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Sample records for tight-binding band structure

  1. Tight binding electronic band structure calculation of achiral boron nitride single wall nanotubes

    International Nuclear Information System (INIS)

    Saxena, Prapti; Sanyal, Sankar P

    2006-01-01

    In this paper we report the Tight-Binding method, for the electronic structure calculations of achiral single wall Boron Nitride nanotubes. We have used the contribution of π electron only to define the electronic band structure for the solid. The Zone-folding method is used for the Brillouin Zone definition. Calculation of tight binding model parameters is done by fitting them to available experimental results of two-dimensional hexagonal monolayers of Boron Nitride. It has been found that all the boron nitride nanotubes (both zigzag and armchair) are constant gap semiconductors with a band gap of 5.27eV. All zigzag BNNTs are found to be direct gap semiconductors while all armchair nanotubes are indirect gap semiconductors. (author)

  2. Tight-Binding Parametrization for Photonic Band Gap Materials

    International Nuclear Information System (INIS)

    Lidorikis, E.; Sigalas, M.M.; Soukoulis, C.M.; Economou, E.N.; Soukoulis, C.M.

    1998-01-01

    The idea of the linear combination of atomic orbitals method, well known from the study of electrons, is extended to the classical wave case. The Mie resonances of the isolated scatterer in the classical wave case are analogous to the atomic orbitals in the electronic case. The matrix elements of the two-dimensional tight-binding (TB) Hamiltonian are obtained by fitting to ab initio results. The transferability of the TB model is tested by reproducing accurately the band structure of different 2D lattices, with and without defects, and at two different dielectric contrasts. copyright 1998 The American Physical Society

  3. LDA+U and tight-binding electronic structure of InN nanowires

    Science.gov (United States)

    Molina-Sánchez, A.; García-Cristóbal, A.; Cantarero, A.; Terentjevs, A.; Cicero, G.

    2010-10-01

    In this paper we employ a combined ab initio and tight-binding approach to obtain the electronic and optical properties of hydrogenated Indium nitride (InN) nanowires. We first discuss InN band structure for the wurtzite structure calculated at the LDA+U level and use this information to extract the parameters needed for an empirical tight-binging implementation. These parameters are then employed to calculate the electronic and optical properties of InN nanowires in a diameter range that would not be affordable by ab initio techniques. The reliability of the large nanowires results is assessed by explicitly comparing the electronic structure of a small diameter wire studied both at LDA+U and tight-binding level.

  4. Consideration of relativistic effects in band structure calculations based on the empirical tight-binding method

    International Nuclear Information System (INIS)

    Hanke, M.; Hennig, D.; Kaschte, A.; Koeppen, M.

    1988-01-01

    The energy band structure of cadmium telluride and mercury telluride materials is investigated by means of the tight-binding (TB) method considering relativistic effects and the spin-orbit interaction. Taking into account relativistic effects in the method is rather simple though the size of the Hamilton matrix doubles. Such considerations are necessary for the interesting small-interstice semiconductors, and the experimental results are reflected correctly in the band structures. The transformation behaviour of the eigenvectors within the Brillouin zone gets more complicated, but is, nevertheless, theoretically controllable. If, however, the matrix elements of the Green operator are to be calculated, one has to use formula manipulation programmes in particular for non-diagonal elements. For defect calculations by the Koster-Slater theory of scattering it is necessary to know these matrix elements. Knowledge of the transformation behaviour of eigenfunctions saves frequent diagonalization of the Hamilton matrix and thus permits a numerical solution of the problem. Corresponding results for the sp 3 basis are available

  5. Multi-band tight-binding calculation of electronic transport in Fe/trans-polyacetylene/Fe tunnel junctions

    International Nuclear Information System (INIS)

    Abedi Ravan, B

    2012-01-01

    In this paper, the electronic transport characteristics of Fe/trans-polyacetylene/Fe magnetic tunnel junctions (MTJs) are investigated using multi-band tight-binding calculations within the framework of nonequilibrium Green function theory. A CH 2 radical is added to different positions on the polymer chain and its effects on the tunnelling magnetoresistance of the MTJ are studied. The ferromagnetic electrodes are assumed to be single-band and their tight-binding parameters are chosen in such a way as to simulate the ab initio density functional calculations of the band structure of bcc-Fe along its [001] crystallographic direction. In building the Hamiltonian of the trans-polyacetylene (t-PA) chain, we have assumed an s orbital on the H atoms and one s and three p(p x ,p y ,p z ) orbitals on the C atoms, and the dimerization effects are taken into account. It is found that moving the radical out of the centre of the polymer chain enhances the tunnelling magnetoresistance of the MTJ.

  6. Band structure and orbital character of monolayer MoS2 with eleven-band tight-binding model

    Science.gov (United States)

    Shahriari, Majid; Ghalambor Dezfuli, Abdolmohammad; Sabaeian, Mohammad

    2018-02-01

    In this paper, based on a tight-binding (TB) model, first we present the calculations of eigenvalues as band structure and then present the eigenvectors as probability amplitude for finding electron in atomic orbitals for monolayer MoS2 in the first Brillouin zone. In these calculations we are considering hopping processes between the nearest-neighbor Mo-S, the next nearest-neighbor in-plan Mo-Mo, and the next nearest-neighbor in-plan and out-of-plan S-S atoms in a three-atom based unit cell of two-dimensional rhombic MoS2. The hopping integrals have been solved in terms of Slater-Koster and crystal field parameters. These parameters are calculated by comparing TB model with the density function theory (DFT) in the high-symmetry k-points (i.e. the K- and Γ-points). In our TB model all the 4d Mo orbitals and the 3p S orbitals are considered and detailed analysis of the orbital character of each energy level at the main high-symmetry points of the Brillouin zone is described. In comparison with DFT calculations, our results of TB model show a very good agreement for bands near the Fermi level. However for other bands which are far from the Fermi level, some discrepancies between our TB model and DFT calculations are observed. Upon the accuracy of Slater-Koster and crystal field parameters, on the contrary of DFT, our model provide enough accuracy to calculate all allowed transitions between energy bands that are very crucial for investigating the linear and nonlinear optical properties of monolayer MoS2.

  7. Relativistic band-structure calculations for CeTIn sub 5 (T=Ir and Co) and analysis of the energy bands by using tight-binding method

    CERN Document Server

    Maehira, T; Ueda, K; Hasegawa, A

    2003-01-01

    In order to investigate electronic properties of recently discovered heavy fermion superconductors CeTIn sub 5 (T=Ir and Co), we employ the relativistic linear augmented-plane-wave (RLAPW) method to clarify the energy band structures and Fermi surfaces of those materials. The obtained energy bands mainly due to the large hybridization between Ce 4 f and In 5 p states well reproduce the Fermi surfaces consistent with the de Haas-van Alphen experimental results. However, when we attempt to understand magnetism and superconductively in CeTIn sub 5 from the microscopic viewpoint, the energy bands obtained in the RLAPW method are too complicated to analyze the system by further including electron correlations. Thus, it is necessary to prepare a more simplified model, keeping correctly the essential characters of the energy bands obtained in the band-structure calculation. For the purpose, we construct a tight-binding model for CeTIn sub 5 by including f-f and p-p hoppings as well as f-p hybridization, which are ex...

  8. The band gap of II-Vi ternary alloys in a tight-binding description

    Energy Technology Data Exchange (ETDEWEB)

    Olguin, Daniel; Blanquero, Rafael [Instituto Politecnico Nacional, Mexico, D.F (Mexico); De Coss, Romeo [Instituto Politecnico Nacional, Yucatan (Mexico)

    2001-02-01

    We present tight-binding calculations for the band gap of II-Vi pseudobinary ternary alloys. We use an sp{sup 3} s* tight-binding Hamiltonian which include spin-orbit coupling. The band gap composition dependence is calculated using a extended version of the virtual crystal approximation, which introduce an empirical correction factor that takes into account the non-linear dependence of the band gap with the composition. The results compare quite well with the experimental data, both for the ternary alloys with wide band gap and for the narrow band gap ones. [Spanish] Presentamos el calculo de la banda de energia prohibida de aleaciones ternarias de compuestos II-VI. El calculo, que incluye interaccion espin-orbita, se hace con el metodo de enlace fuerte, utilizando una base ortogonal de cinco orbitales atomicos por atomo (sp{sup 3} s*), en conjunto con la aproximacion del cristal virtual. En la aproximacion del cristal virtual, incluimos un factor de correccion que toma en cuenta la no linealidad de la banda de energia prohibida como funcion de la concentracion. Con esta correccion nuestros resultados reproducen aceptablemente los datos experimentales hallados en la literatura.

  9. Third nearest neighbor parameterized tight binding model for graphene nano-ribbons

    Directory of Open Access Journals (Sweden)

    Van-Truong Tran

    2017-07-01

    Full Text Available The existing tight binding models can very well reproduce the ab initio band structure of a 2D graphene sheet. For graphene nano-ribbons (GNRs, the current sets of tight binding parameters can successfully describe the semi-conducting behavior of all armchair GNRs. However, they are still failing in reproducing accurately the slope of the bands that is directly associated with the group velocity and the effective mass of electrons. In this work, both density functional theory and tight binding calculations were performed and a new set of tight binding parameters up to the third nearest neighbors including overlap terms is introduced. The results obtained with this model offer excellent agreement with the predictions of the density functional theory in most cases of ribbon structures, even in the high-energy region. Moreover, this set can induce electron-hole asymmetry as manifested in results from density functional theory. Relevant outcomes are also achieved for armchair ribbons of various widths as well as for zigzag structures, thus opening a route for multi-scale atomistic simulation of large systems that cannot be considered using density functional theory.

  10. Empirical tight-binding parameters for solid C60

    International Nuclear Information System (INIS)

    Tit, N.; Kumar, V.

    1993-01-01

    We present a tight-binding model for the electronic structure of C 60 using four (1s and 3p) orbitals per carbon atom. The model has been developed by fitting the tight-binding parameters to the ab-initio pseudopotential calculation of Troullier and Martins (Phys. Rev. B46, 1754 (1992)) in the face-centered cubic (Fm3-bar) phase. Following this, calculations of the energy bands and the density of electronic states have been carried out as a function of the lattice constant. Good agreement has been obtained with the observed lattice-constant dependence of T c using McMillan's formula. Furthermore, calculations of the electronic structure are presented in the simple cubic (Pa3-bar) phase. (author). 43 refs, 3 figs, 1 tab

  11. Microwave emulations and tight-binding calculations of transport in polyacetylene

    Energy Technology Data Exchange (ETDEWEB)

    Stegmann, Thomas, E-mail: stegmann@icf.unam.mx [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Franco-Villafañe, John A., E-mail: jofravil@fis.unam.mx [Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apartado Postal J-48, 72570 Puebla (Mexico); Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Ortiz, Yenni P. [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Kuhl, Ulrich [Université de Nice – Sophia Antipolis, Laboratoire de la Physique de la Matière Condensée, CNRS, Parc Valrose, 06108 Nice (France); Mortessagne, Fabrice, E-mail: fabrice.mortessagne@unice.fr [Université de Nice – Sophia Antipolis, Laboratoire de la Physique de la Matière Condensée, CNRS, Parc Valrose, 06108 Nice (France); Seligman, Thomas H. [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Centro Internacional de Ciencias, 62210 Cuernavaca (Mexico)

    2017-01-05

    A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene. - Highlights: • Electronic transport in individual polyacetylene chains is studied. • Microwave emulation experiments and tight-binding calculations agree well. • In long chains a band-gap opens due the dimerization of the chain. • In short chains edge atoms cause strong resonance peaks in the center of the band-gap.

  12. Microwave emulations and tight-binding calculations of transport in polyacetylene

    International Nuclear Information System (INIS)

    Stegmann, Thomas; Franco-Villafañe, John A.; Ortiz, Yenni P.; Kuhl, Ulrich; Mortessagne, Fabrice; Seligman, Thomas H.

    2017-01-01

    A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene. - Highlights: • Electronic transport in individual polyacetylene chains is studied. • Microwave emulation experiments and tight-binding calculations agree well. • In long chains a band-gap opens due the dimerization of the chain. • In short chains edge atoms cause strong resonance peaks in the center of the band-gap.

  13. Electronic band structure of lithium, sodium and potassium fluorides

    International Nuclear Information System (INIS)

    Jouanin, C.; Albert, J.P.; Gout, C.

    1975-01-01

    A mixed tight-binding, pseudopotential method is proposed to calculate the energy band structure of large-gap crystals and is tested here on LiF, NaF and KF. Three-centre terms are included in the determination of the valence bands by the tight-binding method and for the conduction bands we use a pseudopotential model proposed by Bassani and Giuliano, modified for the positive ions. By taking into account the polarization corrections, transitions calculated from the energy band structures are compared with experimental data and the agreement is generally good

  14. Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

    Science.gov (United States)

    Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

    2018-06-01

    A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

  15. Tight-binding study of the hole subband structure properties of p-type delta-doped quantum wells in Si by using a Thomas-Fermi-Dirac potential

    International Nuclear Information System (INIS)

    Rodriguez-Vargas, I; Madrigal-Melchor, J; Vlaev, S J

    2009-01-01

    We present the hole subband structure of p-type delta-doped single, double, multiple and superlattice quantum wells in Si. We use the first neighbors sp 3 s' tight-binding approximation including spin for the hole level structure analysis. The parameters of the tight-binding hamiltonian were taken from Klimeck et al. [Klimeck G, Bowen R C, Boykin T B, Salazar-Lazaro C, Cwik T A and Stoica A 2000 Superlattice. Microst. 27 77], first neighbors parameters that give realiable results for the valence band of Si. The calculations are based on a scheme previously proposed and applied to delta-doped quantum well systems [Vlaev S J and Gaggero-Sager L M 1998 Phys. Rev. B 58 1142]. The scheme relies on the incorporation of the delta-doped quantum well potential in the diagonal terms of the tight-binding hamiltonian. We give a detail description of the delta-doped quantum well structures, this is, we study the hole subband structure behavior as a function of the impurity density, the interwell distance of the doped planes and the superlattice period. We also compare our results with the available theoretical and experimental data, obtaining a reasonable agreement.

  16. Tight-binding study of the hole subband structure properties of p-type delta-doped quantum wells in Si by using a Thomas-Fermi-Dirac potential

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Vargas, I; Madrigal-Melchor, J; Vlaev, S J, E-mail: isaac@planck.reduaz.m [Unidad Academica de Fisica, Universidad Autonoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, ZAC. (Mexico)

    2009-05-01

    We present the hole subband structure of p-type delta-doped single, double, multiple and superlattice quantum wells in Si. We use the first neighbors sp{sup 3}s' tight-binding approximation including spin for the hole level structure analysis. The parameters of the tight-binding hamiltonian were taken from Klimeck et al. [Klimeck G, Bowen R C, Boykin T B, Salazar-Lazaro C, Cwik T A and Stoica A 2000 Superlattice. Microst. 27 77], first neighbors parameters that give realiable results for the valence band of Si. The calculations are based on a scheme previously proposed and applied to delta-doped quantum well systems [Vlaev S J and Gaggero-Sager L M 1998 Phys. Rev. B 58 1142]. The scheme relies on the incorporation of the delta-doped quantum well potential in the diagonal terms of the tight-binding hamiltonian. We give a detail description of the delta-doped quantum well structures, this is, we study the hole subband structure behavior as a function of the impurity density, the interwell distance of the doped planes and the superlattice period. We also compare our results with the available theoretical and experimental data, obtaining a reasonable agreement.

  17. Tight-binding study of the structural and magnetic properties of vanadium clusters

    International Nuclear Information System (INIS)

    Zhao Jijun; Lain, K.D.

    1995-01-01

    The structural and magnetic properties of small vanadium clusters are studied in the framework of tight-binding theory. According to parameters of the cluster dimer and bulk solid, we developed a tight-binding interatomic potential and calculated the bonding energies for the different possible structures to determine the ground state atomic configurations of the small vanadium clusters. The theoretical bonding energies for the vanadium clusters agree with the experiment much better than the simple droplet model. However, the calculated values for the clusters of odd atomic number are somewhat higher than the measured ones, corresponding to the pair occupation of delocalized 4s 1 electrons. Based on the optimized geometries, we study the magnetic properties of these clusters through a parametrized Hubbard Hamiltonian. We find the small V clusters of ground-state structures exhibit antiferromagnetic behavior while the alignment of local moments in the clusters with the unoptimized structures may show either ferromagnetic or antiferromagnetic characteristics. The average magnetic moments of the clusters decrease nonmonotonically as cluster size increases and the theoretical results are consistent with the upper limits obtained from a recent experiment. (orig.)

  18. Reformulated tight binding calculation for band discontinuity at CdTe/Hg xCd1-xTe heterointerfaces and their type I-type III transitions

    International Nuclear Information System (INIS)

    Ekpunobi, A.J.

    2005-01-01

    A recently reformulated tight binding method is used to calculate the valence band discontinuity at the CdTe/Hg x Cd 1-x Te interface in the s 2 p 2 configuration. The calculated valence band discontinuity of 0.31 eV at CdTe/HgTe interface is in good agreement with self-consistent calculation and accepted experimental value. Calculations were extended to alloy interfaces, which enabled the investigation of the band-offset problem at the transition point. Both valence band discontinuity ratio and conduction band discontinuity ratio show inflexions at the transition point

  19. Tight binding simulation study on zigzag single-walled carbon nanotubes

    Science.gov (United States)

    Sharma, Deepa; Jaggi, Neena; Gupta, Vishu

    2018-01-01

    Tight binding simulation studies using the density functional tight binding (DFTB) model have been performed on various zigzag single-walled carbon-nanotubes (SWCNTs) to investigate their electronic properties using DFTB module of the Material Studio Software version 7.0. Various combinations of different eigen-solvers and charge mixing schemes available in the DFTB Module have been tried to chalk out the electronic structure. The analytically deduced values of the bandgap of (9, 0) SWCNT were compared with the experimentally determined value reported in the literature. On comparison, it was found that the tight binding approximations tend to drastically underestimate the bandgap values. However, the combination of Anderson charge mixing method with standard eigensolver when implemented using the smart algorithm was found to produce fairly close results. These optimized model parameters were then used to determine the band structures of various zigzag SWCNTs. (9, 0) Single-walled Nanotube which is extensively being used for sensing NH3, CH4 and NO2 has been picked up as a reference material since its experimental bandgap value has been reported in the literature. It has been found to exhibit a finite energy bandgap in contrast to its expected metallic nature. The study is of utmost significance as it not only probes and validates the simulation route for predicting suitable properties of nanomaterials but also throws light on the comparative efficacy of the different approximation and rationalization quantum mechanical techniques used in simulation studies. Such simulation studies if used intelligently prove to be immensely useful to the material scientists as they not only save time and effort but also pave the way to new experiments by making valuable predictions.

  20. Tight-binding calculation of Ti-Rh--type phase diagram

    International Nuclear Information System (INIS)

    Sluiter, M.; Turchi, P.; Fu Zezhong; de Fontaine, D.

    1988-01-01

    Tight-binding electronic band-structure calculations were combined with a free-energy expression from a statistical mechanical method called the cluster-variation method. The effective pair interactions used in the cluster-variation calculation were evaluated by the generalized perturbation method. Only d orbitals were included and the numbers of d electrons per atom were taken to be three for the pure A element and eight for the pure B. A phase diagram was constructed incorporating, for the first time, both fcc and bcc lattices and their simple-ordered superstructures. The calculated diagram agreed reasonably well with those determined empirically for Ti-Rh or Ti-Ir

  1. Transferable tight binding model for strained group IV and III-V heterostructures

    Science.gov (United States)

    Tan, Yaohua; Povolotskyi, Micheal; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

    Modern semiconductor devices have reached critical device dimensions in the range of several nanometers. For reliable prediction of device performance, it is critical to have a numerical efficient model that are transferable to material interfaces. In this work, we present an empirical tight binding (ETB) model with transferable parameters for strained IV and III-V group semiconductors. The ETB model is numerically highly efficient as it make use of an orthogonal sp3d5s* basis set with nearest neighbor inter-atomic interactions. The ETB parameters are generated from HSE06 hybrid functional calculations. Band structures of strained group IV and III-V materials by ETB model are in good agreement with corresponding HSE06 calculations. Furthermore, the ETB model is applied to strained superlattices which consist of group IV and III-V elements. The ETB model turns out to be transferable to nano-scale hetero-structure. The ETB band structures agree with the corresponding HSE06 results in the whole Brillouin zone. The ETB band gaps of superlattices with common cations or common anions have discrepancies within 0.05eV.

  2. Handbook of the band structure of elemental solids from Z = 1 to Z = 112

    CERN Document Server

    Papaconstantopoulos, Dimitris A

    2015-01-01

    This handbook presents electronic structure data and tabulations of Slater-Koster parameters for the whole periodic table. This second edition presents data sets for all elements up to Z = 112, Copernicium, whereas the first edition contained only 53 elements. In this new edition, results are given for the equation of state of the elements together with the parameters of a Birch fit, so that the reader can regenerate the results and derive additional information, such as Pressure-Volume relations and variation of Bulk Modulus with Pressure. For each element, in addition to the equation of state, the energy bands, densities of states, and a set of tight-binding parameters is provided. For a majority of elements, the tight-binding parameters are presented for both a two- and three-center approximation. For the hcp structure, new three-center tight-binding results are given. Other new material in this edition include: energy bands and densities of states of all rare-earth metals, a discussion of the McMillan-Gas...

  3. Tuning the electronic properties of gated multilayer phosphorene: A self-consistent tight-binding study

    Science.gov (United States)

    Li, L. L.; Partoens, B.; Peeters, F. M.

    2018-04-01

    By taking account of the electric-field-induced charge screening, a self-consistent calculation within the framework of the tight-binding approach is employed to obtain the electronic band structure of gated multilayer phosphorene and the charge densities on the different phosphorene layers. We find charge density and screening anomalies in single-gated multilayer phosphorene and electron-hole bilayers in dual-gated multilayer phosphorene. Due to the unique puckered lattice structure, both intralayer and interlayer charge screenings are important in gated multilayer phosphorene. We find that the electric-field tuning of the band structure of multilayer phosphorene is distinctively different in the presence and absence of charge screening. For instance, it is shown that the unscreened band gap of multilayer phosphorene decreases dramatically with increasing electric-field strength. However, in the presence of charge screening, the magnitude of this band-gap decrease is significantly reduced and the reduction depends strongly on the number of phosphorene layers. Our theoretical results of the band-gap tuning are compared with recent experiments and good agreement is found.

  4. Reformulated tight binding calculation for band discontinuity at CdTe/Hg {sub x}Cd{sub 1-x}Te heterointerfaces and their type I-type III transitions

    Energy Technology Data Exchange (ETDEWEB)

    Ekpunobi, A.J. [Department of Physics and Industrial Physics, Nnamdi Azikiwe University, P.M.B. 5025, Awka, Anambra State (Nigeria)

    2005-02-25

    A recently reformulated tight binding method is used to calculate the valence band discontinuity at the CdTe/Hg {sub x}Cd{sub 1-x}Te interface in the s{sup 2}p{sup 2} configuration. The calculated valence band discontinuity of 0.31 eV at CdTe/HgTe interface is in good agreement with self-consistent calculation and accepted experimental value. Calculations were extended to alloy interfaces, which enabled the investigation of the band-offset problem at the transition point. Both valence band discontinuity ratio and conduction band discontinuity ratio show inflexions at the transition point.

  5. Theory of the electronic structure of dilute bismide and bismide-nitride alloys of GaAs: Tight-binding and k.p models

    International Nuclear Information System (INIS)

    Usman, Muhammad; Broderick, Christopher A.; O'Reilly, Eoin P.

    2013-01-01

    The addition of dilute concentrations of bismuth (Bi) into GaAs to form GaBi x As 1−x alloys results in a large reduction of the band gap energy (E g ) accompanied by a significant increase of the spin-orbit-splitting energy (Δ SO ), leading to an E g SO regime for x ∼ 10% which is technologically relevant for the design of highly efficient photonic devices. The quaternary alloy GaBi x N y As 1−x−y offers further flexibility for band gap tuning, because both nitrogen and bismuth can independently induce band gap reduction. This work reports sp 3 s* tight binding and 14-band k⋅p models for the study of the electronic structure of GaBi x As 1−x and GaBi x N y As 1−x−y alloys. Our results are in good agreement with the available experimental data

  6. Energy spectrum of two-dimensional tight-binding electrons in a spatially varying magnetic field

    International Nuclear Information System (INIS)

    Oh, G.Y.; Lee, M.H.

    1996-01-01

    The electronic energy spectrum of a two-dimensional lattice in a spatially varying magnetic field is studied within the framework of the tight-binding model by using the scheme of the transfer matrix. It is found that, in comparison with the case of a uniform magnetic field, the energy spectrum exhibits more complicated behavior; band broadening (or gap closing) and band splitting (or gap opening) occur depending on characteristic parameters of the lattice. The origin of these phenomena lies in the existence of direct touching and indirect overlapping between neighboring subbands. Dependence of direct touching and indirect overlapping, and thus the electronic band structure together with the density of states, on characteristic parameters of the lattice is elucidated in detail. copyright 1996 The American Physical Society

  7. The complex band structure for armchair graphene nanoribbons

    International Nuclear Information System (INIS)

    Zhang Liu-Jun; Xia Tong-Sheng

    2010-01-01

    Using a tight binding transfer matrix method, we calculate the complex band structure of armchair graphene nanoribbons. The real part of the complex band structure calculated by the transfer matrix method fits well with the bulk band structure calculated by a Hermitian matrix. The complex band structure gives extra information on carrier's decay behaviour. The imaginary loop connects the conduction and valence band, and can profoundly affect the characteristics of nanoscale electronic device made with graphene nanoribbons. In this work, the complex band structure calculation includes not only the first nearest neighbour interaction, but also the effects of edge bond relaxation and the third nearest neighbour interaction. The band gap is classified into three classes. Due to the edge bond relaxation and the third nearest neighbour interaction term, it opens a band gap for N = 3M − 1. The band gap is almost unchanged for N = 3M + 1, but decreased for N = 3M. The maximum imaginary wave vector length provides additional information about the electrical characteristics of graphene nanoribbons, and is also classified into three classes

  8. Empirical tight-binding modeling of ordered and disordered semiconductor structures; Empirische Tight-Binding-Modellierung geordneter und ungeordneter Halbleiterstrukturen

    Energy Technology Data Exchange (ETDEWEB)

    Mourad, Daniel

    2010-11-30

    In this thesis, we investigate the electronic and optical properties of pure as well as of substitutionally alloyed II-VI and III-V bulk semiconductors and corresponding semiconductor quantum dots by means of an empirical tight-binding (TB) model. In the case of the alloyed systems of the type A{sub x}B{sub 1-x}, where A and B are the pure compound semiconductor materials, we study the influence of the disorder by means of several extensions of the TB model with different levels of sophistication. Our methods range from rather simple mean-field approaches (virtual crystal approximation, VCA) over a dynamical mean-field approach (coherent potential approximation, CPA) up to calculations where substitutional disorder is incorporated on a finite ensemble of microscopically distinct configurations. In the first part of this thesis, we cover the necessary fundamentals in order to properly introduce the TB model of our choice, the effective bond-orbital model (EBOM). In this model, one s- and three p-orbitals per spin direction are localized on the sites of the underlying Bravais lattice. The matrix elements between these orbitals are treated as free parameters in order to reproduce the properties of one conduction and three valence bands per spin direction and can then be used in supercell calculations in order to model mixed bulk materials or pure as well as mixed quantum dots. Part II of this thesis deals with unalloyed systems. Here, we use the EBOM in combination with configuration interaction calculations for the investigation of the electronic and optical properties of truncated pyramidal GaN quantum dots embedded in AlN with an underlying zincblende structure. Furthermore, we develop a parametrization of the EBOM for materials with a wurtzite structure, which allows for a fit of one conduction and three valence bands per spin direction throughout the whole Brillouin zone of the hexagonal system. In Part III, we focus on the influence of alloying on the electronic

  9. The tight binding model study of the role of band filling on the charge gap in graphene-on-substrate in paramagnetic state

    Science.gov (United States)

    Panda, Rudrashish; Sahu, Sivabrata; Rout, G. C.

    2017-05-01

    We communicate here a tight binding theoretical model study of the band filling effect on the charge gap in graphene-on-substrate. The Hamiltonian consists of nearest neighbor electron hopping and substrate induced gap. Besides this the Coulomb interaction is considered here within mean-field approximation in the paramagnetic limit. The electron occupancies at two sublattices are calculated by Green's function technique and are solved self consistently. Finally the charge gap i.e. Δ ¯=U [ - ] is calculated and computed numerically. The results are reported.

  10. Electronic band structure

    International Nuclear Information System (INIS)

    Grosso, G.

    1986-01-01

    The aim of this chapter is to present, in detail, some theoretical methods used to calculate electronic band structures in crystals. The basic strategies employed to attack the problem of electronic-structure calculations are presented. Successive sections present the basic formulations of the tight-binding, orthogonalized-plane-wave, Green'sfunction, and pseudopotential methods with a discussion of their application to perfect solids. Exemplifications in the case of a few selected problems provide further insight by the author into the physical aspects of the different methods and are a guide to the use of their mathematical techniques. A discussion is offered of completely a priori Hartree-Fock calculations and attempts to extend them. Special aspects of the different methods are also discussed in light of recently published related work

  11. Bulk and interface dielectric functions: New results within the tight-binding approximation

    International Nuclear Information System (INIS)

    Elvira, V.D.; Duran, J.C.

    1991-01-01

    A tight-binding approach is used to analyze the dielectric behaviour of bulk semiconductors and semiconductor interfaces. This time interactions between second nearest neighbours are taken into account and several electrostatic models are proposed for the induced charge density around the atoms. The bulk dielectric function of different semiconductors (Si, Ge, GaAs and AlAs) are obtained and compared with other theoretical and experimental results. Finally, the energy band offset for GaAs-AlAs(1,0,0) interface is obtained and related to bulk properties of both semiconductors. The results presented in this paper show how the use of very simple but more realistic electrostatic models improve the analysis of the screening properties in semiconductors, giving a new support to the consistent tight-binding method for studying characteristics related to those properties. (Author)

  12. Absence of zero-temperature transmission rate of a double-chain tight-binding model for DNA with random sequence of nucleotides in thermodynamic limit

    International Nuclear Information System (INIS)

    Xiong Gang; Wang, X.R.

    2005-01-01

    The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While the whole spectrum tends to zero in thermodynamic limit, regardless of the strength of inter-chain coupling. It is also shown that a more faithful model for real DNA with periodic sugar-phosphate chains in backbone structures can be mapped into the above simple double-chain tight-binding model. Combined with above results, the transmission rate of real DNA with long random sequence of nucleotides is expected to be poor

  13. Dielectric response of molecules in empirical tight-binding theory

    Science.gov (United States)

    Boykin, Timothy B.; Vogl, P.

    2002-01-01

    In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

  14. Empirical tight-binding modeling of ordered and disordered semiconductor structures

    International Nuclear Information System (INIS)

    Mourad, Daniel

    2010-01-01

    In this thesis, we investigate the electronic and optical properties of pure as well as of substitutionally alloyed II-VI and III-V bulk semiconductors and corresponding semiconductor quantum dots by means of an empirical tight-binding (TB) model. In the case of the alloyed systems of the type A x B 1-x , where A and B are the pure compound semiconductor materials, we study the influence of the disorder by means of several extensions of the TB model with different levels of sophistication. Our methods range from rather simple mean-field approaches (virtual crystal approximation, VCA) over a dynamical mean-field approach (coherent potential approximation, CPA) up to calculations where substitutional disorder is incorporated on a finite ensemble of microscopically distinct configurations. In the first part of this thesis, we cover the necessary fundamentals in order to properly introduce the TB model of our choice, the effective bond-orbital model (EBOM). In this model, one s- and three p-orbitals per spin direction are localized on the sites of the underlying Bravais lattice. The matrix elements between these orbitals are treated as free parameters in order to reproduce the properties of one conduction and three valence bands per spin direction and can then be used in supercell calculations in order to model mixed bulk materials or pure as well as mixed quantum dots. Part II of this thesis deals with unalloyed systems. Here, we use the EBOM in combination with configuration interaction calculations for the investigation of the electronic and optical properties of truncated pyramidal GaN quantum dots embedded in AlN with an underlying zincblende structure. Furthermore, we develop a parametrization of the EBOM for materials with a wurtzite structure, which allows for a fit of one conduction and three valence bands per spin direction throughout the whole Brillouin zone of the hexagonal system. In Part III, we focus on the influence of alloying on the electronic and

  15. Band nesting, massive Dirac fermions, and valley Landé and Zeeman effects in transition metal dichalcogenides: A tight-binding model

    Science.gov (United States)

    Bieniek, Maciej; Korkusiński, Marek; Szulakowska, Ludmiła; Potasz, Paweł; Ozfidan, Isil; Hawrylak, Paweł

    2018-02-01

    We present here the minimal tight-binding model for a single layer of transition metal dichalcogenides (TMDCs) MX 2(M , metal; X , chalcogen) which illuminates the physics and captures band nesting, massive Dirac fermions, and valley Landé and Zeeman magnetic field effects. TMDCs share the hexagonal lattice with graphene but their electronic bands require much more complex atomic orbitals. Using symmetry arguments, a minimal basis consisting of three metal d orbitals and three chalcogen dimer p orbitals is constructed. The tunneling matrix elements between nearest-neighbor metal and chalcogen orbitals are explicitly derived at K ,-K , and Γ points of the Brillouin zone. The nearest-neighbor tunneling matrix elements connect specific metal and sulfur orbitals yielding an effective 6 ×6 Hamiltonian giving correct composition of metal and chalcogen orbitals but not the direct gap at K points. The direct gap at K , correct masses, and conduction band minima at Q points responsible for band nesting are obtained by inclusion of next-neighbor Mo-Mo tunneling. The parameters of the next-nearest-neighbor model are successfully fitted to MX 2(M =Mo ; X =S ) density functional ab initio calculations of the highest valence and lowest conduction band dispersion along K -Γ line in the Brillouin zone. The effective two-band massive Dirac Hamiltonian for MoS2, Landé g factors, and valley Zeeman splitting are obtained.

