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    Dynamics of Protein-Embedded Vesicles in Simple Shear Flow

    , M.Sc. Thesis Sharif University of Technology Hoore, Masoud (Author) ; Jalali, Mir Abbas (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
    Abstract
    Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical... 

    Oxidation of Sulfides and Olefins in the Presence of Nanocluster Polyoxotungstate–intercalated Layered Double Hydroxide Nanoparticles as a Catalyst

    , M.Sc. Thesis Sharif University of Technology Qoreishi Kavardi, Atefeh Sadat (Author) ; Bagherzadeh, Mojtaba (Supervisor)
    Abstract
    In this study, polyoxometalate (POM) intercalated in the layered double hydroxide (LDH) was synthesized by a selective ion-exchange method. For this purpose, the nanocluster [VW12O40]3- was immobilized on the Mg2+/A13+/Cl–LDH support. The heterogeneous catalyst was characterized by FT-IR, XRD, SEM and analysis of ICP. The LDH-POM was applied as a catalyst in efficient oxidation of sulfides to sulfoxides using UHP as oxidant and CH3OH/ CH¬2¬Cl¬2 ¬as a solvent at room temperature, as well as epoxidation of olefins using TBHP as an oxidants and C¬2H4Cl2 as a solvent in 84°C. This catalyst showed excellent catalytic activities for a substrate/catalyst ratio (200:1). For example, this catalytic... 

    Effects of Graphene Nanopores and Temperature on DNA Sequencing Using Molecular Dynamics

    , M.Sc. Thesis Sharif University of Technology Majdi, Amin (Author) ; Meghdari, Ali (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
    Abstract
    Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,... 

    Long Period Variable Stars in the Local Group Galaxies

    , M.Sc. Thesis Sharif University of Technology Hashemi, Azim (Author) ; Rahvar, Sohrab (Supervisor) ; Javadi, Atefeh (Co-Supervisor)
    Abstract
    In this thesis, the star formation history and evolution of IC 1613 dwarf galaxy and NGC 5128 giant elliptical galaxy has been studied. About IC 1613, our result shows that the star formation history of the galaxy is roughly constant in 5 Gyr ago and this support that the galaxy had been isolated at least in 5 Gyr ago. About NGC 5128, we can see that the star formation rate has suddenly increased in 700 Myr and 3.5 Gyr ago. This results in very good agreement with literature support that the galaxy has experienced some mergers with smaller gas rich galaxies  

    Study and Comparison the Incidence of Dutch Disease in Iranian Economy in Two Periods of Oil Shock

    , M.Sc. Thesis Sharif University of Technology Momeni, Atefeh Sadat (Author) ; nili, Masoud (Supervisor) ; Madanizadeh, Ali (Supervisor)
    Abstract
    This paper studies and compares the effect of "Dutch disease" in Iranian economy in two periods of rising oil price (1973-1978) and (2004-2010). The study presents a DSGE model to analysis the behavior of economic variable in both periods and to address this question that whether or not policy maker has learning behavior. The model consists of households, final goods producers who divided in tradable goods and non-tradable goods sector and the government. I use calibration methods to estimate models parameters.Comparison of simulated results and the actual macroeconomic variables in Iran during 1338-1390 indicates that, first of all Dutch disease effect occur in both periods of oil shock so... 

    3D distributed modeling of trolling-mode AFM during 2D manipulation of a spherical cell

    , Article Journal of Nanoparticle Research ; Volume 23, Issue 4 , 2021 ; 13880764 (ISSN) Mohammadi, S.Z ; Nejat Pishkenari, H ; Mohammadi Moghaddam, M ; Sharif University of Technology
    Springer Science and Business Media B.V  2021
    Abstract
    In this study, a general 3D distributed modeling of Trolling-Mode AFM (TR-AFM) as a nanorobot is presented to analyze the 2D manipulation process of a spherical cell. To this aim, the analysis is categorized into 3 sections. In the first section, 6 deformations of TR-AFM are taken into account, and the standard model of the system is obtained. Moreover, the system is simulated in ANSYS Workbench. The results of modal and transient analyses of the system from both analytical and software methods reveal high agreement, which confirms the accuracy of the presented analytical model. In the second section, by utilizing the 3D derived model, displacement of a spherical yeast single cell (W303)... 

