scholarly journals 3P129 Effects of Lennard-Jones potential parameters between the solute and solvent on the solvation dynamics(07. Water & Hydration & Electrolyte,Poster)

2013 ◽  
Vol 53 (supplement1-2) ◽  
pp. S233
Author(s):  
Yoshito Kondo ◽  
Tetsuro Nagai ◽  
Takuya Takahashi
Keyword(s):  
Solvation Dynamics ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones ◽  
Potential Parameters

Hydrogen Adsorption of Carbon Nanocone Arrays: Influences of Cone Arrangements

2013 ◽  
Vol 845 ◽  
pp. 345-349
Author(s):  
I Ling Chang ◽  
Ming Liang Liao ◽  
Chi Hsiang Chuang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Adsorption ◽  
Md Simulations ◽  
Critical Value ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Weight Percentage ◽  
Curvature Effects ◽  
Lennard Jones ◽  
Potential Parameters

This paper used molecular dynamics (MD) simulations to investigate influences of cone arrangements (including the cone orientation, arrangement pattern and cone spacing) on hydrogen adsorption of open-tip carbon nanocone (CNC) arrays at temperatures of 100 and 300 K. To consider curvature effects for the cone structure of the CNCs, the curvature-modified Lennard-Jones potential parameters were adopted to describe the interactions between the hydrogen and carbon atoms. It was found that the cone orientation (aligned, opposite, and alternate) does not have obvious influences on hydrogen adsorption of the CNC arrays. The arrangement pattern (square and triangular), however, had significant influences on the hydrogen adsorption. The square-patterned CNC array was noticed to have higher storage weight percentage than the triangular-patterned one. Regarding to the influences of cone spacing, the storage weight percentage grew with the increase of the cone spacing and arrived at a stable value as the cone spacing reached a certain critical value. The influences cone arrangements could be ascribed to repulsive effects, which are evident as cone spacing become narrow.

scholarly journals Quantitative determination of the interaction potential between two surfaces using frequency-modulated atomic force microscopy

2020 ◽  
Vol 11 ◽  
pp. 729-739
Author(s):  
Nicholas Chan ◽  
Carrie Lin ◽  
Tevis Jacobs ◽  
Robert W Carpick ◽  
Philip Egberts
Keyword(s):  
Atomic Force Microscopy ◽  
Interaction Potential ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Force Microscopy ◽  
Lennard Jones ◽  
Atomic Force ◽  
Potential Form ◽  
Sample Separation ◽  
Potential Parameters

The interaction potential between two surfaces determines the adhesive and repulsive forces between them. It also determines interfacial properties, such as adhesion and friction, and is a key input into mechanics models and atomistic simulations of contacts. We have developed a novel methodology to experimentally determine interaction potential parameters, given a particular potential form, using frequency-modulated atomic force microscopy (AFM). Furthermore, this technique can be extended to the experimental verification of potential forms for any given material pair. Specifically, interaction forces are determined between an AFM tip apex and a nominally flat substrate using dynamic force spectroscopy measurements in an ultrahigh vacuum (UHV) environment. The tip geometry, which is initially unknown and potentially irregularly shaped, is determined using transmission electron microscopy (TEM) imaging. It is then used to generate theoretical interaction force–displacement relations, which are then compared to experimental results. The method is demonstrated here using a silicon AFM probe with its native oxide and a diamond sample. Assuming the 6-12 Lennard-Jones potential form, best-fit values for the work of adhesion (W adh) and range of adhesion (z 0) parameters were determined to be 80 ± 20 mJ/m2 and 0.6 ± 0.2 nm, respectively. Furthermore, the shape of the experimentally extracted force curves was shown to deviate from that calculated using the 6-12 Lennard-Jones potential, having weaker attraction at larger tip–sample separation distances and weaker repulsion at smaller tip–sample separation distances. This methodology represents the first experimental technique in which material interaction potential parameters were verified over a range of tip–sample separation distances for a tip apex of arbitrary geometry.

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