  16. Gate dielectric strength dependent performance of CNT MOSFET and CNT TFET: A tight binding study

    Directory of Open Access Journals (Sweden)

    Md. Shamim Sarker

    Full Text Available This paper presents a comparative study between CNT MOSFET and CNT TFET taking into account of different dielectric strength of gate oxide materials. Here we have studied the transfer characteristics, on/off current (ION/IOFF ratio and subthreshold slope of the device using Non Equilibrium Greens Function (NEGF formalism in tight binding frameworks. The results are obtained by solving the NEGF and Poisson’s equation self-consistently in NanoTCADViDES environment and found that the ON state performance of CNT MOSFET and CNT TFET have significant dependency on the dielectric strength of the gate oxide materials. The figure of merits of the devices also demonstrates that the CNT TFET is promising for high-speed and low-power logic applications. Keywords: CNT TFET, Subthreshold slop, Barrier width, Conduction band (C.B and Valance band (V.B, Oxide dielectric strength, Tight binding approach

  17. Energy band structure of Cr by the Slater-Koster interpolation scheme

    International Nuclear Information System (INIS)

    Seifu, D.; Mikusik, P.

    1986-04-01

    The matrix elements of the Hamiltonian between nine localized wave-functions in tight-binding formalism are derived. The symmetry adapted wave-functions and the secular equations are formed by the group theory method for high symmetry points in the Brillouin zone. A set of interaction integrals is chosen on physical ground and fitted via the Slater-Koster interpolation scheme to the abinito band structure of chromium calculated by the Green function method. Then the energy band structure of chromium is interpolated and extrapolated in the Brillouin zone. (author)

  18. Simulation of the Band Structure of Graphene and Carbon Nanotube

    International Nuclear Information System (INIS)

    Mina, Aziz N; Awadallah, Attia A; Ahmed, Riham R; Phillips, Adel H

    2012-01-01

    Simulation technique has been performed to simulate the band structure of both graphene and carbon nanotube. Accordingly, the dispersion relations for graphene and carbon nanotube are deduced analytically, using the tight binding model and LCAO scheme. The results from the simulation of the dispersion relation of both graphene and carbon nanotube were found to be consistent with those in the literature which indicates the correctness of the process of simulation technique. The present research is very important for tailoring graphene and carbon nanotube with specific band structure, in order to satisfy the required electronic properties of them.

  19. Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

    Science.gov (United States)

    2016-06-01

    unlimited IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS by Joon H. Kim June 2016 Thesis Advisor...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS 5. FUNDING...repulsive potentials for use in density-functional tight binding (DFTB) simulations of low-valence aluminum metalloid clusters . These systems are under

  20. Tight-binding calculation of radiation loss in photonic crystal CROW.

    Science.gov (United States)

    Ma, Jing; Martínez, Luis Javier; Fan, Shanhui; Povinelli, Michelle L

    2013-01-28

    The tight binding approximation (TBA) is used to relate the intrinsic, radiation loss of a coupled resonator optical waveguide (CROW) to that of a single constituent resonator within a light cone picture. We verify the validity of the TBA via direct, full-field simulation of CROWs based on the L2 photonic crystal cavity. The TBA predicts that the quality factor of the CROW increases with that of the isolated cavity. Moreover, our results provide a method to design CROWs with low intrinsic loss across the entire waveguide band.

  1. Band structure of hydrogenated Si nanosheets and nanotubes

    International Nuclear Information System (INIS)

    Guzman-Verri, G G; Lew Yan Voon, L C

    2011-01-01

    The band structures of fully hydrogenated Si nanosheets and nanotubes are elucidated by the use of an empirical tight-binding model. The hydrogenated Si sheet is a semiconductor with an indirect band gap of about 2.2 eV. The symmetries of the wavefunctions allow us to explain the origin of the gap. We predict that, for certain chiralities, hydrogenated Si nanotubes represent a new type of semiconductor, one with coexisting direct and indirect gaps of exactly the same magnitude. This behavior is different from that governed by the Hamada rule established for non-hydrogenated carbon and silicon nanotubes. A comparison to the results of an ab initio calculation is made.

  2. Electro-optical properties of zigzag and armchair boron nitride nanotubes under a transverse electric field: Tight binding calculations

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2012-02-01

    The electro-optical properties of zigzag and armchair BNNTs in a uniform transverse electric field are investigated within tight binding approximation. It is found that the electric field modifies the band structure and splits band degeneracy where these effects reflect in the DOS and JDOS spectra. A decrease in the band gap, as a function of the electric field, is observed. This gap reduction increases with the diameter and it is independent of chirality. An analytic function to estimate the electric field needed for band gap closing is proposed which is in good agreement with DFT results. In additional, we show that the larger diameter tubes are more sensitive than small ones. Number and position of peaks in DOS and JDOS spectra for armchair and zigzag tubes with similar radius are dependent on electric field strength.

  3. From structure to spectra. Tight-binding theory of InGaAs quantum dots

    International Nuclear Information System (INIS)

    Goldmann, Elias

    2014-01-01

    Self-assembled semiconductor quantum dots have raised considerable interest in the last decades due to a multitude of possible applications ranging from carrier storage to light emitters, lasers and future quantum communication devices. Quantum dots offer unique electronic and photonic properties due to the three-dimensional confinement of charge carriers and the coupling to a quasi-continuum of wetting layer and barrier states. In this work we investigate the electronic structure of In x Ga 1-x As quantum dots embedded in GaAs, considering realistic quantum dot geometries and Indium concentrations. We utilize a next-neighbour sp 3 s * tight-binding model for the calculation of electronic single-particle energies and wave functions bound in the nanostructure and account for strain arising from lattice mismatch of the constituent materials atomistically. With the calculated single-particle wave functions we derive Coulomb matrix elements and include them into a configuration interaction treatment, yielding many-particle states and energies of the interacting many-carrier system. Also from the tight-binding single-particle wave functions we derive dipole transition strengths to obtain optical quantum dot emission and absorption spectra with Fermi's golden rule. Excitonic fine-structure splittings are obtained, which play an important role for future quantum cryptography and quantum communication devices for entanglement swapping or quantum repeating. For light emission suited for long-range quantum-crypted fiber communication InAs quantum dots are embedded in an In x Ga 1-x As strain-reducing layer, shifting the emission wavelength into telecom low-absorption windows. We investigate the influence of the strain-reducing layer Indium concentration on the excitonic finestructure splitting. The fine-structure splitting is found to saturate and, in some cases, even reduce with strain-reducing layer Indium concentration, a result being counterintuitively. Our result

  4. From structure to spectra. Tight-binding theory of InGaAs quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Goldmann, Elias

    2014-07-23

    Self-assembled semiconductor quantum dots have raised considerable interest in the last decades due to a multitude of possible applications ranging from carrier storage to light emitters, lasers and future quantum communication devices. Quantum dots offer unique electronic and photonic properties due to the three-dimensional confinement of charge carriers and the coupling to a quasi-continuum of wetting layer and barrier states. In this work we investigate the electronic structure of In{sub x}Ga{sub 1-x}As quantum dots embedded in GaAs, considering realistic quantum dot geometries and Indium concentrations. We utilize a next-neighbour sp{sup 3}s{sup *} tight-binding model for the calculation of electronic single-particle energies and wave functions bound in the nanostructure and account for strain arising from lattice mismatch of the constituent materials atomistically. With the calculated single-particle wave functions we derive Coulomb matrix elements and include them into a configuration interaction treatment, yielding many-particle states and energies of the interacting many-carrier system. Also from the tight-binding single-particle wave functions we derive dipole transition strengths to obtain optical quantum dot emission and absorption spectra with Fermi's golden rule. Excitonic fine-structure splittings are obtained, which play an important role for future quantum cryptography and quantum communication devices for entanglement swapping or quantum repeating. For light emission suited for long-range quantum-crypted fiber communication InAs quantum dots are embedded in an In{sub x}Ga{sub 1-x}As strain-reducing layer, shifting the emission wavelength into telecom low-absorption windows. We investigate the influence of the strain-reducing layer Indium concentration on the excitonic finestructure splitting. The fine-structure splitting is found to saturate and, in some cases, even reduce with strain-reducing layer Indium concentration, a result being

  5. Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

    Science.gov (United States)

    Tan, Yaohua P.; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

    2015-08-01

    Empirical tight-binding (ETB) methods are widely used in atomistic device simulations. Traditional ways of generating the ETB parameters rely on direct fitting to bulk experiments or theoretical electronic bands. However, ETB calculations based on existing parameters lead to unphysical results in ultrasmall structures like the As-terminated GaAs ultrathin bodies (UTBs). In this work, it is shown that more transferable ETB parameters with a short interaction range can be obtained by a process of mapping ab initio bands and wave functions to ETB models. This process enables the calibration of not only the ETB energy bands but also the ETB wave functions with corresponding ab initio calculations. Based on the mapping process, ETB models of Si and GaAs are parameterized with respect to hybrid functional calculations. Highly localized ETB basis functions are obtained. Both the ETB energy bands and wave functions with subatomic resolution of UTBs show good agreement with the corresponding hybrid functional calculations. The ETB methods can then be used to explain realistically extended devices in nonequilibrium that cannot be tackled with ab initio methods.

  6. A tight binding model study of tunneling conductance spectra of spin and orbitally ordered CMR manganites

    Science.gov (United States)

    Panda, Saswati; Sahoo, D. D.; Rout, G. C.

    2018-04-01

    We report here a tight binding model for colossal magnetoresistive (CMR) manganites to study the pseudo gap (PG) behavior near Fermi level. In the Kubo-Ohata type DE model, we consider first and second nearest neighbor interactions for transverse spin fluctuations in core band and hopping integrals in conduction band, in the presence of static band Jahn-Teller distortion. The model Hamiltonian is solved using Zubarev's Green's function technique. The electron density of states (DOS) is found out from the Green's functions. We observe clear PG near Fermi level in the electron DOS.

  7. Chirality dependence of dipole matrix element of carbon nanotubes in axial magnetic field: A third neighbor tight binding approach

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2014-02-01

    We have studied the electronic structure and dipole matrix element, D, of carbon nanotubes (CNTs) under magnetic field, using the third nearest neighbor tight binding model. It is shown that the 1NN and 3NN-TB band structures show differences such as the spacing and mixing of neighbor subbands. Applying the magnetic field leads to breaking the degeneracy behavior in the D transitions and creates new allowed transitions corresponding to the band modifications. It is found that |D| is proportional to the inverse tube radius and chiral angle. Our numerical results show that amount of filed induced splitting for the first optical peak is proportional to the magnetic field by the splitting rate ν11. It is shown that ν11 changes linearly and parabolicly with the chiral angle and radius, respectively.

  8. Theoretical study of the structure, energetics, and dynamics of silicon and carbon systems using tight-binding approaches

    International Nuclear Information System (INIS)

    Xu, Chunhui.

    1991-01-01

    Semiempirical interatomic potentials are developed for silicon and carbon by modeling the total energy of the system using tight-binding approaches. The parameters of the models were obtained by fitting to results from accurate first-principles Local Density Functional calculations. Applications to the computation of phonons as a function of volume for diamond-structured silicon and carbon and the thermal expansions for silicon and diamond yields results which agree well with experiment. The physical origin of the negative thermal expansion observed in silicon is explained. A tight-binding total energy model is generated capable of describing carbon systems with a variety of atomic coordinations and topologies. The model reproduces the total energy versus volume curves of various carbon polytypes as well as phonons and elastic constants of diamond and graphite. The model has also been used in the molecular-dynamics simulation of the properties of carbon clusters. The calculated ground-state geometries of small clusters (C 2 --C 10 ) correlates well with results from accurate quantum chemical calculations, and the structural trend of clusters from C 2 to C 60 are investigated. 67 refs., 19 figs

  9. MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

    Energy Technology Data Exchange (ETDEWEB)

    DARYLE H BUSCH RICHARD S GIVENS

    2004-12-10

    even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

  10. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    International Nuclear Information System (INIS)

    Aradi, Balint; Frauenheim, Thomas

    2015-01-01

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

  11. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

    Science.gov (United States)

    Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

    2015-07-14

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

  12. Tuning the band gap in hybrid tin iodide perovskite semiconductors using structural templating.

    Science.gov (United States)

    Knutson, Jeremy L; Martin, James D; Mitzi, David B

    2005-06-27

    Structural distortions within the extensive family of organic/inorganic hybrid tin iodide perovskite semiconductors are correlated with their experimental exciton energies and calculated band gaps. The extent of the in- and out-of-plane angular distortion of the SnI4(2-) perovskite sheets is largely determined by the relative charge density and steric requirements of the organic cations. Variation of the in-plane Sn-I-Sn bond angle was demonstrated to have the greatest impact on the tuning of the band gap, and the equatorial Sn-I bond distances have a significant secondary influence. Extended Hückel tight-binding band calculations are employed to decipher the crystal orbital origins of the structural effects that fine-tune the band structure. The calculations suggest that it may be possible to tune the band gap by as much as 1 eV using the templating influence of the organic cation.

  13. Ab-initio electronic band structure calculations for beryllium chalcogenides

    International Nuclear Information System (INIS)

    Kalpana, G.; Pari, G.; Yousuf, Mohammad

    1997-01-01

    The first principle tight-binding linear muffin-tin orbital method within the local density approximation (LDA) has been used to calculate the ground state properties, structural phase transition and pressure dependence of band gap of BeS, BeSe and BeTe. We have calculated the energy-volume relations for these compounds in the B3 and B8 phases. The calculated lattice parameters, bulk modulus and the pressure-volume relation were found to be in good agreement with the recent experimental results. The calculated B3→B8 structural transition pressure for BeS, BeSe and BeTe agree well with the recent experimental results. Our calculations show that these compounds are indirect band gap (Γ-X) semiconductors at ambient conditions. The calculated band gap values are found to be underestimated by 20-30% which is due to the usage of LDA. After the structural transition to the B8 phase, BeS continues to be indirect band gap semiconductors and ultimately above 100 GPa it metallises, BeSe and BeTe are metallic at the B3→B8 structural transition. (author)

  14. Band gap engineering for poly(p-phenylene) and poly(p-phenylene vinylene) copolymers using the tight-binding approach

    Science.gov (United States)

    Giro, R.; Caldas, M. J.; Galvão, D. S.

    The interest in poly(p-phenylene) (PPP) and poly(p-phenylene vinylene) (PPV) copolymers stems from the fact that these homopolymers present interesting optical and electronic properties that allow a great variety of technological applications. Combining different numbers of PPP and PPV units it is possible, in principle, to obtain new structures presenting intermediate gap values (2.8 eV and 2.4 eV for PPP and PPV, respectively). For this study we used a Hückel Hamiltonian tight-binding coupled to the negative factor counting (NFC) technique. We carried out a systematic search to determine optimum relative concentrations for disordered binary polymeric alloys with predefined gap values. Once these structures were obtained, we used the semiempirical methods AM1/PM3 and ZINDO/S-CI for geometrical and optical studies, respectively. Our theoretical results show that it is possible to obtain copolymers of PPP and PPV with intermediate gap values of their parent structures.

  15. Electronic band structure study of colossal magnetoresistance in Tl 2Mn 2O 7

    Science.gov (United States)

    Seo, D.-K.; Whangbo, M.-H.; Subramanian, M. A.

    1997-02-01

    The electronic structure of Tl 2Mn 2O 7 was examined by performing tight binding band calculations. The overlap between the Mn t 2g- and Tl 6 s-block bands results in a partial filling of the Tl 6 s-block bands. The associated Fermi surface consists of 12 cigar-shape electron pockets with each electron pocket about {1}/{1000} of the first Brillouin zone in size. The Tl 6 s-block bands have orbital contributions from the Mn atoms, and the carrier density is very low. These are important for the occurrence of a colossal magnetoresistance in Tl 2Mn 2O 7.

  16. Substrate-Triggered Exosite Binding: Synergistic Dendrimer/Folic Acid Action for Achieving Specific, Tight-Binding to Folate Binding Protein.

    Science.gov (United States)

    Chen, Junjie; van Dongen, Mallory A; Merzel, Rachel L; Dougherty, Casey A; Orr, Bradford G; Kanduluru, Ananda Kumar; Low, Philip S; Marsh, E Neil G; Banaszak Holl, Mark M

    2016-03-14

    Polymer-ligand conjugates are designed to bind proteins for applications as drugs, imaging agents, and transport scaffolds. In this work, we demonstrate a folic acid (FA)-triggered exosite binding of a generation five poly(amidoamine) (G5 PAMAM) dendrimer scaffold to bovine folate binding protein (bFBP). The protein exosite is a secondary binding site on the protein surface, separate from the FA binding pocket, to which the dendrimer binds. Exosite binding is required to achieve the greatly enhanced binding constants and protein structural change observed in this study. The G5Ac-COG-FA1.0 conjugate bound tightly to bFBP, was not displaced by a 28-fold excess of FA, and quenched roughly 80% of the initial fluorescence. Two-step binding kinetics were measured using the intrinsic fluorescence of the FBP tryptophan residues to give a KD in the low nanomolar range for formation of the initial G5Ac-COG-FA1.0/FBP* complex, and a slow conversion to the tight complex formed between the dendrimer and the FBP exosite. The extent of quenching was sensitive to the choice of FA-dendrimer linker chemistry. Direct amide conjugation of FA to G5-PAMAM resulted in roughly 50% fluorescence quenching of the FBP. The G5Ac-COG-FA, which has a longer linker containing a 1,2,3-triazole ring, exhibited an ∼80% fluorescence quenching. The binding of the G5Ac-COG-FA1.0 conjugate was compared to poly(ethylene glycol) (PEG) conjugates of FA (PEGn-FA). PEG2k-FA had a binding strength similar to that of FA, whereas other PEG conjugates with higher molecular weight showed weaker binding. However, no PEG conjugates gave an increased degree of total fluorescence quenching.

  17. Transferable tight-binding model for strained group IV and III-V materials and heterostructures

    Science.gov (United States)

    Tan, Yaohua; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

    2016-07-01

    It is critical to capture the effect due to strain and material interface for device level transistor modeling. We introduce a transferable s p3d5s* tight-binding model with nearest-neighbor interactions for arbitrarily strained group IV and III-V materials. The tight-binding model is parametrized with respect to hybrid functional (HSE06) calculations for varieties of strained systems. The tight-binding calculations of ultrasmall superlattices formed by group IV and group III-V materials show good agreement with the corresponding HSE06 calculations. The application of the tight-binding model to superlattices demonstrates that the transferable tight-binding model with nearest-neighbor interactions can be obtained for group IV and III-V materials.

  18. Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

    Science.gov (United States)

    Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

    2018-01-18

    Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

  19. Perspectives from ab-initio and tight-binding: Applications to transition metal compounds and superlattices

    Science.gov (United States)

    Venkataraman, Vijay Shankar

    a tight-binding model for the 4d orbitals. We further compare these results with energies obtained from DFT calculations. We obtain a zig-zag magnetic ground state for this compound, in all the three approaches. Within DFT, we find that correlations enhance the spin-orbit coupling in this compound and that the anisotropic Kitaev interactions between the spins are dominant in a strong-coupling model. Then, we move on to study the electronic band structures of the higher manganese silicides, which are good thermoelectric materials. Using results from DFT calculations on Mn4Si7 and structural arguments, we construct an effective tight-binding model for the first three members of this series - Mn4Si7, Mn11Si19, and Mn15Si26.

  20. Stokes shift and fine structure splitting in composition-tunable Zn{sub x}Cd{sub 1−x}Se nanocrystals: Atomistic tight-binding theory

    Energy Technology Data Exchange (ETDEWEB)

    Sukkabot, Worasak, E-mail: w.sukkabot@gmail.com

    2017-02-01

    I report on the atomistic correlation of the structural properties and excitonic splitting of ternary alloy Zn{sub x}Cd{sub 1−x}Se wurtzite nanocrystals using the sp{sup 3}s* empirical tight-binding method with the description of the first nearest neighbouring interaction and bowing effect. Based on a successful model, the computations are presented under various Zn compositions (x) and diameters of alloy Zn{sub x}Cd{sub 1−x}Se nanocrystals with the experimentally synthesized compositions and sizes. With increasing Zn contents (x), the optical band gaps and electron-hole coulomb energies are improved, while ground electron-hole wave function overlaps, electron-hole exchange energies, stokes shift and fine structure splitting are reduced. A composition-tunable emission from blue to yellow wavelength is obviously demonstrated. The optical band gaps, ground electron-hole wave function overlaps, electron-hole interactions, stokes shift and fine structure splitting are progressively decreased with the increasing diameters. Alloy Zn{sub x}Cd{sub 1−x}Se nanocrystal with Zn rich and large diameter is the best candidate to optimistically be used as a source of entangled photon pairs. The agreement with the experimental data is remarkable. Finally, the present systematic study on the structural properties and excitonic splitting predominantly opens a new perspective to understand the size- and composition-dependent properties of Zn{sub x}Cd{sub 1−x}Se nanocrystals with a comprehensive strategy to design the optoelectronic devices.

  1. First-principles real-space tight-binding LMTO calculation of electronic structures for atomic clusters

    International Nuclear Information System (INIS)

    Xie, Z.L.; Dy, K.S.; Wu, S.Y.

    1997-01-01

    A real-space scheme has been developed for a first-principles calculation of electronic structures and total energies of atomic clusters. The scheme is based on the combination of the tight-binding linear muffin-tin orbital (TBLMTO) method and the method of real-space Green close-quote s function. With this approach, the local electronic density of states can be conveniently determined from the real-space Green close-quote s function. Furthermore, the full electron density of a cluster can be directly calculated in real space. The scheme has been shown to be very efficient due to the incorporation of the method of real-space Green close-quote s function and Delley close-quote s method of evaluating multicenter integrals. copyright 1996 The American Physical Society

  2. Analysis of the tight-binding description of the structure of metallic 2D systems

    International Nuclear Information System (INIS)

    Baquero, R.

    1990-12-01

    Bidimensional metallic systems as interfaces, quantum wells and superlattices with sharp interfaces became recently available and their properties can now be experimentally studied in detail. To calculate the Local Density of States (LDOS) for surfaces, interfaces, quantum wells and superlattices we use empirical tight-binding Hamiltonians together with the Green function matching method (GFM). In this paper we show some examples of our results employing the method just outlined to describe metallic 2D systems. In particular, we refer briefly to the effect on the LDOS of the very recently established contraction of the first interatomic layer distance in the Ta(001) surface. We then discuss the Nb-V ideal (100) interface and conclude that under certain conditions the V-side of an interface can show magnetism as the V(001) surface does. As a last example, we present a calculation that relates the changes with gold coverage of the reaction rate of the catalytic reaction of cyclohexene into benzene on a Pt(001) surface to the changes on the LDOS of the outermost Pt atomic layer. We show that the behavior of the LDOS around the Fermi level is an important factor to the explanation of the behavior of this catalytic reaction. We conclude by stating that the empirical tight-binding method is a very simple and useful tool for the description of 2D metallic systems. The advantage is that the computational demands are low and all the ingredients to take full profit of this method are available (reliable tight-binding parameters and suitable methods for the calculation of the Green function). (author). 14 refs, 3 figs

  3. A comparative study of density functional and density functional tight binding calculations of defects in graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

    2012-02-15

    The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  4. Strain effect on graphene nanoribbon carrier statistic in the presence of non-parabolic band structure

    International Nuclear Information System (INIS)

    Izuani Che Rosid, N A; Ahmadi, M T; Ismail, Razali

    2016-01-01

    The effect of tensile uniaxial strain on the non-parabolic electronic band structure of armchair graphene nanoribbon (AGNR) is investigated. In addition, the density of states and the carrier statistic based on the tight-binding Hamiltonian are modeled analytically. It is found that the property of AGNR in the non-parabolic band region is varied by the strain. The tunable energy band gap in AGNR upon strain at the minimum energy is described for each of n-AGNR families in the non-parabolic approximation. The behavior of AGNR in the presence of strain is attributed to the breakable AGNR electronic band structure, which varies the physical properties from its normality. The linear relation between the energy gap and the electrical properties is featured to further explain the characteristic of the deformed AGNR upon strain. (paper)

  5. Phononic crystals of spherical particles: A tight binding approach

    Energy Technology Data Exchange (ETDEWEB)

    Mattarelli, M., E-mail: maurizio.mattarelli@fisica.unipg.it [NiPS Laboratory, Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06100 Perugia (Italy); Secchi, M. [CMM - Fondazione Bruno Kessler, Via Sommarive 18, 38123 Trento (Italy); Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy); Montagna, M. [Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento (Italy)

    2013-11-07

    The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.

  6. Dispersion relation and self-collimation frequency of spoof surface plasmon using tight binding model

    International Nuclear Information System (INIS)

    Bhattacharya, Sayak; Shah, Kushal

    2015-01-01

    The analytical dispersion relation of spoof surface plasmon (SSP) is known only in the low-frequency limit and thus cannot be used to describe various practically important characteristics of SSP in the high-frequency limit (such as multimodal nature, anisotropic propagation, self-collimation). In this article, we consider a square lattice of holes made on a perfect electric conductor and derive a closed form expression of the SSP dispersion relation in the high-frequency limit using a tight binding model. Instead of using prior knowledge of the band diagram along the entire first Brillouin zone (BZ) edge, we analytically determine the hopping parameters by using the eigenfrequencies only at the three high-symmetry points of the square lattice. Using this dispersion relation, we derive an expression for the self-collimation frequency of SSP. We show that this analytical formulation is also applicable to dielectric photonic crystals and can be used to predict the frequencies corresponding to centimetre-scale supercollimation and second band self-collimation in these structures. Finally, we show that our analytical results are in agreement with the simulation results for both SSP and photonic crystals. (paper)

  7. Surface Passivation in Empirical Tight Binding

    OpenAIRE

    He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

    2015-01-01

    Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameter...

  8. A Density Functional Tight Binding Study of Acetic Acid Adsorption on Crystalline and Amorphous Surfaces of Titania

    Directory of Open Access Journals (Sweden)

    Sergei Manzhos

    2015-02-01

    Full Text Available We present a comparative density functional tight binding study of an organic molecule attachment to TiO2 via a carboxylic group, with the example of acetic acid. For the first time, binding to low-energy surfaces of crystalline anatase (101, rutile (110 and (B-TiO2 (001, as well as to the surface of amorphous (a- TiO2 is compared with the same computational setup. On all surfaces, bidentate configurations are identified as providing the strongest adsorption energy, Eads = −1.93, −2.49 and −1.09 eV for anatase, rutile and (B-TiO2, respectively. For monodentate configurations, the strongest Eads = −1.06, −1.11 and −0.86 eV for anatase, rutile and (B-TiO2, respectively. Multiple monodentate and bidentate configurations are identified on a-TiO2 with a distribution of adsorption energies and with the lowest energy configuration having stronger bonding than that of the crystalline counterparts, with Eads up to −4.92 eV for bidentate and −1.83 eV for monodentate adsorption. Amorphous TiO2 can therefore be used to achieve strong anchoring of organic molecules, such as dyes, that bind via a -COOH group. While the presence of the surface leads to a contraction of the band gap vs. the bulk, molecular adsorption caused no appreciable effect on the band structure around the gap in any of the systems.

  9. Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

    2015-06-09

    The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

  10. Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface

    International Nuclear Information System (INIS)

    Jałochowski, M; Kwapiński, T; Łukasik, P; Nita, P; Kopciuszyński, M

    2016-01-01

    Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed. (paper)

  11. Density-functional tight-binding investigation of the structure, stability and material properties of nickel hydroxide nanotubes

    Science.gov (United States)

    Jahangiri, Soran; Mosey, Nicholas J.

    2018-01-01

    Nickel hydroxide is a material composed of two-dimensional layers that can be rolled up to form cylindrical nanotubes belonging to a class of inorganic metal hydroxide nanotubes that are candidates for applications in catalysis, energy storage, and microelectronics. The stabilities and other properties of this class of inorganic nanotubes have not yet been investigated in detail. The present study uses self-consistent-charge density-functional tight-binding calculations to examine the stabilities, mechanical properties, and electronic properties of nickel hydroxide nanotubes along with the energetics associated with the adsorption of water by these systems. The tight-binding model was parametrized for this system based on the results of first-principles calculations. The stabilities of the nanotubes were examined by calculating strain energies and performing molecular dynamics simulations. The results indicate that single-walled nickel hydroxide nanotubes are stable at room temperature, which is consistent with experimental investigations. The nanotubes possess size-dependent mechanical properties that are similar in magnitude to those of other inorganic nanotubes. The electronic properties of the nanotubes were also found to be size-dependent and small nickel oxyhydroxide nanotubes are predicted to be semiconductors. Despite this size-dependence, both the mechanical and electronic properties were found to be almost independent of the helical structure of the nanotubes. The calculations also show that water molecules have higher adsorption energies when binding to the interior of the nickel hydroxide nanotubes when compared to adsorption in nanotubes formed from other two-dimensional materials such as graphene. The increased adsorption energy is due to the hydrophilic nature of nickel hydroxide. Due to the broad applications of nickel hydroxide, the nanotubes investigated here are also expected to be used in catalysis, electronics, and clean energy production.

  12. From lattice Hamiltonians to tunable band structures by lithographic design

    Science.gov (United States)

    Tadjine, Athmane; Allan, Guy; Delerue, Christophe

    2016-08-01

    Recently, new materials exhibiting exotic band structures characterized by Dirac cones, nontrivial flat bands, and band crossing points have been proposed on the basis of effective two-dimensional lattice Hamiltonians. Here, we show using atomistic tight-binding calculations that these theoretical predictions could be experimentally realized in the conduction band of superlattices nanolithographed in III-V and II-VI semiconductor ultrathin films. The lithographed patterns consist of periodic lattices of etched cylindrical holes that form potential barriers for the electrons in the quantum well. In the case of honeycomb lattices, the conduction minibands of the resulting artificial graphene host several Dirac cones and nontrivial flat bands. Similar features, but organized in different ways, in energy or in k -space are found in kagome, distorted honeycomb, and Lieb superlattices. Dirac cones extending over tens of meV could be obtained in superlattices with reasonable sizes of the lithographic patterns, for instance in InAs/AlSb heterostructures. Bilayer artificial graphene could be also realized by lithography of a double quantum-well heterostructure. These new materials should be interesting for the experimental exploration of Dirac-based quantum systems, for both fundamental and applied physics.

  13. Quantum tight-binding chains with dissipative coupling

    International Nuclear Information System (INIS)

    Mogilevtsev, D; Slepyan, G Ya; Garusov, E; Kilin, S Ya; Korolkova, N

    2015-01-01

    We present a one-dimensional tight-binding chain of two-level systems coupled only through common dissipative Markovian reservoirs. This quantum chain can demonstrate anomalous thermodynamic behavior contradicting Fourier law. Population dynamics of individual systems of the chain is polynomial with the order determined by the initial state of the chain. The chain can simulate classically hard problems, such as multi-dimensional random walks. (paper)

  14. Atomic and electronic structures of a-SiC:H from tight-binding molecular dynamics

    CERN Document Server

    Ivashchenko, V I; Shevchenko, V I; Ivashchenko, L A; Rusakov, G V

    2003-01-01

    The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp sup 3 s sup * tight-binding force model with molecular dynamics simulations. The parameters of a repulsive pairwise potential are determined from ab initio pseudopotential calculations. Both carbides are generated from dilute vapours condensed from high temperature, with post-annealing at low temperature for a-SiC:H. A plausible model for the inter-atomic correlations and electronic states in a-SiC:H is suggested. According to this model, the formation of the amorphous network is weakly sensitive to the presence of hydrogen. Hydrogen passivates effectively only the weak bonds of threefold-coordinated atoms. Chemical ordering is very much affected by the cooling rate and the structure of the high-temperature vapour. The as-computed characteristics are in rather good agreement with the results for a-SiC and a-Si:H from ab initio calculations.

  15. Efficient self-consistency for magnetic tight binding

    Science.gov (United States)

    Soin, Preetma; Horsfield, A. P.; Nguyen-Manh, D.

    2011-06-01

    Tight binding can be extended to magnetic systems by including an exchange interaction on an atomic site that favours net spin polarisation. We have used a published model, extended to include long-ranged Coulomb interactions, to study defects in iron. We have found that achieving self-consistency using conventional techniques was either unstable or very slow. By formulating the problem of achieving charge and spin self-consistency as a search for stationary points of a Harris-Foulkes functional, extended to include spin, we have derived a much more efficient scheme based on a Newton-Raphson procedure. We demonstrate the capabilities of our method by looking at vacancies and self-interstitials in iron. Self-consistency can indeed be achieved in a more efficient and stable manner, but care needs to be taken to manage this. The algorithm is implemented in the code PLATO. Program summaryProgram title:PLATO Catalogue identifier: AEFC_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 228 747 No. of bytes in distributed program, including test data, etc.: 1 880 369 Distribution format: tar.gz Programming language: C and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux, Mac OS X, Windows XP Has the code been vectorised or parallelised?: Yes. Up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Catalogue identifier of previous version: AEFC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2616 Does the new version supersede the previous version?: Yes Nature of problem: Achieving charge and spin self-consistency in magnetic tight binding can be very

  16. An efficient magnetic tight-binding method for transition metals and alloys

    DEFF Research Database (Denmark)

    Barreteau, Cyrille; Spanjaard, Daniel; Desjonquères, Marie-Catherine

    2016-01-01

    that does not necessitate any further fitting is proposed to deal with systems made of several chemical elements. This model is extended to spin (and orbital) polarized materials by adding Stoner-like and spin–orbit interactions. Collinear and non-collinear magnetism as well as spin-spirals are considered......An efficient parameterized self-consistent tight-binding model for transition metals using s, p and d valence atomic orbitals as a basis set is presented. The parameters of our tight-binding model for pure elements are determined from a fit to bulk ab-initio calculations. A very simple procedure...

