded tensile or compressive stress in different directions.The ratio of γsf/γusf, which is related to the energy barrier for full dislocation nucleation, and the ratio of γutf/γusf, which is related to the energy barrier for twinning formation are plotted each as a function of the preloading stress. The results of this study reveal that the stress state can change the energy barrier of defect nucleation in the crystal lattice, and thereby can play an important role in the deformation mechanism of nanocrystalline material.

All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.

Structure and dynamical properties during solidification of liquid aluminum induced by cooling and compression

The structural transformation from a liquid into a crystalline solid is an important subject in condensed matter physics and materials science. In the present study, first-principles molecular dynamics calculations are performed to investigate the structure and properties of aluminum during the solidification which is induced by cooling and compression. In the cooling process and compression process, it is found that the icosahedral short-range order is initially enhanced and then begin to decay, the face-centered cubic short-range order eventually becomes dominant before it transforms into a crystalline solid.

Effects of Mg2+ on the binding of the CREB/CRE complex:Full-atom molecular dynamics simulations

Metal ions play critical roles in the interaction between deoxyribonucleic acid(DNA) and protein.The experimental research has demonstrated that the Mg^2+ ion can affect the binding between transcription factor and DNA.In our work,by full-atom molecular dynamic simulation, the effects of the Mg^2+ ion on the cyclic adenosine monophosphate(cAMP)response element binding protein(CREB)/cAMP response elements(CRE) complex are investigated.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg^2+ ion is added.Hence, an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg^2+ ion can enhance the stability of the DNA–protein complex.

The effect of dislocations on the thermodynamic properties of Ta single crystal under high pressure by molecular dynamics simulation

The thermodynamic properties of Ta metal under high pressure are studied by molecular dynamics simulation. For dislocation-free Ta crystal, all the thermodynamic properties considered are in good agreement with the results from exper- iments or higher level calculations. If dislocations are included in the Ta crystal, it is found that as the dislocation density increases, the hydrostatic pressure at the phase transition point of bcc-＋hcp and hcp--＋fcc decreases, while the Hugoniot temperature increases. Meanwhile, the impact pressure at the elastic-plastic transition point is found to depend on the crys- tallographic orientation of the pressure. As the dislocation density increases, the pressure of the elastic-plastic transition point decreases rapidly at the initial stage, then gradually decreases with the increase of the dislocation density.

Coalescence of heteroclusters Au_(767) and Ag_(767):a molecular-dynamics study

This paper studies the coalescence of heteroclusters Au767 and Ag767 by using molecular dynamics with the embedded atom method, where layer atomic energy is employed to describe the potential energy variation of per atom in different layers along radial direction. The results show that the coalescence is driven by releasing the atomic energy of the coalesced zone. The deformation, which is induced by substitutional and vacancy diffusion during the coalescence, makes the coalesced cluster disorder. If the summation of the thermal energy and the released atomic energy is large enough to keep the disorder state, the clusters form a metastable liquid droplet; otherwise, the clusters coalesce into a solid cluster when the coalesced cluster reaches the equilibrium state, and the coalesced cluster experiences liquid to solid ordering changes during the coalescence of a solid Au767 with a liquid Ag767 and a liquid Au767 with a liquid Ag767. The centre of figure of the cluster system is shifted during the coalescence process, and higher coalescence temperature causes larger shift degree.