scholarly journals IMAGING A NANOSTRUCTURE BY THE LYAPUNOV EXPONENT COMPUTATION

2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Saša Nježić ◽  
Dragana Malivuk ◽  
Sreten Lekić ◽  
Saša Sekulić ◽  
Enes Škrgić ◽  
...  

A model of the AFM (atomic force microscope) with certain tip-nanostructure interaction, cantilever elasticity and damping of its oscillations is proposed. Stable and unstable motion of the AFM tip interacting with the graphene sheet is investigated by the Lyapunov exponent computation. In our approximation, a hundred Si atoms (top of the AFM tip) interact with C atoms of the nanostructure. Тhis interaction is described by Lennard-Jones potential, and the distance between the top and the center of the cantilever mass is a constant. Complex influence of the initial tip-nanostructure distance and nanostructure size on stability has been examined. We discuss a possible new mode of the AFM operation based on the Lyapunov exponent computation. Maxima and minima of the Lyapunov exponent show where certain parts of the elementary cells are placed.

Author(s):  
Lingyun Ding ◽  
Zhongliang Gong ◽  
Ping Huang

A new model named as the coupled-oscillator model, is proposed to study the atomic-scale static friction. The Maugis-Dugdal model is used to approximately substitute the Lennard-Jones potential of the interfacial friction in new model. Then, the formulas for static friction force and coefficient calculation are deduced. A comparison between the theoretical result and the experimental value obtained by an atomic force microscope is presented to show the model and the formulas practically feasible.


2013 ◽  
Vol 61 (2) ◽  
pp. 535-539
Author(s):  
S. Babicz ◽  
J. Smulko ◽  
A. Zieliński

Abstract Motion of a tip used in an atomic force microscope can be described by the Lennard-Jones potential, approximated by the van der Waals force in a long-range interaction. Here we present a general framework of approximation of the tip motion by adding three terms of Taylor series what results in non-zero harmonics in an output signal. We have worked out a measurement system which allows recording of an excitation tip signal and its non-linear response. The first studies of spectrum showed that presence of the second and the third harmonics in cantilever vibrations may be observed and used as a new method of the investigated samples characterization.


2020 ◽  
Vol 11 ◽  
pp. 729-739
Author(s):  
Nicholas Chan ◽  
Carrie Lin ◽  
Tevis Jacobs ◽  
Robert W Carpick ◽  
Philip Egberts

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.


RSC Advances ◽  
2016 ◽  
Vol 6 (52) ◽  
pp. 46658-46667 ◽  
Author(s):  
Kanes Sumetpipat ◽  
Duangkamon Baowan ◽  
Barry J. Cox ◽  
James M. Hill

Mathematical modelling, comprising Lennard–Jones potential and calculus of variations, is utilized to obtain the energy equations arising from AFM probe and substrate, leading to deflection equations of AFM cantilever.


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.


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