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    Temperature dependence study of nonocontact AFM images using molecular dynamics simulations [electronic resource]

    , Article Int. Journal of Modern Physics ; 2012, Vol. 5, pp. 418-432 Nejat Pishkenari, H. (Hossein) ; Meghdar, Ali ; Sharif University of Technology
    Abstract
    The effect of temperature on the noncontact atomic force microscopy (NC-AFM) surface imaging is investigated with the aid of molecular dynamics (MD) analysis based on the Sutton-Chen (SC) interatomic potential. Particular attention is devoted to the tip and sample flexibility at different temperatures. When a gold coated probe is brought close to the Au (001) surface at high temperatures, the tip and surface atoms are pulled together and their distance becomes smaller. The tip and sample atoms displacement varies in the different environment temperatures and this leads to the different interaction forces. Along this line, to study the effect of temperature on the resulting images, we have... 

    Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces

    , Article Central European Journal of Physics ; Volume 9, Issue 2 , 2011 , pp 454-465 ; 1644-3608 Mahboobi, S. H ; Meghdari, A. (Ali) ; Jalili, N. (Nader) ; Amiri, F. (Farshid) ; Sharif University of Technology
    Abstract
    Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on stepped surfaces. Five surface forms are considered in the simulations. The system parts are made of pure transition metals and Sutton-Chen many-body potential is used as interatomic potential. The conditions which are subjected to change in the tests include: materials used for particles and substrate, and surface step conditions. In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Simulation results show the effect of the aforementioned working conditions on... 

    Molecular dynamics simulation of manipulation of metallic nanoclusters on double-layer substrates [electronic resource]

    , Article Physica E: Low-dimensional Systems and Nanostructures ; 2010, Vol. 42, No. 9, pp. 2364-2374 Mahboobi, H. (Hanif) ; Meghdari, Ali ; Jalili, Nader ; Amiri, Farshid ; Sharif University of Technology
    Abstract
    Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on double-layer surfaces. The system parts are made of transition metals. The conditions which are subjected to change in the tests are material combinations for cluster, main substrate and lubricant layer (adlayer). In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines, which guarantee better success in the manipulation process  

    Planar molecular dynamics simulation of Au clusters in pushing process

    , Article International Journal of Nanomanufacturing ; Vol.5, No.3/4 , 2010 , pp.288-296 Mahboobi, S. H ; Meghdari, A. (Ali) ; Jalili, N. (Nader) ; Amiri, F. (Farshid) ; Sharif University of Technology
    Abstract
    Based on the fact that the manipulation of fine nanoclusters calls for more precise modelling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. In the present research, 2D molecular dynamics simulations have been used to investigate such behaviours. Performing the planar simulations can provide a fairly acceptable qualitative tool for our purpose while the computation time is reduced extremely in comparison to 3D simulations. To perform this study, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behaviour of the aforementioned system. Pushing of... 

    Water electrolyte transport through corrugated carbon nanopores [electronic resource]

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 90, Issue 1, July 2014, Article number 012304 Moghimi Kheirabadi . A ; Moosavi. A
    Abstract
    We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

    Molecular dynamics simulation of melting, solidification and remelting processes of aluminum [electronic resource]

    , Article Iranian Journal of Science and Technology ( IJST): Transactions of Mechanical Engineering ; 2012, Vol.36, No. M1, P.13-23 Solhjoo, S ; Simchi, A. (Abdolreza) ; Aashuri, H ; Sharif University of Technology
    Abstract
    A molecular dynamics simulation study has been performed to investigate the solidification and remelting of aluminum using Sutton - Chen many body potential. Different numbers of atoms from 108 to 2048 atoms were considered to find an adequate size for the system. Three different cooling and heating rates, i.e. 1 0 12 K/s, 10 13 K/s and 10 14 K/s, were used. The structure of the system was examined using radial distribution function. The melting and crystallization temperatures of aluminum were evaluated by calculating the variation of heat capacity during the phase t ransformation. Additionally, Wendt – Abraham parameters were calculated to determine the glass transition temperature. It is... 

