Investigations on the influence of the dihedral angle distribution on the atomic radial distribution function in amorphous Ge and Si

1974 ◽  
Vol 16 (1) ◽  
pp. 101-109 ◽  
Author(s):  
J. Boissonade ◽  
M. Gandais ◽  
M.L. Theye
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Dihedral Angle ◽  
Radial Distribution ◽  
Angle Distribution ◽  
Atomic Radial Distribution ◽  
Atomic Radial Distribution Function

Molecular dynamics studies the effect of structure MgSiO3 bulk on formation process geology of the Earth

2019 ◽  
Vol 08 (03) ◽  
pp. 1950011 ◽  
Author(s):  
Nguyen Trong Dung ◽  
Nguyen Chinh Cuong ◽  
Duong Quoc Van
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Total Energy ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Formation Process ◽  
Pair Interaction ◽  
Effect Of Temperature ◽  
Angle Distribution ◽  
The Earth

The paper studies the effect of temperature ([Formula: see text]), ([Formula: see text], 3200, 4000, 5000, 6000, 7000[Formula: see text]K) at pressure [Formula: see text][Formula: see text]GPa; pressure ([Formula: see text]), ([Formula: see text], 100, 200, 300, 350, 400[Formula: see text]GPa) at [Formula: see text][Formula: see text]K and thermal annealing time ([Formula: see text]), [Formula: see text][Formula: see text]ps (after 105 steps) at [Formula: see text][Formula: see text]K, [Formula: see text][Formula: see text]Gpa) on the structure of MgSiO3 bulk 3000 atoms by Molecular Dynamics (MD) simulation using Born–Mayer (BM) pair interaction potential and periodic boundary conditions. The structural results are analyzed through the Radial Distribution Function (RDF), the Coordination Number (CN), the angle distribution, size ([Formula: see text]), total energy of the system ([Formula: see text]) and the bonding lengths. The results show that the temperature and pressure had influenced the structural properties of MgSiO3 bulk and formation process geology of the Earth. In addition, the center of the Earth with [Formula: see text][Formula: see text]K and [Formula: see text][Formula: see text]GPa has appearance and disappearance of the Si–Si, Si–O, O–O, Si–Mg, O–Mg, Mg–Mg bonds and SiO4, SiO5, SiO6, MgO3, MgO4, MgO5, MgO6, MgO7, MgO8, MgO9, MgO[Formula: see text], MgO[Formula: see text], MgO[Formula: see text] angle distributions. When increasing the depth of the Earth’s surface [Formula: see text] lead to size [Formula: see text] of MgSiO3 decreases, total energy of the system ([Formula: see text]) increases, position of first peak of Radial Distribution Function (RDF) is [Formula: see text], height of RDF is [Formula: see text] varies greatly with [Formula: see text] from [Formula: see text][Formula: see text]km to [Formula: see text][Formula: see text]km, gradually decreasing with [Formula: see text] from [Formula: see text][Formula: see text]km to [Formula: see text][Formula: see text]km and the smallest structural change with [Formula: see text][Formula: see text]km that shows has influence affects on the geological formation of the Earth.

The Influence of Hydrogen atoms on the Performance of Radial Distribution Function Based Descriptors in the Chemoinformatic Studies of HIV-1 Prote-ase Complexes with Inhibitors.

2020 ◽  
Vol 17 ◽  
Author(s):  
Jurica Novak ◽  
Maria A. Grishina ◽  
Vladimir A. Potemkin
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Current Model ◽  
Direct Interaction ◽  
Hydroxyl Group ◽  
Linear Regression Method ◽  
Hydrogen Atoms ◽  
Protease Enzyme ◽  
Hiv 1

: In this letter the newly introduced approach based on the radial distribution function (RDF) weighted by the number of va-lence shell electrons is applied for a series of HIV-1 protease enzyme and its complexes with inhibitors to evaluate the influ-ence of hydrogen atoms on the performance of the model. The multiple linear regression method was used for the selection of the relevant descriptors. Two groups of residues having dominant contribution to the RDF descriptor are identified as relevant for the inhibition. In the first group are residues like Arg8, Asp25, Thr26, Gly27 and Asp29, which establish direct interaction with the inhibitor, while the second group consists of the amino acids at the interface of the two homodimer sub-units or with the solvent. The crucial motif pointed out by our approach as the most important for inhibition of the enzyme’s activity and present in all inhibitors is hydroxyl group that establish hydrogen bond with Asp25 side chain. Additionally, the comparison to the model without hydrogen showed that both models are of similar quality, but the downside of the current model is the need for the determination of residues’ protonation states.

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