scholarly journals Correlation between structure characteristics and pair radial distribution function in Silica glass under compression

2018 ◽  
Vol 34 (4) ◽  
Author(s):  
Lan Mai Thi
Keyword(s):  
High Pressure ◽  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Silica Glass ◽  
Structural Phase ◽  
Dynamics Simulation ◽  
Pairwise Interactions ◽  
Fcc Structure ◽  
Second Peak

We have studied structure of silica glass at different pressures and temperature of 300K by using Molecular Dynamics simulation (MD) method. The model consists of 6000 atoms (2000 Si, 4000 O atoms) with the periodic boundary condition. We applied the Morse-Stretch potentials which describe the pairwise interactions between ions for SiO2 system. There is structural phase transformation from tetrahedra (SiO4) to octahedra (SiO6) network structure. There is splitting in the Si-Si pair radial distribution function (PRDF) at high pressure (100 GPa). The original of this splitting relates to the edge- and face-sharing bonds. The new second peak of the O-O PRDF at the high pressure originates from oxygen atoms of the edge-sharing bonds. Thus, there is rearrangement of O atoms. O atoms have tendency to more order arrangement that leads to form some oxygen hcp and fcc structure in the model at high pressure.

A comparative study between effects of shadowing potential and ODS on Coulomb crystal formation

2010 ◽  
Vol 77 (4) ◽  
pp. 547-557 ◽  
Author(s):  
SWATI BARUAH ◽  
NILAKSHI DAS
Keyword(s):  
Distribution Function ◽  
Comparative Study ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Coupling Parameter ◽  
Dynamics Simulation ◽  
Crystal Formation ◽  
Coulomb Crystal ◽  
Screening Parameter

AbstractIn dusty plasma, the overlapping Debye spheres around dust grains produce an attractive force. Shadowing force is exerted between neighboring particles because of mutual distortion of ion or neutral flux to the particles. A comparative study has been made on the role of these two forces on 2D structure of dusty system. Radial distribution function for the particles is a comparative study between the effect of the coupled Yukawa-shadowing potential and the coupled Yukawa-Overlapping Debye Sphere (ODS) potential on 2D dust crystal formation, which has been performed by using molecular dynamics simulation. The structure of the system is investigated by calculating the radial distribution function (g(r)) for different values of Γ, κ and dust number densities nd. It is seen from our study that the Coulomb coupling parameter does not have significant effect on both ODS and shadowing forces. The attractive shadowing force is more dominant for grains with large screening parameter. However, the ODS force becomes dominant with the increasing value of the dust number density. The results for the Yukawa-Shadowing and the ODS potential are also compared with experimental results and a close agreement is obtained for attractive shadowing force.

ORDERED MICROPHASES OF SYMMETRIC DIBLOCK COPOLYMER IN SELECTIVE SOLVENT: DISSIPATIVE PARTICLE DYNAMICS SIMULATION AND RADIAL DISTRIBUTION FUNCTION ANALYSIS

2011 ◽  
Vol 10 (06) ◽  
pp. 731-745 ◽  
Author(s):  
HAINAN SUN ◽  
BAIQING LI ◽  
CHANGQIAO ZHANG ◽  
CHUNLING WANG ◽  
CHENGBU LIU
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Diblock Copolymer ◽  
Self Assembly ◽  
Function Analysis ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Dynamics Simulation ◽  
Selective Solvent

The self-assembly process of a symmetric diblock copolymer A5B5 in a selective solvent is studied using the dissipative particle dynamics method. Four types of morphologies can form, including lamellae, perforated lamellae, cylinders and spheres. Three phase diagrams are presented to demonstrate the effect of the concentration and interaction parameters on the ordered microstructures. Radial distribution function (RDF) characterizing the spatial correlations of the blocks is calculated. RDF not only confirms the morphological observations, but also provides more quantitative details. The evolution process of hexagonally packed cylinder and lamellae is also illustrated.

scholarly journals MOLECULAR DYNAMICS SIMULATION OF RAPID SOLIDIFICATION OF ALUMINUM UNDER PRESSURE

2008 ◽  
Vol 22 (17) ◽  
pp. 2781-2785 ◽  
Author(s):  
A. SARKAR ◽  
P. BARAT ◽  
P. MUKHERJEE
Keyword(s):  
Molecular Dynamics ◽  
High Pressure ◽  
Distribution Function ◽  
Molecular Dynamics Simulation ◽  
Radial Distribution Function ◽  
Rapid Solidification ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Eam Potential ◽  
Crystallization Tendency

Molecular dynamics simulation study based on the EAM potential is carried out to investigate the effect of pressure on the rapid solidification of Aluminum. The radial distribution function is used to characterize the structure of the Al solidified under different pressures. It is indicated that a high pressure leads to strong crystallization tendency during cooling.

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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