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    Nucleoside Structure using Ab-Initio Computational Methods

    , M.Sc. Thesis Sharif University of Technology Chashmniam, Saeed (Author) ; Tafazzoli, Mohsen (Supervisor)
    Abstract
    The spin – spin coupling constants have been calculated by the Gaussian 2009 program in order to study the nucleosides conformation. To study the effect of solvent, the calculations were performed in four solvent including water, DMSO, chloroform and Carbon tetrachloride.
    Also, the comparison is done on two computing methods including DFT (B3LYP) and HF using 6-311++g** and 6-311g basis set.One bonding (1JC-H), two bonding (2JN-H, 2JC-H) and three bonging coupling constants (3JC-H) have been calculated for unpaired adenosine, thymidine and uridine molecules.Formation of intra-molecular hydrogen bond and electron pair repulsion, respectively, makes the compounds stable and unstable.... 

    Ab initio calculations of characteristic lengths of crystalline materials in first strain gradient elasticity

    , Article Mechanics of Materials ; Volume 61 , 2013 , Pages 73-78 ; 01676636 (ISSN) Shodja, H. M ; Zaheri, A ; Tehranchi, A ; Sharif University of Technology
    2013
    Abstract
    Incorporation of the first gradient of strain, in addition to the strain itself, into the strain energy density of an elastic solid leads to Mindlin's first strain gradient theory, which is useful for examination of size effect as well as other mechanical phenomena at the nano-scale. For isotropic elastic solids, the first strain gradient theory, in addition to the two independent Lamé constants, gives rise to five new material constants which in turn reduce to two material parameters, ℓ1 and ℓ2 with dimension of length. The evaluation of these parameters, however, has posed serious challenges, both experimentally and theoretically. In this work ab initio method is used to compute the... 

    The importance of electron correlation in graphene and hydrogenated graphene

    , Article European Physical Journal B ; Volume 88, Issue 10 , October , 2015 ; 14346028 (ISSN) Hadipour, H ; Jafari, S. A ; Sharif University of Technology
    springer berlin  2015
    Abstract
    Local density approximation (LDA) and Green function effective Coulomb (GW) calculations are performed to investigate the effect of electronic correlations on the electronic properties of both graphene and graphane. The size of band gap in graphane increases from 3.7 eV in LDA to 4.9 eV in GW approximation. By calculating maximally localized Wannier wave functions, we evaluate the necessary integrals to get the Hubbard U and the exchange J interaction from first principles for both graphene and graphane. Our ab-initio estimates indicate that in the case of graphene, in addition to the hopping amplitude t ∼ 2.8 eV giving rise to the Dirac nature of low lying excitations, the Hubbard U value... 

    Coupling of the electronic band structure with Ag phonon modes in Y123 and Y124 systems

    , Article 4th International Conference on Magnetic and Superconducting Materials, MSM'05, Agadir, 5 September 2006 through 8 September 2006 ; Volume 3, Issue 9 , 2006 , Pages 3140-3143 ; 18626351 (ISSN) Khosroabadi, H ; Mossalla, B ; Akhavan, M ; Sharif University of Technology
    2006
    Abstract
    Ab initio frozen-phonon calculations have been performed for k = 0 A g Raman modes of two superconducting systems Y123 and Y124. We have used the local density approximation pseudopotential method in our calculations by VASP code. Results have been compared with other computational and experimental data for similar systems. Then we present changes of electronic band structure with the change of ionic positions in each Ag mode for both systems. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA  

    Gas phase kinetics and mechanism of 2,2-dimethyl but-3-enal and 1-methyl-6-methylenecyclohexa-2,4-diene-1-carbaldehyde retro-cheletropic ene reaction

    , Article Journal of Molecular Structure: THEOCHEM ; Volume 672, Issue 1-3 , 2004 , Pages 61-66 ; 01661280 (ISSN) Gholami, M. R ; Izadyar, M ; Sharif University of Technology
    Elsevier  2004
    Abstract
    Structural and kinetic aspects of the retro-cheletropic ene reactions of 2,2-dimethyl but-3-enal, 1-methyl-6-methylenecyclohexa-2,4-diene-1-carbaldehyde and their deuterated derivatives were investigated using a variety of computational methods. Theoretical calculations were carried out with ab initio and DFT methods at the RHF, MP2 and B3LYP levels of the theory, using the 6-31G* basis set. Vibrational frequency analysis confirmed the stationary states including the transition state (TSs) structures. Intrinsic reaction coordinate calculations show the localized TSs connect with the corresponding minima associated with the reactants and the products. The mechanistic studies on the... 

