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    A Coupling Atomistic-continuum Approach for Modeling Dislocation in Plastic Behavior of Nano-structures

    , M.Sc. Thesis Sharif University of Technology Omrani Pournava, Amir Mohsen (Author) ; Khoei, Amir Reza (Supervisor) ; Jahanshahi, Mohsan (Co-Advisor)
    In this study, a novel multi-scale hierarchical method has been employed to explore the role of edge dislocation on Nano-plates with hexagonal atomic structure in large deformation. multiscale hierarchical atomistic/molecular dynamics (MD) finite element (FE) coupling methods are proposed to demonstrate the impact of dislocation on mechanical properties of Magnesium in large deformation. The atomic nonlinear elastic parameters are attained via computing first-order derivation of stress with respect to strain of Representative Volume Element (RVE). To associate between atomistic and continuum level, the mechanical characteristics are captured in the atomistic scale and transferred to the... 

    DNA Chains Entanglement in Confined Geometries

    , M.Sc. Thesis Sharif University of Technology Ahmadian, Zahra (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    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... 

    Transition from the Down State to the Up State of RBD Protein in SARS -CoV- 2

    , M.Sc. Thesis Sharif University of Technology Taeb, Hoda (Author) ; Ejtehadi, Mohammad Reza (Supervisor) ; Ghasemi Tarei, Maryam (Co-Supervisor)
    Since the first observed case in December 2019, millions of people have been infected by Coronavirus disease 2019 (COVID-¬19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS¬-CoV-¬2). Located on the viral membrane, trimeric spike glycoprotein is one of the most crucial parts of the virus’ structure as it is responsible for the attachment and entry of the virus to host cells. The spike glycoprotein undergoes hinge-like conformational movements and its receptor¬binding domains (RBD) can be in either an accessible (up) state or an inaccessible (down) state to the host cell receptors, such as ACE2. Having performed Molecular Dynamics Simulations and Targeted Molecular... 

    Ionic Polymer-Metal Nanocomposite; Multiscale Simulation, Fabrication and Mechanical Characterization

    , Ph.D. Dissertation Sharif University of Technology Ozmaian, Masoumeh (Author) ; Naghdabadi, Reza (Supervisor) ; Irajizad, Azam (Supervisor) ; Ejtehadi, Mohammad Reza (Co-Advisor)
    Ionic polymer metal nanocomposites (IPMNCs) are among the advance materials which have been widely used recently as smart materials. These nanocomposites, which are made of polymeric layers (Nafion) plated by metallic or non-metallic conductive electrodes, show large deformations under low applied voltages. The advance materials like these nanocomposites have resolved the problems of the conventional actuators and helped in producing accurate systems.
    Several methods have been used to predict the behavior of IPMNCs which any of them consider some simplifying assumptions. In these materials physical phenomena happen at the molecular scale and deformations observed at the large scale.... 

    Comparing Glass Formability of Cu-Zr and Ni-Zr Systems by Molecular Dynamics Simulation

    , M.Sc. Thesis Sharif University of Technology Ghaemi, Milad (Author) ; Tavakoli, Rohollah (Supervisor)
    Metallic glasses (MG) are a group of materials that have unique properties such as high yielding strength and high elastic deformation. Because of limitation in the production of these materials, a few industrial materials of MG have been made so far. A few of binary alloys, like binary alloys made of Cu-Zr, have high Glass Forming Ability (GFA) in medium cooling rates. Between two binary systems of Cu-Zr and Ni-Zr, although constituent elements in aspect of atomic radius, electronic structure, physical properties, phase diagrams and intermetallic compounds are so similar to each other, but GFA between them are very different. For example, in Cu-Zr system there are compounds, such as... 

    Investigation of Stability and Electromechanical Properties of a Nano Capacitor Made of Two Graphene Sheets

    , M.Sc. Thesis Sharif University of Technology Borhanpanah Mooshaki, Mohammad Reza (Author) ; Dehghani Firouz-Abadi, Rouhollah (Supervisor)
    Investigation of electrostatic properties of a nano capacitor made of graphene sheets, is the aim of current research. This nano capacitor is made of two adjacent parallel gr¬aphene sheets. Applying a voltage make an electric field between the sheets, which attracts the sheets together. This change in geometry, affects the electric field between sheets, therefore, the sheet's deformation and the electric field between them are coupled to each other. For modeling the deformation of the sheets, molecular dynamics analysis is employed. The electrostatic equations are used for modeling the electric field. The electric field is assumed to be static in this research, which means that the... 

