The Optimum Maximum Allowed Displacement in Monte Carlo Simulation of Lennard-Jones Potential Point Particles = الحد الأقصى الأمثل للنزوح المسموح به في محاكاة مونت كارلو لجزيئات لينار جونز النقطية

2018 ◽  
Vol 4 (1) ◽  
pp. 18-32
Author(s):  
Iyad Suwan ◽  
Hayel H. Al-Shraydeh ◽  
Abdelrahman Abulebdeh
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Point Particles ◽  
Lennard Jones

Pressure in Ultra Thin Perfluoropolyether Film

2005 ◽  
Author(s):  
N. Kubota ◽  
A. Kobayashi ◽  
M. S. Mayeed ◽  
T. Kato
Keyword(s):  
Thin Film ◽  
Monte Carlo ◽  
Free Surface ◽  
Substrate Surface ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones ◽  
Flat Substrate ◽  
Pressure Distributions ◽  
Head Surface

The density and pressure variations in the ultra thin liquid perfluoropolyether (PFPE) film (2nm) are carried out by Monte Carlo simulations of Lennard-Jones systems. First of all, the variations of density and pressure of ultra thin PFPE film that has a free surface on the flat substrate are carried out. The substrate is assumed to be continuous without atomic structure and exerting Lennard-Jones potential on liquid molecules in the ultra thin film. Next, the variations of density and pressure in the ultra thin PFPE liquid film between the two solids are examined. This is assumed to be due to the contact between the flying head and the PFPE film. From results of the 2500 steps calculation, it is clarified that the density distribution between two solids becomes symmetrical in shape and the pressure distributions concentrate on the substrate surface and the flying head surface do not occur in the liquid between the two surfaces.

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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