VACANCY GENERATION AND ADSORPTION OF Cu ATOM AT Ag(1 1 1) SURFACE DURING DIFFUSION OF Cu-TRIMER

2014 ◽  
Vol 21 (05) ◽  
pp. 1450072 ◽  
Author(s):  
ZULFIQAR ALI SHAH ◽  
SARDAR SIKANDAR HAYAT ◽  
Z. REHMAN ◽  
SARDAR SIDDIQUE RAHMAN ◽  
FARIDA BOUAFIA
Keyword(s):  
Molecular Dynamics ◽  
Surface Layer ◽  
Time Evolution ◽  
Adsorption Energy ◽  
Md Simulation ◽  
Vacant Site ◽  
Substitutional Site ◽  
Constant Energy ◽  
Self Diffusion ◽  
Vacancy Generation

In this paper, the vacancy generation at (1 1 1) surface of silver ( Ag ) and the adsorption of copper ( Cu ) atom in the vacant site at Ag (1 1 1) surface has been studied using molecular dynamics (MD) simulation technique. The run of micro-canonical constant energy (NVE) ensemble results the generation of vacancy at 700 K in the presence of Cu -trimer, and its migration is observed toward the island as a result of self-diffusion of the surface layer atom. The energy of vacancy generation at Ag surface is found to be Ev = 1.078 eV , in the presence of Cu -trimer. The popped-up Ag adatom combines with Cu -trimer, making a mixed-tetramer ( Cu 3– Ag island). The adsorption energy of the Cu -atom among the mixed-tetramer island into the substitutional site is Es = ~ -0.813 eV , leaving a mixed-trimer ( Cu 2– Ag island) at Ag (1 1 1). Moreover, the presence of the island creates some anharmonic effects like dislocations and fissures at the surface. These dislocations and fissures show a trend of attraction to each other and also migrate toward the island, during the time evolution of the system.

New View of Low-Temperature Sintering Phenomenon of Nanometer-Size Particles Based on Molecular Dynamics Study

MRS Advances ◽  
2016 ◽  
Vol 1 (30) ◽  
pp. 2167-2172
Author(s):  
Norie Matsubara ◽  
Shinji Munetoh ◽  
Osamu Furukimi
Keyword(s):  
Molecular Dynamics ◽  
Surface Layer ◽  
Diffusion Coefficient ◽  
Heating Temperature ◽  
Md Simulations ◽  
Atomic Scale ◽  
Self Diffusion ◽  
The Mean ◽  
The Relationship ◽  
Self Diffusion Coefficient

ABSTRACTIn this study, we have investigated a behavior of particle with diameter several ten nanometers size at the time of heating on an atomic scale by numerical analysis using the molecular dynamics (MD) simulation. On solving the equation of motion, the Langevin equation was adopted. The Finnis-Sinclair potential, which can well reproduce the mechanical properties of a BCC-metal, was used as the interatomic force. We determined the relationship between the melting point (Tm) of the nano-sized particles and its diameter by MD simulations. We have also investigated the self-diffusion coefficient of each atom-forming at a temperature larger or less than Tm of the submicron-size metal particles . As a result, even in case of heating at a temperature larger than Tm, the mean self-diffusion coefficient at the center of a particle was 10-7–10-6 cm2/sec. On the other hand, at the surface layer of the particle was two to three orders of magnitude larger than that at the center. Those particles were in a quasi-molten state. It is conceivable that the thickness of the surface layer can explain a phenomenon that sintering progresses as the heating temperature increases.

Molecular dynamics simulation of interhalogen compounds. 1. Liquid chlorine trifluoride (ClF3): structure and thermodynamics

1992 ◽  
Vol 70 (1) ◽  
pp. 34-38 ◽  
Author(s):  
Ramesh K. Wadi ◽  
Vivek Saxena
Keyword(s):  
Molecular Dynamics ◽  
Thermodynamic Properties ◽  
Md Simulation ◽  
Pair Potential ◽  
Liquid Structure ◽  
Spectroscopic Studies ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Laser Raman

The results of a molecular dynamics (MD) simulation study of liquid chlorine trifluoride (ClF3) at 217, 260, and 287 K are reported. The cubic simulation cell consists of 108 ClF3 molecules assumed to be interacting via site–site Lennard–Jones 12–6 pair potential. The parameters for F–F and Cl–Cl interaction are the same as used for the simulation of F2, and Cl2, respectively, and those for the Cl–F cross interaction are calculated using Lorentz–Berthelot rules. These results are then used to calculate various radial distribution functions characteristic of the liquid structure. Thermodynamic properties, namely, configurational energy, constant volume specific heat, and internal pressure are also reported. The time-dependent properties, mean square force and torque, self diffusion coefficient, and the quantum corrections to the free energy, were also obtained. The dimer configuration drawn based on the observed contact distances was found to be in good agreement with the results of matrix isolation infrared and laser Raman spectroscopic studies. Keywords: MD simulation, interhalogens, liquid structure, thermodynamic properties.