    Electronic and phonon structures of BaFe2As2 superconductor by Ab-initio density functional theory

    , Article Journal of Superconductivity and Novel Magnetism ; Volume 26, Issue 1 , January , 2013 , Pages 93-100 ; 15571939 (ISSN) Sandoghchi, M ; Khosroabadi, H ; Almasi, H ; Akhavan, M ; Sharif University of Technology
    2013
    Abstract
    Electronic and phonon structures of the BaFe2As2 superconductor in the magnetic-orthorhombic phase have been investigated by the ab-initio density functional theory using the pseudopotential Quantum Espresso code. Density of state and electronic band structure for this phase has been studied, but phonon dispersion has been obtained only for the nonmagnetic-orthorhombic phase. Electronic band structure and density of states are in good agreement with other calculations in the literature. The electronic state near the Fermi energy are essentially made from Fe3d and As4p orbital that indicate in-plane conductivity in FeAs layers in this system. Comparing calculated phonon dispersions with... 

    A combined first principles and analytical treatment for determination of the surface elastic constants: Application to Si(001) ideal and reconstructed surfaces

    , Article Philosophical Magazine Letters ; Volume 92, Issue 1 , Sep , 2012 , Pages 7-19 ; 09500839 (ISSN) Ojaghnezhad, F ; Shodja, H. M ; Sharif University of Technology
    2012
    Abstract
    Behavior of nanostructures, which are characterized by a large surface-to-volume ratio, is greatly influenced by their surface parameters, such as surface elastic moduli tensor. Accurate determination of the surface elastic constants by first principles is of particular interest. To this end, through consideration of the fundamental thermodynamic arguments for free solid surfaces, an analytical formulation for the change in specific Helmholtz surface free energy is developed. Relating this formulation to the corresponding energy calculated via first principles leads to the determination of the surface elastic moduli tensor. The surface mechanical properties, namely surface energy, surface... 

    Tunable bandgap opening in the proposed structure of silicon-doped graphene

    , Article Micro and Nano Letters ; Volume 6, Issue 8 , 2011 , Pages 582-585 ; 17500443 (ISSN) Azadeh, M. S. S ; Kokabi, A ; Hosseini, M ; Fardmanesh, M ; Sharif University of Technology
    2011
    Abstract
    A specific structure of doped graphene with substituted silicon impurity is introduced and ab initio density-functional approach is applied for the energy band structure calculation of the proposed structure. Using the band structure calculation for different silicon sites in the host graphene, the effect of silicon concentration and unit cell geometry on the bandgap of the proposed structure is also investigated. Chemically, silicon-doped graphene results in an energy gap as large as 2eV according to density-functional theory calculations. As the authors will show, in contrast to previous bandgap engineering methods, such structure has significant advantages including wide gap tuning... 

    Atomistic study of the effect of crystallographic orientation on the twinning and detwinning behavior of NiTi shape memory alloys

    , Article Computational Materials Science ; Volume 203 , 2022 ; 09270256 (ISSN) Fazeli, S ; Izadifar, M ; Dolado, J. S ; Ramazani, A ; Sadrnezhaad, S. K ; Sharif University of Technology
    Elsevier B.V  2022
    Abstract
    Understanding the effect of crystallographic orientation on the twinnin/detwinning mechanisms in NiTi shape memory alloys at an atomistic scale can help to control and tune the mechanical properties and failure behavior of such materials. In this work, we employed classical molecular dynamics (MD) and density functional theory (DFT) computational methods to better understand how twinning and detwinning occurs through a combination of slip, twin, and shuffle on 〈0 1 0〉, 〈1 1 0〉, and 〈1 1 1〉 crystallographic orientations under uniaxial tensile test. Elastic constants including Young's Modulus (E), Bulk modulus (B), Poisson's ratio (ν), and Shear Modulus (G) are obtained and computed for... 

    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)
    Abstract
    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... 

