Papers by Keyword: Molecular Dynamics Simulation

Abstract: The objective of this study is to suggest a method for judging jumping periods, which means an atom moves significantly in a short time in liquid metal. In this study, molecular dynamics (MD) simulation of liquid Pb at 773 K was performed. The self-diffusion coefficient was calculated to confirm that the simulation adequately reproduces liquid Pb and was almost consistent with the reliable experimental data. In the evaluation of jumping period, atomic motion during jumping was considered. A method for estimating jumping period by using each atomic speed and 1st-peak of pair distribution function was suggested by using a time when speed is at a local minimum value.

Abstract: Molecular docking and molecular dynamics on substituted indole derivatives-Leucine Trasporter had been performed. Indole derivatives with methoxy and fluorine group are chosen and specific amino acid residue Arg30 and Asp404 are π-alkyl and π-cation interactions. The suggested molecule containing methoxy groups has an RMSD value of 1.95 Å, a binding energy of-4.00 kcal mol^-1, and an inhibition constant of 1.17 μM. The hypothesized fluorine-containing compound's RMSD value, binding energy, and inhibition constant were each 1.88 Å; -5.97 kcal mol^-1; and 41.88 μM, respectively. The substituted indole derivative with the methoxy group was stable, according to the findings of a 200-ns molecular dynamics simulation, while the substituted indole derivative with the fluorine group was less stable. Based on the examination of RMSD, RMSF, RoG, the quantity of hydrogen, and the level of contact stability of the ligands with the particular amino acid residues for the antidepressant drug, the dynamical interaction of ligands against LeuT was determined.

Abstract: Carbon nanotube (CNT) is an innovative material with significant potential for a wide range of applications, including but not limited to the development of lightweight composite materials or superconductors. A single CNT demonstrates an exceptional degree of tensile strength. CNTs are commonly employed in a structure of yarn, wherein several CNT strands are arranged and aligned together. CNT yarns, on the other hand, have a lower tensile strength than individual CNTs due to the different parameters of the yarn. This study aimed to investigate the effect of different structural parameters on the mechanical properties of CNT yarn. Sixty CNT yarn models with different structures were simulated with the molecular dynamic (MD) simulation. The varied parameters are the chirality of the CNTs, CNTs’ inner diameter, number of walls, crosslink density, and yarn twist angle. Tensile strength results from the simulations were compared concerning the varied parameters, and their influence on the nominal tensile strength of the CNT yarn was studied. It was found that the parameters for the CNT yarn that yields a higher tensile strength are the armchair type CNT with a small diameter, a large number of walls, crosslink density higher than approximately 1%, and a low twist angle.

Abstract: We have used molecular dynamics simulations to investigate the decomposition mechanisms of residual C defects near the interface of 4H-SiC/SiO₂ during NO annealing. We have observed drastically rapid defect decomposition by NO and O₂ mixed gas, which is thermodynamically more realistic, compared with single NO or O₂ gas annealing. We have constructed simplified defect decomposition model. This model numerically reproduced the simulation results, suggesting that multi-step and cooperative reactions caused by the coexistence of NO and O₂ during NO annealing effectively promote the decomposition of residual C defects.

Abstract: The strain rate exerts a profound influence on the mechanical characteristics of nanomaterials. To investigate this phenomenon, the molecular dynamics approach was employed to examine the impact of uniaxial compression along the [100] crystallographic direction in monocrystalline Al. The purpose of this research was to determine the differences in reactions observed during the elastic and plastic phases. It employed the Embedded Atom Method (EAM) as well as the Modified Embedded Atom Method (MEAM) potentials at 300 K. A comparative analysis of the outcomes from these potentials demonstrated considerable disparities. The results encompassed the percentage distribution of crystal structures (fcc, hcp, bcc, and others) as well as their atomic configurations. Several analytical factors were examined, including the strain-stress curve, the radial distribution function (RDF), the common neighbor analysis (CAN). The applied MEAM potential represents a subsequent occurrence of transitions following EAM, encompassing both increasing and decreasing phase transitions.

