scholarly journals Molecular diffusion in gases and liquids

2021 ◽  
Vol 2119 (1) ◽  
pp. 012122
Author(s):  
G V Kharlamov
Keyword(s):  
Experimental Data ◽  
Diffusion Coefficients ◽  
Molecular Diffusion ◽  
Liquid Argon ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones ◽  
Liquid Benzene ◽  
Simulation Results ◽  
Dynamics Method

Abstract The diffusion coefficients in gases and liquids calculated by the molecular dynamics method with the use of the hard absolutely rough elastic spheres model are compared with those calculated using the Lennard-Jones potential. It is shown that dependences of reduced diffusion coefficients on density are similar, but differ numerically for different intermolecular interaction models. The simulation results have been compared with the experimental data on the diffusion in gaseous and liquid argon and in liquid benzene.

scholarly journals Calculated Self-Diffusion Coefficients for Liquid Argon

1972 ◽  
Vol 25 (5) ◽  
pp. 529 ◽  
Author(s):  
RA Fisher ◽  
RO Watts
Keyword(s):  
Diffusion Coefficients ◽  
Pair Potential ◽  
Liquid Argon ◽  
The Self ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Self Diffusion ◽  
Lennard Jones ◽  
Method Of Molecular Dynamics ◽  
Experimental Values

The method of molecular dynamics has been applied with the Barker?Bobetic pair potential for argon interactions to calculate the self-diffusion coefficients of liquid and dense gaseous argon. These self-diffusion coefficients are compared with experimental values and with values obtained from the Lennard?Jones potential. There are significant differences between the calculated and experimental values at high densities.

KIHARA POTENTIAL AND LENNARD-JONES AND DEVONSHIRE EQUATION OF STATE OF LIQUIDS AND DENSE GASES

1966 ◽  
Vol 44 (22) ◽  
pp. 2651-2656 ◽  
Author(s):  
Isamu Nagata
Keyword(s):  
Experimental Data ◽  
Heat Capacity ◽  
Present Theory ◽  
Cell Theory ◽  
Lennard Jones Potential ◽  
Perfect Gas ◽  
Jones Potential ◽  
Dense Gases ◽  
Lennard Jones ◽  
Kihara Potential

The Kihara potential has been applied to the Lennard-Jones and Devonshire cell theory in place of the Lennard-Jones potential. The expressions for the internal energy, heat capacity, and entropy, as well as the compressibility, are given in excess over those of a perfect gas. A comparison between experimental data and the present theory is made.

scholarly journals Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential

2021 ◽  
Vol 22 (11) ◽  
pp. 5914
Author(s):  
Mengsheng Zha ◽  
Nan Wang ◽  
Chaoyang Zhang ◽  
Zheng Wang
Keyword(s):  
Single Cell ◽  
Loss Function ◽  
Gaussian Function ◽  
Three Dimensional ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Cubic Lattice ◽  
Lennard Jones ◽  
3D Fish ◽  
Well Depth

Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis–Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.

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