Molecular Dynamics Simulation of YCl_3 Melt

The molecular dynamics method has been used to study the YCl3 molten salt. The results of the molecular dynamics simulation agree with those of the neutron diffraction experiment. It is found that there are like-octahedral structure of YCl or its fragment. The diffusion coefficients of Y3+ and Cl- in the YCl3 melt are also calculated.

Local structure of calcium silicate melts from classical molecular dynamics simulation and a newly constructed thermodynamic model

The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.

Molecular Dynamics Simulations for Melting Temperatures of SrF2 and BaF2

The shell-model molecular dynamics method was applied to simulate the melting temper- atures of SrF2 and BaF2 at elevated temperatures and high pressures. The same method was used to calculate the equations of state for SrF2 and BaF2 over the pressure range of 0.1 MPa-3 GPa and 0.1 MPa-7 GPa. Compared with previous results for equations of state, the maximum errors are 0.3% and 2.2%, respectively. Considering the pre-melting in the fluorite-type crystals, we made the necessary corrections for the simulated melting temper- atures of SrF2 and BaF2. Consequently, the melting temperatures of SrF2 and BaF2 were obtained for high pressures. The melting temperatures of SrF2 and BaF2 that were obtained by the simulation are in good agreement with available experimental data.

Molecular dynamics simulation of Ni_3Al melting

With the Voter-Chen version of embedded-atom model （EAM） potential and molecular dynamics, the melting of Ni3Al alloy was simulated by one-phase （conventional） and two-phase approaches. It is shown that the simulated melting point is dependent on the potential and the simulation method. The structures of the melts obtained by different simulation methods were analyzed by the pair correlation function, the coordination number, and the distribution of atom pair type （indexed by the Honeycutt-Andersen pair analysis technique）. The results show that the structures are very similar.

Molecular Dynamics Simulation of MgO Melting at High Pressure

Molecular dynamics simulation was used to study the melting of MgO at high pressures. The melting temperature of MgO was accurately obtained at elevated temperature and high pressure after corrections based on the modern theory of melting. The calculated melting curve was compared with the available experimental data and other theoretical results at the pressure range of 0-135 GPa. The corrected melting temperature of MgO is in good agreement with the results from Lindemann melting equation and the two- phase simulated results below 15 GPa.

Molecular dynamics simulation of relationship between local structure and dynamics during glass transition of Mg_7Zn_3 alloy

The rapid solidification process of Mg7Zn3 alloy was simulated by the molecular dynamics method. The relationship between the local structure and the dynamics during the liquid-glass transition was deeply investigated. It was found that the Mg-centered FK polyhedron and the Zn-centered icosahedron play a critical role in the formation of Mg7Zn3 metallic glass. The self-diffusion coefficients of Mg and Zn atoms deviate from the Arrhenius law near the melting temperature and then satisfy the power law. According to the time correlation functions of mean-square displacement, incoherent intermediate scattering function and non-Gaussian parameter, it was found that the β-relaxation in Mg7Zn3 supercooled liquid becomes more and more evident with decreasing temperature, and the α-relaxation time rapidly increases in the VFT law. Moreover, the smaller Zn atom has a faster relaxation behavior than the Mg atom. Some local atomic structures with short-range order have lower mobility, and they play a critical role in the appearance of cage effect in theβ-relaxation regime. The dynamics deviates from the Arrhenius law just at the temperature as the number of local atomic structures begins to rapidly increase. The dynamic glass transition temperature （Tc） is close to the glass transition point in structure （TgStr）.

Molecular Docking, 3D-QSAR and Molecular Dynamics Simulation Studies of Substituted Pyrimidines as Selective Covalent Janus Kinase 3 Inhibitors

Janus kinase 3（JAK3） is a member of Janus kinase（JAK） family, and it represents a promising target for the treatment of immune diseases and cancers. However, no highly selective inhibitors of JAK3 have been developed. For discovering the binding mechanism of JAK3 and these inhibitors, a molecular modeling study combining molecular docking, three-dimensional quantitative structure-activity relationships（3D-QSAR）, molecular dynamics and binding free energy calculations was performed on a series of pyrimidine-based compounds which could bind with the unique residue Cys909 of JAK3 kinase as the selective inhibitors of JAK3 in this work. The optimum Co MFA and Co MSIA models were generated based on the conformations obtained by molecular docking. The results showed that the models have satisfactory predicted capacity in both internal and external validation. Furthermore, a 50 ns molecular dynamics simulation was carried out to determine the detailed binding process of inhibitors with different activities. It was demonstrated that hydrogen bond interactions with Leu828, Glu903, Tyr904, Leu905 and Leu956 of JAK3 are significant for activity increase, and the Van der Waals interaction is mainly responsible for stable complex.