Translational and rotational dynamics in supercritical methanol from molecular dynamics simulation

2004 ◽  
Vol 76 (1) ◽  
pp. 203-213 ◽  
Author(s):  
Michalis Chalaris ◽  
J. Samios
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Time Correlation ◽  
The Self ◽  
Dynamics Simulation ◽  
Supercritical Methanol ◽  
Reorientational Motion ◽  
Self Diffusion ◽  
Theoretical Predictions

The purpose of this paper is to review our latest molecular dynamics (MD) simulation studies on the temperature and density dependence of the translational and reorientational motion in supercritical (SC) methanol. In the present treatment, Jorgensen's [W. L. Jorgensen. J. Phys. Chem. A102, 8641 (1998)] transferable potential model, tested in a recent MD study of hydrogen bonds in this fluid [M. Chalaris and J. Samios, J. Phys. Chem. B103, 1161 (1999)], was employed to simulate the dynamics of the system. The simulations were performed in the canonical (NVT) ensemble along the isotherms 523, 623, and 723 K and densities corresponding to the pressures from 10 to 30 MPa. Several dynamical properties of the fluid have been obtained and analyzed in terms of appropriate time-correlation functions (CFs). With respect to the translational dynamics, the self-diffusion coefficients obtained have been used to test the applicability of the well-known Chapman-Enskog kinetic theory. We have found that the theoretical predictions for the self-diffusion coefficients are only in qualitative agreement with the MD results over the whole temperature and density range studied. Finally, the inspection of the reorientational CFs and their corresponding correlation times lead to the conclusion that the reorientational motion of the SC methanol molecules in the sample is anisotropic.

Dipropargyl ether bisphenol A based boron-containing polymer: synthesis, characterization and molecular dynamics simulations of the resulting pyrolysis and carbonization

RSC Advances ◽  
2015 ◽  
Vol 5 (5) ◽  
pp. 3390-3398 ◽  
Author(s):  
N. Gao ◽  
X. Jiang ◽  
Y. H. Liu
Keyword(s):  
Molecular Dynamics ◽  
Bisphenol A ◽  
Molecular Dynamics Simulations ◽  
Time Evolution ◽  
Small Molecule ◽  
Md Simulation ◽  
Polymer Synthesis ◽  
Color Code ◽  
Pyrolysis Products ◽  
Dynamics Simulations

The time evolution of major pyrolysis products including small-molecule species of a dipropargyl ether bisphenol A based novel boron-containing polymer was examined via ReaxFF-MD simulation (Color code: C, grey; O, red; H, white; B, yellow).

Some Properties of Molten KCl at High Density Studied by MD Simulation

1981 ◽  
Vol 36 (10) ◽  
pp. 1106-1111 ◽  
Author(s):  
Ryuzo Takagi ◽  
Isao Okada ◽  
Kazutaka Kawamura
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Thermodynamic Properties ◽  
Diffusion Coefficients ◽  
Md Simulation ◽  
Ambient Pressure ◽  
The Self ◽  
Self Diffusion ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular dynamics simulations of molten KCl have been performed at 1173 K with the molar volumes of 52.0 (the value under ambient pressure), 50.0, 48.0 and 45.0 cm3 mol-1 . Some thermodynamic properties at higher densities have been evaluated, which are generally in good agreement with the experimentally obtained ones and Monte Carlo results. Both at normal and higher densities, the self-exchange velocities of neighbouring unlike ions (SEV) are found to be proportional to the internal mobilities with nearly the same constant as derived previously for molten LiCl, RbCl and their 1 : 1 mixture. Calculated transport properties such as the SEV and the self-diffusion coefficients considerably decrease with increasing density, while the configuration does not change much.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

scholarly journals Molecular Dynamics Simulation on the Interaction between Palygorskite Coating and Linear Chain Alkane Base Lubricant

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 286
Author(s):  
Jin Zhang ◽  
Lv Yang ◽  
Yue Wang ◽  
Huaichao Wu ◽  
Jiabin Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Molecular Diffusion ◽  
Linear Chain ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Experimental Development ◽  
Practical Applications ◽  
Self Diffusion

Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C12, tetradecane C14, hexadecane C16, and octadecane C18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C12 molecule exhibited higher self-diffusion coefficient values than C14, C16 and C18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

scholarly journals Self-diffusion of Fe and Pt in L1-Ordered FePt: Molecular Dynamics simulation

2021 ◽  
Vol 192 ◽  
pp. 110337
Author(s):  
S.I. Konorev ◽  
R. Kozubski ◽  
M. Albrecht ◽  
I.A. Vladymyrskyi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Self Diffusion

scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

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