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    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,... 

    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... 

    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... 

    U-Shaped Assembly Line Rebalancing With Cost Minimization Objectives

    , M.Sc. Thesis Sharif University of Technology Khoshnood, Sara (Author) ; Akbari, Javad (Supervisor)
    Abstract
    U-shaped assembly lines usually are more effective than straight lines. Therefore special attention has been paid to u-shaped line balancing problem in recent years. On the other hand most articles on the line balancing problems are investigated for the first time. However, within the lifetime of an ALB, the balancing problems do not occur only once prior to its construction, but rather continuously as rebalancing. For example whenever the demand structure or production technology changes or producing seasonal products, the ALB needs to be reconfigured. So many balancing issues in the real world are related to re-balancing of production lines.
    Therefore in this study, U-shaped assembly... 

    Diffusion of Lipid and Protein Molecules in Cell Membranes

    , Ph.D. Dissertation Sharif University of Technology Khoshnood, Atefeh (Author) ; Jalali, Abbas (Supervisor)
    Abstract
    Lipid membranes are fundamental constituents of cell membranes and are now used in lap-on-a-chip technology. Membranes in living cells contain a significant fraction of proteins, which undergo lateral random movements due to thermal fluctuations and shear forces imposed by the solvent fluid. Prominent natural and biotechnological systems where membranes are highly sheared include the plasma membrane of endothelial cells, and membranes used in biosensors for high throughput screening of drug candidates, and in water purification devices. In these systems membrane is in direct contact with the mainstream suspension flow, which is driven by pressure gradients. The efficiency and function of... 

    Long-lived and unstable modes of Brownian suspensions in microchannels

    , Article Journal of Fluid Mechanics ; Volume 701 , 2012 , Pages 407-418 ; 00221120 (ISSN) Khoshnood, A ; Jalali, M. A ; Sharif University of Technology
    2012
    Abstract
    We investigate the stability of the pressure-driven, low-Reynolds-number flow of Brownian suspensions with spherical particles in microchannels. We find two general families of stable/unstable modes: (i) degenerate modes with symmetric and antisymmetric patterns; (ii) single modes that are either symmetric or antisymmetric. The concentration profiles of degenerate modes have strong peaks near the channel walls, while single modes diminish there. Once excited, both families would be detectable through high-speed imaging. We find that unstable modes occur in concentrated suspensions whose velocity profiles are sufficiently flattened near the channel centreline. The patterns of growing unstable... 

    Anomalous diffusion of proteins in sheared lipid membranes

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 88, Issue 3 , September , 2013 ; 15393755 (ISSN) Khoshnood, A ; Jalali, M. A ; Sharif University of Technology
    2013
    Abstract
    We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,... 

    Lipid membranes with transmembrane proteins in shear flow

    , Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) Khoshnood, A ; Noguchi, H ; Gompper, G ; Sharif University of Technology
    2010
    Abstract
    The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins... 

    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  

    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... 

    Assisted passive snake robots: Conception and dynamic modeling using kane's method

    , Article 2005 ASME International Mechanical Engineering Congress and Exposition, IMECE 2005, Orlando, FL, 5 November 2005 through 11 November 2005 ; Volume 74 DSC, Issue 2 PART B , 2005 , Pages 1475-1482 ; 0791842169 (ISBN); 9780791842164 (ISBN) Pendar, H ; Vossoughi, G ; Khoshnood, A ; Poursamad, A ; Sharif University of Technology
    2005
    Abstract
    In this paper conception and dynamic modeling of a snake-like robot with passive wheels and compliant joints is investigated. The proposed robot has the ability to follow a socalled Serpenoid curve passively by using an appropriate set of initial conditions. Introduction of a unique structure at each joint enables the robot to achieve passive motion. A torsional spring is used in series with an actuator between each two consecutive links. Using wheels at the middle of each link imposes many non-holonomic constraints to the system. These constraints reduce the degrees of freedom of the system to only two. Due to the existence of these non-holonomic constraints, dynamic equations governing the... 

    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...