    Study of the Gating Mechanism of Mechanosensitive Membrane Channels

    , M.Sc. Thesis Sharif University of Technology Rasouli, Ali (Author) ; Nejat Pishkenari, Hoessein (Supervisor) ; Zohour, Hassan (Supervisor) ; Jamali, Yousef (Co-Advisor)
    Mechanosensitive membrane channels are indispensable part of cells that sense and respond to mechanical signals. Hence, malfunction of these channels may cause various diseases. Despite numerous studies of these channels, there are still many unanswered questions surrounding these channels and their gating mechanism. Although there have been valuable experimental studies in this field, the need for modelling and computational studies are still felt since experiments face many limitations in this area. Thus, a channel that its crystallographic structure has been recently determined was chosen and studied using computational tools. In this study, gating of the channel under surface tension has... 

    Study of Tangential Coefficient of Restitution in Nano-particles Collision

    , M.Sc. Thesis Sharif University of Technology Shahbakhti, Abbas (Author) ; Sayyadi, Hasan (Supervisor) ; Nejat, Hosein (Co-Supervisor)
    In this thesis, the collisions of two fluorine-C60 nanoparticles have been studied using molecular dynamics simulation. The main purpose of this thesis is to present a completely new method based on the definition of the vertical and tangential coefficient of restitution, although by using the combination of the simulation and theory results, we can obtain the approximate parameters of physical properties of nanoparticles, such as hardness coefficient, surface tension, friction coefficient, etc.At first, two fluorine C60 under different conditions, including collision velocity, collision angle, initial temperature, initial rotational angle of the molecule, and various potential applications... 

    Study of Microstructure Evolution During Cyclic Martensitic Transformations in Shape Memory Alloys with Molecular Dynamics Simulation

    , M.Sc. Thesis Sharif University of Technology Moravvej, Amin (Author) ; Nejat, Hossein (Supervisor) ; Arghavani, Jamal (Supervisor)
    Shape memory alloys (SMA) exhibit a number of features which are not easily explained by equilibrium thermodynamics, including hysteresis in the phase transformation and ‘‘reverse’’ shape memory in the high symmetry phase. Processing can change these features: repeated cycling can ‘‘train’’ the reverse shape memory effect, while changing the amount of hysteresis and other functional properties. These effects are likely to be due to formations of localised defects and these can be studied by atomistic methods. Here we present a molecular dynamics simulation study of such behaviour employing a two-dimensional, binary Lennard–Jones model. Our atomistic model exhibits a symmetry breaking,... 

    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... 

    Theoretical Investigation of Ab-initio MD Approach to Increase the Efficiency and Accuracy of VCD Spectrum Calculation

    , M.Sc. Thesis Sharif University of Technology Hadi, Hossein (Author) ; Jamshidi, Zahra (Supervisor)
    Understanding of the Molecules is the main purpose of the chemistry. Ab-initio molecular dynamics (AIMD) as a branch of the computational chemistry, tries to give us a deep comprehension of the molecule, and its chemical, physical and optical activities. This comprehension, relies on the accuracy of quantum mechanics, in addition to the speed of the classical mechanics. The mixing of the quantum mechanics and the classical mechanics could simulate activities of the atoms in the time-domain, provided the mixing is done with precaution. This, in turn, helps us to forecast the response of a molecule in different situations, and also translating the macroscopic phenomena in a nanoscopic... 

    Theoretical Study of Solvent and Substituent Effects on Kinetic and Mechanism of Organic Reactions and Theoretical Study of Enzyme Reactions

    , Ph.D. Dissertation Sharif University of Technology Irani, Mehdi (Author) ; Gholami, Mohammad Reza (Supervisor)
    Computational chemistry is used to study solvent and substituent effects on kinetics and mechanism of some organic reactions. It also is used to study enzyme reactions and enzyme structures. Organic reactions were studied by ab initio quantum mechanics and Monte Carlo simulations. The enzyme studies were done by QM/MM and MD methods in Lund University. The studied organic reactions are 1) Reactions of hydroxylamine and aminoxide anion with methyl iodide. 2) Rearrangement of allyl p-tolyl ether. 3) Reactions of 1,4-Benzoquinone with Cyclopentadiene and Cyclohexadiene derivatives and reaction of cyclopentadiene and vinyl acetate. In the enzyme studies the catalytic reaction of Glyoxalase... 