    Mechanics and Morphology of Single-Walled Carbon Nanotubes

    , Ph.D. Dissertation Sharif University of Technology Delfani, Mohammad Rasoul (Author) ; Mohammadi Shoja, Hossein (Supervisor)
    Abstract
    Vibration is one of the most important factors in design, operation and lifetime of drill strings. There for, investigation of vibrations in drill string, like every other rotary machine, is very important. The main goal of this research is developing a nonlinear model for a drill string system dynamics in an inclined well. Effects of drilling mud flow rate, weight on bit, angular velocity along with viscous damping, on the stability and vibration of a drill string are studied. Dynamic equation of the model is developed considering axial displacement and lateral bending geometric nonlinear coupling. The effect of drilling mud flow is modeled using Paidoussis formulations. Equation of motion... 

    Ab-initio Calculations of Electronic and Phonon Structures of Ba1-xKxFe2As2 (x = 0,0.5,1) Superconductor

    , M.Sc. Thesis Sharif University of Technology Sandoghchi, Mohammad (Author) ; Khosroabadi, Hossien (Supervisor) ; Akhavan Farshchi, Mohammad (Supervisor)
    Abstract
    After discovery of superconductivity in 1911 people try to find superconductors with higher Tc. High Tc superconductivity in cuprates and iron based superconductors was discovered in 1986 and 2008 respectively. However, there is not any unit theory for high Tc superconductivity in cuprates or iron based superconductors. Study of electronic and phonon structures of high Tc superconductor compounds can lead to find theory of high Tc superconductivity.
    In this dissertation electronic structure of Ba1-xKxFe2As2, which belongs to class of 122 of iron based superconductor, under potassium doping x=0,0.5,1 has been studied. To this end ab-initio method and Density functional theory have been... 

    Structural analysis of Y3Ba5Cu8O 19-δ high-Tc superconductor by ab initio density functional theory

    , Article Physica C: Superconductivity and its Applications ; Volume 497 , 15 February , 2014 , 2014, Pages 84-88 ; ISSN: 09214534 Khosroabadi, H ; Rasti, M ; Akhavan, M ; Sharif University of Technology
    Abstract
    The details of the crystal structure of the recently discovered Y 3Ba5Cu8O18+δ (Y358) superconductor have been determined by ab initio density functional theory. Total energy calculation has been performed for three different suggested structures with different oxygen content. The structure with a center of inversion symmetry and the highest oxygen concentration has the lowest total energy. Thus, it is the best choice for the Y358 crystal structure. By investigating the detailed structure, it is seen that this compound is arranged either of YBa2Cu3O7 and YBaCu2O 5 or YBaCu2O5 and BaCuO2 substructural blocks in the c direction. The difference between the total energy of Y358 compound and the... 

    Ab initio study of electronic effects in the ZnO/TiO2 core/shell interface: Application in dye sensitized solar cells

    , Article RSC Advances ; Vol. 4, issue. 1 , April , 2014 , p. 301-307 Pazoki, M ; Nafari, N ; Taghavinia, N ; Sharif University of Technology
    Abstract
    Core/shell structure of ZnO nanowires coated with a monolayer of TiO 2 is investigated using Density Functional Theory (DFT). The electronic states of the semiconductor is calculated and compared before and after coating of the TiO2 monolayer on a ZnO [101 0] surface. The effect of TiO2 coating induce surface states changes and shifts the conduction and valence band edges to higher energies. Our results, in qualitative agreement with the experimental work of Matt Law et al. (J. Phys. Chem. B, 110, 22652), show an increase in open circuit voltage and a decrease in short circuit current in ZnO/TiO2 core shell dye sensitized solar cells. Regarding the semiconductor density of states (DOS), TiO2... 

    Hydration strongly affects the molecular and electronic structure of membrane phospholipids

    , Article Journal of Chemical Physics ; Volume 136, Issue 11 , 2012 ; 00219606 (ISSN) Mashaghi, A ; Partovi Azar, P ; Jadidi, T ; Nafari, N ; Maass, P ; Tabar, M. R. R ; Bonn, M ; Bakker, H. J ; Sharif University of Technology
    Abstract
    We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells  

    Investigation of quantum conductance in semiconductor single-wall carbon nanotubes: Effect of strain and impurity

    , Article Journal of Applied Physics ; Volume 110, Issue 6 , 2011 ; 00218979 (ISSN) Rabiee Golgir, H ; Faez, R ; Pazoki, M ; Karamitaheri, H ; Sarvari, R ; Sharif University of Technology
    2011
    Abstract
    In this paper the effect of strain and impurity on the quantum conductance of semiconducting carbon nanotubes (CNTs) have been studied by ab-initio calculations. The effect of strain and impurity on the CNT conducting behavior and physical characteristics, like density of states (DOS), band structure, and atomic local density of state (LDOS), is considered and discussed separately and simultaneously. Our results show that the quantum conductance of semiconductor CNTs is increased by compression strain, elongation strain, and replacing nitrogen and boron doping in its structure. The amount of increasing in the conductance depends on the type of strain and impurity. Conductance of CNT can be... 