    Sol-gel nanostructured titanium dioxide: Controlling the crystal structure, crystallite size, phase transformation, packing and ordering

    , Article Microporous and Mesoporous Materials ; Volume 112, Issue 1-3 , 2008 , Pages 392-402 ; 13871811 (ISSN) Mohammadi, M. R ; Fray, D. J ; Mohammadi, A ; Sharif University of Technology
    2008
    Abstract
    The anatase phase of titania was stabilised with physically modifying particulate sol-gel process. Two major parameters, peptisation temperature and drying temperature, were identified which were responsible for retarding the anatase to rutile phase transformation, crystal growth and packing of primary particles. The critical nucleus size of transformation was controlled by natural (at 25 °C) and artificial (at 50 and 70 °C) peptisation techniques. Moreover, sintering of primary particles was controlled by cool (at 0 and 5 °C) and normal (at 25 °C) drying techniques. Fourier transform infrared spectroscopy (FT-IR) analysis confirmed that a full conversion of titanium isopropoxide is obtained... 

    The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes

    , M.Sc. Thesis Sharif University of Technology Jafarinia, Hamid Reza (Author) ; Ahmadiyan, Mohammad Taghi (Supervisor) ; Jalali, Mir Abbas (Co-Advisor) ; Khoshnood, Atefeh (Co-Advisor)
    Abstract
    Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with... 

    Electrokinetic mixing and displacement of charged droplets in hydrogels

    , Article Transport in Porous Media ; Vol. 104, Issue. 3 , Jun , 2014 , pp. 469-499 ; ISSN: 01693913 Mohammadi, A ; Sharif University of Technology
    2014
    Abstract
    Mixing in droplets is an essential task in a variety of microfluidic systems. Inspired by electrokinetic mixing, electric field-induced hydrodynamic flow inside a charged droplet embedded in an unbounded polyelectrolyte hydrogel is investigated theoretically. In this study, the polyelectrolyte hydrogel is modeled as a soft, and electrically charged porous solid saturated with a salted Newtonian fluid, and the droplet is considered an incompressible Newtonian fluid. The droplet-hydrogel interface is modeled as a surface, which is located at the plane of shear, with the electrostatic potential ζ. The fluid inside the droplet attains a finite velocity owing to hydrodynamic coupling with the... 

    Electric-field-induced response of a droplet embedded in a polyelectrolyte gel

    , Article Physics of Fluids ; Volume 25, Issue 8 , 2013 ; 10706631 (ISSN) Mohammadi, A ; Sharif University of Technology
    2013
    Abstract
    The electric-field induced response of a droplet embedded in a quenched polyelectrolyte gel is calculated theoretically. The response comprises the droplet translation and the electric-field induced flow fields within the droplet. The gel is modeled as a soft, and electrically charged porous solid saturated with a salted Newtonian fluid. The droplet is considered an incompressible Newtonian fluid with no free charge. An analytical solution, using the perturbation methodology and linear superposition, is obtained for the leading-order steady response to a DC electric-field. The fluid within the droplet is driven due to hydrodynamic coupling with the electroosmotic flow. The fluid velocity... 

    Oscillatory response of charged droplets in hydrogels

    , Article Journal of Non-Newtonian Fluid Mechanics ; Volume 234 , 2016 , Pages 215-235 ; 03770257 (ISSN) Mohammadi, A ; Sharif University of Technology
    Elsevier  2016
    Abstract
    Characterization of droplet-hydrogel interfaces is of crucial importance to engineer droplet-hydrogel composites for a variety of applications. In order to develop electrokinetic diagnostic tools for probing droplet-hydrogel interfaces, the displacement of a charged droplet embedded in a polyelectrolyte hydrogel exposed to an oscillating electric field is determined theoretically. The polyelectrolyte hydrogel is modeled as an incompressible, charged, porous, and elastic solid saturated with a salted Newtonian fluid. The droplet is considered an incompressible Newtonian fluid with no charges within the droplet. The droplet-hydrogel interface is modeled as a surface with the thickness of zero... 