Learning physical states of bulk crystalline materials from atomic trajectories in molecular dynamics simulation

Melting of crystalline material is a common physical phenomenon,yet it remains elusive owing to the diversity in physical pictures.In this work,we proposed a deep learning architecture to learn the physical states(solid-or liquidphase)from the atomic trajectories of the bulk crystalline materials with four typical lattice types.The method has ultrahigh accuracy(higher than 95%)for the classification of solid-liquid atoms during the phase transition process and is almost insensitive to temperature.The atomic physical states are identified from atomic behaviors without considering any characteristic threshold parameter,which yet is necessary for the classical methods.The phase transition of bulk crystalline materials can be correctly predicted by learning from the atomic behaviors of different materials,which confirms the close correlation between atomic behaviors and atomic physical states.These evidences forecast that there should be a more general undiscovered physical quantity implicated in the atomic behaviors and elucidate the nature of bulk crystalline melting.

Molecular Dynamics Simulation of Dealloyed Layer-induced Tensile Stress in Cu_3Au

During stress corrosion cracking of Cu3Au alloy, there is a dealloyed layer on its surface because of preferential dissolution of Cu, and there is a linear distribution of Cu vacancy concentration in the dealloyed layer. Molecular dynamics simulation has been done on the three-dimensional crystal (about 148 000 atoms) by employing the embedded-atom method (EAM) potential. Simulation shows that Cu3Au crystal in which there is a dealloyed layer on one surface and one end is fixed will be deflected after relaxing for a long time because of a tensile stress generated at or near the dealloyed layer interface. The deflection and then the tensile stress increase with increasing the depth of dealloyed layer and the vacancy concentration in the dealloyed layer.

Molecular Dynamics Simulation Studies on the Micromorphology and Proton Transport of Nafion/Ti_(3)C_(2)T_(x) Composite Membrane

The perfluorosulfonic acid(PFSA) membrane doped with two-dimensional conductive filler Ti_(3)C_(2)T_(x) is a fuel cell proton exchange membrane with high application potential. Experimental studies showed that the proton conductivity of Nafion/Ti_(3)C_(2)T_(x) composite membrane is improved significantly compared with that in pure Nafion. However, the microscopic mechanism of doping on the enhancement of membrane performance is remain unclear now. In this work, molecular dynamics simulation was used to investigate the microscopic morphology and proton transport behaviors of Nafion/Ti_(3)C_(2)T_(x) composite membrane at the molecular level. The results shown that there were significant differences about the diffusion kinetics of water molecules and hydroxium ions in Nafion/Ti_(3)C_(2)T_(x) at low and high hydration levels in the nanoscale region.With the increase of water content, Ti_(3)C_(2)T_(x) in membrane was gradually surrounded by ambient water molecules to form a hydration layer, and forming a relatively continuous proton transport channel between Nafion polymer and Ti_(3)C_(2)T_(x) monomer. The continuous proton transport channel could increase the number of binding sites of proton and thus achieving high proton conductivity and high mobility of water molecules at higher hydration level. The current work can provide a theoretical guidance for designing new type of Nafion composite membranes.

Molecular Dynamics Simulations of Stretch-Induced Crystal Changes in Crystallized Polyethylene/Carbon Nanotubes Nanocomposites

Understanding deformation mechanisms in semi-crystalline polymers during stretching is useful for guiding the processing of highperformance polymer products. In the current work, molecular dynamics simulations were performed to investigate the crystal changes in crystallized polyethylene/carbon nanotube nanocomposites during uniaxial stretching. Both crystal fragmentation and melting occur at low strains. Crystals with small sizes are easier to melt, while those with large sizes would break into smaller crystals. In addition, crystals in interfacial regions are more likely to melt or break due to the orientation motion of carbon nanotubes. It was also found that the recrystallization process is closely related to the stretch-induced orientation of chain segments. After orientation of chain segments along stretching direction is saturated,the recrystallization of highly oriented segments dominates. The current simulation findings are effective complements to the theories of the mechanism of plastic deformation in semicrystalline polymers.

