scholarly journals A new method to reconstruct three-dimensional spatial distribution function from radial distribution function in solvation structure

2005 ◽  
Vol 123 (21) ◽  
pp. 211102 ◽  
Author(s):  
Daisuke Yokogawa ◽  
Hirofumi Sato ◽  
Shigeyoshi Sakaki
Keyword(s):  
Distribution Function ◽  
Spatial Distribution ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Three Dimensional ◽  
New Method ◽  
Spatial Distribution Function ◽  
Solvation Structure

scholarly journals A method for computing the three-dimensional radial distribution function of cloud particles from holographic images

2018 ◽  
Vol 11 (7) ◽  
pp. 4261-4272 ◽  
Author(s):  
Michael L. Larsen ◽  
Raymond A. Shaw
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Laboratory Data ◽  
Three Dimensional ◽  
Periodic Boundary Conditions ◽  
Numerical Techniques ◽  
Cloud Droplets ◽  
Microphysical Processes

Abstract. Reliable measurements of the three-dimensional radial distribution function for cloud droplets are desired to help characterize microphysical processes that depend on local drop environment. Existing numerical techniques to estimate this three-dimensional radial distribution function are not well suited to in situ or laboratory data gathered from a finite experimental domain. This paper introduces and tests a new method designed to reliably estimate the three-dimensional radial distribution function in contexts in which (i) physical considerations prohibit the use of periodic boundary conditions and (ii) particle positions are measured inside a convex volume that may have a large aspect ratio. The method is then utilized to measure the three-dimensional radial distribution function from laboratory data taken in a cloud chamber from the Holographic Detector for Clouds (HOLODEC).

scholarly journals A Method for Computing the Three-Dimensional Radial Distribution Function of Cloud Particles from Holographic Images

2018 ◽  
Author(s):  
Michael L. Larsen ◽  
Raymond A. Shaw
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Laboratory Data ◽  
Three Dimensional ◽  
Periodic Boundary Conditions ◽  
Numerical Techniques ◽  
Cloud Droplets ◽  
Microphysical Processes

Abstract. Reliable measurements of the three-dimensional radial distribution function for cloud droplets are desired to help characterize microphysical processes that depend on local drop environment. Existing numerical techniques to estimate this three-dimensional radial distribution function are not well suited to in situ or laboratory data gathered from a finite experimental domain. This manuscript introduces and tests a new method designed to reliably estimate the three-dimensional radial distribution function in contexts where (i) physical considerations prohibit the use of periodic boundary conditions and (ii) particle positions are measured inside a convex volume that may have a large aspect ratio. The method is then utilized to measure the three-dimensional radial distribution function from laboratory data taken in a cloud chamber from the Holographic Detector for Clouds (HOLODEC).

scholarly journals New method for calculation of radial distribution function

2008 ◽  
Vol 98 (1) ◽  
pp. 012007
Author(s):  
A V Bondarev ◽  
I L Bataronov ◽  
Yu V Barmin ◽  
O A Kordin
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
New Method

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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