  17. Robust flat bands in RCo5 (R=rare earth) compounds

    OpenAIRE

    Ochi, Masayuki; Arita, Ryotaro; Matsumoto, Munehisa; Kino, Hiori; Miyake, Takashi

    2014-01-01

    The mechanism to realize the peculiar flat bands generally existing in RCo5 (R=rare earth) compounds is clarified by analyzing the first-principles band structures and the tight-binding model. These flat bands are constructed from the localized eigenstates, the existence of which is guaranteed by the partial cancelation between the intersite hopping amplitudes among the Co-3d states at the Kagome sites and those between the Kagome and honeycomb sites. Their relative positions to other bands c...

  18. Calculation of elastic constants of BCC transition metals: tight-binding recursion method

    International Nuclear Information System (INIS)

    Masuda, K.; Hamada, N.; Terakura, K.

    1984-01-01

    The elastic constants of BCC transition metals (Fe, Nb, Mo and W) are calculated by using the tight-binding d band and the Born-Mayer repulsive potential. Introducing a small distortion characteristic to C 44 (or C') elastic deformation and calculating the energy change up to second order in the atomic displacement, the shear elastic constants C 44 and C' are determined. The elastic constants C 11 and C 12 are then calculated by using the relations B=1/3(C 11 + 2C 12 ) and C'=1/2(C 11 -C 12 ), where B is the bulk modulus. In general, the agreement between the present results and the experimental values is satisfactory. The characteristic elasticity behaviour, i.e. the strong Nsub(d) (number of d electrons) dependence of the observed anisotropy factor A=C 44 /C', will also be discussed. (author)

  19. Slater-Koster Tight-Binding parametrization of single and few-layer Black-Phosphorus from first-principles calculations

    Science.gov (United States)

    Menezes, Marcos; Capaz, Rodrigo

    Black Phosphorus (BP) is a promising material for applications in electronics, especially due to the tuning of its band gap by increasing the number of layers. In single-layer BP, also called Phosphorene, the P atoms form two staggered chains bonded by sp3 hybridization, while neighboring layers are bonded by Van-der-Waals interactions. In this work, we present a Tight-Binding (TB) parametrization of the electronic structure of single and few-layer BP, based on the Slater-Koster model within the two-center approximation. Our model includes all 3s and 3p orbitals, which makes this problem more complex than that of graphene, where only 2pz orbitals are needed for most purposes. The TB parameters are obtained from a least-squares fit of DFT calculations carried on the SIESTA code. We compare the results for different basis-sets used to expand the ab-initio wavefunctions and discuss their applicability. Our model can fit a larger number of bands than previously reported calculations based on Wannier functions. Moreover, our parameters have a clear physical interpretation based on chemical bonding. As such, we expect our results to be useful in a further understanding of multilayer BP and other 2D-materials characterized by strong sp3 hybridization. CNPq, FAPERJ, INCT-Nanomateriais de Carbono.

  20. Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids.

    Science.gov (United States)

    Addicoat, Matthew A; Stefanovic, Ryan; Webber, Grant B; Atkin, Rob; Page, Alister J

    2014-10-14

    Density functional tight binding (DFTB), which is ∼100-1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5-10 kcal/mol. The structures and thermodynamic stabilities of n -alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data.

  1. Tight-binding tunneling amplitude of an optical lattice

    Science.gov (United States)

    Arzamasovs, Maksims; Liu, Bo

    2017-11-01

    The particle in a periodic potential is an important topic in an undergraduate quantum mechanics curriculum and a stepping stone on the way to more advanced topics, such as courses on interacting electrons in crystalline solids, and graduate-level research in solid-state and condensed matter physics. The interacting many-body phenomena are usually described in terms of the second quantized lattice Hamiltonians which treat single-particle physics on the level of tight-binding approximation and add interactions on top of it. The aim of this paper is to show how the tight-binding tunneling amplitude can be related to the strength of the periodic potential for the case of a cosine potential used in the burgeoning field of ultracold atoms. We show how to approach the problem of computing the tunneling amplitude of a deep lattice using the JWKB (Jeffreys-Wentzel-Kramers-Brillouin, also known as semiclassical) approximation. We also point out that care should be taken when applying the method of the linear combination of atomic orbitals (LCAO) in an optical lattice context. A summary of the exact solution in terms of Mathieu functions is also given.

  2. Tight-binding tunneling amplitude of an optical lattice

    International Nuclear Information System (INIS)

    Arzamasovs, Maksims; Liu, Bo

    2017-01-01

    The particle in a periodic potential is an important topic in an undergraduate quantum mechanics curriculum and a stepping stone on the way to more advanced topics, such as courses on interacting electrons in crystalline solids, and graduate-level research in solid-state and condensed matter physics. The interacting many-body phenomena are usually described in terms of the second quantized lattice Hamiltonians which treat single-particle physics on the level of tight-binding approximation and add interactions on top of it. The aim of this paper is to show how the tight-binding tunneling amplitude can be related to the strength of the periodic potential for the case of a cosine potential used in the burgeoning field of ultracold atoms. We show how to approach the problem of computing the tunneling amplitude of a deep lattice using the JWKB (Jeffreys–Wentzel–Kramers–Brillouin, also known as semiclassical) approximation. We also point out that care should be taken when applying the method of the linear combination of atomic orbitals (LCAO) in an optical lattice context. A summary of the exact solution in terms of Mathieu functions is also given. (paper)

  3. Atomistic tight-binding computations of the structural and optical properties of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals

    Science.gov (United States)

    Sukkabot, Worasak

    2018-05-01

    A study of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals is carried out using atomistic tight-binding theory and the configuration interaction method to provide information for applications in bioimaging, biolabeling, display devices and near-infrared electronic instruments. The calculations yield the dependences of the internal and external passivated shells on the natural behaviours of CdTe/CdX (X=S and Se)/ZnS core/shell/shell nanocrystals. The reduction of the optical band gaps is observed with increasing numbers of monolayers in the external ZnS shell due to quantum confinement. Interestingly, the optical band gaps of CdTe/CdS/ZnS core/shell/shell nanocrystals are greater than those of CdTe/CdSe/ZnS core/shell/shell nanocrystals. In the presence of an external ZnS-coated shell, electron-hole wave function overlaps, oscillation strengths, ground-state exchange energies and Stokes shift are improved, whereas ground-state coulomb energies and fine-structure splitting are reduced. The oscillation strengths, Stokes shift and fine-structure splitting are reduced with the increase in external ZnS shell thickness. The oscillation strengths, Stokes shift and fine-structure splitting of CdTe/CdS/ZnS core/shell/shell nanocrystals are larger than those of CdTe/CdSe/ZnS core/shell/shell nanocrystals. Reduction of the atomistic electron-hole interactions is observed with increasing external ZnS shell size. The strong electron-hole interactions are more probed in CdTe/CdS/ZnS core/shell/shell nanocrystals than in CdTe/CdSe/ZnS core/shell/shell nanocrystals.

  4. Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

    Science.gov (United States)

    Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

    2016-12-01

    Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

  5. Environment-dependent crystal-field tight-binding based on density-functional theory

    International Nuclear Information System (INIS)

    Urban, Alexander

    2012-01-01

    Electronic structure calculations based on Kohn-Sham density-functional theory (DFT) allow the accurate prediction of chemical bonding and materials properties. Due to the high computational demand DFT calculations are, however, restricted to structures containing at most several hundreds of atoms, i.e., to length scales of a few nanometers. Though, many processes of technological relevance, for example in the field of nanoelectronics, are governed by phenomena that occur on a slightly larger length scale of up to 100 nanometers, which corresponds to tens of thousands of atoms. The semiempirical Slater-Koster tight-binding (TB) method makes it feasible to calculate the electronic structure of such large systems. In contrast to first-principles-based DFT, which is universally applicable to almost all chemical species, the TB method is based on parametrized models that are usually specialized for a particular application or for one certain class of compounds. Usually the model parameters (Slater-Koster tables) are empirically adjusted to reproduce either experimental reference data (e.g., geometries, elastic constants) or data from first-principles methods such as DFT. The construction of a new TB model is therefore connected with a considerable effort that is often contrasted by a low transferability of the parametrization. In this thesis we develop a systematic methodology for the derivation of accurate and transferable TB models from DFT calculations. Our procedure exploits the formal relationship between the two methods, according to which the TB total energy can be understood as a direct approximation of the Kohn--Sham energy functional. The concept of our method is different to previous approaches such as the DFTB method, since it allows to extract TB parameters from converged DFT wave functions and Hamiltonians of arbitrary reference structures. In the following the different subjects of this thesis are briefly summarized. We introduce a new technique for the

  6. Structural analysis, electronic properties, and band gaps of a graphene nanoribbon: A new 2D materials

    Science.gov (United States)

    Dass, Devi

    2018-03-01

    Graphene nanoribbon (GNR), a new 2D carbon nanomaterial, has some unique features and special properties that offer a great potential for interconnect, nanoelectronic devices, optoelectronics, and nanophotonics. This paper reports the structural analysis, electronic properties, and band gaps of a GNR considering different chirality combinations obtained using the pz orbital tight binding model. In structural analysis, the analytical expressions for GNRs have been developed and verified using the simulation for the first time. It has been found that the total number of unit cells and carbon atoms within an overall unit cell and molecular structure of a GNR have been changed with the change in their chirality values which are similar to the values calculated using the developed analytical expressions thus validating both the simulation as well as analytical results. Further, the electronic band structures at different chirality values have been shown for the identification of metallic and semiconductor properties of a GNR. It has been concluded that all zigzag edge GNRs are metallic with very small band gaps range whereas all armchair GNRs show both the metallic and semiconductor nature with very small and high band gaps range. Again, the total number of subbands in each electronic band structure is equal to the total number of carbon atoms present in overall unit cell of the corresponding GNR. The semiconductors GNRs can be used as a channel material in field effect transistor suitable for advanced CMOS technology whereas the metallic GNRs could be used for interconnect.

  7. Surface Passivation in Empirical Tight Binding

    Science.gov (United States)

    He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

    2016-03-01

    Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameters. This method is applied to a Si quantum well and a Si ultra-thin body transistor oxidized with SiO2 in several oxidation configurations. Comparison with ab-initio results and experiments verifies the presented method. Oxidation configurations that severely hamper the transistor performance are identified. It is also shown that the commonly used implicit H atom passivation overestimates the transistor performance.

  8. Bandstructure modulation for Si-h and Si-g nanotubes in a transverse electric field: Tight binding approach

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2013-11-01

    We have investigated the electronic properties of SiNTs, under the external electric field, using Tight Binding (TB) approximation. It was found that the energy levels, energy gaps, and density of states (DOS) strongly depend on the electric field strength. The large electric strength leads to coupling the neighbor subbands and induce destruction of subband degeneracy, increase of low-energy states, and strong modulation of energy gap which these effects reflect in the DOS spectrum. It has been shown that, the band gap reduction of Si g-NTs is linearly proportional to the electric field strength. The band gap variation for Si h-NTs increases first and later decreases (Metallic) or first remains constant and then decreases (semiconductor). Also we show that the larger diameter tubes are more sensitive to the field strength than smaller ones. The semiconducting metallic transition or vice versa can be achieved through an increasing of applied fields. Number and position of peaks in DOS spectrum are dependent on electric field strength.

  9. Complex band structures of transition metal dichalcogenide monolayers with spin–orbit coupling effects

    International Nuclear Information System (INIS)

    Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

    2016-01-01

    Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2 , where M   =  Mo, W; X   =  S, Se, Te) while including spin–orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed. (paper)

  10. Complex band structures of transition metal dichalcogenide monolayers with spin-orbit coupling effects

    Science.gov (United States)

    Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

    2016-09-01

    Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2, where M  =  Mo, W; X  =  S, Se, Te) while including spin-orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed.

  11. OLIFE: Tight Binding Code for Transmission Coefficient Calculation

    Science.gov (United States)

    Mijbil, Zainelabideen Yousif

    2018-05-01

    A new and human friendly transport calculation code has been developed. It requires a simple tight binding Hamiltonian as the only input file and uses a convenient graphical user interface to control calculations. The effect of magnetic field on junction has also been included. Furthermore the transmission coefficient can be calculated between any two points on the scatterer which ensures high flexibility to check the system. Therefore Olife can highly be recommended as an essential tool for pretesting studying and teaching electron transport in molecular devices that saves a lot of time and effort.

  12. DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

    Science.gov (United States)

    Humeniuk, Alexander; Mitrić, Roland

    2017-12-01

    A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

  13. Electronic Properties of SiNTs Under External Electric and Magnetic Fields Using the Tight-Binding Method

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2014-02-01

    We investigated the electronic properties of silicon nanotubes (SiNTs) under external transverse electric fields and axial magnetic fields using the tight-binding approximation. It was found that, after switching on the electric and magnetic fields, band modifications such as distortion of degeneracy, change in energy dispersion and subband spacing, and bandgap size reduction occur. The bandgap of silicon gear-like nanotubes (Si g-NTs) decreases linearly with increasing electric field strength, but the bandgap for silicon hexagonal nanotubes (Si h-NTs) first increases and then decreases (metallic) or first remains constant and then decreases (semiconducting). Our results show that the bandgap of Si h-NTs is very sensitive to both electric and magnetic fields, unlike Si g-NTs, which are more sensitive to electric than magnetic fields.

  14. Atomistic Tight-Binding Theory of Electron-Hole Exchange Interaction in Morphological Evolution of CdSe/ZnS Core/Shell Nanodisk to CdSe/ZnS Core/Shell Nanorod

    Directory of Open Access Journals (Sweden)

    Worasak Sukkabot

    2016-01-01

    Full Text Available Based on the atomistic tight-binding theory (TB and a configuration interaction (CI description, the electron-hole exchange interaction in the morphological transformation of CdSe/ZnS core/shell nanodisk to CdSe/ZnS core/shell nanorod is described with the aim of understanding the impact of the structural shapes on the change of the electron-hole exchange interaction. Normally, the ground hole states confined in typical CdSe/ZnS core/shell nanocrystals are of heavy hole-like character. However, the atomistic tight-binding theory shows that a transition of the ground hole states from heavy hole-like to light hole-like contribution with the increasing aspect ratios of the CdSe/ZnS core/shell nanostructures is recognized. According to the change in the ground-state hole characters, the electron-hole exchange interaction is also significantly altered. To do so, optical band gaps, ground-state electron character, ground-state hole character, oscillation strengths, ground-state coulomb energies, ground-state exchange energies, and dark-bright (DB excitonic splitting (stoke shift are numerically demonstrated. These atomistic computations obviously show the sensitivity with the aspect ratios. Finally, the alteration in the hole character has a prominent effect on dark-bright (DB excitonic splitting.

  15. Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Rout, G. C., E-mail: siva1987@iopb.res.in, E-mail: skp@iopb.res.in, E-mail: gcr@iopb.res.in [Physics Enclave, Plot No-664/4825, Lane-4A, Shree Vihar, Bhubaneswar-751031, Odisha (India); Sahu, Sivabrata [School of Applied Sciences (Physics), KIIT University, Bhubaneswar-751024, Odisha (India); Panda, S. K. [K.D. Science College, Pochilima, Hinjilicut,Pin-761101 Ganjam, Orissa (India)

    2016-04-13

    We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution of the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).

  16. Effect of impurity doping on tunneling conductance in AB-stacked bi-layer graphene: A tight-binding study

    International Nuclear Information System (INIS)

    Rout, G. C.; Sahu, Sivabrata; Panda, S. K.

    2016-01-01

    We report here a microscopic tight-binding model calculation for AB-stacked bilayer graphene in presence of biasing potential between the two layers and the impurity effects to study the evolution of the total density of states with special emphasis on opening of band gap near Dirac point. We have calculated the electron Green’s functions for both the A and B sub-lattices by Zubarev technique. The imaginary part of the Green’s function gives the partial and total density of states of electrons. The density of states are computed numerically for 1000 × 1000 grid points of the electron momentum. The evolution of the opening of band gap near van-Hove singularities as well as near Dirac point is investigated by varying the different interlayer hoppings and the biasing potentials. The inter layer hopping splits the density of states at van-Hove singularities and produces a V-shaped gap near Dirac point. Further the biasing potential introduces a U shaped gap near Dirac point with a density minimum at the applied potential(i.e. at V/2).

  17. Structural properties of metal-organic frameworks within the density-functional based tight-binding method

    Energy Technology Data Exchange (ETDEWEB)

    Lukose, Binit; Supronowicz, Barbara; Kuc, Agnieszka B.; Heine, Thomas [School of Engineering and Science, Jacobs University Bremen (Germany); Petkov, Petko S.; Vayssilov, Georgi N. [Faculty of Chemistry, University of Sofia (Bulgaria); Frenzel, Johannes [Lehrstuhl fuer Theoretische Chemie, Ruhr-Universitaet Bochum (Germany); Seifert, Gotthard [Physikalische Chemie, Technische Universitaet Dresden (Germany)

    2012-02-15

    Density-functional based tight-binding (DFTB) is a powerful method to describe large molecules and materials. Metal-organic frameworks (MOFs), materials with interesting catalytic properties and with very large surface areas, have been developed and have become commercially available. Unit cells of MOFs typically include hundreds of atoms, which make the application of standard density-functional methods computationally very expensive, sometimes even unfeasible. The aim of this paper is to prepare and to validate the self-consistent charge-DFTB (SCC-DFTB) method for MOFs containing Cu, Zn, and Al metal centers. The method has been validated against full hybrid density-functional calculations for model clusters, against gradient corrected density-functional calculations for supercells, and against experiment. Moreover, the modular concept of MOF chemistry has been discussed on the basis of their electronic properties. We concentrate on MOFs comprising three common connector units: copper paddlewheels (HKUST-1), zinc oxide Zn{sub 4}O tetrahedron (MOF-5, MOF-177, DUT-6 (MOF-205)), and aluminum oxide AlO{sub 4}(OH){sub 2} octahedron (MIL-53). We show that SCC-DFTB predicts structural parameters with a very good accuracy (with less than 5% deviation, even for adsorbed CO and H{sub 2}O on HKUST-1), while adsorption energies differ by 12 kJ mol{sup -1} or less for CO and water compared to DFT benchmark calculations. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Incipient localization and tight-binding superconductivity: Tsub(c) calculation

    International Nuclear Information System (INIS)

    Kolley, E.; Kolley, W.

    1984-01-01

    Localization effects on the superconducting transition temperature Tsub(c) are examined in strongly disordered three-dimensional systems. A tight-binding formulation of strong-coupling superconductivity is combined, after configuration averaging, with the self-consistent treatment of Anderson localization developed by Vollhardt and Woelfle. The Coulomb interaction becomes retarded via the joint local local density of states, giving rise to an enhancement of the pseudopotential. Numerical Tsub(c) results as a function of disorder are compared with another theoretical work and experimental values for some high-Tsub(c) materials. (orig.)

  19. Zonula occludens toxin structure-function analysis. Identification of the fragment biologically active on tight junctions and of the zonulin receptor binding domain.

    Science.gov (United States)

    Di Pierro, M; Lu, R; Uzzau, S; Wang, W; Margaretten, K; Pazzani, C; Maimone, F; Fasano, A

    2001-06-01

    Zonula occludens toxin (Zot) is an enterotoxin elaborated by Vibrio cholerae that increases intestinal permeability by interacting with a mammalian cell receptor with subsequent activation of intracellular signaling leading to the disassembly of the intercellular tight junctions. Zot localizes in the bacterial outer membrane of V. cholerae with subsequent cleavage and secretion of a carboxyl-terminal fragment in the host intestinal milieu. To identify the Zot domain(s) directly involved in the protein permeating effect, several zot gene deletion mutants were constructed and tested for their biological activity in the Ussing chamber assay and their ability to bind to the target receptor on intestinal epithelial cell cultures. The Zot biologically active domain was localized toward the carboxyl terminus of the protein and coincided with the predicted cleavage product generated by V. cholerae. This domain shared a putative receptor-binding motif with zonulin, the Zot mammalian analogue involved in tight junction modulation. Amino acid comparison between the Zot active fragment and zonulin, combined with site-directed mutagenesis experiments, confirmed the presence of an octapeptide receptor-binding domain toward the amino terminus of the processed Zot.

  20. Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study

    International Nuclear Information System (INIS)

    Ramírez-Morales, A.; Martínez-Orozco, J. C.; Rodríguez-Vargas, I.

    2014-01-01

    The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented

  1. Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez-Morales, A.; Martínez-Orozco, J. C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac. (Mexico)

    2014-05-15

    The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented.

  2. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    NARCIS (Netherlands)

    Ruger, R.; Niehaus, T.; van Lenthe, E.; Heine, T.; Visscher, L.

    2016-01-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nu- clear wavefunction.

  3. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  4. Quantitative analysis on electric dipole energy in Rashba band splitting.

    Science.gov (United States)

    Hong, Jisook; Rhim, Jun-Won; Kim, Changyoung; Ryong Park, Seung; Hoon Shim, Ji

    2015-09-01

    We report on quantitative comparison between the electric dipole energy and the Rashba band splitting in model systems of Bi and Sb triangular monolayers under a perpendicular electric field. We used both first-principles and tight binding calculations on p-orbitals with spin-orbit coupling. First-principles calculation shows Rashba band splitting in both systems. It also shows asymmetric charge distributions in the Rashba split bands which are induced by the orbital angular momentum. We calculated the electric dipole energies from coupling of the asymmetric charge distribution and external electric field, and compared it to the Rashba splitting. Remarkably, the total split energy is found to come mostly from the difference in the electric dipole energy for both Bi and Sb systems. A perturbative approach for long wave length limit starting from tight binding calculation also supports that the Rashba band splitting originates mostly from the electric dipole energy difference in the strong atomic spin-orbit coupling regime.

  5. Rate concept and retarded master equations for dissipative tight-binding models

    International Nuclear Information System (INIS)

    Egger, R.; Mak, C.H.; Weiss, U.

    1994-01-01

    Employing a ''noninteracting-cluster approximation,'' the dynamics of multistate dissipative tight-binding models has been formulated in terms of a set of generalized retarded master equations. The rates for the various pathways are expressed as power series in the intersite couplings. We apply this to the superexchange mechanism, which is relevant for bacterial photosynthesis and bridged electron transfer systems. This approach provides a general and unified description of both incoherent and coherent transport

  6. Band gap engineering of BC2N for nanoelectronic applications

    Science.gov (United States)

    Lim, Wei Hong; Hamzah, Afiq; Ahmadi, Mohammad Taghi; Ismail, Razali

    2017-12-01

    The BC2N as an example of boron-carbon-nitride (BCN), has the analogous structure as the graphene and boron nitride. It is predicted to have controllable electronic properties. Therefore, the analytical study on the engineer-able band gap of the BC2N is carried out based on the schematic structure of BC2N. The Nearest Neighbour Tight Binding (NNTB) model is employed with the dispersion relation and the density of state (DOS) as the main band gap analysing parameter. The results show that the hopping integrals having the significant effect on the band gap, band structure and DOS of BC2N nanowire (BC2NNW) need to be taken into consideration. The presented model indicates consistent trends with the published computational results around the Dirac points with the extracted band gap of 0.12 eV. Also, it is distinguished that wide energy gap of boron nitride (BN) is successfully narrowed by this carbon doped material which assures the application of BC2N on the nanoelectronics and optoelectronics in the near future.

  7. A general intermolecular force field based on tight-binding quantum chemical calculations

    Science.gov (United States)

    Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

    2017-10-01

    A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

  8. Low-order moment expansions to tight binding for interatomic potentials: Successes and failures

    International Nuclear Information System (INIS)

    Kress, J.D.; Voter, A.F.

    1995-01-01

    We discuss the use of moment-based approximations to tight binding. Using a maximum entropy form for the electronic density of states, we show that a general interatomic potential can be defined that is suitable for molecular-dynamics simulations and has several other desirable features. For covalent materials (C and Si), properties where the atoms are in equivalent environments are well converged at low-order moments. For defect environments, which offer a more critical (and relevant) test, the method is found to give less satisfactory results. For example, the vacancy formation energy for Si is too low by ∼2 eV at 10 moments relative to exact tight binding. Attempts to improve the accuracy were unsuccessful, leading to the conclusion that potentials based on this approach are inadequate for covalent materials. We speculate that this may be a deficiency of low-order moment methods in general. For metals, in contrast to the covalent systems, we find that the low-order moment approach is better behaved. This finding is consistent with the success of existing empirical fourth-moment potentials for metals

  9. Relaxation and cross section effects in valence band photoemission spectroscopy

    International Nuclear Information System (INIS)

    McFeely, F.R.

    1976-09-01

    Various problems relating to the interpretation of valence band x-ray photoemission (XPS) spectra of solids are discussed. The experiments and calculations reported herein deal with the following questions: (1) To what extent do many-body effects manifest themselves in an XPS valence band spectrum, and thus invalidate a direct comparison between the photoemission energy distribution, I(E), and the density of states, N(E), calculated on the basis of ground-state one-electron theory. (2) The effect of the binding-energy-dependent photoemission cross section on I(E) at XPS energies. (3) In favorable cases indicated by (1) and (2) we examine the effect of the interaction of the crystal field with the apparent spin-orbit splittings of core levels observed in XPS spectra. (4) The use of tight binding band structure calculations to parameterize the electronic band structure from XPS and other data is described. (5) The use of high energy angle-resolved photoemission on oriented single crystals to gain orbital symmetry information is discussed. (6) The evolution of the shape of the photoemission energy distribution (of polycrystalline Cu) as a function of photon energy from 50 less than or equal h ω less than or equal 175 is discussed

  10. Coupling of Hubbard fermions with phonons in La{sub 2} CuO{sub 4}: A combined study using density-functional theory and the generalized tight-binding method

    Energy Technology Data Exchange (ETDEWEB)

    Shneyder, E.I., E-mail: shneyder@iph.krasn.ru [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation); Reshetnev Siberian State Aerospace University, Krasnoyarsk 660014 (Russian Federation); Spitaler, J. [Materials Center Leoben Forschung GmbH, Rosegger-Straße 18, A-8700 Leoben (Austria); Kokorina, E.E.; Nekrasov, I.A. [Institute of Electrophysics UB RAS, Amundsena Str. 106, 620016 Yekaterinburg (Russian Federation); Gavrichkov, V.A. [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation); Draxl, C. [Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin (Germany); Ovchinnikov, S.G. [Kirensky Institute of Physics SB RAS, Krasnoyarsk 660036 (Russian Federation)

    2015-11-05

    We present results for the electron-phonon interaction of the Γ-point phonons in the tetragonal high-temperature phase of La{sub 2} CuO{sub 4} obtained from a hybrid scheme, combining density-functional theory (DFT) with the generalized tight-binding approach. As a starting point, eigenfrequencies and eigenvectors for the Γ-point phonons are determined from DFT within the frozen phonon approach utilizing the augmented plane wave + local orbitals method. The so obtained characteristics of electron-phonon coupling are converted into parameters of the generalized tight-binding method. This approach is a version of cluster perturbation theory and takes the strong on-site electron correlations into account. The obtained parameters describe the interaction of phonons with Hubbard fermions which form quasiparticle bands in strongly correlated electron systems. As a result, it is found that the Γ-point phonons with the strongest electron-phonon interaction are the A{sub 2u} modes (236 cm{sup −1}, 131 cm{sup −1} and 476 cm{sup −1}). Finally it is shown, that the single-electron spectral-weight redistribution between different Hubbard fermion quasiparticles results in a suppression of electron-phonon interaction which is strongest for the triplet Hubbard band with z oriented copper and oxygen electrons. - Highlights: • Electron-phonon interaction in strongly correlated electron systems is analyzed. • Interaction parameters between strongly correlated electrons and phonons are obtained. • The suppression of these parameters by strong electron correlations is demonstrated.

  11. Localization length and fractal dimension of band centre states for 1-d off-diagonal disordered systems

    International Nuclear Information System (INIS)

    Roman, E.; Wiecko, C.

    1985-08-01

    We study and characterize the eigenstates near the centre of the band of a 1-d tight binding model with off-diagonal disorder Wsub(T). We find a new exponent for the localization length lambda on an energy-dependent range of disorder Wsub(T). We correlate this feature with a change of structure of the wave-function displayed by the behaviour of its fractal dimensionality. (author)

  12. Comparative study of the two-phonon Raman bands of silicene and graphene

    International Nuclear Information System (INIS)

    Popov, Valentin N; Lambin, Philippe

    2016-01-01

    We present a computational study of the two-phonon Raman spectra of silicene and graphene within a density-functional non-orthogonal tight-binding model. Due to the presence of linear bands close to the Fermi energy in the electronic structure of both structures, the Raman scattering by phonons is resonant. We find that the Raman spectra exhibit a crossover behavior for laser excitation close to the π-plasmon energy. This phenomenon is explained by the disappearance of certain paths for resonant Raman scattering and the appearance of other paths beyond this energy. Besides that, the electronic joint density of states (DOS) is divergent at this energy, which is reflected on the behavior of the Raman bands of the two structures in a qualitatively different way. Additionally, a number of Raman bands, originating from divergent phonon DOS at the M point and at points, inside the Brillouin zone, is also predicted. The calculated spectra for graphene are in excellent agreement with available experimental data. The obtained Raman bands can be used for structural characterization of silicene and graphene samples by Raman spectroscopy. (paper)

  13. Tight-Binding simulations of InAs/GaAs quantum dots; Tight-Binding Simulationen von InAs/GaAs Quantenpunkten

    Energy Technology Data Exchange (ETDEWEB)

    Kleinsorge, Alexander

    2008-06-23

    For several years, the technological potential of self-organized grown quantum dots (QD) has been known. Their usage as an effective light source or memory requires the precise prediction of their electronic properties. Hence, this report will study InAs quantum dots at GaAs substrate. After relaxing the atomic positions with a many body potential of Abell-Tersoff type, I calculated the electronic structure using the Tight-Binding method which is reasonable for large systems. During the investigation of wavefunctions depend on the shape, size and temperature, the impact of strain showed up as the main reason for the p-splitting. Typically flat QDs (relative to lateral dimensions) are grown, therefore the energy of bound states depends mostly on their height. The crystal's orientation had a strong impact on the wavefunctions. Moreover, the understanding of STS experiments, which inspected the connection between shape and wavefunction, is better now. Because of the possible simultaneous occupation of semiconductor quantum dots with an electron and a hole, there is a dipole moment of the exciton (due to their different behaviour inside the QD). This is a further experimental access to inner details of the QD. I ascertained the interplay of composition profile and dipole moment. The force caused by additional potentials (piezoelectricity, outer homogeneous and inhomogeneous electrical fields) was also an subject of my inquiries. To conclude, I executed kMC simulations, to better apprehend the annealing experiments. I was able to explain the narrowing of the PL peak width better. Furthermore I showed a ramification of the strain field to the diffusion development (and the following electronic properties). (orig.)

  14. Nanoscale capacitance: A quantum tight-binding model

    Science.gov (United States)

    Zhai, Feng; Wu, Jian; Li, Yang; Lu, Jun-Qiang

    2017-01-01

    Landauer-Buttiker formalism with the assumption of semi-infinite electrodes as reservoirs has been the standard approach in modeling steady electron transport through nanoscale devices. However, modeling dynamic electron transport properties, especially nanoscale capacitance, is a challenging problem because of dynamic contributions from electrodes, which is neglectable in modeling macroscopic capacitance and mesoscopic conductance. We implement a self-consistent quantum tight-binding model to calculate capacitance of a nano-gap system consisting of an electrode capacitance C‧ and an effective capacitance Cd of the middle device. From the calculations on a nano-gap made of carbon nanotube with a buckyball therein, we show that when the electrode length increases, the electrode capacitance C‧ moves up while the effective capacitance Cd converges to a value which is much smaller than the electrode capacitance C‧. Our results reveal the importance of electrodes in modeling nanoscale ac circuits, and indicate that the concepts of semi-infinite electrodes and reservoirs well-accepted in the steady electron transport theory may be not applicable in modeling dynamic transport properties.

  15. Resonant enhancement of band-to-band tunneling in in-plane MoS2/WS2 heterojunctions

    Science.gov (United States)

    Kuroda, Tatsuya; Mori, Nobuya

    2018-04-01

    The band-to-band (BTB) tunneling current J through in-plane MoS2/WS2 heterojunctions is calculated by the nonequilibrium Green function method combined with tight-binding approximation. Types A and B of band configurations are considered. For type-A (type-B) heterojunctions, a potential notch exists (or is absent) at the heterointerface. Both type-A and type-B MoS2/WS2 heterojunctions can support a higher BTB current than MoS2 and WS2 homojunctions. For type-A heterojunctions, the resonant enhancement of J occurs resulting in a significantly higher BTB tunneling current.

  16. A bird’s eye view on the flat and conic band world of the honeycomb and Kagome lattices: towards an understanding of 2D metal-organic frameworks electronic structure

    Science.gov (United States)

    Barreteau, C.; Ducastelle, F.; Mallah, T.

