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    Effect of copper content on tensile mechanical properties of ternary NiTiCu alloy nanowire: molecular dynamics simulation

    , Article Materials Today: Proceedings ; Volume 5, Issue 1 , 2018 , Pages 1552-1555 ; 22147853 (ISSN) Fazeli, S ; Vahedpour, M ; Sadrnezhaad, K ; Sharif University of Technology
    Elsevier Ltd  2018
    Abstract
    Molecular dynamics (MD) simulation was used to study of mechanical properties of NiTiCu with different content of copper. It was shown that the percent composition of copper are significantly affects the stress-strain curves curve. The results showed that as the Cu content increased, the Yield Strength and Young's modulus decreased. © 2017 Elsevier Ltd  

    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  

    Molecular dynamics simulation of manipulation of metallic nanoclusters on stepped surfaces

    , Article Central European Journal of Physics ; Volume 9, Issue 2 , 2011 , Pages 454-465 ; 18951082 (ISSN) Mahboobi, S. H ; Meghdari, A ; Jalili, N ; Amiri, F ; 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... 

    Simulation study of the Gachsaran asphaltene behavior within the interface of oil/water emulsion: a case study

    , Article Colloids and Interface Science Communications ; Volume 33 , 2019 ; 22150382 (ISSN) Saeedi Dehaghani, A. H ; Soodbakhsh Taleghani, M ; Badizad, M. H ; Daneshfar, R ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Molecular dynamics (MD) simulation was utilized to study the role of asphaltene extracted from Gachsaran (an Iranian oilfield) at the synthetic oil-water interface. In agreement with experimental data, IFTs predicted by MD simulation for heptol/brine system showed a minima at around 50 vol.% n-heptane, reflecting the highest contribution of asphaltene into the interface. At greater n-heptane fractions, IFT was increased steadily. Simulation results suggest the asphaltene propensity for remaining in the bulk heptol phase rather related to the fraction of toluene in the mixture. Heptol ingredients, i.e., toluene and heptane, act differently with respect to asphaltene, where former tends to... 

    Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response

    , Article Journal of Biomolecular Structure and Dynamics ; 2020 Azimzadeh Irani, M ; Ejtehadi, M. R ; Sharif University of Technology
    Taylor and Francis Ltd  2020
    Abstract
    Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic... 

    Adsorption onto zeolites: molecular perspective

    , Article Chemical Papers ; Volume 75, Issue 12 , 2021 , Pages 6217-6239 ; 03666352 (ISSN) Salmankhani, A ; Mousavi Khadem, S. S ; Seidi, F ; Hamed Mashhadzadeh, A ; Zarrintaj, P ; Habibzadeh, S ; Mohaddespour, A ; Rabiee, N ; Lima, E. C ; Shokouhimehr, M ; Varma, R. S ; Saeb, M. R ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    Abstract
    2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent adsorption properties, zeolites have found application in diverse chemical processes, e.g., gas adsorption, water purification, and wastewater treatment. Prediction of zeolite performance for a targeted application saves time and expense as such projection... 

    DNA Chains Entanglement in Confined Geometries

    , M.Sc. Thesis Sharif University of Technology Ahmadian, Zahra (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    Our bodies are made from billions of individual cells and DNA is the control central of each cell. In addition to linear DNAs, there are circular DNAs in nature. Circular DNAs cause new topological structures such as knots and catenanes. These topological structures form during biological proccesses such as replication. For example during replication, two daughter circular DNAs may link together and form catenanes. Anzymes named topoisomerases can simplify the topology of circular DNAs. Type 2 topoisomerases is used for simplification of catenanes. These anzymes do it with breaking a double-strand DNA and passing through another one. In comparison with DNAs, topoisomerases are very small and... 

    Calculation of Free Energy Barrier for Base Flipping of Thymine Dimer Outward the DNA Double Strand Using Molecular Dynamics

    , M.Sc. Thesis Sharif University of Technology Arab Bagheri, Amin (Author) ; Parsafar, Golam Abbas (Supervisor)
    Abstract
    Formation of Cyclobutane Pyrimidine Dimer (CPD), one of the most abundant types of damages in DNA double helices, is caused by UV radiation and plays a major role in causing skin cancer. DNA photolyase is an efficient enzyme that repairs this UV-induced damaged DNA-base. Previous studies have shown that the enzyme flips the dimer out of the DNA double helix into its binding pocket.
    In this project, several nanoseconds of molecular dynamics simulations was performed to investigate the process of base flipping energetically. These simulations are consist of equilibration of repaired and damaged double strands for 3 and 8 nanoseconds respectively. All these simulations ran over NVT... 

    Protein-Nanoparticle Interactions

    , M.Sc. Thesis Sharif University of Technology Moharamkhani, Halime (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    In this thesis, proteinnanoparticle interactions have been studied using Molecular Dynamics simulation. sT fN, is the studied protein in this work. It is one of the most important proteins in the blood fluid. In this work, nanoparticle has been modeled as a surface; because the radius of gyration of sT fN is less than 3nm, so when it is near an enough big nanoparticle (100200 nm), nanoparticle seems as a surface from the view of protein. The surface of nanoparticle consists of sodium ions. Surface of nanoparticle, has been modeled using two types of surface:flat surface and nonflat surface. Protein interaction with surface, has been studied in two different initial orientations with respect... 