    Molecular dynamics investigation of β-SiC behavior under three-axial tensile loading [electronic resource]

    , Article Journal of Computational and Theoretical Nanoscience ; November 2011, Volume 8, Number 11, PP. 2187-2192 Mortazavi, B ; Simchi, A. (Abdolreza) ; Besharati-Givi, M.K ; Rajabpour, A ; Sharif University of Technology
    Abstract
    Molecular dynamics (MD) simulations were used to study the mechanical behaviour of β-SiC at nano-scale under tensile loading. Effects of loading rate and tensile temperature on the mechanical properties and failure were studied. Modified embedded-atom method (MEAM) potential and Berendsen thermostat were utilized for modelling. Periodic boundary conditions were employed and the behaviour of material was analyzed under three-axial loading condition at which the stress–strain relation was acceptably size independent. It is shown that with increasing the loading rate from 5 m/s to 70 m/s, the failure strain increases without a remarkable change in the stress–strain relationship. The MD... 

    Temperature-dependent multi-scale modeling of surface effects on nano-materials

    , Article Mechanics of Materials ; Volume 46 , March , 2012 , PP. 94–112 Khoei, A. R. (Amir Reza) ; Ghahremani, P ; Sharif University of Technology
    Abstract
    In this paper, a novel temperature-dependent multi-scale method is developed to investigate the role of temperature on surface effects in the analysis of nano-scale materials. In order to evaluate the temperature effect in the micro-scale (atomic) level, the temperature related Cauchy–Born hypothesis is implemented by employing the Helmholtz free energy, as the energy density of equivalent continua relating to the inter-atomic potential. The multi-scale technique is applied in atomistic level (nano-scale) to exhibit the temperature related characteristics. The first Piola–Kirchhoff stress and tangential stiffness tensor are computed, as the first and second derivatives of the free energy... 

    Validity and size-dependency of cauchy–born hypothesis with Tersoff potential in silicon nano-structures

    , Article Computational Materials Science ; Volume 63 , October , 2012 , PP. 168–177 Khoei, A. R. (Amir Reza) ; Dormohammadi, H. (Hossein) ; Sharif University of Technology
    Abstract
    One of the most popular constitutive rules that correlate the continuum and atomic properties in multi-scale models is the Cauchy–Born (CB) hypothesis. Based on this constitutive law of continuum media, it assumes that all atoms follow the deformation subjected to the boundary of crystal. In this paper, the validity and failure of CB hypothesis are investigated for the silicon nano-structure by comparison of the continuum and atomic properties. In the atomistic level, the stresses and position of atoms are calculated using the molecular dynamics (MD) simulation based on the Tersoff inter-atomic potential. The stresses and strains are compared between the atomistic and continuous media to... 

    Introducing structural approximation method for modeling nanostructures

    , Article Journal of Computational and Theoretical Nanoscience ; Vol. 7, Issue 2 , 2010 , p. 423-428 ; ISSN: 15461955 Momeni, K ; Alasty, A ; Sharif University of Technology
    Abstract
    In this work a new method for analyzing nanostructured materials has been proposed to accelerate the simulations for solid crystalline materials. The proposed Structural Approximation Method (SAM) is based on Molecular Dynamics (MD) and the accuracy of the results can also be improved in a systematic manner by sacrificing the simulation speed. In this method a virtual material is used instead of the real one, which has less number of atoms and therefore fewer degrees of freedom, compared to the real material. The number of differential equations that must be integrated in order to specify the state of the system will decrease significantly, and the simulation speed increases. To generalize... 