    2017-11-01

    We present a thorough tight-binding analysis of the band structure of a wide variety of lattices belonging to the class of honeycomb and Kagome systems including several mixed forms combining both lattices. The band structure of these systems are made of a combination of dispersive and flat bands. The dispersive bands possess Dirac cones (linear dispersion) at the six corners (K points) of the Brillouin zone although in peculiar cases Dirac cones at the center of the zone (Γ point) appear. The flat bands can be of different nature. Most of them are tangent to the dispersive bands at the center of the zone but some, for symmetry reasons, do not hybridize with other states. The objective of our work is to provide an analysis of a wide class of so-called ligand-decorated honeycomb Kagome lattices that are observed in a 2D metal-organic framework where the ligand occupy honeycomb sites and the metallic atoms the Kagome sites. We show that the p x -p y graphene model is relevant in these systems and there exists four types of flat bands: Kagome flat (singly degenerate) bands, two kinds of ligand-centered flat bands (A2 like and E like, respectively doubly and singly degenerate) and metal-centered (three fold degenerate) flat bands.

  17. Optically Unraveling the Edge Chirality-Dependent Band Structure and Plasmon Damping in Graphene Edges.

    Science.gov (United States)

    Duan, Jiahua; Chen, Runkun; Cheng, Yuan; Yang, Tianzhong; Zhai, Feng; Dai, Qing; Chen, Jianing

    2018-05-01

    The nontrivial topological origin and pseudospinorial character of electron wavefunctions make edge states possess unusual electronic properties. Twenty years ago, the tight-binding model calculation predicted that zigzag termination of 2D sheets of carbon atoms have peculiar edge states, which show potential application in spintronics and modern information technologies. Although scanning probe microscopy is employed to capture this phenomenon, the experimental demonstration of its optical response remains challenging. Here, the propagating graphene plasmon provides an edge-selective polaritonic probe to directly detect and control the electronic edge state at ambient condition. Compared with armchair, the edge-band structure in the bandgap gives rise to additional optical absorption and strongly absorbed rim at zigzag edge. Furthermore, the optical conductivity is reconstructed and the anisotropic plasmon damping in graphene systems is revealed. The reported approach paves the way for detecting edge-specific phenomena in other van der Waals materials and topological insulators. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Characterization of the Fermi surface of BEDT-TTF4[Hg2Cl6].PhCl by electronic band structure calculations

    International Nuclear Information System (INIS)

    Veiros, L.F.; Canadell, E.

    1994-01-01

    Tight-binding band structure calculations for the room temperature structure of BEDT-TTF 4 [Hg 2 Cl 6 ]-PhCl show the existence of closed electron and hole Fermi surfaces, in agreement with the 2D metallic conductivity of this salt. It is shown that these closed Fermi surfaces result from the hybridization of two hidden 1D Fermi surfaces. However, our study also shows that a transition associated with either a usual or a hidden nesting type mechanism is unlikely. This explains why this salt retains its metallic properties without any resistivity anomaly down to 1.3 K. Our study suggests that BEDT-TTF 4 [Hg 2 Cl 6 ]-PhCl is somewhat anisotropic 2D semimetal and should exhibit Shubnikov-de Haas oscillations corresponding to a cross-sectional area of approximately 13% of the first Brillouin zone. (orig.)

  19. Some Effective Tight-Binding Models for Electrons in DNA Conduction: A Review

    International Nuclear Information System (INIS)

    Yamada, H.; Iguchi, K.

    2010-01-01

    Quantum transport for DNA conduction has been widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works concerning the electronic states and the conduction/transfer in DNA polymers. We have mainly investigated the energy-band structure and the correlation effects of localization property in the two- and three-chain systems (ladder model) with long-range correlation as a simple model for electronic property in a double strand of DNA by using the tight-bindingmodel. In addition, we investigated the localization properties of electronic states in several actual DNA sequences such as bacteriophages of Escherichia coli, human-chromosome 22, compared with those of the artificial disordered sequences with correlation. The charge-transfer properties for poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA polymers are also presented in terms of localization lengths within the frameworks of the polaron models due to the coupling between the charge carriers and the lattice vibrations of the double strand of DNA

  20. A study of the performance of tight-binding models for silicon and silicon-germanium alloys

    Science.gov (United States)

    Roberts, Amanda Killen

    1998-11-01

    An important challenge in achieving small-scale semiconductor devices is to confine dopants to small, well-defined regions because device performance depends on their accurate placement. However, semiconductor processing involves repeated annealing cycles which can cause dopants to diffuse away from their intended locations. For this reason, it is important to understand the basic physical processes of dopant diffusion on atomic length scales. Tight binding models offer the possibility of studying diffusion in larger systems and for longer time scales than is possible with current LDA methods. However, while a wide variety of tight binding models exist for silicon, these models are not necessarily suited for dynamical studies and they are rarely extended to elements which are dopants in silicon, or to multicomponent systems. This dissertation addresses these issues. We present the first systematic comparison of three parameterized, two-center, sp-based, tight binding models which, because of their simplicity, are suitable for dynamical studies. The models we considered are those by Goodwin et al. (GSP), Kwon et al., and Sawada. We evaluated these models for Si to determine their relative strengths and weaknesses in comparison to experimental and LDA results. Our results show that none of these models is outstanding over the others, and all give acceptable representations of the properties of Si which are of interest for dynamical studies. Having carefully investigated the fitting process to find simple ways to fit tight binding parameters, we have provided information as to the role of each of the GSP parameters in the fitting procedure. As a result, we have recorded a detailed prescription for fitting which can be followed by researchers wanting to extend the models to additional species. Based on our findings about the performance of the Si models, we extended the GSP model to second-nearest neighbors and produced new parameter sets for Si, Ge, and SiGe. This has

  1. Development of tight-binding based GW algorithm and its computational implementation for graphene

    Energy Technology Data Exchange (ETDEWEB)

    Majidi, Muhammad Aziz [Departemen Fisika, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); NUSNNI-NanoCore, Department of Physics, National University of Singapore (NUS), Singapore 117576 (Singapore); Singapore Synchrotron Light Source (SSLS), National University of Singapore (NUS), 5 Research Link, Singapore 117603 (Singapore); Naradipa, Muhammad Avicenna, E-mail: muhammad.avicenna11@ui.ac.id; Phan, Wileam Yonatan; Syahroni, Ahmad [Departemen Fisika, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia); Rusydi, Andrivo [NUSNNI-NanoCore, Department of Physics, National University of Singapore (NUS), Singapore 117576 (Singapore); Singapore Synchrotron Light Source (SSLS), National University of Singapore (NUS), 5 Research Link, Singapore 117603 (Singapore)

    2016-04-19

    Graphene has been a hot subject of research in the last decade as it holds a promise for various applications. One interesting issue is whether or not graphene should be classified into a strongly or weakly correlated system, as the optical properties may change upon several factors, such as the substrate, voltage bias, adatoms, etc. As the Coulomb repulsive interactions among electrons can generate the correlation effects that may modify the single-particle spectra (density of states) and the two-particle spectra (optical conductivity) of graphene, we aim to explore such interactions in this study. The understanding of such correlation effects is important because eventually they play an important role in inducing the effective attractive interactions between electrons and holes that bind them into excitons. We do this study theoretically by developing a GW method implemented on the basis of the tight-binding (TB) model Hamiltonian. Unlike the well-known GW method developed within density functional theory (DFT) framework, our TB-based GW implementation may serve as an alternative technique suitable for systems which Hamiltonian is to be constructed through a tight-binding based or similar models. This study includes theoretical formulation of the Green’s function G, the renormalized interaction function W from random phase approximation (RPA), and the corresponding self energy derived from Feynman diagrams, as well as the development of the algorithm to compute those quantities. As an evaluation of the method, we perform calculations of the density of states and the optical conductivity of graphene, and analyze the results.

  2. Development of tight-binding based GW algorithm and its computational implementation for graphene

    International Nuclear Information System (INIS)

    Majidi, Muhammad Aziz; Naradipa, Muhammad Avicenna; Phan, Wileam Yonatan; Syahroni, Ahmad; Rusydi, Andrivo

    2016-01-01

    Graphene has been a hot subject of research in the last decade as it holds a promise for various applications. One interesting issue is whether or not graphene should be classified into a strongly or weakly correlated system, as the optical properties may change upon several factors, such as the substrate, voltage bias, adatoms, etc. As the Coulomb repulsive interactions among electrons can generate the correlation effects that may modify the single-particle spectra (density of states) and the two-particle spectra (optical conductivity) of graphene, we aim to explore such interactions in this study. The understanding of such correlation effects is important because eventually they play an important role in inducing the effective attractive interactions between electrons and holes that bind them into excitons. We do this study theoretically by developing a GW method implemented on the basis of the tight-binding (TB) model Hamiltonian. Unlike the well-known GW method developed within density functional theory (DFT) framework, our TB-based GW implementation may serve as an alternative technique suitable for systems which Hamiltonian is to be constructed through a tight-binding based or similar models. This study includes theoretical formulation of the Green’s function G, the renormalized interaction function W from random phase approximation (RPA), and the corresponding self energy derived from Feynman diagrams, as well as the development of the algorithm to compute those quantities. As an evaluation of the method, we perform calculations of the density of states and the optical conductivity of graphene, and analyze the results.

  3. Self-consistent tight-binding model of B and N doping in graphene

    DEFF Research Database (Denmark)

    Pedersen, Thomas Garm; Pedersen, Jesper Goor

    2013-01-01

    . The impurity potential depends sensitively on the impurity occupancy, leading to a self-consistency requirement. We solve this problem using the impurity Green's function and determine the self-consistent local density of states at the impurity site and, thereby, identify acceptor and donor energy resonances.......Boron and nitrogen substitutional impurities in graphene are analyzed using a self-consistent tight-binding approach. An analytical result for the impurity Green's function is derived taking broken electron-hole symmetry into account and validated by comparison to numerical diagonalization...

  4. Influence of the aggregate state on band structure and optical properties of C60 computed with different methods

    Science.gov (United States)

    Pal, Amrita; Arabnejad, Saeid; Yamashita, Koichi; Manzhos, Sergei

    2018-05-01

    C60 and C60 based molecules are efficient acceptors and electron transport layers for planar perovskite solar cells. While properties of these molecules are well studied by ab initio methods, those of solid C60, specifically its optical absorption properties, are not. We present a combined density functional theory-Density Functional Tight Binding (DFTB) study of the effect of solid state packing on the band structure and optical absorption of C60. The valence and conduction band edge energies of solid C60 differ on the order of 0.1 eV from single molecule frontier orbital energies. We show that calculations of optical properties using linear response time dependent-DFT(B) or the imaginary part of the dielectric constant (dipole approximation) can result in unrealistically large redshifts in the presence of intermolecular interactions compared to available experimental data. We show that optical spectra computed from the frequency-dependent real polarizability can better reproduce the effect of C60 aggregation on optical absorption, specifically with a generalized gradient approximation functional, and may be more suited to study effects of molecular aggregation.

  5. Magnetoband structures of AB-stacked zigzag nanographite ribbons

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.P.; Chiu, C.W.; Shyu, F.L.; Chen, R.B.; Lin, M.F

    2002-12-30

    Magnetoband structures of AB-stacked zigzag nanographite ribbons are studied by the tight-binding model. The magnetic field changes band width, energy space, and energy dispersions (the produce of Landau subbands and Landau levels). It causes many zero energy points. Such points and corresponding localized states are studied in detail. There are certain important differences between localized states and edge states. Oscillation period of Landau subbands are determined by these points. The interribbon interactions also affect magnetoband structures, such as energy dispersions, band width, oscillation period of Landau subbands, and flux dependence of Hofstadter butterflies.

  6. Band structure of semiconductors

    CERN Document Server

    Tsidilkovski, I M

    2013-01-01

    Band Structure of Semiconductors provides a review of the theoretical and experimental methods of investigating band structure and an analysis of the results of the developments in this field. The book presents the problems, methods, and applications in the study of band structure. Topics on the computational methods of band structure; band structures of important semiconducting materials; behavior of an electron in a perturbed periodic field; effective masses and g-factors for the most commonly encountered band structures; and the treatment of cyclotron resonance, Shubnikov-de Haas oscillatio

  7. Investigation on cored-eutectic structure in Ni60/WC composite coatings fabricated by wide-band laser cladding

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Qunshuang, E-mail: maqunshuang@126.com; Li, Yajiang, E-mail: yajli@sdu.edu.cn; Wang, Juan, E-mail: jwang@sdu.edu.cn; Liu, Kun, E-mail: liu_kun@163.com

    2015-10-05

    Highlights: • Perfect composite coatings were fabricated using wide-band laser cladding. • Special cored-eutectic structure was synthesized in Ni60/WC composite coatings. • Cored-eutectic consists of hard carbide compounds and fine lamellar eutectic of M{sub 23}C{sub 6} carbides and γ-Ni(Fe). • Wear resistance of coating layer was significantly improved due to precipitation of M{sub 23}C{sub 6} carbides. - Abstract: Ni60 composite coatings reinforced with WC particles were fabricated on the surface of Q550 steel using LDF4000-100 fiber laser device. The wide-band laser and circular beam laser used in laser cladding were obtained by optical lens. Microstructure, elemental distribution, phase constitution and wear properties of different composite coatings were investigated. The results showed that WC particles were partly dissolved under the effect of wide-band fiber laser irradiation. A special cored-eutectic structure was synthesized due to dissolution of WC particles. According to EDS and XRD results, the inside cores were confirmed as carbides of M{sub 23}C{sub 6} enriched in Cr, W and Fe. These complex carbides were primarily separated out in the molten metal when solidification started. Eutectic structure composed of M{sub 23}C{sub 6} carbides and γ-Ni(Fe) grew around carbides when cooling. Element content of Cr and W is lower at the bottom of cladding layer. In consequence, the eutectic structure formed in this region did not have inside carbides. The coatings made by circular laser beam were composed of dendritic matrix and interdendritic eutectic carbides, lacking of block carbides. Compared to coatings made by circular laser spot, the cored-eutectic structure formed in wide-band coatings had advantages of well-distribution and tight binding with matrix. The uniform power density and energy distribution and the weak liquid convection in molten pool lead to the unique microstructure evolution in composite coatings made by wide-band laser

  8. Model construction and superconductivity analysis of organic conductors β-(BDA-TTP)2MF6 (M = P, As, Sb and Ta) based on first-principles band calculation

    Science.gov (United States)

    Aizawa, H.; Kuroki, K.; Yasuzuka, S.; Yamada, J.

    2012-11-01

    We perform a first-principles band calculation for a group of quasi-two-dimensional organic conductors β-(BDA-TTP)2MF6 (M = P, As, Sb and Ta). The ab-initio calculation shows that the density of states is correlated with the bandwidth of the singly occupied (highest) molecular orbital, while it is not necessarily correlated with the unit-cell volume. The direction of the major axis of the cross section of the Fermi surface lies in the Γ-B-direction, which differs from that obtained by the extended Hückel calculation. Then, we construct a tight-binding model which accurately reproduces the ab-initio band structure. The obtained transfer energies give a smaller dimerization than in the extended Hückel band. As to the difference in the anisotropy of the Fermi surface, the transfer energies along the inter-stacking direction are smaller than those obtained in the extended Hückel calculation. Assuming spin-fluctuation-mediated superconductivity, we apply random phase approximation to a two-band Hubbard model. This two-band Hubbard model is composed of the tight-binding model derived from the first-principles band structure and an on-site (intra-molecule) repulsive interaction taken as a variable parameter. The obtained superconducting gap changes sign four times along the Fermi surface like in a d-wave gap, and the nodal direction is different from that obtained in the extended Hückel model. Anion dependence of Tc is qualitatively consistent with the experimental observation.

  9. Model construction and superconductivity analysis of organic conductors β-(BDA-TTP)2MF6 (M = P, As, Sb and Ta) based on first-principles band calculation

    International Nuclear Information System (INIS)

    Aizawa, H; Kuroki, K; Yasuzuka, S; Yamada, J

    2012-01-01

    We perform a first-principles band calculation for a group of quasi-two-dimensional organic conductors β-(BDA-TTP) 2 MF 6 (M = P, As, Sb and Ta). The ab-initio calculation shows that the density of states is correlated with the bandwidth of the singly occupied (highest) molecular orbital, while it is not necessarily correlated with the unit-cell volume. The direction of the major axis of the cross section of the Fermi surface lies in the Γ–B-direction, which differs from that obtained by the extended Hückel calculation. Then, we construct a tight-binding model which accurately reproduces the ab-initio band structure. The obtained transfer energies give a smaller dimerization than in the extended Hückel band. As to the difference in the anisotropy of the Fermi surface, the transfer energies along the inter-stacking direction are smaller than those obtained in the extended Hückel calculation. Assuming spin-fluctuation-mediated superconductivity, we apply random phase approximation to a two-band Hubbard model. This two-band Hubbard model is composed of the tight-binding model derived from the first-principles band structure and an on-site (intra-molecule) repulsive interaction taken as a variable parameter. The obtained superconducting gap changes sign four times along the Fermi surface like in a d-wave gap, and the nodal direction is different from that obtained in the extended Hückel model. Anion dependence of T c is qualitatively consistent with the experimental observation. (paper)

  10. Band Gap Changes Of Single Walled Carbon Nanotubes Under Uniaxial Strain

    International Nuclear Information System (INIS)

    Dereli, G.

    2010-01-01

    The study of the band gap variation with mechanical deformation is important in manipulations of Single Walled Carbon Nanotubes (SWCNT). In this study we investigated the electronic band structure and the mechanical properties of (12,0) and (13,0) SWCNTs under the effect of uniaxial strain. Electronic and mechanical properties are studied using a parallel, order N, tight-binding molecular dynamics (O(N) TBMD) simulation code designed by G. Dereli et. al. We showed the effect of uniaxial strain on the variations of band gaps and the total energy per atom of (12,0) and (13,0) SWCNTs. We calculated Young's modulus and the Poisson ratio of these SWCNTs. The research reported here was supported through the Yildiz Technical University Research Found Project No: 24-01-01-04. Simulations are performed in parallel environment at Carbon Nanotube Simulation Laboratory of Yildiz Technical University.

  11. Structural and electronic properties of thallium compounds

    International Nuclear Information System (INIS)

    Paliwal, Neetu; Srivastava, Vipul

    2016-01-01

    The tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA has been used to calculate structural and electronic properties of thallium pnictides TlX (X=Sb, Bi) at high pressure. As a function of volume, the total energy is evaluated. Apart from this, the lattice parameter (a_0), bulk modulus (B_0), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed metallic behaviour in TlSb and TlBi compounds. The values of equilibrium lattice constants and bulk modulus are agreed well with the available data.

  12. Structural and electronic properties of thallium compounds

    Energy Technology Data Exchange (ETDEWEB)

    Paliwal, Neetu, E-mail: neetumanish@gmail.com [Department of Physics, AISECT University Bhopal, 464993 (India); Srivastava, Vipul [Department of Engineering Physics, NRI Institute of Research & Technology, Raisen Road, Bhopal, 462021 (India)

    2016-05-06

    The tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA has been used to calculate structural and electronic properties of thallium pnictides TlX (X=Sb, Bi) at high pressure. As a function of volume, the total energy is evaluated. Apart from this, the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed metallic behaviour in TlSb and TlBi compounds. The values of equilibrium lattice constants and bulk modulus are agreed well with the available data.

  13. Tight-binding electrons on triangular and kagome lattices under staggered modulated magnetic fields: quantum Hall effects and Hofstadter butterflies

    International Nuclear Information System (INIS)

    Li Juan; Wang Yifei; Gong Changde

    2011-01-01

    We consider the tight-binding models of electrons on a two-dimensional triangular lattice and kagome lattice under staggered modulated magnetic fields. Such fields have two components: a uniform-flux part with strength φ, and a staggered-flux part with strength Δφ. Various properties of the Hall conductances and Hofstadter butterflies are studied. When φ is fixed, variation of Δφ leads to the quantum Hall transitions and Chern numbers of Landau subbands being redistributed between neighboring pairs. The energy spectra with nonzero Δφs have similar fractal structures but quite different energy gaps compared with the original Hofstadter butterflies of Δφ = 0. Moreover, the fan-like structure of Landau levels in the low magnetic field region is also modified appreciably by Δφ.

  14. Tight-binding electrons on triangular and kagome lattices under staggered modulated magnetic fields: quantum Hall effects and Hofstadter butterflies

    Energy Technology Data Exchange (ETDEWEB)

    Li Juan; Wang Yifei; Gong Changde, E-mail: yfwang_nju@hotmail.com [Center for Statistical and Theoretical Condensed Matter Physics, and Department of Physics, Zhejiang Normal University, Jinhua 321004 (China)

    2011-04-20

    We consider the tight-binding models of electrons on a two-dimensional triangular lattice and kagome lattice under staggered modulated magnetic fields. Such fields have two components: a uniform-flux part with strength {phi}, and a staggered-flux part with strength {Delta}{phi}. Various properties of the Hall conductances and Hofstadter butterflies are studied. When {phi} is fixed, variation of {Delta}{phi} leads to the quantum Hall transitions and Chern numbers of Landau subbands being redistributed between neighboring pairs. The energy spectra with nonzero {Delta}{phi}s have similar fractal structures but quite different energy gaps compared with the original Hofstadter butterflies of {Delta}{phi} = 0. Moreover, the fan-like structure of Landau levels in the low magnetic field region is also modified appreciably by {Delta}{phi}.

  15. Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

    Science.gov (United States)

    Nishimoto, Yoshio; Fedorov, Dmitri G.

    2018-02-01

    The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.

  16. A model for the direct-to-indirect band-gap transition in monolayer ...

    Indian Academy of Sciences (India)

    Abstract. A monolayer of MoSe2 is found to be a direct band-gap semiconductor. We show, ... In order to determine appropriate basis for the tight-binding model, the Mo and Se ..... RD thanks the Council of Scientific and Industrial Research.

  17. Interplay between magnetism and energetics in Fe-Cr alloys from a predictive noncollinear magnetic tight-binding model

    DEFF Research Database (Denmark)

    Soulairol, R.; Barreteau, Cyrille; Fu, Chu-Chun

    2016-01-01

    Magnetism is a key driving force controlling several thermodynamic and kinetic properties of Fe-Cr systems. We present a tight-binding model for Fe-Cr, where magnetism is treated beyond the usual collinear approximation. A major advantage of this model consists in a rather simple fitting procedur...

  18. Surface passivation for tight-binding calculations of covalent solids

    International Nuclear Information System (INIS)

    Bernstein, N

    2007-01-01

    Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp 3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system

  19. Lanthanide 4f-electron binding energies and the nephelauxetic effect in wide band gap compounds

    International Nuclear Information System (INIS)

    Dorenbos, Pieter

    2013-01-01

    Employing data from luminescence spectroscopy, the inter 4f-electron Coulomb repulsion energy U(6, A) in Eu 2+/3+ impurities together with the 5d-centroid energy shift ϵ c (1,3+,A) in Ce 3+ impurities in 40 different fluoride, chloride, bromide, iodide, oxide, sulfide, and nitride compounds has been determined. This work demonstrates that the chemical environment A affects the two energies in a similar fashion; a fashion that follows the anion nephelauxetic sequence F, O, Cl, Br, N, I, S, Se. One may then calculate U(6, A) from well established and accurate ϵ c (1,3+,A) values which are then used as input to the chemical shift model proposed in Dorenbos (2012) [19]. As output it provides the chemical shift of 4f-electron binding energy and therewith the 4f-electron binding energy relative to the vacuum energy. In addition this method provides a tool to routinely establish the binding energy of electrons at the top of the valence band (work function) and the bottom of the conduction band (electron affinity) throughout the entire family of inorganic compounds. How the electronic structure of the compound and lanthanide impurities therein change with type of compound and type of lanthanide is demonstrated. -- Highlights: ► A relationship between 5d centroid shift and 4f-electron Coulomb repulsion energy is established. ► Information on the absolute 4f-electron binding energy of lanthanides in 40 compounds is provided. ► A new tool to determine absolute binding energies of electrons in valence and conduction bands is demonstrated

  20. Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

    Science.gov (United States)

    Nishimoto, Yoshio

    2015-09-07

    We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

  1. Hydroxychloroquine binding to cytoplasmic domain of Band 3 in human erythrocytes: Novel mechanistic insights into drug structure, efficacy and toxicity.

    Science.gov (United States)

    Nakagawa, Mizuki; Sugawara, Kotomi; Goto, Tatsufumi; Wakui, Hideki; Nunomura, Wataru

    2016-05-13

    Hydroxychloroquine (HCQ) is a widely used drug in the treatment of autoimmune diseases, such as arthritis and systemic lupus erythematosus. It has also been prescribed for the treatment of malaria owing to its lower toxicity compared to its closely related compound chloroquine (CQ). However, the mechanisms of action of HCQ in erythrocytes (which bind preferentially this drug) have not been documented and the reasons underlying the lower side effects of HCQ compared to CQ remain unclear. Here we show that, although the activity of erythrocyte lactate dehydrogenase (LDH), but not GAPDH, was inhibited by both HCQ and CQ in vitro, LDH activity in erythrocytes incubated with 20 mM HCQ was not significantly reduced within 5 h in contrast to CQ did. Using HCQ coupled Sepharose chromatography (HCQ-Sepharose), we identified Band 3, spectrin, ankyrin, protein 4.1R and protein 4.2 as HCQ binding proteins in human erythrocyte plasma membrane. Recombinant cytoplasmic N-terminal 43 kDa domain of Band 3 bound to HCQ-Sepharose and was eluted with 40 mM (but not 20 mM) HCQ. Band 3 transport activity was reduced by only 23% in the presence of 20 mM HCQ. Taken together, these data demonstrate that HCQ binds to the cytoplasmic N-terminal domain of Band 3 in human erythrocytes but does not inhibit dramatically its transport activity. We hypothesize that the trapping of HCQ on Band 3 contributes to the lower side effects of the drug on energy production in erythrocytes. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Band structure and Fermi surface of UPd2Al3 studied by angle-resolved photoemission spectroscopy

    International Nuclear Information System (INIS)

    Fujimori, Shin-ichi; Saitoh, Yuji; Okane, Tetsuo; Yamagami, Hiroshi; Fujimori, Atsushi; Haga, Yoshinori; Yamamoto, Etsuji; Onuki, Yoshichika

    2007-01-01

    We have observed the band structure and Fermi surfaces of the heavy Fermion superconductor UPd 2 Al 3 by angle-resolved photoemission experiments in the soft X-ray region. We observed renormalized quasi-particle bands in the vicinity of the Fermi level and strongly dispersive bands on the higher binding energy side. Our observation suggests that the structure previously assigned to contributions from localized states in the U 5f spectrum has strong energy dispersions

  3. Influence of chemical disorder on the electronic level spacing distribution of the Ag{sub 5083} nanoparticle: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Medrano, L.R., E-mail: leonardoms20@gmail.com [Faculty of Physical Sciences, National University of San Marcos, P.O. Box 14-0149, Lima 14 (Peru); Landauro, C.V., E-mail: clandauros@unmsm.edu.pe [Faculty of Physical Sciences, National University of San Marcos, P.O. Box 14-0149, Lima 14 (Peru)

    2013-03-01

    In the present work we study, employing a tight-binding Hamiltonian, the influence of chemical disorder on the electronic level spacing distribution of a silver nanoparticle containing 5083 atoms (∼ 5.5 nm). This nanoparticle was obtained by molecular dynamics simulations with a tight-binding atomic potential. The results indicate that in the absence of disorder the level spacing distributions are similar to those expected for systems belonging to the Gaussian Orthogonal Ensemble. Whereas, after increasing the chemical disorder, the electronic level spacing distribution and the Σ{sub 2} statistics tend to the corresponding form for the Poisson Ensemble, i.e., the silver nanoparticle acquires an insulating character which is expected for strongly disordered systems. Hence, this kind of disorder produces the localization of the electronic states of the nanoparticle.

  4. Tight-binding molecular dynamics simulation of charge state effects in semiconductors

    CERN Document Server

    Khakimov, Z M; Sulaymonov, N T; Kiv, A E; Levin, A A

    2002-01-01

    New model of Si-H bond dissociation has been proposed and tested in the cluster Si sub 1 sub 0 H sub 1 sub 6 by the simulation approach that combines classical molecular dynamics method and the self-consistent tight-binding electronic and total energy calculation one. It is shown that the monohydride Si-H bond is unstable with respect to formation of silicon dangling bond and bend bridge Si-H-Si bond when this cluster traps the single positive charge. In this case hydrogen atom migrates rather rotating around Si-Si bond than crossing the center of this bond (the bond-centered position). The model can be useful for understanding hydrogen related phenomena at surfaces, interfaces, internal voids of various hydrogenated silicon systems: electronic devices, silicon solar cells, and nanocrystalline and porous silicon. (author)

  5. Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

    Science.gov (United States)

    Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

    2018-06-27

    We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

  6. Combinatorial computational chemistry approach of tight-binding quantum chemical molecular dynamics method to the design of the automotive catalysts

    International Nuclear Information System (INIS)

    Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    2006-01-01

    Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support

  7. Computational Design of Flat-Band Material

    Science.gov (United States)

    Hase, I.; Yanagisawa, T.; Kawashima, K.

    2018-02-01

    Quantum mechanics states that hopping integral between local orbitals makes the energy band dispersive. However, in some special cases, there are bands with no dispersion due to quantum interference. These bands are called as flat band. Many models having flat band have been proposed, and many interesting physical properties are predicted. However, no real compound having flat band has been found yet despite the 25 years of vigorous researches. We have found that some pyrochlore oxides have quasi-flat band just below the Fermi level by first principles calculation. Moreover, their valence bands are well described by a tight-binding model of pyrochlore lattice with isotropic nearest neighbor hopping integral. This model belongs to a class of Mielke model, whose ground state is known to be ferromagnetic with appropriate carrier doping and on-site repulsive Coulomb interaction. We have also performed a spin-polarized band calculation for the hole-doped system from first principles and found that the ground state is ferromagnetic for some doping region. Interestingly, these compounds do not include magnetic element, such as transition metal and rare-earth elements.

  8. An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhi [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, Xiang-Wei; Li, Shu-Shen [State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2014-03-24

    We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10{sup 5} atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose.

  9. An efficient atomistic quantum mechanical simulation on InAs band-to-band tunneling field-effect transistors

    International Nuclear Information System (INIS)

    Wang, Zhi; Jiang, Xiang-Wei; Li, Shu-Shen; Wang, Lin-Wang

    2014-01-01

    We have presented a fully atomistic quantum mechanical simulation method on band-to-band tunneling (BTBT) field-effect transistors (FETs). Our simulation approach is based on the linear combination of bulk band method with empirical pseudopotentials, which is an atomist method beyond the effective-mass approximation or k.p perturbation method, and can be used to simulate real-size devices (∼10 5 atoms) efficiently (∼5 h on a few computational cores). Using this approach, we studied the InAs dual-gate BTBT FETs. The I-V characteristics from our approach agree very well with the tight-binding non-equilibrium Green's function results, yet our method costs much less computationally. In addition, we have studied ways to increase the tunneling current and analyzed the effects of different mechanisms for that purpose

  10. Geometrical and band-structure effects on phonon-limited hole mobility in rectangular cross-sectional germanium nanowires

    International Nuclear Information System (INIS)

    Tanaka, H.; Mori, S.; Morioka, N.; Suda, J.; Kimoto, T.

    2014-01-01

    We calculated the phonon-limited hole mobility in rectangular cross-sectional [001], [110], [111], and [112]-oriented germanium nanowires, and the hole transport characteristics were investigated. A tight-binding approximation was used for holes, and phonons were described by a valence force field model. Then, scattering probability of holes by phonons was calculated taking account of hole-phonon interaction atomistically, and the linearized Boltzmann's transport equation was solved to calculate the hole mobility at low longitudinal field. The dependence of the hole mobility on nanowire geometry was analyzed in terms of the valence band structure of germanium nanowires, and it was found that the dependence was qualitatively reproduced by considering an average effective mass and the density of states of holes. The calculation revealed that [110] germanium nanowires with large height along the [001] direction show high hole mobility. Germanium nanowires with this geometry are also expected to exhibit high electron mobility in our previous work, and thus they are promising for complementary metal-oxide-semiconductor (CMOS) applications

  11. Electronic structure investigation of MoS2 and MoSe2 using angle-resolved photoemission spectroscopy and ab initio band structure studies.

    Science.gov (United States)

    Mahatha, S K; Patel, K D; Menon, Krishnakumar S R

    2012-11-28

    Angle-resolved photoemission spectroscopy (ARPES) and ab initio band structure calculations have been used to study the detailed valence band structure of molybdenite, MoS(2) and MoSe(2). The experimental band structure obtained from ARPES has been found to be in good agreement with the theoretical calculations performed using the linear augmented plane wave (LAPW) method. In going from MoS(2) to MoSe(2), the dispersion of the valence bands decreases along both k(parallel) and k(perpendicular), revealing the increased two-dimensional character which is attributed to the increasing interlayer distance or c/a ratio in these compounds. The width of the valence band and the band gap are also found to decrease, whereas the valence band maxima shift towards the higher binding energy from MoS(2) to MoSe(2).

  12. Identification of Critical Residues for the Tight Binding of Both Correct and Incorrect Nucleotides to Human DNA Polymerase λ

    Science.gov (United States)

    Brown, Jessica A.; Pack, Lindsey R.; Sherrer, Shanen M.; Kshetry, Ajay K.; Newmister, Sean A.; Fowler, Jason D.; Taylor, John-Stephen; Suo, Zucai

    2010-01-01

    DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β (Pol β). Pre-steady state kinetic studies have shown that the Pol λ•DNA complex binds both correct and incorrect nucleotides 130-fold tighter on average than the Pol β•DNA complex, although, the base substitution fidelity of both polymerases is 10−4 to 10−5. To better understand Pol λ’s tight nucleotide binding affinity, we created single- and double-substitution mutants of Pol λ to disrupt interactions between active site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding with each of the common structural moieties in the following order: triphosphate ≫ base > ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and template base led to a moderate increase in the Kd. The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template. PMID:20851705

  13. DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

    Science.gov (United States)

    Gaus, Michael; Cui, Qiang; Elstner, Marcus

    2012-04-10

    The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.

