Computer simulation of CaSiO3glass under compression: correlation between Si–Si pair radial distribution function and intermediate range order structure

2017 ◽  
Vol 4 (6) ◽  
pp. 065201 ◽  
Author(s):  
Mai Thi Lan ◽  
Tran Thuy Duong ◽  
Toshiaki Iitaka ◽  
Nguyen Van Hong
Keyword(s):  
Computer Simulation ◽  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Range Order ◽  
Order Structure ◽  
Intermediate Range ◽  
Intermediate Range Order

Medium range order and the radial distribution function

2006 ◽  
Vol 352 (2) ◽  
pp. 116-122 ◽  
Author(s):  
A. Bodapati ◽  
M.M.J. Treacy ◽  
M. Falk ◽  
J. Kieffer ◽  
P. Keblinski
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Range Order ◽  
Medium Range Order ◽  
Medium Range

Simulation of Structure and Dynamics of Amorphous SiO2

1996 ◽  
Vol 446 ◽  
Author(s):  
Y. Kogure ◽  
M. Doyama
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Amorphous Structure ◽  
Amorphous Sio2 ◽  
Coordination Numbers ◽  
Structure And Dynamics ◽  
External Stresses

AbstractA molecular dynamics computer simulation of amorphous SiO2 has been made to investigate the structure and dynamics. The effects of the external stresses on the amorphous structure were investigated through the radial distribution function, the distribution of Si‐O‐Si bond angles, and the distribution of coordination numbers.

Lysozyme Protein Solution with an Intermediate Range Order Structure

2011 ◽  
Vol 115 (22) ◽  
pp. 7238-7247 ◽  
Author(s):  
Yun Liu ◽  
Lionel Porcar ◽  
Jinhong Chen ◽  
Wei-Ren Chen ◽  
Peter Falus ◽  
...  
Keyword(s):  
Range Order ◽  
Order Structure ◽  
Protein Solution ◽  
Intermediate Range ◽  
Intermediate Range Order

Study on the Local Structure of PAN-Based Carbon Fiber Using Radial Distribution Function Based on XRD

2013 ◽  
Vol 664 ◽  
pp. 614-619 ◽  
Author(s):  
Xue Lin ◽  
Cheng Guo Wang ◽  
Mei Jie Yu ◽  
Zhi Tao Lin ◽  
Shan Zhang
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Long Range ◽  
Carbon Fibers ◽  
Radial Distribution ◽  
Local Structure ◽  
Range Order ◽  
Structure Evolution ◽  
Long Range Order ◽  
Rigid Rod

The local structure evolution of polyacrylonitrile (PAN) fibers during pre-oxidation and carbonization was studied using X-ray diffraction (XRD) and radial distribution function (RDF). The nearest inter-chains distance of PAN is 6.88 Å, which is close to the diameter of the “rigid rod” model proposed by Warner. The third neighbor distances of carbon fibers are greater than that of graphite, indicating the planar six-member rings are absent in the carbon fibers from 500 to 1250°C. The structure of fibers transforms from long-range order to long-range disorder during the pre-oxidation process, then transforms from short-range order to long-range order during the carbonization process.

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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