Spectroscopic constants and molecular properties of rare-gas diatomic molecule in Lennard-Jones potential: Ab initio and density functional study

2006 ◽  
Vol 107 (4) ◽  
pp. 824-831 ◽  
Author(s):  
N. C. Bera ◽  
I. Bhattacharyya ◽  
A. K. Das
Keyword(s):  
Ab Initio ◽  
Diatomic Molecule ◽  
Density Functional ◽  
Molecular Properties ◽  
Spectroscopic Constants ◽  
Functional Study ◽  
Rare Gas ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Performance of modified Lennard–Jones potential to seed ab initio calculations of small cadmium clusters

2013 ◽  
Vol 1021 ◽  
pp. 249-255 ◽  
Author(s):  
Macarena Muñoz ◽  
Alejandro Varas ◽  
Carlos Cárdenas ◽  
José Rogan ◽  
Patricio Fuentealba
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

A continuum approximation of the rare-gas liquids

1994 ◽  
Vol 72 (5-6) ◽  
pp. 206-209
Author(s):  
P. Mohazzabi ◽  
Timothy H. Popadic
Keyword(s):  
Nearest Neighbors ◽  
Potential Energy Function ◽  
Heat Of Fusion ◽  
Continuum Approximation ◽  
Rare Gas ◽  
Lennard Jones Potential ◽  
Neutron Diffraction Data ◽  
Jones Potential ◽  
Latent Heat Of Fusion ◽  
Lennard Jones

Potential energies and the number of nearest neighbors in liquid neon, argon, krypton, and xenon are calculated using a continuum approximation and the Lennard–Jones potential energy function. The number of nearest neighbors obtained in this way compare very well to those obtained from the neutron diffraction data. The potential energies are used to calculate the latent heat of fusion for these elements, which are in excellent agreement with the experimental data in all cases.

A Combined ab initio and Density Functional Study of the Electronic Structure of Thymine and 2-Thiothymine Radicals

2003 ◽  
Vol 68 (12) ◽  
pp. 2322-2334 ◽  
Author(s):  
Robert Vianello ◽  
Zvonimir B. Maksić
Keyword(s):  
Ab Initio ◽  
Spin Density ◽  
Density Functional ◽  
Radical Cations ◽  
Functional Study ◽  
Theory Approach ◽  
Functional Theory ◽  
Adiabatic Ionization Potential ◽  
Highest Occupied Molecular Orbital ◽  
Positively Charged

The electronic and energetic properties of thymine (1) and 2-thiothymine (2) and their neutral and positively charged radicals are considered by a combined ab initio and density functional theory approach. It is conclusively shown that ionization of 1 and 2 greatly facilitates deprotonation of the formed radical cations thus making the proton transfer between charged and neutral precursor species thermodynamically favourable. The adiabatic ionization potential of 1 and 2 are analysed. It appears that ADIP(1) is larger than ADIP(2) by 10 kcal/mol, because of greater stability of the highest occupied molecular orbital (HOMO) of the former. It is also shown beyond any doubt that the spin density in neutral and cationic radical of 2 is almost exclusively placed on the σ-3p AO of sulfur implying that these two systems represent rather rare sigma-radicals. In contrast, the spin density of radicals of 1 is distributed over their π-network.

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.

Sign in / Sign up

Export Citation Format

Share Document