Search for: molecular-dynamics
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    Mechanism of 1,12-Dicarba-closo-dodecaborane Mobility on Gold Substrate as a Nanocar Wheel

    , Article Journal of Physical Chemistry C ; Volume 120, Issue 26 , 2016 , Pages 14048-14058 ; 19327447 (ISSN) Hosseini Lavasani, S.M ; Nejat Pishkenari, H ; Meghdari, A ; Sharif University of Technology
    American Chemical Society  2016
    We studied the mobility of p-carborane on a gold surface by analyzing the potential energy surfaces (PES) and simulating the motion of p-carborane using the classical molecular dynamics (MD) method. In the first section, we calculated the PES of p-carborane molecules on a gold surface during pure translation (sliding) and pure rotation independently and then employed this PES to predict the probable motion of p-carborane. These calculations were performed in several major orientations during sliding as well as different fixed positions during rotational movements to enable us to find the p-carborane motion threshold on a gold surface. In the second section, we use classical MD in isothermal... 

    Disease-related metabolites affect protein-nanoparticle interactions

    , Article Nanoscale ; Volume 10, Issue 15 , 2018 , Pages 7108-7115 ; 20403364 (ISSN) Tavakol, M ; Montazeri, A ; Naghdabadi, R ; Hajipour, M. J ; Zanganeh, S ; Caracciolo, G ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2018
    Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and... 

    Charge asymmetry effect in ion transport through angstrom-scale channels

    , Article Journal of Physical Chemistry C ; Volume 123, Issue 2 , 2019 , Pages 1462-1469 ; 19327447 (ISSN) Yu, Y ; Fan, J ; Esfandiar, A ; Zhu, Y ; Wu, H ; Wang, F ; Sharif University of Technology
    American Chemical Society  2019
    Structural and dynamic properties of ions confined in nanoslits are crucial to understand the fundamental mechanism underlying a wide range of chemical and biological phenomena. K + and Cl - show similar ion mobilities in a bulk aqueous solution, whereas they exhibit a remarkable difference when transporting through an angstrom-scale channel. Our molecular dynamics simulations uncover that such discrepancy originates from the subtle differences in their hydration structures and preferable locations across the channel. Opposite charge causes different water dipolar orientations around ions, mediating the distance and tribological interactions between hydrated ions and channel's walls.... 

    Effects of topological constraints on linked ring polymers in solvents of varying quality

    , Article Soft Matter ; Volume 16, Issue 12 , 2020 , Pages 3029-3038 Ahmadian Dehaghani, Z ; Chubak, I ; Likos, C. N ; Ejtehadi, M. R ; Sharif University of Technology
    Royal Society of Chemistry  2020
    We investigate the effects of topological constraints in catenanes composed of interlinked ring polymers on their size in a good solvent as well as on the location of their θ-point when the solvent quality is worsened. We mainly focus on poly[n]catenanes consisting of n ring polymers each of length m interlocked in a linear fashion. Using molecular dynamics simulations, we study the scaling of the poly[n]catenane's radius of gyration in a good solvent, assuming in general that Rg ∼ mμnν and we find that μ = 0.65 ± 0.02 and ν = 0.60 ± 0.01 for the range of n and m considered. These findings are further rationalized with the help of a mean-field Flory-like theory yielding the values of μ =... 

    Thermal conductivity of the cell membrane in the presence of cholesterol and amyloid precursor protein

    , Article Physical Review E ; Volume 102, Issue 4 , 2020 Rafieiolhosseini, N ; Ejtehadi, M. R ; Sharif University of Technology
    American Physical Society  2020
    The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the... 

    Dynamical time scales of friction dynamics in active microrheology of a model glass

    , Article Soft Matter ; Volume 17, Issue 20 , 2021 , Pages 5162-5169 ; 1744683X (ISSN) Madanchi, A ; Yu, J. W ; Lee, W. B ; Rahimi Tabar, M. R ; Rahbari, S. H. E ; Sharif University of Technology
    Royal Society of Chemistry  2021
    Owing to the local/heterogeneous structures in supercooled liquids, after several decades of research, it is now clear that supercooled liquids are structurally different from their conventional liquid counterparts. Accordingly, an approach based on a local probe should provide a better understanding about the local mechanical properties as well as heterogeneous structures. Recently, the superiority of active microrheology over global rheology has been demonstrated [Yu et al., Sci. Adv., 2020, 6, 8766]. Here, we elaborate this new avenue of research and provide more evidence for such superiority. We report on the results of an extensive molecular dynamics simulation of active microrheology... 

    Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein

    , Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) Asadzadeh, H ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
    Hindawi Limited  2021
    Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

    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)
    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... 

    Simulation of Biomanipulation Using Molecular Dynamics

    , M.Sc. Thesis Sharif University of Technology Mahjour Firouzi, Mohammad Ali (Author) ; Meghdari, Ali (Supervisor) ; Nejat Pishkenari, Hossein (Supervisor)
    This thesis is devoted to the simulation of biomolecules manipulation using Molecular dynamics (MD). In order to investigate the manipulation behavior, we have used the Ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a graphene sample as substrate. Along this line, a lot of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between tip and substrate, initial orientation of protein, and the simulation environment (dry or wet). The results demonstrate that tips with bigger diameters and smaller distances with respect to the substrate increase... 

    Protein-Nanoparticle Interactions

    , M.Sc. Thesis Sharif University of Technology Moharamkhani, Halime (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    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)
    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 the Thermodynamic Properties of Ion Liquid 1-Ethyl 3-Methyl Imidazalium and Anion Hexafluorophosphorus Using the Equation of Mode and Molecular Dynamic Simulation Data

    , M.Sc. Thesis Sharif University of Technology Rezaei, Ramin (Author) ; Parsafar, Gholam Abbas (Supervisor)
    In this thesis, we use two simple simulation models for ionic liquids, and the efficiency of the Lennard Jones equations and the state equation obtained from this potential were investigated. Then, using these models, the temperature-dependent coefficients were calculated in two equations at different temperatures, and then analytical expressions were reported to them. Given that ion fluid data is reported only in a small range of densities, these data were used to evaluate the equations used, using a model in a wider range of densities. For this purpose, simulation of molecular dynamics simulation data was simulated. In these two models, the relative size of cations and anions is different.... 

    Using Molecular Dynamics Simulation for Investigation of Sulfuric Compounds Adsorption on Zeolite

    , M.Sc. Thesis Sharif University of Technology Ramezani Shabolaghi, Kianoush (Author) ; Mohammadi, Aliasghar (Supervisor)
    There are different sulfur compounds in the crude oil, and after combustion all of these sulfuric compounds produce sulfur dioxide, this sulfur dioxide cause acid rain, deactivation of catalysts and also environmental bad effects. So the amount of sulfur that is released should be controlled and this is done by removing sulfuric compounds before combustion. zeolites as adsorbent of sulfuric compounds has been used widely by researches and had given good results. molecular dynamics simulation as an effective way for describing the behavior of these compounds in the molecular level and in scales of angstrom has been used and the effect of van der waals and electrostatic forces between sorbates... 

    Molecular Dynamics Simulation of Nanoscale Effects in Nanomanipulation

    , Ph.D. Dissertation Sharif University of Technology Mahboobi, Hanif (Author) ; Meghdari, Ali (Supervisor)
    Metallic clusters are among the best candidates that may be utilized as building blocks for constructing nanostructures. Despite their great potential, a variety of questions arises about their suitability as building blocks at the nanoscale level. One of the key factors in the assembly of nanoclusters is the precise positioning that is required by a manipulation system. The response of clusters, which are subjected to this process, is of great importance. Currently, the size of clusters used as building blocks is shrinking down to a few nanometers. In such cases, the particle nature of matter plays an important role in manipulator/cluster/substrate interactions. Having a deeper insight into... 

    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)
    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... 

    Study of Melting and Rapid Solidification of TiAl alloy and Formation of its Diffusion Bonded Structure using Molecular Dynamics Simulation

    , M.Sc. Thesis Sharif University of Technology Yazdan Yar, Azade (Author) ; Aashuri, Hossin (Supervisor) ; Simchi, Abdolreza (Co-Advisor)
    The rapid pace of development of nanoscience and nanotechnology and their applications in various fields have made the study of materials in smaller scales more important than any time ever. Having an insight of materials’ microstructure and the mechanism of different phenomena in the atomic scale will be very beneficent in designing new and advanced materials or modifying the current manufacturing processes. Since molecular dynamics (MD) method has been well known as a mean of studying materials in atomic scale, it has been used in this study to investigate two different phenomena. The selection of the appropriate interatomic potential is of great importance in MD; Embedded Atom Method... 

    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
    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
    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... 

    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
    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
    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...