  14. Dirac Cones, Topological Edge States, and Nontrivial Flat Bands in Two-Dimensional Semiconductors with a Honeycomb Nanogeometry

    Directory of Open Access Journals (Sweden)

    E. Kalesaki

    2014-01-01

    Full Text Available We study theoretically two-dimensional single-crystalline sheets of semiconductors that form a honeycomb lattice with a period below 10 nm. These systems could combine the usual semiconductor properties with Dirac bands. Using atomistic tight-binding calculations, we show that both the atomic lattice and the overall geometry influence the band structure, revealing materials with unusual electronic properties. In rocksalt Pb chalcogenides, the expected Dirac-type features are clouded by a complex band structure. However, in the case of zinc-blende Cd-chalcogenide semiconductors, the honeycomb nanogeometry leads to rich band structures, including, in the conduction band, Dirac cones at two distinct energies and nontrivial flat bands and, in the valence band, topological edge states. These edge states are present in several electronic gaps opened in the valence band by the spin-orbit coupling and the quantum confinement in the honeycomb geometry. The lowest Dirac conduction band has S-orbital character and is equivalent to the π-π^{⋆} band of graphene but with renormalized couplings. The conduction bands higher in energy have no counterpart in graphene; they combine a Dirac cone and flat bands because of their P-orbital character. We show that the width of the Dirac bands varies between tens and hundreds of meV. These systems emerge as remarkable platforms for studying complex electronic phases starting from conventional semiconductors. Recent advancements in colloidal chemistry indicate that these materials can be synthesized from semiconductor nanocrystals.

  15. Target molecular weights for red cell band 3 stilbene and mercurial binding sites

    International Nuclear Information System (INIS)

    Verkman, A.S.; Skorecki, K.L.; Jung, C.Y.; Ausiello, D.A.

    1986-01-01

    Radiation inactivation was used to measure the target sizes for binding of disulfonic stilbene anion transport inhibitor 4,4'-dibenzamido-2,2'-disulfonic stilbene (DBDS) and mercurial water transport inhibitor p-chloromercuribenzene sulfonate (pCMBS) to human erythrocytes. The measured target size for erythrocyte ghost acetylcholinesterase was 78 +/- 3 kDa. DBDS binding to ghost membranes was measured by a fluorescence enhancement technique. Radiation (0-26 Mrad) had no effect on total membrane protein and DBDS binding affinity, whereas DBDS binding stoichiometry decreased exponentially with radiation dose, giving a target size of 59 +/- 4 kDa. H2-4,4'-diisothiocyano-2,2'-disulfonic stilbene (H2-DIDS, 5 microM) blocked greater than 95% of DBDS binding at all radiation doses. pCMBS binding was measured from the time course of tryptophan fluorescence quenching in ghosts treated with the sulfhydryl reagent N-ethylmaleimide (NEM). Radiation did not affect the kinetics of tryptophan quenching, whereas the total amplitude of the fluorescence signal inactivated with radiation with a target size of 31 +/- 6 kDa. These results support the notion that DBDS and pCMBS bind to the transmembrane domain of erythrocyte band 3 in NEM-treated ghosts and demonstrate that radiation inactivation may probe a target significantly smaller than a covalently linked protein subunit. The small target size for the band 3 stilbene binding site may correspond to the intramembrane domain of the band 3 monomer (52 kDa), which is physically distinct from the cytoplasmic domain (42 kDa)

  16. Emergent gravity in the cubic tight-binding model of Weyl semimetal in the presence of elastic deformations

    Energy Technology Data Exchange (ETDEWEB)

    Cortijo, Alberto [Instituto de Ciencia de Materiales de Madrid, CSIC, Cantoblanco, 28049 Madrid (Spain); Zubkov, M.A., E-mail: zubkov@itep.ru [ITEP, B. Cheremushkinskaya 25, Moscow, 117259 (Russian Federation); Moscow Institute of Physics and Technology, 9, Institutskii per., Dolgoprudny, Moscow Region, 141700 (Russian Federation); Far Eastern Federal University, School of Biomedicine, 690950 Vladivostok (Russian Federation); National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe highway 31, 115409 Moscow (Russian Federation)

    2016-03-15

    We consider the tight-binding model with cubic symmetry that may be relevant for the description of a certain class of Weyl semimetals. We take into account elastic deformations of the semimetal through the modification of hopping parameters. This modification results in the appearance of emergent gauge field and the coordinate dependent anisotropic Fermi velocity. The latter may be interpreted as emergent gravitational field.

  17. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    International Nuclear Information System (INIS)

    Henke, Paul S.; Mak, Chi H.

    2014-01-01

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure

  18. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    Energy Technology Data Exchange (ETDEWEB)

    Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)

    2014-08-14

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

  19. Adsorbate-induced modification of electronic band structure of epitaxial Bi(111) films

    Energy Technology Data Exchange (ETDEWEB)

    Matetskiy, A.V., E-mail: mateckij@iacp.dvo.ru [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); Bondarenko, L.V.; Tupchaya, A.Y.; Gruznev, D.V. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); Eremeev, S.V. [Institute of Strength Physics and Materials Science, 634021 Tomsk (Russian Federation); Tomsk State University, 634050 Tomsk (Russian Federation); Zotov, A.V. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok (Russian Federation); Department of Electronics, Vladivostok State University of Economics and Service, 690600 Vladivostok (Russian Federation); Saranin, A.A. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok (Russian Federation)

    2017-06-01

    Highlights: • Modification of electronic properties of ultrathin Bi films by adsorbates is demonstrated. • Due to electron doping from Cs adatoms, surface-state bands shift to higher binding energies. • As a result, only electron pockets are left in the Fermi map. • Tin acts as an acceptor dopant for Bi, shifting Fermi level upward. • As a result, only hole pockets are left in the Fermi map. - Abstract: Changes of the electronic band structure of Bi(111) films on Si(111) induced by Cs and Sn adsorption have been studied using angle-resolved photoemission spectroscopy and density functional theory calculations. It has been found that small amounts of Cs when it presents at the surface in a form of the adatom gas leads to shifting of the surface and quantum well states to the higher binding energies due to the electron donation from adsorbate to the Bi film. In contrast, adsorbed Sn dissolves into the Bi film bulk upon heating and acts as an acceptor dopant, that results in shifting of the surface and quantum well states upward to the lower binding energies. These results pave the way to manipulate with the Bi thin film electron band structure allowing to achieve a certain type of conductivity (electron or hole) with a single spin channel at the Fermi level making the adsorbate-modified Bi a reliable base for prospective spintronics applications.

  20. Tight-Binding simulations of InAs/GaAs quantum dots

    International Nuclear Information System (INIS)

    Kleinsorge, Alexander

    2008-01-01

    For several years, the technological potential of self-organized grown quantum dots (QD) has been known. Their usage as an effective light source or memory requires the precise prediction of their electronic properties. Hence, this report will study InAs quantum dots at GaAs substrate. After relaxing the atomic positions with a many body potential of Abell-Tersoff type, I calculated the electronic structure using the Tight-Binding method which is reasonable for large systems. During the investigation of wavefunctions depend on the shape, size and temperature, the impact of strain showed up as the main reason for the p-splitting. Typically flat QDs (relative to lateral dimensions) are grown, therefore the energy of bound states depends mostly on their height. The crystal's orientation had a strong impact on the wavefunctions. Moreover, the understanding of STS experiments, which inspected the connection between shape and wavefunction, is better now. Because of the possible simultaneous occupation of semiconductor quantum dots with an electron and a hole, there is a dipole moment of the exciton (due to their different behaviour inside the QD). This is a further experimental access to inner details of the QD. I ascertained the interplay of composition profile and dipole moment. The force caused by additional potentials (piezoelectricity, outer homogeneous and inhomogeneous electrical fields) was also an subject of my inquiries. To conclude, I executed kMC simulations, to better apprehend the annealing experiments. I was able to explain the narrowing of the PL peak width better. Furthermore I showed a ramification of the strain field to the diffusion development (and the following electronic properties). (orig.)

  1. The adsorption effect of C6H5 on density of states for double wall carbon nanotubes by tight binding model

    International Nuclear Information System (INIS)

    Fathalian, A.

    2012-01-01

    A theoretical approach based on a tight-binding model is developed to study the effects of the adsorption of finite concentrations of C 6 H 5 gas molecules on double-walled carbon nanotube (DWCNT) electronic properties. To obtain proper hopping integrals and random on-site energies for the case of one molecule adsorption, the local density of states for various hopping integrals and random on-site energies are calculated. Since C 6 H 5 molecule is a donor with respect to the carbon nanotubes and their states should appear near the conduction band of the system, effects of various hopping integral deviations and on-site energies for one molecule adsorption are considered to find proper hopping and on-site energies consistent with expected n-type semiconductor. We found that adsorption of C 6 H 5 gas molecules could lead to a (8.0)-(20.0) DWCNT n-type semiconductor. The width of impurity adsorbed gas states in the density of states could be controlled by adsorbed gas concentration.

  2. Human zonulin, a potential modulator of intestinal tight junctions.

    Science.gov (United States)

    Wang, W; Uzzau, S; Goldblum, S E; Fasano, A

    2000-12-01

    Intercellular tight junctions are dynamic structures involved in vectorial transport of water and electrolytes across the intestinal epithelium. Zonula occludens toxin derived from Vibrio cholerae interacts with a specific intestinal epithelial surface receptor, with subsequent activation of a complex intracellular cascade of events that regulate tight junction permeability. We postulated that this toxin may mimic the effect of a functionally and immunologically related endogenous modulator of intestinal tight junctions. Affinity-purified anti-zonula occludens toxin antibodies and the Ussing chamber assay were used to screen for one or more mammalian zonula occludens toxin analogues in both fetal and adult human intestine. A novel protein, zonulin, was identified that induces tight junction disassembly in non-human primate intestinal epithelia mounted in Ussing chambers. Comparison of amino acids in the active zonula occludens toxin fragment and zonulin permitted the identification of the putative receptor binding domain within the N-terminal region of the two proteins. Zonulin likely plays a pivotal role in tight junction regulation during developmental, physiological, and pathological processes, including tissue morphogenesis, movement of fluid, macromolecules and leukocytes between the intestinal lumen and the interstitium, and inflammatory/autoimmune disorders.

  3. Structural insights into human peroxisome proliferator activated receptor delta (PPAR-delta selective ligand binding.

    Directory of Open Access Journals (Sweden)

    Fernanda A H Batista

    Full Text Available Peroxisome proliferator activated receptors (PPARs δ, α and γ are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPARδ more than 300-fold more tightly than PPARα or PPARγ but the structural basis of PPARδ:GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPARδ:GW0742 complex. Comparisons of the PPARδ:GW0742 complex with published structures of PPARs in complex with α and γ selective agonists and pan agonists suggests that two residues (Val312 and Ile328 in the buried hormone binding pocket play special roles in PPARδ selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPARα and γ ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPARδ ligand design.

  4. Leak tight sealants and joint details for concrete structure in RAPP

    International Nuclear Information System (INIS)

    Singha Roy, P.K.; Baste, M.S.

    1975-01-01

    Leak tightness may pertain to either air or water and in extreme cases each will require separate consideration based on general basic requirements. Leak-tight sealants against air pressure are required in the construction joints and around penetrations in the concrete containment structures. The containment structures should be able to withstand the maximum anticipated design pressure during the incident of a MCA with only minimal leakage (0.1% of bldg. volume per day in RAPP) which is mostly through these joints. Apart from proper joint design and preparation the sealant itself must have superb adhesion to the concrete surface and integrify throughout its service life to prevent any rupture or micro-cracks at any section of the joint. Leak tightness pertains to water tightness as well. A critical water-tight joint at the bottom dome of the prestressed concrete dousing tank at its junction with the 36 inches dia dousing water pipes constructed in RAPP-2, which should be able to withstand the water pressure, continuous submergence in the water of the tank and the longitudinal and lateral movement of the water pipes during opening and closure of the dousing valves, has been made and hydrostatically tested when not even the slight sweating was found. The construction and materials of the above joints and the sealant along with the properties and performance observed during testing/use are described. As the sealant used is an imported poly-sulphide caulking compound suggestions have also been made, which may be kept in mind while developing an Indian substitute. (author)

  5. Nature of the band tails in one-dimensional disordered systems

    International Nuclear Information System (INIS)

    Brezini, A.; Sebbani, M.; Benkhaled, N.; Depollier, C.; Kergomard, J.

    1995-12-01

    A theoretical model for the density of states based on a tight-binding scheme for one-dimensional disordered systems is investigated within a self-consistent approach in terms of a probabilistic procedure. In particular an exact analytical expression is worked out for the density of states for the case of a Cauchy distribution for the site energies in the region of localized states. A particular attention is paid to the energies lying in the band tails. It is mainly shown that the band tails are sensitive to the typical nature of the disorder. (author). 35 refs, 1 fig

  6. Investigation of gas molecules adsorption on carbon nano tubes electric properties in tight binding model

    International Nuclear Information System (INIS)

    Moradian, R.; Mohammadi, Y.

    2007-01-01

    Based on tight binding model we investigated effects of bi-atomic molecules gas(in the general form denoted by X 2 )on single-walled carbon nano tubes electronic properties. We found for some specified values of hopping integrals and random on-site energies, adsorbed molecules bound states located inside of the (10,0) single-walled carbon nano tubes energy gap, where it is similar to the reported experimental results for O 2 adsorption while for other values there is no bound states inside of energy gap. This is similar to the N 2 adsorption on semiconductor single-walled carbon nano tubes.

  7. Valence band states in Si-based p-type delta-doped field effect transistors

    International Nuclear Information System (INIS)

    Martinez-Orozco, J C; Vlaev, Stoyan J

    2009-01-01

    We present tight-binding calculations of the hole level structure of δ-doped Field Effect Transistor in a Si matrix within the first neighbors sp 3 s* semi-empirical tight-binding model including spin. We employ analytical expressions for Schottky barrier potential and the p-type δ-doped well based on a Thomas-Fermi approximation, we consider these potentials as external ones, so in the computations they are added to the diagonal terms of the tight-binding Hamiltonian, by this way we have the possibility to study the energy levels behavior as we vary the backbone parameters in the system: the two-dimensional impurity density (p 2d ) of the p-type δ-doped well and the contact voltage (V c ). The aim of this calculation is to demonstrate that the tight-binding approximation is suitable for device characterization that permits us to propose optimal values for the input parameters involved in the device design.

  8. Valence band states in Si-based p-type delta-doped field effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Orozco, J C; Vlaev, Stoyan J, E-mail: jcmover@correo.unam.m [Unidad Academica de Fisica, Universidad Autonoma de Zacatecas, Calzada Solidaridad esquina con Paseo la Bufa S/N, C.P. 98060, Zacatecas, Zac. (Mexico)

    2009-05-01

    We present tight-binding calculations of the hole level structure of delta-doped Field Effect Transistor in a Si matrix within the first neighbors sp{sup 3}s* semi-empirical tight-binding model including spin. We employ analytical expressions for Schottky barrier potential and the p-type delta-doped well based on a Thomas-Fermi approximation, we consider these potentials as external ones, so in the computations they are added to the diagonal terms of the tight-binding Hamiltonian, by this way we have the possibility to study the energy levels behavior as we vary the backbone parameters in the system: the two-dimensional impurity density (p{sub 2d}) of the p-type delta-doped well and the contact voltage (V{sub c}). The aim of this calculation is to demonstrate that the tight-binding approximation is suitable for device characterization that permits us to propose optimal values for the input parameters involved in the device design.

  9. Changes of electronic structure of SnTe due to high concentration of Sn vacancies

    International Nuclear Information System (INIS)

    Masek, J.; Nuzhnyj, D.N.

    1997-01-01

    Non-stoichiometric Sn 1-y Te is a strongly degenerated n-type semiconductor. This is important for understanding unusual features of magnetic behaviour of Sn 1-x Gd x Te where the relative positions of the Fermi energy and the atomic d-level of Gd govern the exchange coupling.The influence of the Sn vacancies on the band structure cannot be neglect if their concentration reaches a few atomic percent. We address this problem by using a tight-binding coherent potential approach and show that although the character of the bands remains unchanged, they are modified so that ε d can come out above the heavy-hole band. (author)

  10. DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

    Science.gov (United States)

    Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

    2013-09-10

    A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

  11. Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

    International Nuclear Information System (INIS)

    Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

    2005-01-01

    The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed

  12. Physics Colloquium - Tight-binding in a new light: Photons in optical lattices

    CERN Multimedia

    Ecole de Physique - Université de Genève

    2011-01-01

    Geneva University Physics Department 24, Quai Ernest Ansermet CH-1211 Geneva 4   Lundi 21 mars 2011, 17h00 Ecole de Physique, Auditoire Stueckelberg Tight-binding in a new light: Photons in optical lattices Dr. Niels Madsen Department of Physics, Swansea University, Singleton Park, Swansea, United Kingdom   Antihydrogen, the bound state of an antiproton and a positron, has been produced at low energies at CERN (the European Organization for Nuclear Research) since 2002. Antihydrogen is of interest for use in a precision test of nature's fundamental symmetries. The charge conjugation/parity/time reversal (CPT) theorem, a crucial part of the foundation of the standard model of elementary particles and interactions, demands that hydrogen and antihydrogen have the same spectrum. Given the current experimental precision of measurements on the hydrogen atom, subjecting antihydrogen to rigorous spectroscopic examination would constitute a compelling, model-independent test of CPT. Antihydrogen co...

  13. Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy

    International Nuclear Information System (INIS)

    Gelzinis, Andrius; Valkunas, Leonas; Abramavicius, Darius; Fuller, Franklin D; Ogilvie, Jennifer P; Mukamel, Shaul

    2013-01-01

    We propose an optimized tight-binding electron–hole model of the photosystem II (PSII) reaction center (RC). Our model incorporates two charge separation pathways and spatial correlations of both static disorder and fast fluctuations of energy levels. It captures the main experimental features observed in time-resolved two-dimensional (2D) optical spectra at 77 K: peak pattern, lineshapes and time traces. Analysis of 2D spectra kinetics reveals that specific regions of the 2D spectra of the PSII RC are sensitive to the charge transfer states. We find that the energy disorder of two peripheral chlorophylls is four times larger than the other RC pigments. (paper)

  14. Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy

    Science.gov (United States)

    Gelzinis, Andrius; Valkunas, Leonas; Fuller, Franklin D.; Ogilvie, Jennifer P.; Mukamel, Shaul; Abramavicius, Darius

    2013-07-01

    We propose an optimized tight-binding electron-hole model of the photosystem II (PSII) reaction center (RC). Our model incorporates two charge separation pathways and spatial correlations of both static disorder and fast fluctuations of energy levels. It captures the main experimental features observed in time-resolved two-dimensional (2D) optical spectra at 77 K: peak pattern, lineshapes and time traces. Analysis of 2D spectra kinetics reveals that specific regions of the 2D spectra of the PSII RC are sensitive to the charge transfer states. We find that the energy disorder of two peripheral chlorophylls is four times larger than the other RC pigments.

  15. Band 3 in aging and neurological disease.

    Science.gov (United States)

    Kay, M M

    1991-01-01

    Senescent cell antigen appears on old cells and marks them for death by initiating the binding of IgG autoantibody and subsequent removal by phagocytes in mammals and other vertebrates. We have created a synthetic aging antigen that blocks binding of IgG to senescent cells in vitro. Synthetic senescent cell antigen might be effective in preventing cellular destruction in vivo in certain diseases, and can be used to manipulate cellular life span in situ. Senescent cell antigen is generated by the modification of an important structural and transport membrane molecule, protein band 3. Band 3 is present in cellular, nuclear, Golgi, and mitochondrial membranes as well as in cell membranes. Band 3 proteins in nucleated cells participate in cell surface patching and capping. Band 3 maintains acid-base balance by mediating the exchange of anions (e.g., chloride, bicarbonate), and is the binding site for glycolytic enzymes. It is responsible for CO2 exchange in all tissues and organs. Thus, it is the most heavily used anion transport system in the body. Band 3 is a major transmembrane structural protein which attaches the plasma membrane to the internal cell cytoskeleton by binding to band 2.1 (ankyrin). Oxidation generates senescent cell antigen in situ. Band 3 is present in the central nervous system, and differences have been described in band 3 between young and aging brain tissue. One autosomal recessive neurological disease, choreoacanthocytosis, is associated with band 3 abnormalities. The 150 residues of the carboxyl terminus segment of band 3 appear to be altered. In brains from Alzheimer's disease patients, antibodies to aged band 3 label the amyloid core of classical plaques and the microglial cells located in the middle of the plaque in tissue sections, and an abnormal band 3 in immunoblots. Band 3 protein(s) in mammalian brain performs the same functions as that of erythroid band 3. These functions is anion transport, ankyrin binding, and generation of

  16. Electronic structure and phase equilibria in ternary substitutional alloys

    International Nuclear Information System (INIS)

    Traiber, A.J.S.; Allen, S.M.; Waterstrat, R.M.

    1996-01-01

    A reliable, consistent scheme to study phase equilibria in ternary substitutional alloys based on the tight-binding approximation is presented. With electronic parameters from linear muffin-tin orbital calculations, the computed density of states and band structures compare well with those from more accurate abinitio calculations. Disordered alloys are studied within the tight-binding coherent-potential approximation extended to alloys; energetics of ordered systems are obtained through effective pair interactions computed with the general perturbation method; and partially ordered alloys are studied with a novel simplification of the molecular coherent-potential approximation combined with the general perturbation method. The formalism is applied to bcc-based Zr-Ru-Pd alloys which are promising candidates for medical implant devices. Using energetics obtained from the above scheme, we apply the cluster- variation method to study phase equilibria for particular pseudo- binary alloys and show that results are consistent with observed behavior of electronic specific heat coefficient with composition for Zr 0.5 (Ru, Pd) 0.5

  17. Structure of an E. coli integral membrane sulfurtransferase and its structural transition upon SCN− binding defined by EPR-based hybrid method

    Science.gov (United States)

    Ling, Shenglong; Wang, Wei; Yu, Lu; Peng, Junhui; Cai, Xiaoying; Xiong, Ying; Hayati, Zahra; Zhang, Longhua; Zhang, Zhiyong; Song, Likai; Tian, Changlin

    2016-01-01

    Electron paramagnetic resonance (EPR)-based hybrid experimental and computational approaches were applied to determine the structure of a full-length E. coli integral membrane sulfurtransferase, dimeric YgaP, and its structural and dynamic changes upon ligand binding. The solution NMR structures of the YgaP transmembrane domain (TMD) and cytosolic catalytic rhodanese domain were reported recently, but the tertiary fold of full-length YgaP was not yet available. Here, systematic site-specific EPR analysis defined a helix-loop-helix secondary structure of the YagP-TMD monomers using mobility, accessibility and membrane immersion measurements. The tertiary folds of dimeric YgaP-TMD and full-length YgaP in detergent micelles were determined through inter- and intra-monomer distance mapping and rigid-body computation. Further EPR analysis demonstrated the tight packing of the two YgaP second transmembrane helices upon binding of the catalytic product SCN−, which provides insight into the thiocyanate exportation mechanism of YgaP in the E. coli membrane. PMID:26817826

  18. Hydrostatic pressure and conduction band non-parabolicity effects on the impurity binding energy in a spherical quantum dot

    International Nuclear Information System (INIS)

    Sivakami, A.; Mahendran, M.

    2010-01-01

    The binding energy of a shallow hydrogenic impurity in a spherical quantum dot under hydrostatic pressure with square well potential is calculated using a variational approach within the effective mass approximation. The effect of conduction band non-parabolicity on these energies is also estimated. The binding energy is computed for GaAs spherical quantum dot as a function of dot size, hydrostatic pressure both in the presence and absence of the band non-parabolicity effect. Our results show that (i) the hydrostatic pressure increases the impurity binding energy when dot radius increases for a given pressure, (ii) the hydrostatic pressure with the band non-parabolicity effect effectively increases the binding energy such that the variation is large for smaller dots and (iii) the maximum contribution by the non-parabolicity effect is about 15% for narrow dots. Our results are in good agreement with Perez-Merchancano et al. [J. Phys. Condens. Matter 19 (2007) 026225] who have not considered the conduction band non-parabolicity effect.

  19. Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

    International Nuclear Information System (INIS)

    Le Trong, Isolde; Chu, Vano; Xing, Yi; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

    2013-01-01

    The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex

  20. Quasiparticle band gap of organic-inorganic hybrid perovskites: Crystal structure, spin-orbit coupling, and self-energy effects

    Science.gov (United States)

    Gao, Weiwei; Gao, Xiang; Abtew, Tesfaye A.; Sun, Yi-Yang; Zhang, Shengbai; Zhang, Peihong

    2016-02-01

    The quasiparticle band gap is one of the most important materials properties for photovoltaic applications. Often the band gap of a photovoltaic material is determined (and can be controlled) by various factors, complicating predictive materials optimization. An in-depth understanding of how these factors affect the size of the gap will provide valuable guidance for new materials discovery. Here we report a comprehensive investigation on the band gap formation mechanism in organic-inorganic hybrid perovskites by decoupling various contributing factors which ultimately determine their electronic structure and quasiparticle band gap. Major factors, namely, quasiparticle self-energy, spin-orbit coupling, and structural distortions due to the presence of organic molecules, and their influences on the quasiparticle band structure of organic-inorganic hybrid perovskites are illustrated. We find that although methylammonium cations do not contribute directly to the electronic states near band edges, they play an important role in defining the band gap by introducing structural distortions and controlling the overall lattice constants. The spin-orbit coupling effects drastically reduce the electron and hole effective masses in these systems, which is beneficial for high carrier mobilities and small exciton binding energies.

  1. Theoretical prediction of low-density hexagonal ZnO hollow structures

    Energy Technology Data Exchange (ETDEWEB)

    Tuoc, Vu Ngoc, E-mail: tuoc.vungoc@hust.edu.vn [Institute of Engineering Physics, Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Huan, Tran Doan [Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136 (United States); Thao, Nguyen Thi [Institute of Engineering Physics, Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Hong Duc University, 307 Le Lai, Thanh Hoa City (Viet Nam); Tuan, Le Manh [Hong Duc University, 307 Le Lai, Thanh Hoa City (Viet Nam)

    2016-10-14

    Along with wurtzite and zinc blende, zinc oxide (ZnO) has been found in a large number of polymorphs with substantially different properties and, hence, applications. Therefore, predicting and synthesizing new classes of ZnO polymorphs are of great significance and have been gaining considerable interest. Herein, we perform a density functional theory based tight-binding study, predicting several new series of ZnO hollow structures using the bottom-up approach. The geometry of the building blocks allows for obtaining a variety of hexagonal, low-density nanoporous, and flexible ZnO hollow structures. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with bulk ZnO. The electronic band structures of the ZnO hollow structures are finally examined in detail.

  2. Dirac cones in isogonal hexagonal metallic structures

    Science.gov (United States)

    Wang, Kang

    2018-03-01

    A honeycomb hexagonal metallic lattice is equivalent to a triangular atomic one and cannot create Dirac cones in its electromagnetic wave spectrum. We study in this work the low-frequency electromagnetic band structures in isogonal hexagonal metallic lattices that are directly related to the honeycomb one and show that such structures can create Dirac cones. The band formation can be described by a tight-binding model that allows investigating, in terms of correlations between local resonance modes, the condition for the Dirac cones and the consequence of the third structure tile sustaining an extra resonance mode in the unit cell that induces band shifts and thus nonlinear deformation of the Dirac cones following the wave vectors departing from the Dirac points. We show further that, under structure deformation, the deformations of the Dirac cones result from two different correlation mechanisms, both reinforced by the lattice's metallic nature, which directly affects the resonance mode correlations. The isogonal structures provide new degrees of freedom for tuning the Dirac cones, allowing adjustment of the cone shape by modulating the structure tiles at the local scale without modifying the lattice periodicity and symmetry.

  3. Finite temperature magnon spectra in yttrium iron garnet from a mean field approach in a tight-binding model

    Science.gov (United States)

    Shen, Ka

    2018-04-01

    We study magnon spectra at finite temperature in yttrium iron garnet using a tight-binding model with nearest-neighbor exchange interaction. The spin reduction due to thermal magnon excitation is taken into account via the mean field approximation to the local spin and is found to be different at two sets of iron atoms. The resulting temperature dependence of the spin wave gap shows good agreement with experiment. We find that only two magnon modes are relevant to the ferromagnetic resonance.

  4. Structural and Thermodynamic Insights into Chitooligosaccharide Binding to Human Cartilage Chitinase 3-like Protein 2 (CHI3L2 or YKL-39)*

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C.; Suginta, Wipa

    2015-01-01

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (−3)(−2)(−1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. PMID:25477513

  5. Determinants for Tight and Selective Binding of a Medicinal Dicarbene Gold(I) Complex to a Telomeric DNA G-Quadruplex: a Joint ESI MS and XRD Investigation.

    Science.gov (United States)

    Bazzicalupi, Carla; Ferraroni, Marta; Papi, Francesco; Massai, Lara; Bertrand, Benoît; Messori, Luigi; Gratteri, Paola; Casini, Angela

    2016-03-18

    The dicarbene gold(I) complex [Au(9-methylcaffein-8-ylidene)2 ]BF4 is an exceptional organometallic compound of profound interest as a prospective anticancer agent. This gold(I) complex was previously reported to be highly cytotoxic toward various cancer cell lines in vitro and behaves as a selective G-quadruplex stabilizer. Interactions of the gold complex with various telomeric DNA models have been analyzed by a combined ESI MS and X-ray diffraction (XRD) approach. ESI MS measurements confirmed formation of stable adducts between the intact gold(I) complex and Tel 23 DNA sequence. The crystal structure of the adduct formed between [Au(9-methylcaffein-8-ylidene)2 ](+) and Tel 23 DNA G-quadruplex was solved. Tel 23 maintains a characteristic propeller conformation while binding three gold(I) dicarbene moieties at two distinct sites. Stacking interactions appear to drive noncovalent binding of the gold(I) complex. The structural basis for tight gold(I) complex/G-quadruplex recognition and its selectivity are described. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Electronic structure and exchange interactions in diluted semimagnetic semiconductors (Zn,Co)Se and (Zn,Mn)Se

    Science.gov (United States)

    Mašek, J.

    1991-05-01

    A comparative study of the electronic structure of (Zn,Co)Se and (Zn,Mn)Se is done by using a tight-binding version of the coherent potential approximation. The densities of states, relevant for a photoemission experiment, are calculated for a magnetically disordered phase. The exchange constant Jpd is obtained from the splitting of the valence band top in the ferromagnetic phase of the mixed crystal; Jdd is estimated from the energy of a spin reversal. We explain the large exchange constant in the Co-based systems as a result of efficient hybridization of the d-states with the valence band.

  7. The electronic band structures of InNxAs1-x, InNxSb1-x and InAsxSb1-x alloys

    International Nuclear Information System (INIS)

    Mohammad, Rezek; Katircioglu, Senay

    2009-01-01

    The band gap bowings of InN x As 1-x , InN x Sb 1-x , and InAs x Sb 1-x alloys defined by the optimized lattice constants are investigated using empirical tight binding (ETB) method. The present ETB energy parameters which take the nearest neighbor interactions into account with sp 3 d 2 basis are determined to be sufficient to provide a typical feature for the band gap bowings of the alloys. The band gap bowing parameter is found to be relatively large in both InN x As 1-x and InN x Sb 1-x compared to InAs x Sb 1-x alloys. Moreover, the variation of the fundamental band gaps of InN x Sb 1-x alloys is sharper than that of InN x As 1-x alloys for small concentrations of N. Besides, a small amount of nitrogen is determined to be more effective in InN x Sb 1-x than in InN x As 1-x alloys to decrease the corresponding effective masses of the electrons around Γ points

  8. Development of tight-binding, chemical-reaction-dynamics simulator for combinatorial computational chemistry

    International Nuclear Information System (INIS)

    Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira

    2004-01-01

    Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated

  9. Complex band structure and electronic transmission eigenchannels

    DEFF Research Database (Denmark)

    Jensen, Anders; Strange, Mikkel; Smidstrup, Soren

    2017-01-01

    and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two...

  10. Tailoring the electronic structure of graphene for catalytic and nanoelectronic applications

    DEFF Research Database (Denmark)

    Vallejo, Federico Calle; García Lastra, Juan Maria

    2011-01-01

    We explore possible routes to tailor the catalytic and electronic properties of graphitic materials through doping. The investigation is carried out by theoretical Density Functional Theory (DFT) and tight-binding calculations. We show that Feporphyrin- like sites inserted in graphitic sheets......, created after doping are active towards the Oxygen Reduction reaction (ORR). On the other hand, we also show that it is possible to tune the opening of a gap in the band structure of graphene by changing the adsorption periodicity of molecules on its surface....

  11. Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance

    International Nuclear Information System (INIS)

    Sattonnay, G; Tétot, R

    2014-01-01

    Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd 2 Ti 2 O 7 and Gd 2 Zr 2 O 7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd 2 Ti 2 O 7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd 2 Zr 2 O 7 . Therefore, the defect stability in A 2 B 2 O 7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd 2 Ti 2 O 7 amorphization induced by irradiation. (paper)

  12. Contribution to the study of electronic structure of crystalline semiconductors (Si, Ge, GaAs, Gap, ZnTe, ZnSe

    Directory of Open Access Journals (Sweden)

    Bouhafs B.

