Simulation of the Diffusion Features of Point Defects in bcc Metals

2006 ◽  
Vol 249 ◽  
pp. 41-46
Author(s):  
Andrey S. Chirkov ◽  
Andrei V. Nazarov
Keyword(s):  
Point Defects ◽  
Density Functional ◽  
Tight Binding ◽  
Interatomic Potentials ◽  
Binding Theory ◽  
Many Body ◽  
Functional Theory ◽  
Bcc Metals ◽  
Diffusion Characteristics ◽  
The Density Functional Theory

This work is devoted to simulation of the diffusion features of point defects in bcc metals. The properties of point defects have been investigated with the usage of many-body interatomic potentials. This approach, based on the density-functional theory, permitted us to derive more adequate diffusion features of solids. This investigation is carried out within the framework of the Finnis-Sinclair formalism, developed for an assembly of N atoms and represents the secondmoment approximation of the tight-binding theory. We used a new model, based on the molecular static method for simulating the atomic structure near the defect and vacancy migration in pure metals. This approach gives the opportunity to simulate the formation and the migration volumes of the point defects, taking into consideration the influence of pressure on structure and consequently on energy. The diffusion characteristics of bcc α-Fe and anomalous β-Zr have been investigated.

STRUCTURE AND MAGNETIC PROPERTIES OF Co12X(X = Ni, Ag, Pt, Au) CLUSTERS

2007 ◽  
Vol 21 (30) ◽  
pp. 5091-5098 ◽  
Author(s):  
Q. L. LU ◽  
J. C. JIANG ◽  
J. G. WAN ◽  
G. H. WANG
Keyword(s):  
Density Functional ◽  
Magnetic Moments ◽  
Stable Configuration ◽  
Many Body ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Au Clusters ◽  
The Density Functional Theory ◽  
Ground State Structures ◽  
Body Potential

The ground state structures of Co 12 X ( X = Ni , Ag , Pt , Au ) clusters are obtained by a genetic algorithm with a Gupta-like many-body potential, and further optimized using the density functional theory with generalized gradient approximation. The structures of Co 12 X have a slightly distorted icosahedral pattern. The X atom is on the surface for the most stable configuration. Their total magnetic moments are 0μ B , 3μ B , 21μ B , and 22μ B , respectively. The reasons for the reduction of magnetism of Co 12 X are discussed in detail.

Graphene-Based Sensors for Monitoring Strain

2013 ◽  
Vol 3 (1) ◽  
pp. 74-83
Author(s):  
M. Mirnezhad ◽  
R. Ansari ◽  
H. Rouhi ◽  
M. Faghihnasiri
Keyword(s):  
Fermi Level ◽  
Band Gap ◽  
Strain Distribution ◽  
Density Functional ◽  
Tight Binding ◽  
Density Functional Theory Calculations ◽  
Generalized Gradient ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Gap Opening

The application of graphene as a nanosensor in measuring strain through its band structure around the Fermi level is investigated in this paper. The mechanical properties of graphene as well as its electronic structure are determined by using the density functional theory calculations within the framework of generalized gradient approximation. In the case of electronic properties, the simulations are applied for symmetrical and asymmetrical strain distributions in elastic range; also the tight-binding approach is implemented to verify the results. It is indicated that the energy band gap does not change with the symmetrical strain distribution but depend on the asymmetric strain distribution, increasing strain leads to band gap opening around the Fermi level.

scholarly journals Getting excited: challenges in quantum-classical studies of excitons in polymeric systems

2016 ◽  
Vol 18 (44) ◽  
pp. 30297-30304 ◽  
Author(s):  
Behnaz Bagheri ◽  
Björn Baumeier ◽  
Mikko Karttunen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Phenylene Ethynylene ◽  
Many Body ◽  
Functional Theory ◽  
Polymeric Systems ◽  
The Density Functional Theory ◽  
Classical Studies

A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) and many-body Green's functions theory (GW-BSE) was performed to describe the conformational and optical properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE).

scholarly journals Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

2021 ◽  
Author(s):  
Bahaa Jawad ◽  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Density Functional ◽  
Vaccine Development ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Tight Binding ◽  
Md Simulations ◽  
Functional Theory ◽  
Generalized Born ◽  
The Density Functional Theory ◽  
Key Residues

<p>The spike protein of SARS-CoV-2 binds to ACE2 receptor <i>via</i> its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two <i>ab initio</i> quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q<sup>493</sup>, Y<sup>505</sup>, Q<sup>498</sup>, N<sup>501</sup>, T<sup>500</sup>, N<sup>487</sup>, Y<sup>449</sup>, F<sup>486</sup>, K<sup>417</sup>, Y<sup>489</sup>, F<sup>456</sup>, Y<sup>495</sup>, and L<sup>455</sup> have been identified as hotspots in RBD, while those in ACE2 are K<sup>353</sup>, K<sup>31</sup>, D<sup>30</sup>, D<sup>355</sup>, H<sup>34</sup>, D<sup>38</sup>, Q<sup>24</sup>, T<sup>27</sup>, Y<sup>83</sup>, Y<sup>41</sup>, E<sup>35</sup>, and E<sup>37</sup>. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q<sup>493</sup>, N<sup>501</sup>, F<sup>486</sup>, K<sup>417</sup>, and F<sup>456</sup> in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N<sup>487</sup>, Q<sup>493</sup>, Y<sup>449</sup>, T<sup>500</sup>, G<sup>496</sup>, G<sup>446</sup> and G<sup>502</sup> in RBD form pairs <i>via</i> specific hydrogen bonding with Q<sup>24</sup>, H<sup>34</sup>, E<sup>35</sup>, D<sup>38</sup>, Y<sup>41</sup>, Q<sup>42</sup> and K<sup>353</sup> in ACE2. </p>

scholarly journals Point defects in turbostratic stacked bilayer graphene

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13725-13730 ◽  
Author(s):  
Chuncheng Gong ◽  
Sungwoo Lee ◽  
Suklyun Hong ◽  
Euijoon Yoon ◽  
Gun-Do Lee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Point Defects ◽  
Density Functional ◽  
Tight Binding ◽  
Bilayer Graphene ◽  
Dynamics Simulation ◽  
Functional Theory ◽  
Transmission Electron ◽  
Aberration Corrected

