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Ab Initio Modeling (ab + initio_modeling)
Selected AbstractsAb initio modeling of small diameter silicon nanowiresPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2006Murat Durandurdu Abstract Using ab initio calculations, we predict stable small diameter silicon nanowires. The wires are constructed from the expended phases of silicon, clathrate Si(34) and Si(46) structures, and found to be energetically more favorable than the diamond type nanowires at the same diameters. Furthermore, the wires are semiconducting with band gap energy of 0.22 eV and 0.34 eV. Chemical passivation of the wires with hydrogen induces a broadening of band gap energy due to the quantum size effect and increases the hardness of the wires. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: Implications for asymmetric cell division in DrosophilaPROTEIN SCIENCE, Issue 5 2008Mohammad S. Yousef Abstract Miranda is a multidomain adaptor protein involved in neuroblast asymmetric division in Drosophila melanogaster. The central domain of Miranda is necessary for cargo binding of the neural transcription factor Prospero, the Prospero-mRNA carrier Staufen, and the tumor suppressor Brat. Here, we report the first solution structure of Miranda central "cargo-binding" domain (residues 460,660) using small-angle X-ray scattering. Ab initio modeling of the scattering data yields an elongated "rod-like" molecule with a maximum linear dimension (Dmax) of ,22 nm. Moreover, circular dichroism and cross-linking experiments indicate that the cargo-binding domain is predominantly helical and forms a parallel coiled-coil homodimer in solution. Based on the results, we modeled the full-length Miranda protein as a double-headed, double-tailed homodimer with a long central coiled-coil region. We discuss the cargo-binding capacity of the central domain and propose a structure-based mechanism for cargo release and timely degradation of Miranda in developing neuroblasts. [source] Multiscale simulation of polycrystal mechanics of textured ,-Ti alloys using ab initio and crystal-based finite element methodsPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 12 2008D. Ma Abstract Crystal-based finite element methods (FEM) are versatile continuum approaches for predicting mechanical properties and deformation-induced crystallographic textures. They can be applied to both, elastic,plastic and elastic problems. The methodology is based on (i) a detailed understanding of the underlying crystal deformation mechanisms and (ii) a number of constitutive material parameters that are often difficult to measure. First principle calculations, that take into account the discrete nature of matter at the atomic scale, are an alternative way to study mechanical properties of single crystals without using empirical parameters. In this study we demonstrate how to combine these two well-established modeling tools, viz., ab initio modeling and crystal mechanical FEM, for an improved approach to design of polycrystalline materials. The combination is based on (i) the determination of basic thermodynamic and elastic parameter trends in metallurgical alloy design using density-functional (DFT) calculations (P. Hohenberg and W. Kohn, Phys. Rev. 136, B864 (1964), W. Kohn and L. J. Sham, Phys. Rev. 140, A1133 (1965) [1, 2], respectively) and (ii) the up-scale transfer of these results into crystal-based finite element simulations which take into account the anisotropic nature of the elastic,plastic deformation of metals. The method is applied to three body-centered cubic (bcc, ,) Ti,Nb alloys for bio-medical applications. The study addresses two technological processes, namely, the prediction of texture evolution during cold rolling (elastic-plastic problem) and elastic bending of textured polycrystals (elastic problem). (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Klockmannite, CuSe: structure, properties and phase stability from ab initio modelingACTA CRYSTALLOGRAPHICA SECTION B, Issue 3-2 2002Victor Milman The details of the electronic and crystal structure, the nature of the interatomic bonding and the phase stability of three modifications of klockmannite, CuSe, are analysed using first principles modeling. The hexagonal modification of CuSe is predicted to be less stable than the orthorhombic phase under pressure. The stabilizing force for the orthorhombic phase is identified as the Cu,Cu bond formation between the Cu atoms in the flat hexagonal CuSe layer and in the buckled Cu2Se2 layer. Furthermore, klockmannite is shown to be unstable under compression with respect to the decomposition into umangite, Cu3Se2, and krutaite, CuSe2 II. [source] | ||||||||||