    2012-06-01

    Full Text Available The band structure of semiconductors was described by several theorists since the Fifties. The main objective of the present paper is to do a comparative study between various families of semi-conductors IV (Si,Ge, III-V (GaAs, GaP and II-VI (ZnSe, ZnTe with both methods; tight Binding1 method and pseudo potential method2. This work enables us to understand as well as the mechanism of conduction process in these semiconductors and powers and limits of the above methods. The obtained results allow to conclude that both methods are in a good agreement to describe the morphology of band structures of the cited semiconductors. This encourages us to study in the future the electronic behaviour through the structure of bands for more complex systems such as the heterostructures.

  13. Structural, electronic and mechanical properties of inner surface modified imogolite nanotubes

    Directory of Open Access Journals (Sweden)

    Maurício Chagas Da Silva

    2015-03-01

    Full Text Available The electronic, structural and mechanical properties of the modified imogolites have been investigated using self consistent charge-density functional-tight binding method with a posteriori treatment of the dispersion interaction (SCC-DFTB-D. The zigzag (12,0 imogolite has been used as the initial structure for the calculations. The functionalization of the interior (12,0 imogolite nanotubes by organosilanes and by heat treatment leading to the dehydroxylation of the silanols were investigated. The reaction of the silanols with the trimethylmethoxysilanes is favored and the arrangement of the different substitutions that leads to the most symmetrical structures are preferred. The Young moduli and band gaps are slightly decreased. However, the dehydroxylation of the silanol groups in the inner surface of the imogolite leads to the increase of the Young moduli and a drastic decrease of the band gap of about 4.4 eV. It has been shown that the degree of the dehydroxylation can be controlled by heat treatment and tune the band gap, eventually, leading to a semiconductor material with well defined nanotube structure.

  14. Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

    First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

  15. Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

    Science.gov (United States)

    Kroonblawd, Matthew; Goldman, Nir

    2017-06-01

    First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

  16. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39).

    Science.gov (United States)

    Ranok, Araya; Wongsantichon, Jantana; Robinson, Robert C; Suginta, Wipa

    2015-01-30

    Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Predicted electronic and structural properties of B{sub x}In{sub 1-x}As

    Energy Technology Data Exchange (ETDEWEB)

    Tayebi, N. [Laboratory of Applied Materials, University of Sidi Bel Abbes, 31 rue de Madagascar, Sidi Bel Abbes (Algeria); Benkabou, K., E-mail: kbenkabou@yahoo.fr [Laboratory of Applied Materials, University of Sidi Bel Abbes, 31 rue de Madagascar, Sidi Bel Abbes (Algeria); Aoumeur-Benkabou, F.Z. [Laboratory of Applied Materials, University of Sidi Bel Abbes, 31 rue de Madagascar, Sidi Bel Abbes (Algeria)

    2012-07-15

    Structural and electronic properties of the B{sub x}In{sub 1-x}As ternary alloy are studied using the tight binding method. The optical band gap bowing is calculated for the first time in the full range of Boron composition x. It is found to be strong. A small deviation from virtual crystal approximation is found for the bond length. New results on elastic constants are reported. The obtained results are in good agreement with the available data in the literature.

  18. Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

    Science.gov (United States)

    Gruden, Maja; Andjeklović, Ljubica; Jissy, Akkarapattiakal Kuriappan; Stepanović, Stepan; Zlatar, Matija; Cui, Qiang; Elstner, Marcus

    2017-09-30

    Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  19. Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

    Science.gov (United States)

    Kowalczyk, Tim; Le, Khoa; Irle, Stephan

    2016-01-12

    We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

  20. Decorin core protein (decoron) shape complements collagen fibril surface structure and mediates its binding.

    Science.gov (United States)

    Orgel, Joseph P R O; Eid, Aya; Antipova, Olga; Bella, Jordi; Scott, John E

    2009-09-15

    Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e(1) bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e(1) bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

  1. Decorin core protein (decoron shape complements collagen fibril surface structure and mediates its binding.

    Directory of Open Access Journals (Sweden)

    Joseph P R O Orgel

    2009-09-01

    Full Text Available Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM. With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein and binding sites in the d and e(1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e(1 bands. This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

  2. Rietveld analysis and electronic bands structure on Tc superconductors systems

    International Nuclear Information System (INIS)

    Aldea, N.; Tiusan, C. V.; Sandu, V.

    1999-01-01

    A procedure for simultaneous refinement of structural and micro-structural disorder parameters for polycrystalline YBa 2 Cu 3 O 7-x system is proposed. It is based on Rietveld method combined with Fourier analysis for broadened peaks Another purpose of this paper consists in electronic structure determination studied by using the self-consistent Tight Binding Linear Muffin-Tin Orbital Atomic Spheres Approximation TB-LMTO-ASA methods. The Rietveld method uses an analytical function that describes the profiles, usually pseudo-Voigt (pV) or Pearson VII (PVII). The parameters of the analytical profiles describe its amplitude, position and peak shape. The full width at half maximum (FWHM) is supposed to vary with the diffraction angle in agreement with the Caglioti, Paoletti and Ricci's relationship. The best structural parameters are determined in the least squares sense by the minimisation a classical residual using the Marquardt method. In this case, the peak profiles were modelled by the pseudo-Voigt function corrected by the instrumental asymmetry. The physical information obtained are: scale factor, lattice parameters, atomic position and displacements, atomic occupation numbers, temperature factor (isotropy or anisotropy), preferred orientation parameter, crystalline size and micro-strain along different crystallographic directions, distributions of crystallite size and micro-strain functions. This procedure was implemented on computer code and it has a friendly graphical interface based on pull down menus technique. From the experimental point of view the X-ray diffraction data were collected using a horizontal powder diffractometer in the Bragg-Brentano (BB) geometry with a Ni filtered CuKα, λ = 1.54178 A, at room temperature using a DRON 2 set-up. The diffraction profiles were measured with a proportional gas detector, a single channel pulse-height discrimination and a standard associated counting circuit. The electronic band calculations are based on the TB

  3. Leak-tightness characteristics concerning the containment structures of the HTTR

    International Nuclear Information System (INIS)

    Sakaba, Nariaki; Iigaki, Kazuhiko; Kondo, Masaaki; Emori, Koichi

    2004-01-01

    The containment structures of the HTTR consist of the reactor containment vessel, the service area, and the emergency air purification system, which minimise the release of fission products in postulated accidents, which lead to fission product release from the reactor facilities. The reactor containment vessel is designed to withstand the temperature and pressure transients and to be leak-tight in the case of a rupture of the primary concentric hot-gas duct, etc. The pressure inside the service area is maintained at a negative pressure by the emergency air purification system. The emergency air purification system will also remove airborne radioactivity and will maintain a correct pressure in the service area. The leak-tightness characteristics of the containment structures are described in this paper. The measured leakage rates of the reactor containment vessel were enough less than the specified leakage limit of 0.1%/d confirmed during the commissioning tests and annual inspections. The service area was kept in a way that the design pressure becomes well below its allowable limitation by the emergency air purification system, which filters efficiency of particle removal and iodine removal well over the limited values. The obtained data demonstrate that the reactor containment structures were fabricated to minimise the release of fission products in the postulated accidents with fission product release from the reactor facilities

  4. Micro-structure and Air-tightness of Squeeze Casting Motor housing for New Energy Vehicle

    Science.gov (United States)

    Jiang, Y. F.; Kang, Z. Q.; Jiang, W. F.; Wang, K. W.; Sha, D. L.; Li, M. L.; Sun, J.

    2018-05-01

    In order to improve the performance of automobile parts, the influence of squeeze casting process parameters on casting defects, material structure and air-tightness of aluminum alloy motor housing for new energy vehicle was studied. The results show that the density of the castings increases with the increase in pressure and mold temperature. With increase in pouring temperature, it increases first and then decreases. Pressure has the greatest influence on the density of the castings. Under a certain pressure, with moderate increase in casting temperature and mold temperature, the grain growth begins to increase; the dendrites become less, the new α - Al grains are spherical and granular, the micro-structure is uniform. Also, with increase in pressure, this effect is more pronounced, the air-tightness of castings improve. In conclusion, when the pressure is 110MPa, pouring temperature is 680° C, mold temperature is 280° C, pressure holding for 30s, and punch speed of 0.1m/s, there is no clear shrinkage in the casting, the structure is uniform, the qualified rate of air-tightness of production reaches 86%, and the performance is excellent.

  5. Band structures in fractal grading porous phononic crystals

    Science.gov (United States)

    Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

    2018-05-01

    In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

  6. Maximally localized Wannier functions in LaMnO3 within PBE + U, hybrid functionals and partially self-consistent GW: an efficient route to construct ab initio tight-binding parameters for eg perovskites.

    Science.gov (United States)

    Franchini, C; Kováčik, R; Marsman, M; Murthy, S Sathyanarayana; He, J; Ederer, C; Kresse, G

    2012-06-13

    Using the newly developed VASP2WANNIER90 interface we have constructed maximally localized Wannier functions (MLWFs) for the e(g) states of the prototypical Jahn-Teller magnetic perovskite LaMnO(3) at different levels of approximation for the exchange-correlation kernel. These include conventional density functional theory (DFT) with and without the additional on-site Hubbard U term, hybrid DFT and partially self-consistent GW. By suitably mapping the MLWFs onto an effective e(g) tight-binding (TB) Hamiltonian we have computed a complete set of TB parameters which should serve as guidance for more elaborate treatments of correlation effects in effective Hamiltonian-based approaches. The method-dependent changes of the calculated TB parameters and their interplay with the electron-electron (el-el) interaction term are discussed and interpreted. We discuss two alternative model parameterizations: one in which the effects of the el-el interaction are implicitly incorporated in the otherwise 'noninteracting' TB parameters and a second where we include an explicit mean-field el-el interaction term in the TB Hamiltonian. Both models yield a set of tabulated TB parameters which provide the band dispersion in excellent agreement with the underlying ab initio and MLWF bands.

  7. Structural phase transition and electronic properties in samarium chalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Panwar, Y. S., E-mail: yspanwar2011@gmail.com [Department of Physics, Govt. New Science College Dewas-455001 (India); Aynyas, Mahendra [Department of Physics, C.S.A. Govt. P.G. College, Sehore, 466001 (India); Pataiya, J.; Sanyal, Sankar P. [Department of Physics, Barkatullah University, Bhopal, 462026 (India)

    2016-05-06

    The electronic structure and high pressure properties of samarium monochalcogenides SmS, SmSe and SmTe have been reported by using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). The total energy as a function of volume is evaluated. It is found that these monochalcogenides are stable in NaCl-type structure under ambient pressure. We predict a structural phase transition from NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-type) structure for these compounds. Phase transition pressures were found to be 1.7, 4.4 and 6.6 GPa, for SmS, SmSe and SmTe respectively. Apart from this, the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure (BS) and density of states (DOS) are calculated. From energy band diagram we observed that these compounds exhibit metallic character. The calculated values of equilibrium lattice parameter and phase transition pressure are in general good agreement with available data.

  8. High-energy band structure of gold

    DEFF Research Database (Denmark)

    Christensen, N. Egede

    1976-01-01

    The band structure of gold for energies far above the Fermi level has been calculated using the relativistic augmented-plane-wave method. The calculated f-band edge (Γ6-) lies 15.6 eV above the Fermi level is agreement with recent photoemission work. The band model is applied to interpret...

  9. Identification of Tight-Binding Plasmepsin II and Falcipain 2 Inhibitors in Aqueous Extracts of Marine Invertebrates by the Combination of Enzymatic and Interaction-Based Assays

    Science.gov (United States)

    Salas-Sarduy, Emir; Guerra, Yasel; Covaleda Cortés, Giovanni; Avilés, Francesc Xavier; Chávez Planes, María A.

    2017-01-01

    Natural products from marine origin constitute a very promising and underexplored source of interesting compounds for modern biotechnological and pharmaceutical industries. However, their evaluation is quite challenging and requires specifically designed assays to reliably identify the compounds of interest in a highly heterogeneous and interfering context. In the present study, we describe a general strategy for the confident identification of tight-binding protease inhibitors in the aqueous extracts of 62 Cuban marine invertebrates, using Plasmodium falciparum hemoglobinases Plasmepsin II and Falcipain 2 as model enzymes. To this end, we first developed a screening strategy that combined enzymatic with interaction-based assays and then validated screening conditions using five reference extracts. Interferences were evaluated and minimized. The results from the massive screening of such extracts, the validation of several hits by a variety of interaction-based assays and the purification and functional characterization of PhPI, a multifunctional and reversible tight-binding inhibitor for Plasmepsin II and Falcipain 2 from the gorgonian Plexaura homomalla, are presented. PMID:28430158

  10. True photonic band-gap mode-control in VCSEL structures

    DEFF Research Database (Denmark)

    Romstad, F.; Madsen, M.; Birkedal, Dan

    2003-01-01

    Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect.......Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect....

  11. Transport in bilayer and trilayer graphene: band gap engineering and band structure tuning

    Science.gov (United States)

    Zhu, Jun

    2014-03-01

    Controlling the stacking order of atomically thin 2D materials offers a powerful tool to control their properties. Linearly dispersed bands become hyperbolic in Bernal (AB) stacked bilayer graphene (BLG). Both Bernal (ABA) and rhombohedral (ABC) stacking occur in trilayer graphene (TLG), producing distinct band structures and electronic properties. A symmetry-breaking electric field perpendicular to the sample plane can further modify the band structures of BLG and TLG. In this talk, I will describe our experimental effort in these directions using dual-gated devices. Using thin HfO2 film deposited by ALD as gate dielectric, we are able to apply large displacement fields D > 6 V/nm and observe the opening and saturation of the field-induced band gap Eg in bilayer and ABC-stacked trilayer graphene, where the conduction in the mid gap changes by more than six decades. Its field and temperature dependence highlights the crucial role played by Coulomb disorder in facilitating hopping conduction and suppressing the effect of Eg in the tens of meV regime. In contrast, mid-gap conduction decreases with increasing D much more rapidly in clean h-BN dual-gated devices. Our studies also show the evolution of the band structure in ABA-stacked TLG, in particular the splitting of the Dirac-like bands in large D field and the signatures of two-band transport at high carrier densities. Comparison to theory reveals the need for more sophisticated treatment of electronic screening beyond self-consistent Hartree calculations to accurately predict the band structures of trilayer graphene and graphenic materials in general.

  12. Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1

    Energy Technology Data Exchange (ETDEWEB)

    Rimon, Gilad; Sidhu, Ranjinder S.; Lauver, D. Adam; Lee, Jullia Y.; Sharma, Narayan P.; Yuan, Chong; Frieler, Ryan A.; Trievel, Raymond C.; Lucchesi, Benedict R.; Smith, William L. (Michigan)

    2010-02-11

    Pain associated with inflammation involves prostaglandins synthesized from arachidonic acid (AA) through cyclooxygenase-2 (COX-2) pathways while thromboxane A{sub 2} formed by platelets from AA via cyclooxygenase-1 (COX-1) mediates thrombosis. COX-1 and COX-2 are both targets of nonselective nonsteroidal antiinflammatory drugs (nsNSAIDs) including aspirin whereas COX-2 activity is preferentially blocked by COX-2 inhibitors called coxibs. COXs are homodimers composed of identical subunits, but we have shown that only one subunit is active at a time during catalysis; moreover, many nsNSAIDS bind to a single subunit of a COX dimer to inhibit the COX activity of the entire dimer. Here, we report the surprising observation that celecoxib and other coxibs bind tightly to a subunit of COX-1. Although celecoxib binding to one monomer of COX-1 does not affect the normal catalytic processing of AA by the second, partner subunit, celecoxib does interfere with the inhibition of COX-1 by aspirin in vitro. X-ray crystallographic results obtained with a celecoxib/COX-1 complex show how celecoxib can bind to one of the two available COX sites of the COX-1 dimer. Finally, we find that administration of celecoxib to dogs interferes with the ability of a low dose of aspirin to inhibit AA-induced ex vivo platelet aggregation. COX-2 inhibitors such as celecoxib are widely used for pain relief. Because coxibs exhibit cardiovascular side effects, they are often prescribed in combination with low-dose aspirin to prevent thrombosis. Our studies predict that the cardioprotective effect of low-dose aspirin on COX-1 may be blunted when taken with coxibs.

  13. The surface electronic structure of Y(0001)

    International Nuclear Information System (INIS)

    Searle, C.

    1998-12-01

    Yttrium has been grown epitaxially on W(110). The growth was monitored by using photoemission spectroscopy with a synchrotron radiation source. The film thickness has been gauged by the attenuation of the W 4f 7/2 bulk component. The films have been grown reproducibly and show a prominent surface state which is indicative of good order and low contamination. Angle-Resolved Ultra-Violet Photoemission Spectroscopy has been used to examine the valence band of these ultra-thin films. The films show a very different structure to the valence band of a bulk crystal of yttrium. The differences have been investigated by a series of model calculations using the LMASA-46 tight-binding LMTO program. The calculations suggest that the ultra-thin film surface state may be hybridised with a tungsten orbital having (x 2 - y 2 ) character. (author)

  14. Emergence of quasiparticle Bloch states in artificial crystals crafted atom-by-atom

    Directory of Open Access Journals (Sweden)

    Jan Girovsky, Jose L. Lado, Floris E. Kalff, Eleonora Fahrenfort, Lucas J. J. M. Peters, Joaquín Fernández-Rossier, Alexander F. Otte

    2017-06-01

    Full Text Available The interaction of electrons with a periodic potential of atoms in crystalline solids gives rise to band structure. The band structure of existing materials can be measured by photoemission spectroscopy and accurately understood in terms of the tight-binding model, however not many experimental approaches exist that allow to tailor artificial crystal lattices using a bottom-up approach. The ability to engineer and study atomically crafted designer materials by scanning tunnelling microscopy and spectroscopy (STM/STS helps to understand the emergence of material properties. Here, we use atom manipulation of individual vacancies in a chlorine monolayer on Cu(100 to construct one- and two-dimensional structures of various densities and sizes. Local STS measurements reveal the emergence of quasiparticle bands, evidenced by standing Bloch waves, with tuneable dispersion. The experimental data are understood in terms of a tight-binding model combined with an additional broadening term that allows an estimation of the coupling to the underlying substrate.

  15. The tight binding model study of the role of anisotropic AFM spin ordering in the charge ordered CMR manganites

    Science.gov (United States)

    Kar, J. K.; Panda, Saswati; Rout, G. C.

    2017-05-01

    We propose here a tight binding model study of the interplay between charge and spin orderings in the CMR manganites taking anisotropic effect due to electron hoppings and spin exchanges. The Hamiltonian consists of the kinetic energies of eg and t2g electrons of manganese ion. It further includes double exchange and Heisenberg interactions. The charge density wave interaction (CDW) describes an extra mechanism for the insulating character of the system. The CDW gap and spin parameters are calculated using Zubarev's Green's function technique and computed self-consistently. The results are reported in this communication.

  16. Bulletin of Materials Science | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    ... independent reflections. The donors form a trimerized column, and the band structure calculated by the tight-binding approximation shows band insulator properties. The temperature dependent of the d.c. resistivity shows a semiconducting behaviour with room temperature resistivity along the -axis; ρ 290 K = 5.6 ohm ...

  17. Modulation of Tight Junction Structure and Function by Kinases and Phosphatases Targeting Occludin

    Directory of Open Access Journals (Sweden)

    Max Johannes Dörfel

    2012-01-01

    Full Text Available Tight junctions (TJs typically represent the most apical contacts in epithelial and endothelial cell layers where they play an essential role in the separation of extracellular or luminal spaces from underlying tissues in the body. Depending on the protein composition, TJs define the barrier characteristics and in addition maintain cell polarity. Two major families of integral membrane proteins form the typical TJ strand network, the tight junction-associated MARVEL protein (TAMP family members occludin, tricellulin, and MarvelD3 as well as a specific set of claudins. Occludin was the first identified member of these tetraspanins and is now widely accepted as a regulator of TJ assembly and function. Therefore, occludin itself has to be tightly regulated. Phosphorylation of occludin appears to be of central importance in this context. Here we want to summarize current knowledge on the kinases and phosphatases directly modifying occludin, and their role in the regulation of TJ structure, function, and dynamics.

  18. Amniotic band-like structures | Govender | Obstetrics and ...

    African Journals Online (AJOL)

    Intra-amniotic band-like structures are seen fairly commonly on routine obstetric scans, especially during the first and second trimesters of pregnancy. It is important to establish the cause for such findings in order to determine their clinical significance and to assess prognosis. The vast majority of band-like structures are ...

  19. Atomistic modeling of zirconium hydride precipitation: methodology for deriving a tight-binding potential

    International Nuclear Information System (INIS)

    Dufresne, Alice

    2014-01-01

    The zirconium-hydrogen system is of nuclear safety interest, as the hydride precipitation leads to the cladding embrittlement, which is made of zirconium-based alloys. The cladding is the first safety barrier confining the radioactive products: its integrity shall be kept during the entire fuel-assemblies life, in reactor, including accidental situation, and post-operation (transport and storage). Many uncertainties remain regarding the hydrides precipitation kinetics and the local stress impact on their precipitation. The atomic scale modeling of this system would bring clarifications on the relevant mechanisms. The usual atomistic modeling methods are based on thermo-statistic approaches, whose precision and reliability depend on the interatomic potential used. However, there was no potential allowing a rigorous study of the Zr-H system. The present work has indeed addressed this issue: a new tight-binding potential for zirconium hydrides modeling is now available. Moreover, this thesis provides a detailed manual for deriving such potentials accounting for spd hybridization, and fitted here on DFT results. This guidebook has be written in light of modeling a pure transition metal followed by a metal-covalent coupling (metallic carbides, nitrides and silicides). (author)

  20. Effective one-band approach for the spin splittings in quantum wells

    Science.gov (United States)

    Alekseev, P. S.; Nestoklon, M. O.

    2017-03-01

    The spin-orbit interaction of two-dimensional electrons in quantum wells grown from the III-V semiconductors consists of two parts with different symmetry: the Bychkov-Rashba and the Dresselhaus terms. The last term is usually attributed to the bulk spin-orbit Hamiltonian which reflects the Td symmetry of the zincblende lattice. While it is known that the quantum well interfaces may also contribute to the Dresselhaus term, the exact structure and relative importance of the interface and bulk contributions are not well understood. To deal with this problem, we perform tight-binding calculations of the spin splittings of the electron levels in [100] GaAs/AlGaAs quantum wells. We show that the obtained spin splittings can be adequately described within the one-band electron Hamiltonian containing, together with the bulk contribution, the two interface contributions to the Dresselhaus term. The magnitude of the interface contribution to the spin-orbit interaction for sufficiently narrow quantum wells is of the same order as the bulk contribution.

  1. Wakefield Band Partitioning in LINAC Structures

    International Nuclear Information System (INIS)

    Jones, Roger M

    2003-01-01

    In the NLC project multiple bunches of electrons and positrons will be accelerated initially to a centre of mass of 500 GeV and later to 1 TeV or more. In the process of accelerating 192 bunches within a pulse train, wakefields are excited which kick the trailing bunches off axis and can cause luminosity dilution and BBU (Beam Break Up). Several structures to damp the wakefield have been designed and tested at SLAC and KEK and these have been found to successfully damp the wakefield [1]. However, these 2π/3 structures suffered from electrical breakdown and this has prompted us to explore lower group velocity structures operating at higher fundamental mode phase advances. The wakefield partitioning amongst the bands has been found to change markedly with increased phase advance. Here we report on general trends in the kick factor and associated wakefield band partitioning in dipole bands as a function of phase advance of the synchronous mode in linacs. These results are applicable to both TW (travelling wave) and SW (standing wave) structures

  2. Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection.

    Science.gov (United States)

    Pernigo, Stefano; Fukuzawa, Atsushi; Beedle, Amy E M; Holt, Mark; Round, Adam; Pandini, Alessandro; Garcia-Manyes, Sergi; Gautel, Mathias; Steiner, Roberto A

    2017-01-03

    The sarcomeric cytoskeleton is a network of modular proteins that integrate mechanical and signaling roles. Obscurin, or its homolog obscurin-like-1, bridges the giant ruler titin and the myosin crosslinker myomesin at the M-band. Yet, the molecular mechanisms underlying the physical obscurin(-like-1):myomesin connection, important for mechanical integrity of the M-band, remained elusive. Here, using a combination of structural, cellular, and single-molecule force spectroscopy techniques, we decode the architectural and functional determinants defining the obscurin(-like-1):myomesin complex. The crystal structure reveals a trans-complementation mechanism whereby an incomplete immunoglobulin-like domain assimilates an isoform-specific myomesin interdomain sequence. Crucially, this unconventional architecture provides mechanical stability up to forces of ∼135 pN. A cellular competition assay in neonatal rat cardiomyocytes validates the complex and provides the rationale for the isoform specificity of the interaction. Altogether, our results reveal a novel binding strategy in sarcomere assembly, which might have implications on muscle nanomechanics and overall M-band organization. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  3. A unique distortion in K{sub 1/3}Ba{sub 2/3}AgTe{sub 2}: X-ray diffraction determination and electronic band structure analysis of its incommensurately modulated structure

    Energy Technology Data Exchange (ETDEWEB)

    Gourdon, O; Hanko, J; Boucher, F; Petricek, V; Whangbo, M H; Kanatzidis, M G; Evain, M

    2000-04-03

    The incommensurately modulated structure of a square Te-net, namely that of K{sub 1/3}Ba{sub 2/3}AgTe{sub 2}, is determined from single-crystal X-ray diffraction data within a (3+1)D higher dimension formalism. The phase is shown to crystallize in the monoclinic symmetry, P2{sub 1}({alpha}0{gamma}) superspace group with the following lattice parameters: a = 4.6441(10) {angstrom}, b = 4.6292(12) {angstrom}, c = 23.765(9) {angstrom}, and {beta} = 101.28(2){degree} with q = 0.3248(6)a* {minus}0.07(8)c*, that is, in a symmetry different from that reported for the average structure (tetragonal) or that assumed from electron diffraction measurements (orthorhombic). After the introduction of a crenel function for the Te displacive description, the refinement converged to a residual factor R = 0.033 for 2583 observed reflections and 115 parameters (R = 0.024 and 0.101 for 1925 main reflections and 658 first-order satellites, respectively). The [Ag{sub 2}-Te{sub 2}] and the Ba/K layers are found to be only weakly modulated. The modulation of the square Te-net is, however, both substantial and unique. Namely, it results in two different units: a V-shaped Te{sub 3} trimer and a W-shaped Te{sub 5} pentamer. To examine both unit types, which are segregated in domains that aperiodically alternate within the Te layers, first principles electronic band structure calculations were carried out for three model commensurate structures using the tight-binding linear-muffin-tin-orbital method (LMTO). The calculations show that the distorted structures of V-pattern (model 2) and W-pattern (model 3) are more stable than the average structure (model 1) and that the V-pattern distortion provides a slightly larger stabilization than does the W-pattern distortion. The Fermi surface calculated for the average structure shows nesting vectors that are consistent with the occurrence of the V- and W-pattern distortions in the Te layers. However, these vectors do not predict the observed modulation

  4. Pass-band reconfigurable spoof surface plasmon polaritons

    Science.gov (United States)

    Zhang, Hao Chi; He, Pei Hang; Gao, Xinxin; Tang, Wen Xuan; Cui, Tie Jun

    2018-04-01

    In this paper, we introduce a new scheme to construct the band-pass tunable filter based on the band-pass reconfigurable spoof surface plasmon polaritons (SPPs), whose cut-off frequencies at both sides of the passband can be tuned through changing the direct current (DC) bias of varactors. Compared to traditional technology (e.g. microstrip filters), the spoof SPP structure can provide more tight field confinement and more significant field enhancement, which is extremely valuable for many system applications. In order to achieve this scheme, we proposed a specially designed SPP filter integrated with varactors and DC bias feeding structure to support the spoof SPP passband reconfiguration. Furthermore, the full-wave simulated result verifies the outstanding performance on both efficiency and reconfiguration, which has the potential to be widely used in advanced intelligent systems.

  5. Band-Structure of Thallium by the LMTO Method

    DEFF Research Database (Denmark)

    Holtham, P. M.; Jan, J. P.; Skriver, Hans Lomholt

    1977-01-01

    by an energy gap. The 6d and 7s bands were found to be far above the Fermi level and the 5d states were found to be far below it. Fermi surface properties and the electronic specific heat are computed and compared with experiment. The joint density of states has also been computed and is in reasonable...... and p bands for the HCP structure. Energy bands have been evaluated both with and without spin-orbit coupling which is particularly large in thallium. Energy bands close to the Fermi level were found to be mainly 6p like in character. The 6s states lay below the 6p bands and were separated from them......The relativistic band structure of thallium has been calculated using the linear muffin-tin orbital (LMTO) method. The positions and extents of the bands were found to follow the Wigner-Seitz rule approximately, and the origin of the dispersion of the bands was established from the canonical s...

  6. The Marvels of Electromagnetic Band Gap (EBG) Structures

    Science.gov (United States)

    2003-11-01

    terminology of "Electromagnetic conference papers and journal articles dealing with Band- gaps (EBG)". Recently, many researchers the characterizations...Band Gap (EBG) Structures 9 utilized to reduce the mutual coupling between Structures: An FDTD/Prony Technique elements of antenna arrays. based on the...Band- Gap of several patents. He has had pioneering research contributions in diverse areas of electromagnetics,Snteructure", Dymposiget o l 21 IE 48

  7. Band structures in near spherical 138Ce

    Science.gov (United States)

    Bhattacharjee, T.; Chanda, S.; Bhattacharyya, S.; Basu, S. K.; Bhowmik, R. K.; Das, J. J.; Pramanik, U. Datta; Ghugre, S. S.; Madhavan, N.; Mukherjee, A.; Mukherjee, G.; Muralithar, S.; Singh, R. P.

    2009-06-01

    The high spin states of N=80138Ce have been populated in the fusion evaporation reaction 130Te( 12C, 4n) 138Ce at E=65 MeV. The γ transitions belonging to various band structures were detected and characterized using an array of five Clover Germanium detectors. The level scheme has been established up to a maximum spin and excitation energy of 23 ℏ and 9511.3 keV, respectively, by including 53 new transitions. The negative parity ΔI=1 band, developed on the 6536.3 keV 15 level, has been conjectured to be a magnetic rotation band following a semiclassical analysis and comparing the systematics of similar bands in the neighboring nuclei. The said band is proposed to have a four quasiparticle configuration of [πgh]⊗[. Other band structures are interpreted in terms of multi-quasiparticle configurations, based on Total Routhian Surface (TRS) calculations. For the low and medium spin states, a shell model calculation using a realistic two body interaction has been performed using the code OXBASH.

  8. Intrinsic optical confinement for ultrathin InAsN quantum well superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Sakri, A.; Robert, C.; Pedesseau, L.; Cornet, C.; Durand, O.; Even, J.; Jancu, J.-M. [Université Europeenne de Bretagne, INSA Rennes,France and CNRS, UMR 6082, Foton, 20 avenues des Buttes de Coësmes, 35708 Rennes (France)

    2013-12-04

    We study energy-band engineering with InAsN monolayer in GaAs/GaP quantum well structure. A tight-binding calculation indicates that both type I alignment along with direct band-gap behavior can be obtained. We show that the optical transitions are less sensitive to the position of the probe.

  9. Organometallic DNA-B12 Conjugates as Potential Oligonucleotide Vectors: Synthesis and Structural and Binding Studies with Human Cobalamin-Transport Proteins.

    Science.gov (United States)

    Mutti, Elena; Hunger, Miriam; Fedosov, Sergey; Nexo, Ebba; Kräutler, Bernhard

    2017-11-16

    The synthesis and structural characterization of Co-(dN) 25 -Cbl (Cbl: cobalamin; dN: deoxynucleotide) and Co-(dN) 39 -Cbl, which are organometallic DNA-B 12 conjugates with single DNA strands consisting of 25 and 39 deoxynucleotides, respectively, and binding studies of these two DNA-Cbl conjugates to three homologous human Cbl transporting proteins, transcobalamin (TC), intrinsic factor (IF), and haptocorrin (HC), are reported. This investigation tests the suitability of such DNA-Cbls for the task of eventual in vivo oligonucleotide delivery. The binding of DNA-Cbl to TC, IF, and HC was investigated in competition with either a fluorescent Cbl derivative and Co-(dN) 25 -Cbl, or radiolabeled vitamin B 12 ( 57 Co-CNCbl) and Co-(dN) 25 -Cbl or Co-(dN) 39 -Cbl. Binding of the new DNA-Cbl conjugates was fast and tight with TC, but poorer with HC and IF, which extends a similar original finding with the simpler DNA-Cbl, Co-(dN) 18 -Cbl. The contrasting affinities of TC versus IF and HC for the DNA-Cbl conjugates are rationalized herein by a stepwise mechanism of Cbl binding. Critical contributions to overall affinity result from gradual conformational adaptations of the Cbl-binding proteins to the DNA-Cbl, which is first bound to the respective β domains. This transition is fast with TC, but slow with IF and HC, with which weaker binding results. The invariably tight interaction of the DNA-Cbl conjugates with TC makes the Cbl moiety a potential natural vector for the specific delivery of oligonucleotide loads from the blood into cells. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

    Science.gov (United States)

    Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

    2013-06-01

    RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous 'polyamide amino acids' (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy-entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.