    Molecular Dynamics Simulation of Aβ42 Neurotoxicity Inhibition in Order to Alzheimer’s Disease Treatment

    , M.Sc. Thesis Sharif University of Technology Khandan, Vahid (Author) ; Firoozabadi, Bahar (Supervisor) ; Saeedi, Mohammad Saeed (Supervisor)
    Abstract
    Alzheimer’s disease (AD) is the most common type of dementia in the elderly. The neuropathology and treatment of AD is not precisely determined yet, but according to the pathological studies, AD is associated with presence of toxic soluble oligomers and insoluble senile plaques formed by amyloidosis of Amyloid Beta (Aβ) in neocortical region of brain. An attractive therapeutic approach to treat AD is to identify small ligands that are capable of binding to critical residues in order to inhibit or reverse Aβ amyloidosis process as source of neurotoxicity. In this area, therapeutic efforts designed various organic agents and most of them focused on the N-terminal sequence of Aβ. The aim of... 

    Calculation of Interfacial Tension in Water-Methane System at High Pressures Using Molecular Simulation

    , M.Sc. Thesis Sharif University of Technology Salami, Hossein (Author) ; Ghotbi, Cyrus (Supervisor) ; Taghikhani, Vahid (Supervisor) ; Robert, Marc (Supervisor)
    Abstract
    Interfacial tension has wide application in surface engineering and specially oil and gas industry. One has to do work to transfer a molecule from bulk to the surface of a fluid. The amount of this work is proportional to Interfacial tension.Molecular simulation is a fundumental approach for calculating the thermophisycal properties of matter such asInterfacial tension.In this thesis we have investigated the effect of pressure and temperature on surface tension of pure water and interfacial tension of Water-Methane system. The TIP4P potential model was used for Water molecules and OPLS for Methane molecules. In the first part, Water heat capacity and Methane density were calculated for... 

    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... 

    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... 

    Multiscale modeling of the effect of carbon nanotube orientation on the shear deformation properties of reinforced polymer-based composites

    , Article Physics Letters, Section A: General, Atomic and Solid State Physics ; Volume 375, Issue 14 , 2011 , Pages 1588-1597 ; 03759601 (ISSN) Montazeri, A ; Sadeghi, M ; Naghdabadi, R ; Rafii Tabar, H ; Sharif University of Technology
    Abstract
    A combination of molecular dynamics (MD), continuum elasticity and FEM is used to predict the effect of CNT orientation on the shear modulus of SWCNT-polymer nanocomposites. We first develop a transverse-isotropic elastic model of SWCNTs based on the continuum elasticity and MD to compute the transverse-isotropic elastic constants of SWCNTs. These constants are then used in an FEM-based simulation to investigate the effect of SWCNT alignment on the shear modulus of nanocomposites. Furthermore, shear stress distributions along the nanotube axis and over its cross-sectional area are investigated to study the effect of CNT orientation on the shear load transfer  

    Comparison of the mechanical properties of NiTi/Cu bilayer by nanoindentation and tensile test: Molecular dynamics simulation

    , Article Materials Research Express ; Volume 3, Issue 12 , 2016 ; 20531591 (ISSN) Fazeli, S ; Vahedpour, M ; Sadrnezhaad, S. K ; Sharif University of Technology
    Institute of Physics Publishing  2016
    Abstract
    Molecular dynamics simulation was used to study of mechanical properties of NiTi/Cu bilayer by nanoindentation and tensile testing. A comparison has been made among mechanical properties measured and plastic deformation process at different copper thickness during nanoindnetation and tensile test of the samples. Embedded atom method potentials for describing of inter-Atomic interaction and Nose-Hoover thermostat and barostat are employed in the simulation at 400 K. The results showed that as the copper film thickness decreased, the maximum load and hardness values increased during nanoindetation. Saha and Nix model is used to describe reduced young's modulus behaviour of the bilayer system... 

    What is the copper thin film thickness effect on thermal properties of NiTi/Cu bi-layer?

    , Article Materials Research Express ; Volume 4, Issue 2 , 2017 ; 20531591 (ISSN) Fazeli, S ; Vahedpour, M ; Sadrnezhaad, S. K ; Sharif University of Technology
    Institute of Physics Publishing  2017
    Abstract
    Molecular dynamics (MD) simulation was used to study of thermal properties of NiTi/Cu. Embedded atom method (EAM) potentials for describing of inter-atomic interaction and Nose-Hoover thermostat and barostat are employed. The melting of the bi-layers was considered by studying the temperature dependence of the cohesive energy and mean square displacement. To highlight the differences between bi-layers with various copper layer thickness, the effect of copper film thickness on thermal properties containing the cohesive energy, melting point, isobaric heat capacity and latent heat of fusion was estimated. The results show that thermal properties of bi-layer systems are higher than that of... 

    Effects of the temperature and the ph on the main protease of sars-cov-2: A molecular dynamics simulation study

    , Article Biointerface Research in Applied Chemistry ; Volume 12, Issue 6 , 2022 , Pages 7239-7248 ; 20695837 (ISSN) Kordzadeh, A ; Saadatabadi, A. R ; Sharif University of Technology
    AMG Transcend Association  2022
    Abstract
    The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was... 

    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... 

    Multiscale molecular dynamics simulation of nanobio membrane in interaction with protein

    , Article ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology, NEMB 2013 ; 2013 ; ISBN: 9780791845332 Maftouni, N ; Amininasab, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
    2013
    Abstract
    One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of...