Molecular Dynamics Studies of Defects in Si

1990 ◽  
Vol 209 ◽  
Author(s):  
M.S. Duesbery ◽  
D.J. Michel ◽  
Efthimios Kaxiras ◽  
B. Joos
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamic Simulation ◽  
Experimental Evidence ◽  
Dynamic Simulation ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Recent Literature ◽  
Empirical Potentials ◽  
Generalized Stacking Fault ◽  
Generalized Stacking Fault Energy

ABSTRACTThe efficacy of three modern empirical potentials in the molecular dynamic simulation of the configurations, energies and mobility of dislocation cores and their excitations is assessed in the light of recent literature. The results are found to be inconsistent both between different potentials and with experimental evidence. It is argued that the discrepancies are rooted in the limited databases which have been used in the construction of empirical potentials. The reason for the discrepancies is demonstrated by comparing empirical and density functional calculations of the generalized stacking fault energy.

Study on Nanolithography Process of Polycrystalline Copper Using Molecular Dynamic Simulation

2007 ◽  
Vol 340-341 ◽  
pp. 961-966
Author(s):  
Chan Il Kim ◽  
Young Suk Kim ◽  
Sang Il Hyun ◽  
Seung Han Yang ◽  
Jun Young Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Diamond Like Carbon ◽  
Polycrystalline Copper ◽  
Berkovich Indenter ◽  
Contact Surfaces ◽  
Dynamics Simulations

Molecular dynamics simulations are performed to verify the effect of grain boundary on nanolithography process. The model with about two hundred thousand copper (Cu) atoms is composed of two different crystal orientations of which contact surfaces are (101) and (001) planes. The grain boundary is located on the center of model and has 45 degreeangle in xz-plane. The tool is made of diamond-like-carbon with the shape of Berkovich indenter. As the tool is indented and plowed on the surface, dislocations are generated. Moreover, during the plowing process, the steps as well as the typical pile-ups are formed in front of the tool. These defects propagate into the surface of the substrate. As the tool approaches to the grain boundary, the defects are seen to be accumulated near the grain boundary. The shape of the grain boundary is also significantly deformed after the tool passes it. We observed the forces exerted on the tool by the contact with substrate, so that the friction coefficients can be obtained to address the effect of the grain boundary on the friction characteristics.

Hydrogen doping in wide-bandgap amorphous In–Ga–O semiconductors

2020 ◽  
Vol 8 (43) ◽  
pp. 15436-15449
Author(s):  
Julia E. Medvedeva ◽  
Bishal Bhattarai
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Long Range ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Structural Transformations ◽  
Wide Bandgap ◽  
Computationally Intensive ◽  
Dynamics Simulations

Microscopic mechanisms of the formation of H defects and their role in passivation of under-coordinated atoms, short- and long-range structural transformations, and the resulting electronic properties of amorphous In–Ga–O with In : Ga = 6 : 4 are investigated using computationally-intensive ab initio molecular dynamics simulations and accurate density-functional calculations.

scholarly journals MOLECULAR DYNAMICS SIMULATIONS OF SEVERAL SELECTED COMPOUNDS FROM THE HERBAL DATABASE OF INDONESIA RESULTS OF MOLECULAR DOCKING AGAINST DNA METHYLTRANSFERASE ENZYME

2018 ◽  
Vol 10 (1) ◽  
pp. 285
Author(s):  
Muhamad Fikri Ihsan ◽  
Arry Yanuar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Dna Methyltransferase ◽  
Positive Control ◽  
Amino Acid Residues ◽  
Dynamics Simulations ◽  
Ucsf Chimera

Objective: This study aimed to investigate the interactions of DNA methyltransferase (DNMT) enzymes and potential ligands as DNMT inhibitorsthrough molecular dynamics simulations.Methods: This study was conducted using tools in the form of hardware (primary and secondary computers) and software (OpenBabel, AutoDockTools, Amber MD, Amber Tools, VMD, PuTTY, LigandScout, and UCSF Chimera).Results: Results of molecular docking of cassiamin C, procyanidin B2, epicatechin-4alphaent-8-ent-epicatechin, epicatechin-4beta-8-epicatechin-3-O-gallate, neorhusflavanone, 3-O-galloylepigallocatechin -4beta-6-epicatechin-3-O-gallate, withanolide, 3-O-galloylepigallocatechin-4beta-6-epigallocatechin-3-O-gallate, cyanidin-3-6″-caffeylsophoroside-5-glucoside, epifriedelinol, gallocatechin-4alpha-8-epicatechin, scutellarein-7-glucosyl-1-4-rhamnoside, epigallocatechin-3-gallate (EGCG) (positive control), and sinefungin (co-crystal) compounds showed ΔG values −9.34,−10.95, −7.95, −11.01, −8.78, −8.87, −11.49, −7.98, −5.92, −8.92, −9.17, −8.76, −9.70, and −9.11 kcal/mol, respectively. Cassiamin C, procyanidin B2,epicatechin-4-beta-8-epicatechin-3-O-gallate, withanolide, and gallocatechin-4alpha-8-epicatechin compounds had lower ΔG than sinefungin (cocrystal)and EGCG (positive control) compounds. The results of molecular dynamic simulation of seven selected compounds showed the best overallactivities were procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, and gallocatechin-4alpha-8-epi-catechin compounds.Conclusions: The best overall activities based on molecular docking and molecular dynamic simulation were procyanidin B2, epicatechin-4beta-8-epicatechin-3-O-gallate, and gallocatechin-4alpha-8-epi-catechin compounds. Amino acid residues that are important for the activity of DNMT1inhibitor are Phe1145, Glu1168, Met1169, Cys1191, Glu1266, Ala1579, and Val1580.

Sign in / Sign up

Export Citation Format

Share Document