Alignment of Buckingham Parameters to Generalized Lennard-Jones Potential Functions

2009 ◽  
Vol 64 (3-4) ◽  
pp. 200-204 ◽  
Author(s):  
Teik-Cheng Lim

Abstract The Lennard-Jones(12-6) and the Exponential-6 potential functions are commonly used in computational softwares for describing the van der Waals interaction energy. Some softwares allow switching between these two potentials under prescribed condition(s) that attempt to connect the parameter relationship between the two functions. Here we propose a technique by which the parameter relationship between both potentials is extracted by simultaneously imposing an equal force constant at the well depth’s minimum and an equal mean interatomic energy from the point of equilibrium to the point of total separation. The former imposition induces good agreement for the interatomic compression and a small change in the interatomic distance near the equilibrium while the latter enables good agreement for large interatomic separation. The excellent agreement exhibited by the plots validates the technique of combined criteria proposed herein

2021 ◽  
Vol 22 (11) ◽  
pp. 5914
Author(s):  
Mengsheng Zha ◽  
Nan Wang ◽  
Chaoyang Zhang ◽  
Zheng Wang

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.


1967 ◽  
Vol 47 (7) ◽  
pp. 2491-2494 ◽  
Author(s):  
Bruce Hartmann ◽  
Zaka I. Slawsky

Sign in / Sign up

Export Citation Format

Share Document