Molecular mechanics and dynamics simulation of hydrogen diffusion in aluminum melt

The main impurities in aluminum melt are hydrogen and Al_2O_3,which can deteriorate melt quality and materials performance.However,the diffusion process of H atoms in aluminum melt and the interactions among Al atoms,Al_2O_3 and hydrogen have been studied rarely.Molecular mechanics and dynamics simulations are employed to study the diffusion behaviors of different types of hydrogen,such as free H atoms,H atoms in H_2 and H^+ions in H_2O using COMPASS force field.Correspondingly,force field types h,h1h and h1o are used to describe different types of hydrogen which are labeled as H_h,H_(h1h) and H_(h1o).The results show that the adsorption areas are maximum for H_(h1o),followed by H_(h1h) and H_h.The diffusion ability of H_(h1o) is the strongest whereas H_h is hard to diffuse in aluminum melt because of the differences in radius and potential well depth of various types of hydrogen.Al_2O_3 cluster makes the Al atoms array disordered,creating the energy conditions for hydrogen diffusion in aluminum melt.Al_2O_3 improves the diffusion of H_h and H_(h1o),and constrains H_(h1h) which accumulates around it and forms gas porosities in aluminum.H_(h1o) is the most dispersive in aluminum melt,moreover,the distance of Al-H_(h1o) is shorter than that of Al-H_(h1h),both of which are detrimental to the removal of H_(h1o).The simulation results indicate that the gas porosities can be eliminated by the removal of Al_2O_3 inclusions,and the dispersive hydrogen can be removed by adsorption function of gas bubbles or molten fluxes.

Discovery of Novel Acetaldehyde Dehydrogenase 1A1(ALDH1A1) Inhibitors by Utilizing 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation

Acetaldehyde dehydrogenase 1A1 is a hopeful therapeutic target to ovarian cancer. In this present work, 3D-QSAR, molecular docking and molecular dynamics(MD) simulations were implemented on a series of quinoline-based ALDH1A1 inhibitors to investigate novel acetaldehyde dehydrogenase 1A1 inhibitors as anticancer adjuvant drugs for ovarian cancer. Two reliable CoMFA(Q^(2) = 0.583, R^(2) = 0.967) and CoMSIA(Q^(2) = 0.640, R^(2) = 0.977) models of ALDH1A1 inhibitors were established. Novel ALDH1A1 inhibitors were predicted by the 3D-QSAR models. Molecular docking reveals important residues for protein-compound interactions, and the results revealed ALDH1A1 inhibitors had stronger electrostatic interaction and binding affinity with key residues of protein, such as Phe171, Val174 and Cys303. Molecular dynamics simulations further verified the results of molecular docking. The above information provided significant guidance for the design of novel ALDH1A1 inhibitors.

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.

Relationship between Voronoi entropy and the viscosity of Zr_(36)Cu_(64) alloy melt based on molecular dynamics

Molecular dynamics simulation is used to investigate the relationship between Voronoi entropy and viscosity for rapid solidification processing of Zr36Cu64 binary alloy melt. The simulation results at different temperatures, cooling rates, and pressures, show that Voronoi entropy is able to accurately describe the relationship of the transition between the cluster structure and the viscosity of Zr36Cu64 binary alloy melt through Voronoi polyhedron analysis. That is, the higher the degree of order of the microstructure, the lower the Voronoi entropy is and the higher the viscosity is. The simulation provides an important reference for studying metallic glass with high glass-forming ability.

3D-QSAR,Molecular Docking and Molecular Dynamics Simulations of 3-Phenylsulfonylaminopyridine Derivatives as Novel PI3Kα Inhibitors

The p110α,catalytic subunit of PI3Ka,was the primary phosphoinositide 3-kinases(PI3Ks)isoform involved in oncogenic RTK signaling and tumorigenesis.In this study,the three-dimensional quantitative structure-activity relationship(3D-QSAR),molecular docking and molecular dynamics simulation were employed to study the binding mode between 3-phenylsulfonylaminopyridine derivatives and PI3Kα.The stable and reliable 3D-QSAR models were constructed based on the application of the comparative molecular field analysis(CoMFA)model(q^(2)=0.704,r^(2)=0.994)and comparative molecular similarity index analysis(CoMSIA)model(q^(2)=0.804,r^(2)=0.996).The contour maps illustrated relationship between structure and biological activity.The conformation obtained after MD simulation was more stable than the docked conformation.MD simulation was performed in a more realistic environment,and was much closer to physiological conditions.As a result,five novel PI3Kα inhibitors were designed with better biological activity than the template compound 8.