The point defects in turbostratic bilayer graphene are characterized using aberration-corrected transmission electron microscopy, density functional theory, and tight-binding molecular dynamics simulation.

scholarly journals Size engineering optoelectronic features of C, Si and CSi hybrid diamond-shaped quantum dots

RSC Advances ◽  
2019 ◽  
Vol 9 (49) ◽  
pp. 28609-28617 ◽  
Author(s):  
H. Ouarrad ◽  
F.-Z. Ramadan ◽  
L. B. Drissi
Keyword(s):  
Density Functional Theory ◽  
Quantum Dots ◽  
Ab Initio ◽  
Density Functional ◽  
Optoelectronic Properties ◽  
Many Body ◽  
Functional Theory ◽  
The Density Functional Theory

Based on the density functional theory and many-body ab initio calculations, we investigate the optoelectronic properties of diamond-shaped quantum dots based graphene, silicene and graphene–silicene hybrid.

scholarly journals Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

2021 ◽  
Author(s):  
Bahaa Jawad ◽  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Density Functional ◽  
Vaccine Development ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Tight Binding ◽  
Md Simulations ◽  
Functional Theory ◽  
Generalized Born ◽  
The Density Functional Theory ◽  
Key Residues

<p>The spike protein of SARS-CoV-2 binds to ACE2 receptor <i>via</i> its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analysis at molecular, amino acid (AA) and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex, including the MD simulations with molecular mechanics generalized Born surface area (MM-GBSA) method to predict binding free energy (BFE) and to determine the actual interacting AAs, as well as two <i>ab initio</i> quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q<sup>493</sup>, Y<sup>505</sup>, Q<sup>498</sup>, N<sup>501</sup>, T<sup>500</sup>, N<sup>487</sup>, Y<sup>449</sup>, F<sup>486</sup>, K<sup>417</sup>, Y<sup>489</sup>, F<sup>456</sup>, Y<sup>495</sup>, and L<sup>455</sup> have been identified as hotspots in RBD, while those in ACE2 are K<sup>353</sup>, K<sup>31</sup>, D<sup>30</sup>, D<sup>355</sup>, H<sup>34</sup>, D<sup>38</sup>, Q<sup>24</sup>, T<sup>27</sup>, Y<sup>83</sup>, Y<sup>41</sup>, E<sup>35</sup>, and E<sup>37</sup>. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q<sup>493</sup>, N<sup>501</sup>, F<sup>486</sup>, K<sup>417</sup>, and F<sup>456</sup> in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. The DFT results reveal that N<sup>487</sup>, Q<sup>493</sup>, Y<sup>449</sup>, T<sup>500</sup>, G<sup>496</sup>, G<sup>446</sup> and G<sup>502</sup> in RBD form pairs <i>via</i> specific hydrogen bonding with Q<sup>24</sup>, H<sup>34</sup>, E<sup>35</sup>, D<sup>38</sup>, Y<sup>41</sup>, Q<sup>42</sup> and K<sup>353</sup> in ACE2. </p>

Fitting electron density as a physically sound basis for the development of interatomic potentials of complex alloys

2018 ◽  
Vol 20 (27) ◽  
pp. 18647-18656 ◽  
Author(s):  
Jose M. Ortiz-Roldan ◽  
Gustavo Esteban-Manzanares ◽  
Sergio Lucarini ◽  
Sofía Calero ◽  
Javier Segurado ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Density Functional ◽  
New Method ◽  
Interatomic Potentials ◽  
Functional Theory ◽  
Starting Point ◽  
The Density Functional Theory

A new method to obtain physically sound EAM parameters using the density functional theory electron density as the starting point.

scholarly journals Calculation of Gamma Spectra for Positron Annihilation on Molecules

2010 ◽  
Vol 666 ◽  
pp. 21-24 ◽  
Author(s):  
D.G. Green ◽  
S. Saha ◽  
F. Wang ◽  
G.F. Gribakin ◽  
C.M. Surko
Keyword(s):  
Positron Annihilation ◽  
Density Functional ◽  
Many Body ◽  
Physical Reason ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Many Body Perturbation Theory ◽  
Chemical Trends ◽  
Selection Of ◽  
Gamma Spectra

Calculations of gamma spectra for positron annihilation for a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The contribution to the -spectra from individual molecular orbitals is obtained from electron momentum distributions calculated using the density functional theory (DFT) based B3LYP/TZVP model. For positrons thermalised to room temperature, the calculation, in its simplest form, effectively treats the positron as a plane wave and gives positron annihilation  spectra linewidths that are broader (30–40%) than experiment, although the main chemical trends are reproduced. The main physical reason for this is the neglect of positron repulsion from the nuclei. We show that this effect can be incorporated through momentum-dependent correction factors, determined from positron-atom calculations, e.g., many-body perturbation theory. Inclusion of these factors in the calculation gives linewidths that are in improved agreement with experiment.

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