    Mechanism Investigation of Metallic Nanoparticles Interaction with Biological Molecules using Molecular Dynamic Simulation

    , M.Sc. Thesis Sharif University of Technology Soltani, Nima (Author) ; Gholami, Mohammad Reza (Supervisor)
    Amyloid β (Aβ) peptide is believed to be associated with the progression of Alzheimer's disease. One of the main obstacles in developments of therapeutic agents to combat progression of Alzheimer's disease, is the presence of the blood–brain barrier (BBB), which prevents the penetration of the majority of drugs. However, nanoscale objects are able to cross the BBB at low concentrations. Therefore, it is worthwhile to study the interactions of these peptides at the interface of nanomaterials. In this work we have employed molecular dynamics, and weighted histogram analysis methods in order to study the dynamic behavior and affinity of Aβ25-35 peptide on metallic surfaces of different... 

    Molecular Dynamics Simulation of Actin: An Investigation into the Mechanical Properties

    , M.Sc. Thesis Sharif University of Technology Mehrafrooz, Behzad (Author) ; Shamloo, Amir (Supervisor) ; Firoozbakhsh, Keikhosrow (Supervisor)
    Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

    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... 

    Study on Thermodynamics of Iodine Vapor Adsorption on Cu Nanoparticles by Different Computational Approach

    , M.Sc. Thesis Sharif University of Technology Razavi, Maliheh (Author) ; Outokesh, Mohammad (Supervisor)
    Iodine isotopes are among the most significant medical radioisotopes with a wide range of applications in therapy and diagnosis. The I-131 isotope is usually synthesized by irradiation of natural tellurium in atomic reactors. But there is an alternative route in which this isotopes is produced along with two other significant medical radioisotopes (i.e. Mo-99, Xe-131) by neutronic irradiation of uranium in the reactors. To separate iodine isotopes especially in the extraction process of fission fragments, it is necessary to be selective adsorption of iodine on a selective adsorbent. One of the most selective adsorbent for this application is copper. The aim of this study is to compare the... 

    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)
    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,... 

    Atomistic Study of Iinterface Properties and Structure of Nickel-Silicon and Polyethelene-Ghraphene by Molecular Dynamics Simulation

    , M.Sc. Thesis Sharif University of Technology Amini, Hamed (Author) ; Kokabi, Amir Hossein (Supervisor) ; Simchi, Abdolreza (Supervisor)
    First atomistic simulation was used to study the deformation and fracture mechanisms of Ni-Si interfaces under tensile and shear loads dependent on the crystal structure of interface zone. Modified embedded atom method (MEAM) potential was utilized for molecular dynamics (MD) modeling. The simulation includes analysis of common neighbors, coordination number, least-square atomic local strain, and radial distribution function. The profound effect of interface crystallography on the tensile and shear deformation is shown. The highest tensile strength is obtained for interfaces with high plane density due to lowest atomic disorder while under shear loading planes with low density exhibit a high... 

    A Concurrent Multiscale Modelling of Crack Propagation with the Use of Extended Finite Element Method

    , M.Sc. Thesis Sharif University of Technology Alizadeh, Omid (Author) ; khoei, Amir Reza (Supervisor)
    Crack propagation problem is one of the most important problems that are being investigated for a long time. Plenty of various approaches have been utilized to simulate the crack propagation phenomenon. Continuum based methods like Finite element (FE), Extended Finite element (XFEM), have been successfully applied, and the obtained results are valid in macro scale. However, the stress filed near crack tip in FEM modeling of crack, is not exquisite enough due to inability of continuum based approaches in revealing atomistic aspects of the material.
    In order to gather efficiency of the continuum based domain and the accuracy of the atomistic based domain, Multiscale methods are employed.... 

    Mechanical Model in Cell and Nucleus Deformation

    , M.Sc. Thesis Sharif University of Technology Heydari, Tiam (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Now a days, the ability of measuring the mechanical properties of the living cells in in experiments has been increased. Experiments shows that the stem cells could alter their faith in different mechanical situations, but an integrated model about this phenomenon in literature has not been introduced yet. In this research thesis s minimal cell model (MMC) is developed to capture the behavior of the cells on substrates with varying mechanical properties and morphologies, MMC consists of large scale models for outer membrane of the cell and nuclear envelope, cytoplasmic area, chromatin fibers and Extra cellular matrix. Each component of the MMC will be placed in an integrated software to...