Vibrational analysis of the fullerene family using Tersoff potential

Hossein Nejat Pishkenari,Pooriya Ghaf Ghanbari 한국물리학회 2017 Current Applied Physics Vol.17 No.1

Using Tersoff bond order potential, a vibrational analysis of the spherical fullerene family, namely C60, C80, C180, C240, C260, C320, C500, and C720 was performed. To evaluate the validity of our results, we have compared our simulation results with available experimental data and also with DFT B3LYP/6-31G(d) calculations. In general, molecular stiffness tends to decrease with increasing size, but its variation is limited in cases where mostly the tension-compression interaction sites are active such as the breathing mode. Furthermore, the bond length of each molecule is derived and compared with experimental and theoretical values calculated for graphene. Finally, vibrational frequencies are plotted in a histogram to reveal the common frequency gap and concentration points of the frequency distribution.

Surface elasticity and size effect on the vibrational behavior of silicon nanoresonators

Hossein Nejat Pishkenari,Bahram Afsharmanesh,Ehsan Akbari 한국물리학회 2015 Current Applied Physics Vol.15 No.11

Predominance of nano-scale effects observed in material behavior at small scales requires implementation of new simulation methods which are not merely based on classical continuum mechanic. On the other hand, although the atomistic modeling methods are capable of modeling nano-scale effects, due to the computational cost, they are not suitable for dynamic analysis of nano-structures. In this research, we aim to develop a continuum-based model for nano-beam vibrations which is capable of predicting the results of molecular dynamics (MD) simulations with considerably lower computational effort. In this classical-based modeling, the surface and core regions are taken to have different mechanical properties, where core atoms are assumed to have macroscale properties whereas surface layer is showing a different elastic modulus from the core components. By estimating physical parameters of proposed classical model using molecular dynamics results and the genetic algorithm, calibrated classical EulereBernoulli and Timoshenko beam models are developed. The results demonstrates that a Timoshenko beam model incorporating surface effects and having calibrated parameters, is able to provide almost the same results as molecular dynamics method which can be used to predict the vibrational behavior of nano-beams at different scales from nano to macro.

A close look at the motion of C60 on gold

Hossein Nejat Pishkenari,Alireza Nemati,Ali Meghdari,Saeed Sohrabpour 한국물리학회 2015 Current Applied Physics Vol.15 No.11

In this paper, we have studied the motion of buckminsterfullerene (C60) on a gold surface by analyzing its potential energy and using classical molecular dynamics method. The results can be employed to investigate the motion of C60-based nanocars which have been made in recent years. For this purpose, we have studied the translational and rotational motions of C60 molecule independently. First, we have calculated the potential energy of a C60 molecule on a gold surface in different orientations and positions and employed this data to predict fullerene motion by examining its potential energy. Then we have simulated the motion of C60 at different temperatures using classical molecular dynamics methods. Specifying the regime of the motion at different temperatures is one of main goals of this paper.We have found that the rotational motion of C60 molecule on the gold substrate, was easier than its sliding (translational) motion. Also, the regime of motion of fullerene depended on temperature. The results demonstrate that three different regimes of motion, dependent on temperature, could be observed: rare jumps to adjacent cells, frequent jumps, and continuous motion. Employing the results of this paper not only helps to understand the C60 motion on the gold surface but also provides an appropriate tool for realizing motion of the thermally-driven fullerene-based nanocars.

Surface defects characterization with frequency and force modulation atomic force microscopy using molecular dynamics simulations

Hossein Nejat Pishkenari,Ali Meghdari 한국물리학회 2010 Current Applied Physics Vol.10 No.2

This paper is devoted to the characterization of the surface defects using a recently developed AFM technique called frequency and force modulation AFM (FFM–AFM). The simulated system includes a recently developed gold coated AFM probe which interacts with a sample including single-atom vacancy and impurities. In order to examine the behavior of the above system on different transition metals, the molecular dynamics (MD) simulation with Sutton–Chen (SC) inter-atomic potential is used. In this study,an online imaging simulation of the probe and sample is performed, and the effects of the horizontal scan speed, the effective frequency set-point, the cantilever stiffness, the tip-sample rest position and the cantilever quality factor on the resulting images are investigated. Using a proposed optimum controlling scheme for the excitation force amplitude, the cantilever horizontal speed can be increased.

Study of Biomolecules Imaging Using Molecular Dynamics Simulations

Mohsen Kheirodin,Hossein Nejat Pishkenari,Ali Moosavi,Ali Meghdari 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2015 NANO Vol.10 No.7

The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip–sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a graphene sheet is used as the substrate. The effects of CNT's geometric parameters such as the CNT height, the diameter, the tilt angle, the flexibility and the number of layers on the image quality have been evaluated.

Real-time Topography and Hamaker Constant Estimation in Atomic Force Microscopy Based on Adaptive Fading Extended Kalman Filter

Milad Seifnejad Haghighi,Hossein Nejat Pishkenari 제어·로봇·시스템학회 2021 International Journal of Control, Automation, and Vol.19 No.7

In this study, a novel technique based on adaptive fading extended Kalman filter for atomic force microscopy is proposed to directly estimate the topography of a sample surface without needing any control system. While in conventional imaging techniques, the scanning speed or the bandwidth is limited due to a relatively large settling time, the method proposed in this research is able to address this issue and estimate the topography throughout transient oscillation of the microcantilever. With this aim, an estimation process using an adaptive fading extended Kalman filter (augmented with forgetting factor) as the system observer is designed and coupled with the system dynamics to obtain sample topography. Obtained results demonstrate that the sample height is estimated by this algorithm with high accuracy and a relatively high scanning speed. Moreover, the observer is able to identify the topography and Hamaker constant simultaneously. Therefore, the presented approach can compensate for the low scanning speed of the classical imaging method as well as eliminate the need for a closed-loop controller.

Cellular Injection Using Carbon Nanotube: A Molecular Dynamics Study

Seyed Hanif Mahboobi,Alireza Taheri,Hossein Nejat Pishkenari,Ali Meghdari,Mahya Hemmat 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2015 NANO Vol.10 No.2

Determination of an injection condition which is minimally invasive to the cell membrane is of great importance in drug and gene delivery. For this purpose, a series of molecular dynamics (MD) simulations are conducted to study the penetration of a carbon nanotube (CNT) into a pure POPC cell membrane under various injection velocities, CNT tilt angles and chirality parameters. The simulations are nonequilibrium and all-atom. The force and stress exerted on the nanotube, deformation of the lipid bilayer, and strain of the CNT atoms are inspected during the simulations. We found that a lower nanotube velocity results in successfully entering the membrane with minimum disruption in the CNT and the lipid bilayer, and CNT's chirality distinctly affects the results. Moreover, it is shown that the tilt angle of the CNT influences the nanotube's buckling and may result in destroying the membrane structure during the injection process.