  11. Large-scale calculations of solid oxide fuel cell cermet anode by tight-binding quantum chemistry method

    International Nuclear Information System (INIS)

    Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

    2005-01-01

    Improvement of anode characteristics of solid oxide fuel cells is important for the better cell performance and especially the direct use of hydrocarbons. A mixture of ceramics and metal is generally used as anode, and different combinations of ceramics and metals lead to different electrode characteristics. We performed large-scale calculations to investigate the characteristics of Ni/CeO 2 and Cu/CeO 2 anodes at the electronic level using our tight-binding quantum chemical molecular dynamics program. Charge distribution analysis clarified the electron transfer from metal to oxide in both anodes. The calculations of density of states clarified different contributions of Ni and Cu orbitals to the energy levels at around Fermi level in each cermet. Based on the obtained results, we made considerations to explain different characteristics of both cermet anodes. The effectiveness of our approach for the investigation of complex cermet system was proved

  12. The helical structure of DNA facilitates binding

    International Nuclear Information System (INIS)

    Berg, Otto G; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

    2016-01-01

    The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction–diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general. (paper)

  13. Band structure of CdTe under high pressure

    International Nuclear Information System (INIS)

    Jayam, Sr. Gerardin; Nirmala Louis, C.; Amalraj, A.

    2005-01-01

    The band structures and density of states of cadmium telluride (CdTe) under various pressures ranging from normal to 4.5 Mbar are obtained. The electronic band structure at normal pressure of CdTe (ZnS structure) is analyzed and the direct band gap value is found to be 1.654 eV. CdTe becomes metal and superconductor under high pressure but before that it undergoes structural phase transition from ZnS phase to NaCl phase. The equilibrium lattice constant, bulk modulus and the phase transition pressure at which the compounds undergo structural phase transition from ZnS to NaCl are predicted from the total energy calculations. The density of states at the Fermi level (N(E F )) gets enhanced after metallization, which leads to the superconductivity in CdTe. In our calculation, the metallization pressure (P M = 1.935 Mbar) and the corresponding reduced volume ((V/V 0 ) M = 0.458) are estimated. Metallization occurs via direct closing of band gap at Γ point. (author)

  14. Hofstadter butterflies and magnetically induced band-gap quenching in graphene antidot lattices

    DEFF Research Database (Denmark)

    Pedersen, Jesper Goor; Pedersen, Thomas Garm

    2013-01-01

    We study graphene antidot lattices (GALs) in magnetic fields. Using a tight-binding model and a recursive Green's function technique that we extend to deal with periodic structures, we calculate Hofstadter butterflies of GALs. We compare the results to those obtained in a simpler gapped graphene ...

  15. Intrinsic properties of high-spin band structures in triaxial nuclei

    Science.gov (United States)

    Jehangir, S.; Bhat, G. H.; Sheikh, J. A.; Palit, R.; Ganai, P. A.

    2017-12-01

    The band structures of 68,70Ge, 128,130,132,134Ce and 132,134,136,138Nd are investigated using the triaxial projected shell model (TPSM) approach. These nuclei depict forking of the ground-state band into several s-bands and in some cases, both the lowest two observed s-bands depict neutron or proton character. It was discussed in our earlier work that this anomalous behaviour can be explained by considering γ-bands based on two-quasiparticle configurations. As the parent band and the γ-band built on it have the same intrinsic structure, g-factors of the two bands are expected to be similar. In the present work, we have undertaken a detailed investigation of g-factors for the excited band structures of the studied nuclei and the available data for a few high-spin states are shown to be in fair agreement with the predicted values.

  16. Band structures in the nematic elastomers phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Shuai [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China); School of Civil Engineering and Architecture, Anyang Normal University, Anyang 455000 (China); Liu, Ying, E-mail: yliu5@bjtu.edu.cn [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China); Liang, Tianshu [Department of Mechanics, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044 (China)

    2017-02-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  17. Band structures in the nematic elastomers phononic crystals

    International Nuclear Information System (INIS)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-01-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  18. Proton transfer along water bridges in biological systems with density-functional tight-binding

    Science.gov (United States)

    Reiss, Krystle; Wise, Abigail; Mazzuca, James

    2015-03-01

    When examining the dynamics of charge transfer in high dimensional enzymatic systems, the cost of quantum mechanical treatment of electrons increases exponentially with the size of the system. As a semi-empirical method, density-functional tight-binding aids in shortening these calculation times, but can be inaccurate in the regime where bonds are being formed and broken. To address these inaccuracies with respect to proton transfer in an enzymatic system, DFTB is being used to calculate small model systems containing only a single amino acid residue donor, represented by an imidazole molecule, and a water acceptor. When DFTB calculations are compared to B3LYP geometry calculations of the donor molecule, we observe a bond angle error on the order of 1.2 degrees and a bond length error on the order of 0.011 Å. As we move forward with small donor-acceptor systems, comparisons between DFTB and B3LYP energy profiles will provide a better clue as to what extent improvements need to be made. To improve the accuracy of the DFTB calculations, the internuclear repulsion term may be altered. This would result in energy profiles that closely resemble those produced by higher-level theory. Alma College Provost's Office.

  19. Band connectivity for topological quantum chemistry: Band structures as a graph theory problem

    Science.gov (United States)

    Bradlyn, Barry; Elcoro, L.; Vergniory, M. G.; Cano, Jennifer; Wang, Zhijun; Felser, C.; Aroyo, M. I.; Bernevig, B. Andrei

    2018-01-01

    The conventional theory of solids is well suited to describing band structures locally near isolated points in momentum space, but struggles to capture the full, global picture necessary for understanding topological phenomena. In part of a recent paper [B. Bradlyn et al., Nature (London) 547, 298 (2017), 10.1038/nature23268], we have introduced the way to overcome this difficulty by formulating the problem of sewing together many disconnected local k .p band structures across the Brillouin zone in terms of graph theory. In this paper, we give the details of our full theoretical construction. We show that crystal symmetries strongly constrain the allowed connectivities of energy bands, and we employ graph theoretic techniques such as graph connectivity to enumerate all the solutions to these constraints. The tools of graph theory allow us to identify disconnected groups of bands in these solutions, and so identify topologically distinct insulating phases.

  20. Band structures in Sierpinski triangle fractal porous phononic crystals

    International Nuclear Information System (INIS)

    Wang, Kai; Liu, Ying; Liang, Tianshu

    2016-01-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

  1. Band structures in Sierpinski triangle fractal porous phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Kai; Liu, Ying, E-mail: yliu5@bjtu.edu.cn; Liang, Tianshu

    2016-10-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

  2. Tight closure and vanishing theorems

    International Nuclear Information System (INIS)

    Smith, K.E.

    2001-01-01

    Tight closure has become a thriving branch of commutative algebra since it was first introduced by Mel Hochster and Craig Huneke in 1986. Over the past few years, it has become increasingly clear that tight closure has deep connections with complex algebraic geometry as well, especially with those areas of algebraic geometry where vanishing theorems play a starring role. The purpose of these lectures is to introduce tight closure and to explain some of these connections with algebraic geometry. Tight closure is basically a technique for harnessing the power of the Frobenius map. The use of the Frobenius map to prove theorems about complex algebraic varieties is a familiar technique in algebraic geometry, so it should perhaps come as no surprise that tight closure is applicable to algebraic geometry. On the other hand, it seems that so far we are only seeing the tip of a large and very beautiful iceberg in terms of tight closure's interpretation and applications to algebraic geometry. Interestingly, although tight closure is a 'characteristic p' tool, many of the problems where tight closure has proved useful have also yielded to analytic (L2) techniques. Despite some striking parallels, there had been no specific result directly linking tight closure and L∼ techniques. Recently, however, the equivalence of an ideal central to the theory of tight closure was shown to be equivalent to a certain 'multiplier ideal' first defined using L2 methods. Presumably, deeper connections will continue to emerge. There are two main types of problems for which tight closure has been helpful: in identifying nice structure and in establishing uniform behavior. The original algebraic applications of tight closure include, for example, a quick proof of the Hochster-Roberts theorem on the Cohen-Macaulayness of rings of invariants, and also a refined version of the Brianqon-Skoda theorem on the uniform behaviour of integral closures of powers of ideals. More recent, geometric

  3. Dielectric constant of graphene-on-polarized substrate: A tight ...

    Indian Academy of Sciences (India)

    2017-06-24

    Jun 24, 2017 ... We report here a microscopic tight-binding theoretical study of the dynamic dielectric response of graphene-on-polarizable substrate with impurity. The Hamiltonian consists of first, second and third nearest neighbour electron hopping interactions besides doping and substrate-induced effects on graphene.

  4. Spin-relaxation time in the impurity band of wurtzite semiconductors

    Science.gov (United States)

    Tamborenea, Pablo I.; Wellens, Thomas; Weinmann, Dietmar; Jalabert, Rodolfo A.

    2017-09-01

    The spin-relaxation time for electrons in the impurity band of semiconductors with wurtzite crystal structure is determined. The effective Dresselhaus spin-orbit interaction Hamiltonian is taken as the source of the spin relaxation at low temperature and for doping densities corresponding to the metallic side of the metal-insulator transition. The spin-flip hopping matrix elements between impurity states are calculated and used to set up a tight-binding Hamiltonian that incorporates the symmetries of wurtzite semiconductors. The spin-relaxation time is obtained from a semiclassical model of spin diffusion, as well as from a microscopic self-consistent diagrammatic theory of spin and charge diffusion in doped semiconductors. Estimates are provided for particularly important materials. The theoretical spin-relaxation times compare favorably with the corresponding low-temperature measurements in GaN and ZnO. For InN and AlN we predict that tuning of the spin-orbit coupling constant induced by an external potential leads to a potentially dramatic increase of the spin-relaxation time related to the mechanism under study.

  5. Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

    Energy Technology Data Exchange (ETDEWEB)

    Rüger, Robert, E-mail: rueger@scm.com [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Lenthe, Erik van [Scientific Computing & Modelling NV, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Heine, Thomas [Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig (Germany); Visscher, Lucas [Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

    2016-05-14

    We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.

  6. BAND STRUCTURE OF NON-STEIOCHIOMETRIC LARGE-SIZED NANOCRYSTALLITES

    Directory of Open Access Journals (Sweden)

    I.V.Kityk

    2004-01-01

    Full Text Available A band structure of large-sized (from 20 to 35nm non-steichiometric nanocrystallites (NC of the Si2-xCx (1.04 < x < 1.10 has been investigated using different band energy approaches and a modified Car-Parinello molecular dynamics structure optimization of the NC interfaces. The non-steichiometric excess of carbon favors the appearance of a thin prevailingly carbon-contained layer (with thickness of about 1 nm covering the crystallites. As a consequence, one can observe a substantial structure reconstruction of boundary SiC crystalline layers. The numerical modeling has shown that these NC can be considered as SiC reconstructed crystalline films with thickness of about 2 nm covering the SiC crystallites. The observed data are considered within the different one-electron band structure methods. It was shown that the nano-sized carbon sheet plays a key role in a modified band structure. Independent manifestation of the important role played by the reconstructed confined layers is due to the experimentally discovered excitonic-like resonances. Low-temperature absorption measurements confirm the existence of sharp-like absorption resonances originating from the reconstructed layers.

  7. Electronic and Magnetic Properties of Transition-Metal Oxide Nanocomposites: A Tight-Binding Modeling at Mesoscale

    Science.gov (United States)

    Tai, Yuan-Yen; Zhu, Jian-Xin

    Transition metal oxides (TMOs) exhibit many emergent phenomena ranging from high-temperature superconductivity and giant magnetoresistance to magnetism and ferroelectricity. In addition, when TMOs are interfaced with each other, new functionalities can arise, which are absent in individual components. In this talk, I will present an overview on our recent efforts in theoretical understanding of the electronic and magnetic properties TMO nanocomposites. In particular, I will introduce our recently developed tight-binding modeling of these properties arising from the interplay of competing interactions at the interfaces of planar and pillar nanocomposites. Our theoretical tool package will provide a unique capability to address the emergent phenomena in TMO nanocomposites and their mesoscale response to such effects like strain and microstructures at the interfaces, and ultimately help establish design principles of new multifunctionality with TMOs. This work was carried out under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at LANL under Contract No. DE-AC52-06NA25396, and was supported by the LANL LDRD Program.

  8. Band Structure Characteristics of Nacreous Composite Materials with Various Defects

    Science.gov (United States)

    Yin, J.; Zhang, S.; Zhang, H. W.; Chen, B. S.

    2016-06-01

    Nacreous composite materials have excellent mechanical properties, such as high strength, high toughness, and wide phononic band gap. In order to research band structure characteristics of nacreous composite materials with various defects, supercell models with the Brick-and-Mortar microstructure are considered. An efficient multi-level substructure algorithm is employed to discuss the band structure. Furthermore, two common systems with point and line defects and varied material parameters are discussed. In addition, band structures concerning straight and deflected crack defects are calculated by changing the shear modulus of the mortar. Finally, the sensitivity of band structures to the random material distribution is presented by considering different volume ratios of the brick. The results reveal that the first band gap of a nacreous composite material is insensitive to defects under certain conditions. It will be of great value to the design and synthesis of new nacreous composite materials for better dynamic properties.

  9. Analysis on X-band structure breakdown at GLCTA

    International Nuclear Information System (INIS)

    Suehara, T.; Sanuki, T.; Komamiya, S.; Higo, T.; Hayano, H.; Terunuma, N.; Saeki, T.; Watanabe, K.; Hayakawa, A.; Tsukada, Y.

    2004-01-01

    We have built a new monitoring system for accelerator structure breakdown in the X-band high-gradient test facility at KEK (GLCTA: Global Linear Collider Test Accelerator). An X-band test structure KX01 (made by KEK) has been processed at GLCTA and we have been collecting data for about 3 months using this breakdown monitoring system. We describe overview of the monitoring system and preliminary result of breakdown analysis of the structure. (author)

  10. Atomic structure of the SnO2 (110) surface

    International Nuclear Information System (INIS)

    Godin, T.J.; LaFemina, J.P.

    1991-12-01

    Using a tight-binding, total-energy model, we examine atomic relaxations of the ideal stoichiometric and reduced tin oxide (11) surfaces. In both cases we find a nearly bond-length conserving rumple of the top layer, and a smaller counter-relaxation of the second layer. These calculations show no evidence of surface states in the band gap for either surface

  11. Maximizing band gaps in plate structures

    DEFF Research Database (Denmark)

    Halkjær, Søren; Sigmund, Ole; Jensen, Jakob Søndergaard

    2006-01-01

    periodic plate using Bloch theory, which conveniently reduces the maximization problem to that of a single base cell. Secondly, we construct a finite periodic plate using a number of the optimized base cells in a postprocessed version. The dynamic properties of the finite plate are investigated......Band gaps, i.e., frequency ranges in which waves cannot propagate, can be found in elastic structures for which there is a certain periodic modulation of the material properties or structure. In this paper, we maximize the band gap size for bending waves in a Mindlin plate. We analyze an infinite...... theoretically and experimentally and the issue of finite size effects is addressed....

  12. Band structure analysis in SiGe nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Amato, Michele [' Centro S3' , CNR-Istituto Nanoscienze, via Campi 213/A, 41100 Modena (Italy); Dipartimento di Scienze e Metodi dell' Ingegneria, Universita di Modena e Reggio Emilia, via Amendola 2 Pad. Morselli, I-42100 Reggio Emilia (Italy); Palummo, Maurizia [European Theoretical Spectroscopy Facility (ETSF) (Italy); CNR-INFM-SMC, Dipartimento di Fisica, Universita di Roma, ' Tor Vergata' , via della Ricerca Scientifica 1, 00133 Roma (Italy); Ossicini, Stefano, E-mail: stefano.ossicini@unimore.it [' Centro S3' , CNR-Istituto Nanoscienze, via Campi 213/A, 41100 Modena (Italy) and Dipartimento di Scienze e Metodi dell' Ingegneria, Universita di Modena e Reggio Emilia, via Amendola 2 Pad. Morselli, I-42100 Reggio Emilia (Italy) and European Theoretical Spectroscopy Facility - ETSF (Italy) and Centro Interdipartimentale ' En and Tech' , Universita di Modena e Reggio Emilia, via Amendola 2 Pad. Morselli, I-42100 Reggio Emilia (Italy)

    2012-06-05

    One of the main challenges for Silicon-Germanium nanowires (SiGe NWs) electronics is the possibility to modulate and engine their electronic properties in an easy way, in order to obtain a material with the desired electronic features. Diameter and composition constitute two crucial ways for the modification of the band gap and of the band structure of SiGe NWs. Within the framework of density functional theory we present results of ab initio calculations regarding the band structure dependence of SiGe NWs on diameter and composition. We point out the main differences with respect to the case of pure Si and Ge wires and we discuss the particular features of SiGe NWs that are useful for future technological applications.

  13. Band structure analysis in SiGe nanowires

    International Nuclear Information System (INIS)

    Amato, Michele; Palummo, Maurizia; Ossicini, Stefano

    2012-01-01

    One of the main challenges for Silicon-Germanium nanowires (SiGe NWs) electronics is the possibility to modulate and engine their electronic properties in an easy way, in order to obtain a material with the desired electronic features. Diameter and composition constitute two crucial ways for the modification of the band gap and of the band structure of SiGe NWs. Within the framework of density functional theory we present results of ab initio calculations regarding the band structure dependence of SiGe NWs on diameter and composition. We point out the main differences with respect to the case of pure Si and Ge wires and we discuss the particular features of SiGe NWs that are useful for future technological applications.

  14. Optical properties of 1T and 2H phases of TaS2 and TaSe2

    Indian Academy of Sciences (India)

    10] have observed a phase transition to the H phase induced by a STM tip in ... Several semi-empirical band structure and ligand field models have been ... and Yoffe [12] have applied the semi-empirical tight binding (TB) method to calculate.

  15. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    Energy Technology Data Exchange (ETDEWEB)

    Hegde, Ganesh, E-mail: ghegde@purdue.edu; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard, E-mail: gekco@purdue.edu [Network for Computational Nanotechnology (NCN), Department of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Boykin, Timothy [Department of Electrical and Computer Engineering, University of Alabama, Huntsville, Alabama (United States)

    2014-03-28

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

  16. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    International Nuclear Information System (INIS)

    Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard; Boykin, Timothy

    2014-01-01

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales

  17. An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

    Science.gov (United States)

    Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

    2014-03-01

    Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

  18. Effect of the coupling between electronic structure and crystalline structure on some properties of transition metals; Couplage entre structure electronique et structure cristalline: effet sur quelques proprietes des metaux de transition

    Energy Technology Data Exchange (ETDEWEB)

    Nastar, M

    1994-10-14

    The elastic constants, energetic stabilities and vacancy formation energies in transition metals are calculated within a Tight Binding model. In order to outline the effect of the electronic structure, these properties are represented as functions of band filling. The variation of the shear elastic constants of hexagonal close packed (HCP), body centered cubic (BCC) and face centered cubic (FCC) structures, is in contrast with the roughly parabolic behavior of bulk modulus. The general trends are in very good agreement with available experimental and `ab initio` data. The vacancy formation energy in the BCC structure shows strong deviations from bell shape behavior with a maximum corresponding approximately to the band filling of group 6. This band filling effect contributes to the noticeable decrease of the self diffusion rate between group 4 and group 6. We demonstrate that the abrupt increase of the C` elastic constant, the NT{sub 1} (0.-1.1) phonon frequency, the energy differences between BCC and HCP and between FCC and HCP as well as the vacancy formation energy, that occurs when going from Zr to Mo, is related to the presence of a pseudo-gap in the density of states of the BCC structure. Using the recursion method, we show that the general trends of these properties are correctly reproduced when considering only a few moments of the density of states (about 6). On the other hand, details such as the elastic constant singularities, are displayed only with an exact calculation of the density of states. (Author). 173 refs., 84 figs., 5 tabs.

  19. Dielectric constant of graphene-on-polarized substrate: A tight ...

    Indian Academy of Sciences (India)

    Sivabrata Sahu

    Corresponding author. E-mail: gcr@iopb.res.in. Published online 24 June 2017. Abstract. We report here a microscopic tight-binding theoretical study of the dynamic dielectric response of graphene-on-polarizable substrate with impurity. The Hamiltonian consists of first, second and third nearest- neighbour electron hopping ...

  20. Total energy calculation of perovskite, BaTiO3, by self-consistent

    Indian Academy of Sciences (India)

    Unknown

    rgy, lattice constant, density of states, band structure etc using self-consistent tight binding method. ... share the paraelectric simple-cubic perovskite structure .... of neighbouring ions. In order to find the ground state, we solve the variation problem, minimizing Etot with respect to the coefficients, .*,λµ ic. The final equation is.

  1. Does the low hole transport mass in and Si nanowires lead to mobility enhancements at high field and stress: A self-consistent tight-binding study

    Science.gov (United States)

    Kotlyar, R.; Linton, T. D.; Rios, R.; Giles, M. D.; Cea, S. M.; Kuhn, K. J.; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard

    2012-06-01

    The hole surface roughness and phonon limited mobility in the silicon , , and square nanowires under the technologically important conditions of applied gate bias and stress are studied with the self-consistent Poisson-sp3d5s*-SO tight-binding bandstructure method. Under an applied gate field, the hole carriers in a wire undergo a volume to surface inversion transition diminishing the positive effects of the high and valence band nonparabolicities, which are known to lead to the large gains of the phonon limited mobility at a zero field in narrow wires. Nonetheless, the hole mobility in the unstressed wires down to the 5 nm size remains competitive or shows an enhancement at high gate field over the large wire limit. Down to the studied 3 nm sizes, the hole mobility is degraded by strong surface roughness scattering in and wires. The channels are shown to experience less surface scattering degradation. The physics of the surface roughness scattering dependence on wafer and channel orientations in a wire is discussed. The calculated uniaxial compressive channel stress gains of the hole mobility are found to reduce in the narrow wires and at the high field. This exacerbates the stressed mobility degradation with size. Nonetheless, stress gains of a factor of 2 are obtained for wires down to 3 nm size at a 5×1012 cm-2 hole inversion density per gate area.

  2. Optical properties of InAs/GaAs quantum dot superlattice structures

    Science.gov (United States)

    Imran, Ali; Jiang, Jianliang; Eric, Deborah; Zahid, M. Noaman; Yousaf, M.; Shah, Z. H.

    2018-06-01

    Quantum dot (QD) structure has potential applications in modern highly efficient optoelectronic devices due to their band-tuning. The device dimensions have been miniatured with increased efficiencies by virtue of this discovery. In this research, we have presented modified analytical and simulation results of InAs/GaAs QD superlattice (QDSL). We have applied tight binding model for the investigation of ground state energies using timeindependent Schrödinger equation (SE) with effective mass approximation. It has been investigated that the electron energies are confined due to wave function delocalization in closely coupled QD structures. The minimum ground state energy can be obtained by increasing the periodicity and decreasing the barrier layer thickness. We have calculated electronics and optical properties which includes ground state energies, transition energies, density of states (DOS), absorption coefficient and refractive index, which can be tuned by structure modification. In our results, the minimum ground state energy of QDSL is achieved to be 0.25 eV with a maximum period of 10 QDs. The minimum band to band and band to continuum transition energies are 63 meV and 130 meV with 2 nm barrier layer thickness respectively. The absorption coefficient of our proposed QDSL model is found to be maximum 1.2 × 104 cm-1 and can be used for highly sensitive infrared detector and high efficiency solar cells.

  3. Border Structure of Intercalary Heterochromatin Bands of Drosophila melanogaster Polytene Chromosomes.

    Science.gov (United States)

    Khoroshko, V A; Zykova, T Yu; Popova, O O; Zhimulev, I F

    2018-03-01

    The precise genomic localization of the borders of 62 intercalary heterochromatin bands in Drosophila polytene chromosomes was determined. A new type of bands containing chromatin of different states was identified. This type is a combination of the gray band and the intercalary heterochromatin band, creating a genetic structure that with a light microscope is identified as a continuous band. The border structure of such bands includes the coding regions of genes with ubiquitous activity.

  4. Effect of correlation on the band structure of α-cerium

    International Nuclear Information System (INIS)

    Rao, R.S.; Singh, R.P.

    1975-01-01

    The electronic band structure of f.c.c. phase of the rare earth metal cerium (α-cerium) has been calculated using a formulation of the crystal potential where correlation also has been included in addition to exchange. The Green's function method of Korringa-Kohn and Rostoker has been used due to obvious advantages in calculation. The calculations indicate that the s-d bands are hybridized with the f-levels but the f-bands are fairly narrow and lie slightly above the Fermi level. The structure of the bands is qualitatively similar to those of calculations by others except for a general shift of the entire set of bands by about 0.1 Ryd. Thd density of states has also been calculated from the bands obtained. The spin susceptibility of α-cerium has also been calculated using the Kohn-Sham method. However, the calculated additional contributions to the band structure values cannot still explain the large experimental values reported in the literature. (author)

  5. The cellular approach to band structure calculations

    International Nuclear Information System (INIS)

    Verwoerd, W.S.

    1982-01-01

    A short introduction to the cellular approach in band structure calculations is given. The linear cellular approach and its potantial applicability in surface structure calculations is given some consideration in particular

  6. Structure of a Glomulin-RBX1-CUL1 complex: inhibition of a RING E3 ligase through masking of its E2-binding surface

    Science.gov (United States)

    Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.; Hammel, Michal; Lambert, Lester J.; Waddell, M. Brett; Mittag, Tanja; DeCaprio, James A.; Schulman, Brenda A.

    2012-01-01

    Summary The ~300 human Cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1’s RING domain, regulates the RBX1-CUL1-containing SCFFBW7 complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains the basis for GLMN’s selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition. PMID:22748924

  7. Hermetic compartments leak-tightness enhancement

    International Nuclear Information System (INIS)

    Murani, J.

    2000-01-01

    In connection with the enhancement of the nuclear safety of the Jaslovske Bohunice V-1 NPP actions for the increase of the leak tightness are performed. The reconstruction has been done in the following directions: hermetic compartments leak tightness enhancement; air lock installation; installation of air lock in SP 4 vent system; integrated leakage rate test to hermetic compartments with leak detection. After 'major' leaks on the hermetic boundary components had been eliminated, since 1994 works on a higher qualitative level began. The essence of the works consists in the detection and identification of leaks in the structural component of the hermetic boundary during the planned refueling outages. The results of the Small Reconstruction and gradual enhancement of leak tightness are presented

  8. Hardware device to physical structure binding and authentication

    Science.gov (United States)

    Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

    2013-08-20

    Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

  9. Novel structural flexibility identification in narrow frequency bands

    International Nuclear Information System (INIS)

    Zhang, J; Moon, F L

    2012-01-01

    A ‘Sub-PolyMAX’ method is proposed in this paper not only for estimating modal parameters, but also for identifying structural flexibility by processing the impact test data in narrow frequency bands. The traditional PolyMAX method obtains denominator polynomial coefficients by minimizing the least square (LS) errors of frequency response function (FRF) estimates over the whole frequency range, but FRF peaks in different structural modes may have different levels of magnitude, which leads to the modal parameters identified for the modes with small FRF peaks being inaccurate. In contrast, the proposed Sub-PolyMAX method implements the LS solver in each subspace of the whole frequency range separately; thus the results identified from a narrow frequency band are not affected by FRF data in other frequency bands. In performing structural identification in narrow frequency bands, not in the whole frequency space, the proposed method has the following merits: (1) it produces accurate modal parameters, even for the modes with very small FRF peaks; (2) it significantly reduces computation cost by reducing the number of frequency lines and the model order in each LS implementation; (3) it accurately identifies structural flexibility from impact test data, from which structural deflection under any static load can be predicted. Numerical and laboratory examples are investigated to verify the effectiveness of the proposed method. (paper)

  10. Optimum design of band-gap beam structures

    DEFF Research Database (Denmark)

    Olhoff, Niels; Niu, Bin; Cheng, Gengdong

    2012-01-01

    The design of band-gap structures receives increasing attention for many applications in mitigation of undesirable vibration and noise emission levels. A band-gap structure usually consists of a periodic distribution of elastic materials or segments, where the propagation of waves is impeded...... or significantly suppressed for a range of external excitation frequencies. Maximization of the band-gap is therefore an obvious objective for optimum design. This problem is sometimes formulated by optimizing a parameterized design model which assumes multiple periodicity in the design. However, it is shown...... in the present paper that such an a priori assumption is not necessary since, in general, just the maximization of the gap between two consecutive natural frequencies leads to significant design periodicity. The aim of this paper is to maximize frequency gaps by shape optimization of transversely vibrating...

  11. Phononic band gap structures as optimal designs

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Sigmund, Ole

    2003-01-01

    In this paper we use topology optimization to design phononic band gap structures. We consider 2D structures subjected to periodic loading and obtain the distribution of two materials with high contrast in material properties that gives the minimal vibrational response of the structure. Both in...

  12. Design of an X-band accelerating structure using a newly developed structural optimization procedure

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xiaoxia [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Fang, Wencheng; Gu, Qiang [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Zhao, Zhentang, E-mail: zhaozhentang@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); University of Chinese Academy of Sciences, Beijing 100049 (China)

    2017-05-11

    An X-band high gradient accelerating structure is a challenging technology for implementation in advanced electron linear accelerator facilities. The present work discusses the design of an X-band accelerating structure for dedicated application to a compact hard X-ray free electron laser facility at the Shanghai Institute of Applied Physics, and numerous design optimizations are conducted with consideration for radio frequency (RF) breakdown, RF efficiency, short-range wakefields, and dipole/quadrupole field modes, to ensure good beam quality and a high accelerating gradient. The designed X-band accelerating structure is a constant gradient structure with a 4π/5 operating mode and input and output dual-feed couplers in a racetrack shape. The design process employs a newly developed effective optimization procedure for optimization of the X-band accelerating structure. In addition, the specific design of couplers providing high beam quality by eliminating dipole field components and reducing quadrupole field components is discussed in detail.

  13. Parallel decomposition of the tight-binding fictitious Lagrangian algorithm for molecular dynamics simulations of semiconductors

    International Nuclear Information System (INIS)

    Yeh, M.; Kim, J.; Khan, F.S.

    1995-01-01

    We present a parallel decomposition of the tight-binding fictitious Lagrangian algorithm for the Intel iPSC/860 and the Intel Paragon parallel computers. We show that it is possible to perform long simulations, of the order of 10 000 time steps, on semiconducting clusters consisting of as many as 512 atoms, on a time scale of the order of 20 h or less. We have made a very careful timing analysis of all parts of our code, and have identified the bottlenecks. We have also derived formulas which can predict the timing of our code, based on the number of processors, message passing bandwidth, floating point performance of each node, and the set up time for message passing, appropriate to the machine being used. The time of the simulation scales as the square of the number of particles, if the number of processors is made to scale linearly with the number of particles. We show that for a system as large as 512 atoms, the main bottleneck of the computation is the orthogonalization of the wave functions, which consumes about 90% of the total time of the simulation

  14. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  15. Two band superconductivity for MgB2: Tc and isotope exponent α as a function of the carrier number n and the role of the center of the band

    International Nuclear Information System (INIS)

    Rodriguez-Nunez, J.J.; Schmidt, A.A.; Bianconi, A.; Perali, A.

    2005-08-01

    We study a two band superconducting, assuming that we have two tight binding bands, ε 2 (k-vector) = ε 2 (0) - t 2 [cos(k x ) + cos(k y ) + s 2 cos(k z )] - μ and ε 3 (k-vector) ε 3 (0) - t 3 [cos(k x ) + cos(k y )+s 3 cos(k z )] - μ. We solve the two gap equations at T = T c and calculate T c x n and μ x n for various values of pairing interaction, V, and Debye frequency, ω D . Also, from an expression developed in a previous paper by two of the present authors, we calculate α x n, where n is the number of carriers per site per band and α is the isotope exponent. We take only interband scattering, V, as a first approach. We find that in order to have superconductivity (T c ≠ 0), large values of V are necessary. Also, for V/ω D > 1, we obtain α > 1.00 and for V/ω D >1.00, the isotope exponent becomes less than 1. (author)

  16. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

    Science.gov (United States)

    Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

    2010-05-01

    The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

  17. Structure-function relations in oxaloacetate decarboxylase complex. Fluorescence and infrared approaches to monitor oxomalonate and Na(+ binding effect.

    Directory of Open Access Journals (Sweden)

    Thierry Granjon

    Full Text Available BACKGROUND: Oxaloacetate decarboxylase (OAD is a member of the Na(+ transport decarboxylase enzyme family found exclusively in anaerobic bacteria. OAD of Vibrio cholerae catalyses a key step in citrate fermentation, converting the chemical energy of the decarboxylation reaction into an electrochemical gradient of Na(+ ions across the membrane, which drives endergonic membrane reactions such as ATP synthesis, transport and motility. OAD is a membrane-bound enzyme composed of alpha, beta and gamma subunits. The alpha subunit contains the carboxyltransferase catalytic site. METHODOLOGY/PRINCIPAL FINDINGS: In this report, spectroscopic techniques were used to probe oxomalonate (a competitive inhibitor of OAD with respect to oxaloacetate and Na(+ effects on the enzyme tryptophan environment and on the secondary structure of the OAD complex, as well as the importance of each subunit in the catalytic mechanism. An intrinsic fluorescence approach, Red Edge Excitation Shift (REES, indicated that solvent molecule mobility in the vicinity of OAD tryptophans was more restricted in the presence of oxomalonate. It also demonstrated that, although the structure of OAD is sensitive to the presence of NaCl, oxomalonate was able to bind to the enzyme even in the absence of Na(+. REES changes due to oxomalonate binding were also observed with the alphagamma and alpha subunits. Infrared spectra showed that OAD, alphagamma and alpha subunits have a main component band centered between 1655 and 1650 cm(-1 characteristic of a high content of alpha helix structures. Addition of oxomalonate induced a shift of the amide-I band of OAD toward higher wavenumbers, interpreted as a slight decrease of beta sheet structures and a concomitant increase of alpha helix structures. Oxomalonate binding to alphagamma and alpha subunits also provoked secondary structure variations, but these effects were negligible compared to OAD complex. CONCLUSION: Oxomalonate binding affects the

  18. Effect of the coupling between electronic structure and crystalline structure on some properties of transition metals

    International Nuclear Information System (INIS)

    Nastar, M.