Abstract: We have developed a new interatomic potential of Si-O-C-N with newly added N for classical molecular dynamics simulation of NO annealing at 4H-SiC/SiO₂ interface. By adjusting the potential parameters to reproduce the material properties obtained from first-principles calculations for various kinds of structures, the accuracy of the potential has improved well enough to reproduce the formation of Si₃N termination at the 4H-SiC/SiO₂ interface during NO annealing. We have also observed that the defects with C=C double bonds have been modified into C-N bonds, which is supposed to be the decomposition process of residual C atoms in the NO annealing of 4H-SiC/SiO₂.

Abstract: The effects of the application of constant electric fields on the dynamics of a confined water droplet between two different surfaces are investigated, by using a molecular dynamics method. It is found that the water molecules responded to the electric field, which partially depends on the wettability of the different surfaces. The results reveal that the application of external electric fields causes to create extra pressure on the surfaces, which are theoretically justified. The induced pressure could be experienced by multilayer nano-filters, which are used in desalination processes, with the aid of an external electric field, and may reduce the water filters shelf life.

Abstract: The relationship of geometrical properties and mechanical properties of carbon nanotubes (CNTs) was investigated by using high-throughput molecular simulation. Geometrical properties such as diameter, number of walls, chirality, and crosslink density were considered. As a key factor in determining the mechanical properties of composites reinforced with CNTs, nominal tensile strength is the focus in this study, which can be calculated by fracture force divided by the full cross-sectional area including the hollow core and the wall thickness. The fracture mode, nominal tensile strength, and nominal Young’s modulus under the condition of CNTs outermost tube loading axial tensile test were evaluated. Three types of fracture modes led by different crosslink densities of CNTs were obtained. By data-mining through large amounts of datasets, we showed that CNTs with small diameter, large number of walls, and crosslinks between walls can have high nominal tensile strength. We demonstrated that zigzag-type CNTs with crosslink density of approximately 1.5% - 2.5%, armchair-type CNTs with crosslink density of approximately 3% - 4% can help improve the load transfer from the outer tube to the inner tube the most.

Abstract: Aluminum alloys have been attracting significant attention. Especially Al-Mg-Si alloys can exhibit an excellent balance between strength and ductility. Deformation mechanisms and microstructural evolution are still challenging issues. Accordingly, to describe how the type of phase influence mechanical behaviour of Al/Mg/Si alloys, in this paper atomic simulations are performed to investigate the uniaxial compressive behaviour of Al-Mg-Si ternary phases. The compression is at the same strain rate (3.10¹⁰ s−1); using Modified Embedded Atom Method (MEAM) potential to model the deformation behaviour. From these simulations, we get the total radial distribution function; the stress-strain responses to describe the elastic and plastic behaviors of GP-AlMg₄Si₆, U2-Al₄Mg₄Si₄ and β-Al₃Mg₂Si₆ phases. For a Detailed description of which phase influence hardness and ductility of these alloys; the mechanical properties are determined and presented. These stress-strain curves obtained show a rapid increase in stress up to a maximum followed by a gradual drop when the specimen fails by ductile fracture. From the results, it was found that GP-AlMg₄Si₆ & U2-Al₄Mg₄Si₄ phases are brittle under uniaxial compressive loading while β-Al₃Mg₂Si₆ phase is very ductile under the same compressive loading. The engineering stress-strain relationship suggests that β-Al₃Mg₂Si₆ phase have high elasticity limit, ability to resist deformation and have the advantage of being highly malleable. Molecular dynamics software LAMMPS was used to simulate and build the Al-Mg-Si ternary system.

Abstract: Hydrogen energy has great potential to become one of the clean energies of the future. The current use of hydrogen gas as an energy source still has problems, namely in the distribution and storage system. One solution to overcome these problems is to use the adsorption method. Zeolite material is considered to be a good material to be used as a storage medium for hydrogen gas. Experimental research generally still requires a fairly high cost. Therefore, we need another method that can support it. In this research, the author used the Molecular Dynamics Simulation method. The variation of temperature used in this simulation is 77, 100, 150, 195, 273, and 293 K with a variation of pressure at each temperature is 1, 2, 4, 6, 8, and 10 bar. Our simulation results are then compared with the results of experimental research conducted by other researchers. At low pressure and high temperature, the results of our simulation are close to the results of experimental research. But at high pressure and low temperature, the results of our simulation are significantly different from the results of experimental research.