    Ab-Initio calculations of the CO adsorption and dissociation on substitutional Fe-Cu surface alloys relevant to Fischer-Tropsch Synthesis: Bcc-(Cu)Fe(100) and fcc-(Fe)Cu(100)

    , Article Surface and Interface Analysis ; Volume 45, Issue 7 , 2013 , Pages 1081-1087 ; 01422421 (ISSN) Elahifard, M ; Fazeli, E ; Joshani, A ; Gholami, M ; Sharif University of Technology
    Abstract
    Direct CO dissociation is seen the main path of the first step in the Fischer-Tropsch Synthesis (FTS) on the reactive iron surfaces. Cu/Fe alloy film is addressed with various applications over face-centered-cubic (fcc)-Cu and body-centered-cubic (bcc)-Fe in the FTS, i.e. preventing iron carbide formation (through direct CO dissociation) by moderating the surface reactivity and facilitating the reduction of iron surfaces, respectively. In this study by density functional theory, the stable configurations of CO molecule on various Cu/Fe alloys over fcc-Cu(100) and bcc-Fe(100) surfaces with different CO coverage (25% and 50%) have been evaluated. Our results showed that the ensemble effect... 

    Surfactant binary systems: Ab initio calculations, preferential solvation, and investigation of solvatochromic parameters

    , Article Journal of Chemical and Engineering Data ; Volume 61, Issue 1 , 2016 , Pages 255-263 ; 00219568 (ISSN) Kohantorabi, M ; Salari, H ; Fakhraee, M ; Gholami, M.R ; Sharif University of Technology
    American Chemical Society 
    Abstract
    Solvatochromic UV-vis shifts of three probes 4-nitroaniline, 4-nitroanisol, and Reichardt's dye in binary mixtures of polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (Triton X-100 or TX-100) with methanol, ethanol, 1-propanol, and water have been investigated at 298 K. Structural and intermolecular interactions of solvatochromic probes were determined in these systems. Solvatochromic parameters, including normalized polarity (ETN), dipolarity-polarizability (π∗), hydrogen-bond donor (α), and hydrogen-bond acceptor (β) abilities, were measured at a wide range of mole fraction (0 ≤ X ≤ 1) with 0.1 increment. Interestingly, a similar behavior of ETN and α is observed in... 

    Elastic moduli tensors, ideal strength, and morphology of stanene based on an enhanced continuum model and first principles

    , Article Mechanics of Materials ; Volume 110 , 2017 , Pages 1-15 ; 01676636 (ISSN) Shodja, H. M ; Ojaghnezhad, F ; Etehadieh, A ; Tabatabaei, M ; Sharif University of Technology
    Elsevier B.V  2017
    Abstract
    The present work aims to provide an accurate description of the tensile behavior of the planar as well as low-buckled stanene and to capture their ideal strength in armchair (AC)- and zigzag (ZZ)-directions. For an accurate description of anisotropic response of such hyperelastic materials as stanene, consideration of a highly nonlinear constitutive model in which up to the fourth power of strains is incorporated is inevitable. By utilizing first principles calculations based on density functional theory (DFT), the second, third, fourth, and fifth order elastic moduli tensors corresponding to both planar and low-buckled states are obtained. Moreover, the morphology of the free-standing... 

    Molecular dynamics study of two dimensional silicon dioxides with in-plane negative poisson's ratio

    , Article Computational Materials Science ; Volume 153 , 2018 , Pages 258-267 ; 09270256 (ISSN) Safaei, S ; Tavakoli, R ; Jafary Zadeh, M ; Sharif University of Technology
    Abstract
    In the present work, the mechanical properties, in particular, the Poisson's ratio of four two-dimensional silica structures, called here α,β,γ and δ are studied by means of molecular dynamics simulations. The α structure has been synthesized experimentally and the others have been reported as the most stable low-energy structures that reveal in-plane negative Poisson's ratio based on the first principles calculations. Among these structures, β-silica exhibits the largest in-plane negative Poisson's ratio which is 2–4 times higher than penta-graphene. Our results illustrate that the classical molecular dynamics simulation reproduces results in agreement with those of the first principles...