    Transport in droplet-hydrogel composites: response to external stimuli

    , Article Colloid and Polymer Science ; Volume 293, Issue 3 , March , 2015 , Pages 941-962 ; 0303402X (ISSN) Mohammadi, A ; Sharif University of Technology
    Springer Verlag  2015
    Abstract
    Determination of effective transport properties of droplet-hydrogel composites is essential for various applications. The transport of ions through a droplet-hydrogel composite subjected to an electric field is theoretically studied as an initial step toward quantifying the effective transport properties of droplet-hydrogel composites. A three-phase electrokinetic model is used to derive the microscale characteristics of the polyelectrolyte hydrogel, and the droplet is considered an incompressible Newtonian fluid. The droplet-hydrogel interface is modeled as a surface, which encloses the interior fluid. The surface has the thickness of zero and the electrostatic potential ζ. Standard... 

    A simple particulate sol-gel route to synthesize nanostructural TiO2-Ta2O5 binary oxides and their characteristics

    , Article Materials Science and Engineering B: Solid-State Materials for Advanced Technology ; Volume 142, Issue 1 , 2007 , Pages 16-27 ; 09215107 (ISSN) Mohammadi, M. R ; Fray, D. J ; Sadrnezhaad, S. K ; Mohammadi, A ; Sharif University of Technology
    2007
    Abstract
    Nanostructured and mesoporous TiO2-Ta2O5 films and powders with various TiO2:Ta2O5 molar ratios and high specific surface area (SSA) have been prepared by a straightforward particulate sol-gel route. Titanium isopropoxide and tantalum ethoxide were used as precursors and hydroxypropyl cellulose (HPC) was used as a polymeric fugitive agent (PFA) in order to increase the SSA. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) revealed that powders contained both hexagonal δ-Ta2O5 and monoclinic β-Ta2O5 phases, as well as anatase and rutile. It was observed that Ta2O5 retarded anatase-to-rutile transformation. Furthermore, δ → β phase transformation temperature increased... 

    Correction to: Controlled manipulation of a bio-particle using trolling mode atomic force microscope: a simulation study (Journal of Nanoparticle Research, (2021), 23, 10, (221), 10.1007/s11051-021-05301-6)

    , Article Journal of Nanoparticle Research ; Volume 24, Issue 8 , 2022 ; 13880764 (ISSN) Mohammadi, S. Z ; Nejat Pishkenari, H ; Mohammadi Moghaddam, M ; Sajjadi, M ; Sharif University of Technology
    Springer Science and Business Media B.V  2022
    Abstract
    The original article contained a mistake in Equation 1. The corrected Equation 1 is shown below: MX+Cx+Kx=f.The original article has been updated © Springer Nature B.V. 2022  

    Experimental investigation of thermal resistance of a ferrofluidic closed-loop pulsating heat pipe

    , Article Heat Transfer Engineering ; Vol. 35, issue. 1 , 2014 , pp. 25-33 ; ISSN: 01457632 Mohammadi, M ; Mohammadi, M ; Ghahremani, A. R ; Shafii, M. B ; Mohammadi, N ; Sharif University of Technology
    2014
    Abstract
    For the present article, a pulsating heat pipe (PHP) is fabricated and tested experimentally by bending a copper tube. The effects of working fluid, heat input, charging ratio, inclination angle, magnets location, and ferrofluid (magnetic nanofluid) volumetric concentration have been investigated on the thermal performance of this PHP. Experimental results show that using ferrofluid as a working fluid improves the thermal performance of the PHP significantly. Moreover, applying a magnetic field on a ferrofluidic PHP reduces its thermal resistance. By changing the inclination angle of the PHP from vertical mode to angles close to the horizontal mode, the present PHP has a constant and... 