Discovery of Benzimidazole Derivatives as Novel Aldosterone Synthase Inhibitors:QSAR,Docking Studies,and Molecular Dynamics Simulation

Aldosterone synthase inhibitors can lessen the production of aldosterone in organisms,which effec-tively affecting the treatment of hypertension.A series of computational approaches like QSAR,docking,DFT and molecular dynamics simulation are applied on 40 benzimidazole derivatives of aldosterone synthase(CYP11B2)in-hibitors.Statistical parameters:Q^(2)=0.877,R^(2)=0.983(CoMFA)and Q^(2)=0.848,R^(2)=0.994(CoMSIA)indicate on good predictive power of both models and DFT’s result illustrates the stability of both models.Besides,Y-randomization test is also performed to ensure the robustness of the obtained 3D-QSAR models.Docking studies show inhibitors rely onπ-πinteraction with residues,such as Phe130,Ala313 and Phe481.Molecular dynamics simulation results further confirm that the hydrophobic interaction with proteins enhances the inhibitor’s inhibitory effect.Based on QSAR studies and molecular docking,we designed novel compounds with enhanced activity against aldosterone synthase.Furthermore,the newly designed compounds are analyzed for their ADMET proper-ties and drug likeness and the results show that they all have excellent bioavailability.

Simulation study on non-linear effects of initial melt temperatures on microstructures during solidification process of liquid Mg_7Zn_3 alloy

The non-linear effects of different initial melt temperatures on the microstructure evolution during the solidification process of liquid Mg7Zn3 alloys were investigated by molecular dynamics simulation, The microstructure transformation mechanisms were analyzed by several methods. The system was found to be solidified into amorphous structures from different initial melt temperatures at the same cooling rate of 1×10^12 K/s, and the 1551 bond-type and the icosahedron basic cluster （12 0 12 0 ） played a key role in the microstructure transition. Different initial melt temperatures had significant effects on the final microstructures. These effects only can be clearly observed below the glass transition temperature Tg; and these effects are non-linearly related to the initial melt temperatures, and fluctuated in a certain range. However, the changes of the average atomic energy of the systems are still linearly related with the initial melt temperatures, namely, the higher the initial melt temperature is, the more stable the amorphous structure is and the stronger the glass forming ability will be.

Coordination properties and structural units distribution of Q_T^i in calcium aluminosilicate melts from MD simulation

The distribution of Al （j） and the structural units distribution of Qi T in calcium aluminosilicate melts were studied by means of molecular dynamics simulation. The results show that provided there exists lower-field strength cation relative to Al3+, such as alkaline and alkaline earth metals, Al will be four-coordinated but not six-coordinated. Meanwhile, if there exist a large number of higher-field strength cations such as Si4+ and little lower-field strength cation, six-coordinated aluminum will be formed. The relation of structural units distribution of Qi T with chemical composition shift was also extracted, showing that as Ca2+ exists, the distributions of Qi Si, Qi Al or Qi T have the similar changing trend with the variation of component. Because of high-temperature effect, the Al-tetrahedral units in melts are greatly active and unstable and there exist dynamic transforming equilibria of Al（3）Al（4） and （Al（5））Al（4）. The three-coordinated oxygen and charge-compensated bridging oxygen are proposed to explain phenomena of the negative charge redundancy of AlO4 and location of network modifier with charge-compensated function in aluminosilicate melts.

Simulation of Melting Behavior of the MgSi03 Perovskite Under Lower Mantle Conditions

The melting curve of MgSiO3 perovskite was simulated using molecular dynamics method combining with the effective pair potentials under the lower mantle conditions. It was shown that the state equation simulated for MgSiO3 perovskite is very successful in reproducing accurately the experimental data over a wide range of pressure. The pressure dependence of the simulated melting temperature of MgSiO3 perovskite is in agreement with the recent experimental data. The melting curve simulated for MgSiO3 is very steep at pressures below 60 GPa first, then it becomes smooth with increasing pressure. At the core mantle boundary pressure 135 GPa, MgSiO3 perovskite melts at 6500 K, which is significantly lower than that of the extrapolations of the experimental data from Zerr and Boehler.