    Cell-imprinted substrates act as an artificial niche for skin regeneration

    , Article ACS Applied Materials and Interfaces ; Vol. 6, Issue. 15 , 2014 , Pages 13280-13292 ; ISSN: 19448244 Mashinchian, O ; Bonakdar, S ; Taghinejad, H ; Satarifard, V ; Heidari, M ; Majidi, M ; Sharifi, S ; Peirovi, A ; Saffar, S ; Taghinejad, M ; Abdolahad, M ; Mohajerzadeh, S ; Shokrgozar, M. A ; Rezayat, S. M ; Ejtehadi M. R ; Dalby, M. J ; Mahmoudi, M ; Sharif University of Technology
    Abstract
    Bioinspired materials can mimic the stem cell environment and modulate stem cell differentiation and proliferation. In this study, biomimetic micro/nanoenvironments were fabricated by cell-imprinted substrates based on mature human keratinocyte morphological templates. The data obtained from atomic force microscopy and field emission scanning electron microscopy revealed that the keratinocyte-cell-imprinted poly(dimethylsiloxane) casting procedure could imitate the surface morphology of the plasma membrane, ranging from the nanoscale to the macroscale, which may provide the required topographical cell fingerprints to induce differentiation. Gene expression levels of the genes analyzed... 

    Water electrolyte transport through corrugated carbon nanopores

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Vol. 90, issue. 1 , July , 2014 ; ISSN: 15393755 Moghimi Kheirabadi, A ; Moosavi, A ; Sharif University of Technology
    Abstract
    We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

    Investigation of intense femto-second laser ionization and dissociation of methane with time-dependent density-functional approach

    , Article Chemical Physics Letters ; Vol. 604 , 2014 , Pages 60-67 ; ISSN: 00092614 Irani, E ; Sadighi Bonabi, R ; Anvari, A ; Sharif University of Technology
    Abstract
    Three dimensional calculations of electronic dynamics of CH4 in a strong laser field are presented with time-dependent density-functional theory. Time evolution of dipole moment and electron localization function is presented. The dependence of dissociation rate on the laser characters is shown and optimal effective parameters are evaluated. The optimum field leads to 76% dissociation probability for Gaussian envelope and 40 fs (FWHM) at 10 16 W cm-2. The dissociation probability is calculated by optimum convolution of dual short pulses. By combining of field assisted dissociation process and Ehrenfest molecular dynamics, time variation of bond length, velocity and orientation effect are... 

    Sandwich beam model for free vibration analysis of bilayer graphene nanoribbons with interlayer shear effect

    , Article Journal of Applied Physics ; Vol. 115, issue. 17 , May , 2014 ; ISSN: 00218979 Nazemnezhad, R ; Shokrollahi, H ; Hosseini-Hashemi, S ; Sharif University of Technology
    Abstract
    In this study, sandwich beam model (SM) is proposed for free vibration analysis of bilayer graphene nanoribbons (BLGNRs) with interlayer shear effect. This model also takes into account the intralayer (in-plane) stretch of graphene nanoribbons. The molecular dynamics (MD) simulations using the software LAMMPS and Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential are done to validate the accuracy of the sandwich model results. The MD simulation results include the two first frequencies of cantilever BLGNRs with different lengths and two interlayer shear moduli, i.e., 0.25 and 4.6GPa. These two interlayer shear moduli, 0.25 and 4.6GPa, can be obtained by sliding a small... 

    Molecular dynamics simulation of orientation dependency in the shock-induced phase transition of C60 fullerene single crystals into amorphous diamond

    , Article Phase Transitions ; Vol. 87, Issue. 3 , 2014 , Pages 271-285 ; ISSN: 01411594 Mahnama, M ; Naghdabadi, R ; Sharif University of Technology
    Abstract
    A molecular dynamics simulation of the shock-wave propagation in the face-centered cubic (FCC) structured C60 fullerene along the <100>, <110> and <111> crystallographic directions is performed. For this purpose, the response of the material under different shock-wave loadings is studied through Hugoniot curves. Three regimes of the material behavior have been observed from fully elastic to elastic-plastic to plastic. The Hugoniot elastic limit and the phase transition are also investigated along different crystallographic directions. It is shown that the shock wave travels faster along the <110> and <111> directions than in the <100> direction in the material. Comparing the results with the... 