    Bromo-lithium Exchange Reaction in Organic Synthesis and Continuous Separation of Organic and Aqueous phase Reactions by Microfloid Technique

    , M.Sc. Thesis Sharif University of Technology Pourasghar Mohammadi, Ali (Author) ; Mohammadi, Ali Asghar (Supervisor) ; Bastani, Dariush (Supervisor)
    Abstract
    Today, with the development of micro-technology in chemical reactions, the use of appropriate systems for the separation and purification of synthesized chemicals seems to be necessary. In this study, the continuous synthesis of bromide-lithium exchange reaction and the separation of organic and aqueous phase products in micro systems was investigated.The method used to construct micro-separator and micro reactor, a laser engraving technique, and thermal bonding of glass to glass.In the first step, the factors affecting the separation of organic and aqueous phase in the capillary micro-separator, such as the width of the capillary, the length of the capillary, the number of capillaries and... 

    Semiconductor TiO2-Al2O3 thin film gas sensors derived from aqueous particulate sol-gel process

    , Article Materials Science in Semiconductor Processing ; Vol. 27, issue , 2014 , p. 711-718 Mohammadi, M. R ; Sharif University of Technology
    2014
    Abstract
    Nanostructured TiO2-Al2O3 films and powders were prepared by a straightforward aqueous particulate sol-gel route. Titanium (IV) isopropoxide and aluminum chloride were used as precursors, and hydroxypropyl cellulose was used as a polymeric fugitive agent in order to increase the porosity. The effect of Al:Ti molar ratio was studied on the crystallization behavior of the products. X-ray diffraction (XRD) revealed that the powders crystallized at 800°C, containing anatase-TiO2, rutile-TiO2 and cubic-Al2O3 phases. Furthermore, it was found that Al2O3 retarded the anatase to rutile transformation. Transmission electron microscope (TEM) image showed that one of the smallest crystallite sizes was... 

    Concavity degree: A new feature for chromosome centromere localization

    , Article AISP 2012 - 16th CSI International Symposium on Artificial Intelligence and Signal Processing ; 2012 , Pages 58-63 ; 9781467314794 (ISBN) Mohammadi, M. R ; Sharif University of Technology
    2012
    Abstract
    Analyzing the features of the chromosomes can be very useful for diagnosis of many genetic disorders or prediction of the possible abnormalities that may occur in the future generations. For this purpose, karyotype is often used which to make it, there is necessary to identify each one of the 24 chromosomes from the microscopic images. Definition and extraction of the morphological and band pattern based features for each chromosome is the first step to identify them. An important class of the morphological features is the location of the chromosome's centromere. Thus, centromere localization is an initial step in designing an automatic karyotyping system. In this paper, a novel algorithm... 

    Optimal placement of PMUs for power system observability using topology based formulated algorithms

    , Article Journal of Applied Sciences ; Volume 9, Issue 13 , 2009 , Pages 2463-2468 ; 18125654 (ISSN) Mohammadi Ivatloo, B ; Sharif University of Technology
    2009
    Abstract
    This study presents optimal placement of Phasor Measurement Units (PMUs) for the purpose of power system observability using topology based formulated algorithms. The optimal PMU placement problem is formulated to minimize the number of PMUs installation subject to full network observability. The Branch and Bound (B and B) and genetic algorithm optimization methods are selected to solve the problem, which are suitable for problems with integer and Boolean variables. Topology-based algorithm used for observability analysis and a hybrid method of topology transformation and nonlinear constraint is used to form constraints. The IEEE 14, 30, 57 and 118-bus and the New England 39-bus test systems... 

    Stabilized Meshless Local Petrov-Galerkin (MLPG) method for incompressible viscous fluid flows

    , Article CMES - Computer Modeling in Engineering and Sciences ; Volume 29, Issue 2 , 2008 , Pages 75-94 ; 15261492 (ISSN) Haji Mohammadi, M ; Sharif University of Technology
    2008
    Abstract
    In this paper, the truly Meshless Local Petrov-Galerkin (MLPG) method is extended for computation of steady incompressible flows, governed by the Navier-Stokes equations (NSE), in vorticity-stream function formulation. The present method is a truly meshless method based on only a number of randomly located nodes. The formulation is based on two equations including stream function Poisson equation and vorticity advection-dispersion-reaction equation (ADRE). The meshless method is based on a local weighted residual method with the Heaviside step function and quartic spline as the test functions respectively over a local subdomain. Radial basis functions (RBF) interpolation is employed in shape...