    Vibration analysis of a graphene nanoribbon under harmonic lorentz force using a hybrid modal-molecular dynamics method

    , Article International Journal of Structural Stability and Dynamics ; Vol. 14, issue. 2 , 2014 ; ISSN: 02194554 Firouz-Abadi, R. D ; Mohammadkhani, H ; Amini, H ; Sharif University of Technology
    Abstract
    An efficient hybrid modal-molecular dynamics method is developed for the vibration analysis of large scale nanostructures. Using the reduced order method, presented in this paper, linear and nonlinear vibrations of a suspended graphene nanoribbon (GNR) carrying an electric current in a harmonic magnetic field are investigated. The resonance frequencies as well as the nonlinear vibration response obtained by the present technique and direct molecular dynamic simulations are in very good agreement. Also, the obtained results illustrate the hardening behavior of nonlinear vibrations which is diminished by stretching the GNR  

    Temperature dependence and the effect of charge configuration on water permeation through modified carbon nanotubes: A simulation study

    , Article Fluid Phase Equilibria ; Volume 363 , 15 February , 2014 , Pages 282-289 ; ISSN: 03783812 Alizadeh, A ; Parsafar, G ; Sharif University of Technology
    Abstract
    We have investigated the water permeation through carbon nanotube (CNT) membranes as a model of peptide nanotube channels (PNCs). The effect of different charge configured CNTs which tailored based on some artificial ion channels on the water permeation through the channels have been studied. In addition, the temperature dependence of the permeation has been investigated. We have found that there is a jump in the permeation which is somehow related to the characteristics of each channel and the temperature of this permeation jump changes according to the channel configuration. Our investigation on the channels shows that the temperature at which the permeation jump occurs is related to the... 

    Nanofluidic transport inside carbon nanotubes

    , Article Journal of Physics D: Applied Physics ; Volume 47, Issue 6 , 12 February , 2014 ; ISSN: 00223727 Moghimi Kheirabadi, A ; Moosavi, A ; Akbarzadeh, A. M ; Sharif University of Technology
    Abstract
    Using non-equilibrium molecular dynamics simulations, we investigate the effects of nanotube size, mean flow velocity, ion concentration and temperature of an electrolyte water solution on shearing stress and nominal viscosity. It is shown that the distributed electric field arising from the electrolyte water solution has significant influences on fluid properties. Also, the temperature of the solution, which causes thermal movement, affects nanofluidic transport in nanoenvironments. The nominal viscosity and shearing stress increases as the tube diameter increases. When the temperature of solution increases or ion concentration decreases, the shearing stress and nominal viscosity increase.... 

    A temperature-related boundary Cauchy-Born method for multi-scale modeling of silicon nano-structures

    , Article Physics Letters, Section A: General, Atomic and Solid State Physics ; Vol. 378, issue. 5-6 , 2014 , pp. 551-560 ; ISSN: 03759601 Khoei, A. R ; Dormohammadi, H ; Aramoon, A ; Sharif University of Technology
    Abstract
    The surface, edge and corner effects have significant influences in the electrical and optical properties of silicon nano-structures. In this paper, a novel hierarchical temperature-related multi-scale model is presented based on the boundary Cauchy-Born method to investigate not only the surface but also the edge and corner effects in thermal properties of diamond-like structures such as silicon nano-structures at finite temperature. A combined finite element method and molecular dynamics are respectively employed in macro- and micro-scale levels. The temperature-related Cauchy-Born rule is applied using the Helmholtz free energy, as the energy density of equivalent continua relating to the... 

    Multi-scale modeling of surface effects in nano-materials with temperature-related Cauchy-Born hypothesis via the modified boundary cauchy-born model

    , Article International Journal for Numerical Methods in Engineering ; Vol. 97, issue. 2 , 2014 , pp. 79-110 ; ISSN: 00295981 Khoei, A. R ; Ghahremani, P ; Dormohammadi, H ; Sharif University of Technology
    Abstract
    In nano-structures, the influence of surface effects on the properties of material is highly important because the ratio of surface to volume at the nano-scale level is much higher than that of the macro-scale level. In this paper, a novel temperature-dependent multi-scale model is presented based on the modified boundary Cauchy-Born (MBCB) technique to model the surface, edge, and corner effects in nano-scale materials. The Lagrangian finite element formulation is incorporated into the heat transfer analysis to develop the thermo-mechanical finite element model. The temperature-related Cauchy-Born hypothesis is implemented by using the Helmholtz free energy to evaluate the temperature...