    1994-01-01

    The elastic constants, energetic stabilities and vacancy formation energies in transition metals are calculated within a Tight Binding model. In order to outline the effect of the electronic structure, these properties are represented as functions of band filling. The variation of the shear elastic constants of hexagonal close packed (HCP), body centered cubic (BCC) and face centered cubic (FCC) structures, is in contrast with the roughly parabolic behavior of bulk modulus. The general trends are in very good agreement with available experimental and 'ab initio' data. The vacancy formation energy in the BCC structure shows strong deviations from bell shape behavior with a maximum corresponding approximately to the band filling of group 6. This band filling effect contributes to the noticeable decrease of the self diffusion rate between group 4 and group 6. We demonstrate that the abrupt increase of the C' elastic constant, the NT 1 (0.-1.1) phonon frequency, the energy differences between BCC and HCP and between FCC and HCP as well as the vacancy formation energy, that occurs when going from Zr to Mo, is related to the presence of a pseudo-gap in the density of states of the BCC structure. Using the recursion method, we show that the general trends of these properties are correctly reproduced when considering only a few moments of the density of states (about 6). On the other hand, details such as the elastic constant singularities, are displayed only with an exact calculation of the density of states. (Author). 173 refs., 84 figs., 5 tabs

  19. Location of the valence band maximum in the band structure of anisotropic 1 T'-ReSe2

    Science.gov (United States)

    Eickholt, P.; Noky, J.; Schwier, E. F.; Shimada, K.; Miyamoto, K.; Okuda, T.; Datzer, C.; Drüppel, M.; Krüger, P.; Rohlfing, M.; Donath, M.

    2018-04-01

    Transition-metal dichalcogenides (TMDCs) are a focus of current research due to their fascinating optical and electronic properties with possible technical applications. ReSe2 is an interesting material of the TMDC family, with unique anisotropic properties originating from its distorted 1 T structure (1 T '). To develop a fundamental understanding of the optical and electric properties, we studied the underlying electronic structure with angle-resolved photoemission (ARPES) as well as band-structure calculations within the density functional theory (DFT)-local density approximation (LDA) and GdW approximations. We identified the Γ ¯M¯1 direction, which is perpendicular to the a axis, as a distinct direction in k space with the smallest bandwidth of the highest valence band. Using photon-energy-dependent ARPES, two valence band maxima are identified within experimental limits of about 50 meV: one at the high-symmetry point Z , and a second one at a non-high-symmetry point in the Brillouin zone. Thus, the position in k space of the global valence band maximum is undecided experimentally. Theoretically, an indirect band gap is predicted on a DFT-LDA level, while quasiparticle corrections lead to a direct band gap at the Z point.

  20. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

    Directory of Open Access Journals (Sweden)

    Waqasuddin Khan

    Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.

  1. Three-dimensional measurement of a tightly focused laser beam

    Directory of Open Access Journals (Sweden)

    Xiangsheng Xie

    2013-02-01

    Full Text Available The spatial structure of a tightly focused light field is measured with a double knife-edge scanning method. The measurement method is based on the use of a high-quality double knife-edge fabricated from a right-angled silicon fragment mounted on a photodetector. The reconstruction of the three-dimensional structures of tightly focused spots is carried out with both uniform and partially obstructed linearly polarized incident light beams. The optical field distribution is found to deviate substantially from the input beam profile in the tightly focused region, which is in good agreement with the results of numerical simulations.

  2. Less-tight versus tight control of hypertension in pregnancy.

    Science.gov (United States)

    Magee, Laura A; von Dadelszen, Peter; Rey, Evelyne; Ross, Susan; Asztalos, Elizabeth; Murphy, Kellie E; Menzies, Jennifer; Sanchez, Johanna; Singer, Joel; Gafni, Amiram; Gruslin, Andrée; Helewa, Michael; Hutton, Eileen; Lee, Shoo K; Lee, Terry; Logan, Alexander G; Ganzevoort, Wessel; Welch, Ross; Thornton, Jim G; Moutquin, Jean-Marie

    2015-01-29

    The effects of less-tight versus tight control of hypertension on pregnancy complications are unclear. We performed an open, international, multicenter trial involving women at 14 weeks 0 days to 33 weeks 6 days of gestation who had nonproteinuric preexisting or gestational hypertension, office diastolic blood pressure of 90 to 105 mm Hg (or 85 to 105 mm Hg if the woman was taking antihypertensive medications), and a live fetus. Women were randomly assigned to less-tight control (target diastolic blood pressure, 100 mm Hg) or tight control (target diastolic blood pressure, 85 mm Hg). The composite primary outcome was pregnancy loss or high-level neonatal care for more than 48 hours during the first 28 postnatal days. The secondary outcome was serious maternal complications occurring up to 6 weeks post partum or until hospital discharge, whichever was later. Included in the analysis were 987 women; 74.6% had preexisting hypertension. The primary-outcome rates were similar among 493 women assigned to less-tight control and 488 women assigned to tight control (31.4% and 30.7%, respectively; adjusted odds ratio, 1.02; 95% confidence interval [CI], 0.77 to 1.35), as were the rates of serious maternal complications (3.7% and 2.0%, respectively; adjusted odds ratio, 1.74; 95% CI, 0.79 to 3.84), despite a mean diastolic blood pressure that was higher in the less-tight-control group by 4.6 mm Hg (95% CI, 3.7 to 5.4). Severe hypertension (≥160/110 mm Hg) developed in 40.6% of the women in the less-tight-control group and 27.5% of the women in the tight-control group (Phypertension. (Funded by the Canadian Institutes of Health Research; CHIPS Current Controlled Trials number, ISRCTN71416914; ClinicalTrials.gov number, NCT01192412.).

  3. Band structure of superlattice with δ-like potential

    International Nuclear Information System (INIS)

    Gashimzade, N.F.; Gashimzade, F.M.; Hajiev, A.T.

    1993-08-01

    Band structure of superlattice with δ-like potential has been calculated taking into account interaction of carriers of different kinds. Superlattices of semiconductors with degenerated valence band and zero-gap semiconductors have been considered. For the latter semimetal-semiconductor transition has been obtained. (author). 8 refs, 1 fig

  4. Band structural properties of MoS2 (molybdenite)

    International Nuclear Information System (INIS)

    Gupta, V.P.

    1980-01-01

    Semiconductivity and superconductivity in MoS 2 (molybdenite) can be understood in terms of the band structure of MoS 2 . The band structural properties of MoS 2 are presented here. The energy dependence of nsub(eff) and epsilon(infinity)sub(eff) is investigated. Using calculated values of nsub(eff) and epsilon(infinity)sub(eff), the Penn gap has been determined. The value thus obtained is shown to be in good agreement with the reflectivity data and also with the value obtained from the band structure. The Ravindra and Srivastava formula has been shown to give values for the isobaric temperature gradient of Esub(G)[(deltaEsub(G)/deltaT)sub(P)], which are in agreement with the experimental data, and the contribution to (deltaEsub(G)/deltaT)sub(P) due to the electron lattice interaction has been evaluated. In addition, the electronic polarizability has been calculated using a modified Lorentz-Lorenz relation. (author)

  5. General theoretical description of angle-resolved photoemission spectroscopy of van der Waals structures

    Science.gov (United States)

    Amorim, B.

    2018-04-01

    We develop a general theory to model the angle-resolved photoemission spectroscopy (ARPES) of commensurate and incommensurate van der Waals (vdW) structures, formed by lattice mismatched and/or misaligned stacked layers of two-dimensional materials. The present theory is based on a tight-binding description of the structure and the concept of generalized umklapp processes, going beyond previous descriptions of ARPES in incommensurate vdW structures, which are based on continuous, low-energy models, being limited to structures with small lattice mismatch/misalignment. As applications of the general formalism, we study the ARPES bands and constant energy maps for two structures: twisted bilayer graphene and twisted bilayer MoS2. The present theory should be useful in correctly interpreting experimental results of ARPES of vdW structures and other systems displaying competition between different periodicities, such as two-dimensional materials weakly coupled to a substrate and materials with density wave phases.

  6. First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

    Science.gov (United States)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-04-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

  7. The establishment of a method for evaluating the long-term water-tightness durability of underground concrete structure taking into account some deteriorations

    International Nuclear Information System (INIS)

    Hironaga, Michihiko; Kawanishi, Motoi

    1996-01-01

    To establish a method of evaluating the long-term water-tightness durability of underground concrete structures, the authors firstly studied a deterioration evaluation model to express the deterioration condition of concrete structures and constructed, on the basis of this model, a function evaluation model to estimate the lowering of functions due to deterioration, consequently indicating a 'concept for evaluating the deterioration and functions of concrete structures' which will make it possible to perform the functional evaluation of concrete structures. Based on this concept, the authors then discusses a technique for evaluating the long-term water-tightness durability of underground concrete structures, specifically indicating the technique by means of illustrations. (author)

  8. Measuring the band structures of periodic beams using the wave superposition method

    Science.gov (United States)

    Junyi, L.; Ruffini, V.; Balint, D.

    2016-11-01

    Phononic crystals and elastic metamaterials are artificially engineered periodic structures that have several interesting properties, such as negative effective stiffness in certain frequency ranges. An interesting property of phononic crystals and elastic metamaterials is the presence of band gaps, which are bands of frequencies where elastic waves cannot propagate. The presence of band gaps gives this class of materials the potential to be used as vibration isolators. In many studies, the band structures were used to evaluate the band gaps. The presence of band gaps in a finite structure is commonly validated by measuring the frequency response as there are no direct methods of measuring the band structures. In this study, an experiment was conducted to determine the band structure of one dimension phononic crystals with two wave modes, such as a bi-material beam, using the frequency response at only 6 points to validate the wave superposition method (WSM) introduced in a previous study. A bi-material beam and an aluminium beam with varying geometry were studied. The experiment was performed by hanging the beams freely, exciting one end of the beams, and measuring the acceleration at consecutive unit cells. The measured transfer function of the beams agrees with the analytical solutions but minor discrepancies. The band structure was then determined using WSM and the band structure of one set of the waves was found to agree well with the analytical solutions. The measurements taken for the other set of waves, which are the evanescent waves in the bi-material beams, were inaccurate and noisy. The transfer functions at additional points of one of the beams were calculated from the measured band structure using WSM. The calculated transfer function agrees with the measured results except at the frequencies where the band structure was inaccurate. Lastly, a study of the potential sources of errors was also conducted using finite element modelling and the errors in

  9. Photonic band edge assisted spontaneous emission enhancement from all Er3+ 1-D photonic band gap structure

    Science.gov (United States)

    Chiasera, A.; Meroni, C.; Varas, S.; Valligatla, S.; Scotognella, F.; Boucher, Y. G.; Lukowiak, A.; Zur, L.; Righini, G. C.; Ferrari, M.

    2018-06-01

    All Er3+ doped dielectric 1-D Photonic Band Gap Structure was fabricated by rf-sputtering technique. The structure was constituted by of twenty pairs of SiO2/TiO2 alternated layers doped with Er3+ ions. The scanning electron microscopy was used to check the morphology of the structure. Transmission measurements put in evidence the stop band in the range 1500 nm-1950 nm. The photoluminescence measurements were obtained by optically exciting the sample and detecting the emitted light in the 1.5 μm region at different detection angles. Luminescence spectra and luminescence decay curves put in evidence that the presence of the stop band modify the emission features of the Er3+ ions.

  10. Prime tight frames

    DEFF Research Database (Denmark)

    Lemvig, Jakob; Miller, Christopher; Okoudjou, Kasso A.

    2014-01-01

    to suggest effective analysis and synthesis computation strategies for such frames. Finally, we describe all prime frames constructed from the spectral tetris method, and, as a byproduct, we obtain a characterization of when the spectral tetris construction works for redundancies below two.......We introduce a class of finite tight frames called prime tight frames and prove some of their elementary properties. In particular, we show that any finite tight frame can be written as a union of prime tight frames. We then characterize all prime harmonic tight frames and use thischaracterization...

  11. Effects of axial magnetic field on the electronic and optical properties of boron nitride nanotube

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2011-07-01

    The splitting of band structure and absorption spectrum, for boron nitride nanotubes (BNNTs) under axial magnetic field, is studied using the tight binding approximation. It is found that the band splitting ( ΔE) at the Γ point is linearly proportional to the magnetic field ( Φ/Φ0). Our results indicate that the splitting rate νii, of the two first bands nearest to the Fermi level, is a linear function of n -2 for all (n,0) zigzag BNNTs. By investigation of the dependence of band structure and absorption spectrum to the magnetic field, we found that absorption splitting is equal to band splitting and the splitting rate of band structure can be used to determine the splitting rate of the absorption spectrum.

  12. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

    Directory of Open Access Journals (Sweden)

    Hu Jianjun

    2011-05-01

    Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

  13. Mid-frequency Band Dynamics of Large Space Structures

    Science.gov (United States)

    Coppolino, Robert N.; Adams, Douglas S.

    2004-01-01

    High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

  14. Exciton binding energy in wurtzite InGaN/GaN quantum wells

    International Nuclear Information System (INIS)

    Park, Seoung-Hwan; Kim, Jong-Jae; Kim, Hwa-Min

    2004-01-01

    The internal field and carrier density effects on the exciton binding energies in wurtzite (WZ) InGaN/GaN quantum-well (QW) structures are investigated using the multiband effective-mass theory, and are compared with those obtained from the at-band model and with those of GaN/AlGaN QW structures. The exciton binding energy is significantly reduced with increasing sheet carrier density, suggesting that excitons are nearly bleached at densities around 10 12 cm -2 for both InGaN/GaN and GaN/AlGaN QW structures. With the inclusion of the internal field, the exciton binding energy is substantialy reduced compared to that of the at-band model in the investigated region of the wells. This can be explained by a decrease in the momentum matrix element and an increase in the inverse screening length due to the internal field. The exciton binding energy of the InGaN/GaN structure is smaller than that of the GaN/AlGaN structure because InGaN/GaN structures have a smaller momentum matrix element and a larger inverse screening length than GaN/AlGaN structures.

  15. Characterization of band structure for transverse acoustic phonons in Fibonacci superlattices by a bandedge formalism

    International Nuclear Information System (INIS)

    Hsueh, W J; Chen, R F; Tang, K Y

    2008-01-01

    We present a divergence-free method to determine the characteristics of band structures and projected band structures of transverse acoustic phonons in Fibonacci superlattices. A set of bandedge equations is formulated to solve the band structures for the phonon instead of using the traditional dispersion relation. Numerical calculations show band structures calculated by the present method for the Fibonacci superlattice without numerical instability, which may occur in traditional methods. Based on the present formalism, the band structure for the acoustic phonons has been characterized by closure points and the projected bandgaps of the forbidden bands. The projected bandgaps are determined by the projected band structure, which is characterized by the cross points of the projected bandedges. We observed that the band structure and projected band structure and their characteristics were quite different for different generation orders and the basic layers for the Fibonacci superlattice. In this study, concise rules to determine these characteristics of the band structure and the projected band structure, including the number and the location of closure points of forbidden bands and those of projected bandgaps, in Fibonacci superlattices with arbitrary generation order and basic layers are proposed.

  16. A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

    Science.gov (United States)

    Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

    2014-06-10

    We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

  17. Polarization-dependent diffraction in all-dielectric, twisted-band structures

    Energy Technology Data Exchange (ETDEWEB)

    Kardaś, Tomasz M.; Jagodnicka, Anna; Wasylczyk, Piotr, E-mail: pwasylcz@fuw.edu.pl [Photonic Nanostructure Facility, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warszawa (Poland)

    2015-11-23

    We propose a concept for light polarization management: polarization-dependent diffraction in all-dielectric microstructures. Numerical simulations of light propagation show that with an appropriately configured array of twisted bands, such structures may exhibit zero birefringence and at the same time diffract two circular polarizations with different efficiencies. Non-birefringent structures as thin as 3 μm have a significant difference in diffraction efficiency for left- and right-hand circular polarizations. We identify the structural parameters of such twisted-band matrices for optimum performance as circular polarizers.

  18. Phononic Band Gaps in 2D Quadratic and 3D Cubic Cellular Structures.

    Science.gov (United States)

    Warmuth, Franziska; Körner, Carolin

    2015-12-02

    The static and dynamic mechanical behaviour of cellular materials can be designed by the architecture of the underlying unit cell. In this paper, the phononic band structure of 2D and 3D cellular structures is investigated. It is shown how the geometry of the unit cell influences the band structure and eventually leads to full band gaps. The mechanism leading to full band gaps is elucidated. Based on this knowledge, a 3D cellular structure with a broad full band gap is identified. Furthermore, the dependence of the width of the gap on the geometry parameters of the unit cell is presented.

  19. What is the role of the second "structural" NADP+-binding site in human glucose 6-phosphate dehydrogenase?

    Science.gov (United States)

    Wang, Xiao-Tao; Chan, Ting Fai; Lam, Veronica M S; Engel, Paul C

    2008-08-01

    Human glucose 6-phosphate dehydrogenase, purified after overexpression in E. coli, was shown to contain one molecule/subunit of acid-extractable "structural" NADP+ and no NADPH. This tightly bound NADP+ was reduced by G6P, presumably following migration to the catalytic site. Gel-filtration yielded apoenzyme, devoid of bound NADP+ but, surprisingly, still fully active. Mr of the main component of "stripped" enzyme by gel filtration was approximately 100,000, suggesting a dimeric apoenzyme (subunit Mr = 59,000). Holoenzyme also contained tetramer molecules and, at high protein concentration, a dynamic equilibrium gave an apparent intermediate Mr of 150 kDa. Fluorescence titration of the stripped enzyme gave the K d for structural NADP+ as 37 nM, 200-fold lower than for "catalytic" NADP+. Structural NADP+ quenches 91% of protein fluorescence. At 37 degrees C, stripped enzyme, much less stable than holoenzyme, inactivated irreversibly within 2 d. Inactivation at 4 degrees C was partially reversed at room temperature, especially with added NADP+. Apoenzyme was immediately active, without any visible lag, in rapid-reaction studies. Human G6PD thus forms active dimer without structural NADP+. Apparently, the true role of the second, tightly bound NADP+ is to secure long-term stability. This fits the clinical pattern, G6PD deficiency affecting the long-lived non-nucleate erythrocyte. The Kd values for two class I mutants, G488S and G488V, were 273 nM and 480 nM, respectively (seven- and 13-fold elevated), matching the structural prediction of weakened structural NADP+ binding, which would explain decreased stability and consequent disease. Preparation of native apoenzyme and measurement of Kd constant for structural NADP+ will now allow quantitative assessment of this defect in clinical G6PD mutations.

  20. Structured Laguerre-Gaussian beams for mitigation of spherical aberration in tightly focused regimes

    Science.gov (United States)

    Haddadi, S.; Bouzid, O.; Fromager, M.; Hasnaoui, A.; Harfouche, A.; Cagniot, E.; Forbes, A.; Aït-Ameur, K.

    2018-04-01

    Many laser applications utilise a focused laser beam having a single-lobed intensity profile in the focal plane, ideally with the highest possible on-axis intensity. Conventionally, this is achieved with the lowest-order Laguerre-Gaussian mode (LG00), the Gaussian beam, in a tight focusing configuration. However, tight focusing often involves significant spherical aberration due to the high numerical aperture of the systems involved, thus degrading the focal quality. Here, we demonstrate that a high-order radial LG p0 mode can be tailored to meet and in some instances exceed the performance of the Gaussian. We achieve this by phase rectification of the mode using a simple binary diffractive optic. By way of example, we show that the focusing of a rectified LG50 beam is almost insensitive to a spherical aberration coefficient of over three wavelengths, in contrast with the usual Gaussian beam for which the intensity of the focal spot is reduced by a factor of two. This work paves the way towards enhanced focal spots using structured light.

  1. Empirical optimization of DFT  +  U and HSE for the band structure of ZnO

    Science.gov (United States)

    Bashyal, Keshab; Pyles, Christopher K.; Afroosheh, Sajjad; Lamichhane, Aneer; Zayak, Alexey T.

    2018-02-01

    ZnO is a well-known wide band gap semiconductor with promising potential for applications in optoelectronics, transparent electronics, and spintronics. Computational simulations based on the density functional theory (DFT) play an important role in the research of ZnO, but the standard functionals, like Perdew-Burke-Erzenhof, result in largely underestimated values of the band gap and the binding energies of the Zn3d electrons. Methods like DFT  +  U and hybrid functionals are meant to remedy the weaknesses of plain DFT. However, both methods are not parameter-free. Direct comparison with experimental data is the best way to optimize the computational parameters. X-ray photoemission spectroscopy (XPS) is commonly considered as a benchmark for the computed electronic densities of states. In this work, both DFT  +  U and HSE methods were parametrized to fit almost exactly the binding energies of electrons in ZnO obtained by XPS. The optimized parameterizations of DFT  +  U and HSE lead to significantly worse results in reproducing the ion-clamped static dielectric tensor, compared to standard high-level calculations, including GW, which in turn yield a perfect match for the dielectric tensor. The failure of our XPS-based optimization reveals the fact that XPS does not report the ground state electronic structure for ZnO and should not be used for benchmarking ground state electronic structure calculations.

  2. Quasiparticle band structure of rocksalt-CdO determined using maximally localized Wannier functions.

    Science.gov (United States)

    Dixit, H; Lamoen, D; Partoens, B

    2013-01-23

    CdO in the rocksalt structure is an indirect band gap semiconductor. Thus, in order to determine its band gap one needs to calculate the complete band structure. However, in practice, the exact evaluation of the quasiparticle band structure for the large number of k-points which constitute the different symmetry lines in the Brillouin zone can be an extremely demanding task compared to the standard density functional theory (DFT) calculation. In this paper we report the full quasiparticle band structure of CdO using a plane-wave pseudopotential approach. In order to reduce the computational effort and time, we make use of maximally localized Wannier functions (MLWFs). The MLWFs offer a highly accurate method for interpolation of the DFT or GW band structure from a coarse k-point mesh in the irreducible Brillouin zone, resulting in a much reduced computational effort. The present paper discusses the technical details of the scheme along with the results obtained for the quasiparticle band gap and the electron effective mass.

  3. Structural changes of eIF4E upon binding to the mRNA 5' monomethylguanosine and trimethylguanosine Cap.

    Science.gov (United States)

    Rutkowska-Wlodarczyk, Izabela; Stepinski, Janusz; Dadlez, Michal; Darzynkiewicz, Edward; Stolarski, Ryszard; Niedzwiecka, Anna

    2008-03-04

    Recognition of the 5' cap by the eukaryotic initiation factor 4E (eIF4E) is the rate-limiting step in the ribosome recruitment to mRNAs. The regular cap consists of 7-monomethylguanosine (MMG) linked by a 5'-5' triphosphate bridge to the first transcribed nucleoside, while some primitive eukaryotes possess a N (2), N (2),7-trimethylguanosine (TMG) cap structure as a result of trans splicing. Mammalian eIF4E is highly specific to the MMG form of the cap in terms of association constants and thermodynamic driving force. We have investigated conformational changes of eIF4E induced by interaction with two cap analogues, 7-methyl-GTP and N (2), N (2),7-trimethyl-GTP. Hydrogen-deuterium exchange and electrospray mass spectrometry were applied to probe local dynamics of murine eIF4E in the apo and cap-bound forms. The data show that the cap binding induces long-range conformational changes in the protein, not only in the cap-binding pocket but also in a distant region of the 4E-BP/eIF4G binding site. Formation of the complex with 7-methyl-GTP makes the eIF4E structure more compact, while binding of N (2), N (2),7-trimethyl-GTP leads to higher solvent accessibility of the protein backbone in comparison with the apo form. The results suggest that the additional double methylation at the N (2)-amino group of the cap causes sterical effects upon binding to mammalian eIF4E which influence the overall solution dynamics of the protein, thus precluding formation of a tight complex.

  4. Systematic design of phononic band-gap materials and structures by topology optimization

    DEFF Research Database (Denmark)

    Sigmund, Ole; Jensen, Jakob Søndergaard

    2003-01-01

    Phononic band-gap materials prevent elastic waves in certain frequency ranges from propagating, and they may therefore be used to generate frequency filters, as beam splitters, as sound or vibration protection devices, or as waveguides. In this work we show how topology optimization can be used...... to design and optimize periodic materials and structures exhibiting phononic band gaps. Firstly, we optimize infinitely periodic band-gap materials by maximizing the relative size of the band gaps. Then, finite structures subjected to periodic loading are optimized in order to either minimize the structural...

  5. Valence band electronic structure and band alignment of LaAlO{sub 3}/SrTiO{sub 3}(111) heterointerfaces

    Energy Technology Data Exchange (ETDEWEB)

    Gabel, J.; Scheiderer, P.; Zapf, M.; Schuetz, P.; Sing, M.; Claessen, R. [Physikalisches Institut and Roentgen Center for Complex Material Systems (RCCM), Universitaet Wuerzburg (Germany); Schlueter, C.; Lee, T.L. [Diamond Light Source, Didcot (United Kingdom)

    2015-07-01

    As in the famous LaAlO{sub 3}(LAO)/SrTiO{sub 3}(STO) (001) a two-dimensional electron system (2DES) also forms at the interface between LAO and STO in (111) orientation. A distinct feature of the (111) interface is its peculiar real space topology. Each bilayer represents a buckled honeycomb lattice similar to graphene which is known theoretically to host various topologically non-trivial states. Bilayer STO in proximity to the interface can be regarded as a three-orbital generalization of graphene with enhanced electron correlations making it a promising candidate for the realization of strongly correlated topological phases. We have investigated the electronic structure of the LAO/STO (111) heterostructure in relation to the oxygen vacancy concentration which we can control by synchrotron light irradiation and oxygen dosing. With hard X-ray photoemission we study the core levels, whereas resonant soft X-ray photoemission is used to probe the interfacial valence band (VB) states. Two VB features are found: a peak at the Fermi level associated with the 2DES and in-gap states at higher binding energies attributed to oxygen vacancies. By varying the oxygen vacancy contribution we can tune the emergence of the VB states and engineer the interfacial band alignment.

  6. Deformed configurations, band structures and spectroscopic ...

    Indian Academy of Sciences (India)

    2014-03-20

    Mar 20, 2014 ... The deformed configurations and rotational band structures in =50 Ge and Se nuclei are studied by deformed Hartree–Fock with quadrupole constraint and angular momentum projection. Apart from the `almost' spherical HF solution, a well-deformed configuration occurs at low excitation. A deformed ...

  7. Structural diagenesis in Upper Carboniferous tight gas sandstones. Lessons learned from the Piesberg analog study

    Energy Technology Data Exchange (ETDEWEB)

    Steindorf, P.; Hoehne, M.; Becker, S.; Hilgers, C. [RWTH Aachen Univ. (Germany). Energy and Mineral Resources Group (EMR); Koehrer, B. [Wintershall Holding GmbH, Barnstorf (Germany)

    2013-08-01

    Upper Carboniferous tight gas sandstone reservoirs in NW-Germany consist of thick successions of cyclothems. Our focus is the Westphalian D of the Piesberg quarry near Osnabrueck, which exposes cemented, faulted and jointed third-order coarse- to fine-grained sandstone cycles separated by anthracite coal seams. We characterize the rocks and the lateral variation of rock properties such as porosity to better constrain input data for reservoir modelling. Three cycles are exposed, each approximately 50 m thick. Rock types can be clearly distinguished by spectral gamma ray in the quarry. Sandstones are intensely compacted and cemented with quartz and generally characterized by low porosities < 8 % (Hepycnometry on plugs and cuttings). Porosities are secondary and mainly related to detrital carbonate dissolution. Around faults dissolution is higher and the porosities can increase to up to 25%. The normal faults show different throws in the quarry and bands of shale and coal have smeared into the fault at juxtaposed beds, which may result in compartments. They dominantly strike W-E and NNW-SSE, but subordinate NE-SW striking fault patterns are also present. Joints were analyzed in a 50 x 50 m section of the quarry wall using Lidar (Light detection and ranging) laser scanning, which allows the characterization of the lithology and quantitative measurement of bedding and fracture orientation data in inaccessible areas. NNE-SSW and W-E joint sets are accompanied by northeasterly and northwesterly striking sets. Around faults, fault planes and fractures are cemented with quartz veins, showing localized mass transport. Due to the intense cementation, the sandstones can reach uniaxial strengths of more than 100 MPa normal to bedding, and approximately 50 MPa parallel to bedding. Sandstone beds within and close to faults are leached by fluids, and their uniaxial strength is reduced by a factor of more than two. Our high resolution field data enables a better understanding of

  8. Surface band structures on Nb(001)

    International Nuclear Information System (INIS)

    Fang, B.; Lo, W.; Chien, T.; Leung, T.C.; Lue, C.Y.; Chan, C.T.; Ho, K.M.

    1994-01-01

    We report the joint studies of experimental and theoretical surface band structures of Nb(001). Angle-resolved photoelectron spectroscopy was used to determine surface-state dispersions along three high-symmetry axes bar Γ bar M, bar Γ bar X, and bar M bar X in the surface Brillouin zone. Ten surface bands have been identified. The experimental data are compared to self-consistent pseudopotential calculations for the 11-layer Nb(001) slabs that are either bulk terminated or fully relaxed (with a 12% contraction for the first interlayer spacing). The band calculations for a 12% surface-contracted slab are in better agreement with the experimental results than those for a bulk-terminated slab, except for a surface resonance near the Fermi level, which is related to the spin-orbit interaction. The charge profiles for all surface states or resonances have been calculated. Surface contraction effects on the charge-density distribution and the energy position of surface states and resonances will also be discussed

  9. Analysis of oxygen binding-energy variations for BaO on W

    Science.gov (United States)

    Haas, G. A.; Shih, A.; Mueller, D.; Thomas, R. E.

    Interatomic Auger analyses have been made of different forms of BaO layers on W substrates. Variations in Auger spectroscopy energies of the Ba4dBa5pO2p interatomic Auger transition were found to be largely governed by the O2p binding energy of the BaO adsorbate. This was illustrated by comparing results of the Auger data values with values derived from O2p binding energies using ultraviolet photoelectron spectroscopy. Very good agreement was observed not only for the W substrate but also for the W substrate which showed two oxygen-induced electronics state. Variations in binding energy were noted for different states of BaO lattice formation and for different amounts of oxidation, ranging from the transition of Ba to BaO and continuing to the BaO 2 stoichiometry and beyond. Effects were also reported for adsorbate alignment and thermal activation (i.e., reduction) of the oxidized state. An empirical relationship was found suggesting that the more tightly bound the O2p states of the BaO adsorbate were, the lower its work function would be. This link between binding energy and work function was observed to be valid not only for cases of poisoning by oxidation, but held as well during reactivation by the subsequent reduction of the oxide. In addition, this relationship also appeared to predict the low work function obtained through the introduction of substances such as Sc to the BaO-W system. Possible qualitative reasons which might contribute to this are discussed in terms of enhanced dipole effects and shifts in band structure.

  10. Polarimetric and Structural Properties of a Boreal Forest at P-Band and L-Band

    Science.gov (United States)

    Tebaldini, S.; Rocca, F.

    2010-12-01

    With this paper we investigate the structural and polarimetric of the boreal forest within the Krycklan river catchment, Northern Sweden, basing on multi-polarimetric and multi-baseline SAR surveys at P-Band and L-Band collected in the framework of the ESA campaign BioSAR 2008. The analysis has been carried out by applying the Algebraic Synthesis (AS) technique, recently introduced in literature, which provides a theoretical framework for the decomposition of the backscattered signal into ground-only and volume-only contributions, basing on both baseline and polarization diversity. The availability of multiple baselines allows the formation of a synthetic aperture not only along the azimuth direction but also in elevation. Accordingly, the backscattered echoes can be focused not only in the slant range, azimuth plane, but in the whole 3D space. This is the rationale of the SAR Tomography (T-SAR) concept, which has been widely considered in the literature of the last years. It follows that, as long as the penetration in the scattering volume is guaranteed, the vertical profile of the vegetation layer is retrieved by separating backscatter contributions along the vertical direction, which is the main reason for the exploitation of Tomographic techniques at longer wavelengths. Still, the capabilities of T-SAR are limited to imaging the global vertical structure of the electromagnetic scattering in a certain polarization. It then becomes important to develop methodologies for the investigation of the vertical structure of different Scattering Mechanisms (SMs), such as ground and volume scattering, in such a way as to derive information that can be delivered also outside the field of Radar processing. This is an issue that may become relevant at longer wavelengths, such as P-Band, where the presence of multiple scattering arising from the interaction with terrain could hinder the correct reconstruction of the forest structure. The availability of multiple polarizations

  11. Complete flexural vibration band gaps in membrane-like lattice structures

    International Nuclear Information System (INIS)

    Yu Dianlong; Liu Yaozong; Qiu Jing; Wang Gang; Zhao Honggang

    2006-01-01

    The propagation of flexural vibration in the periodical membrane-like lattice structure is studied. The band structure calculated with the plane wave expansion method indicates the existence of complete gaps. The frequency response function of a finite periodic structure is simulated with finite element method. Frequency ranges with vibration attenuation are in good agreement with the gaps found in the band structure. Much larger attenuations are found in the complete gaps comparing to those directional ones. The existence of complete flexural vibration gaps in such a lattice structure provides a new idea for vibration control of thin plates

  12. Structural Fingerprints of Transcription Factor Binding Site Regions

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2009-03-01

    Full Text Available Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.

  13. Pore Structure and Limit Pressure of Gas Slippage Effect in Tight Sandstone

    Science.gov (United States)

    You, Lijun; Xue, Kunlin; Kang, Yili; Liao, Yi

    2013-01-01

    Gas slip effect is an important mechanism that the gas flow is different from liquid flow in porous media. It is generally considered that the lower the permeability in porous media is, the more severe slip effect of gas flow will be. We design and then carry out experiments with the increase of backpressure at the outlet of the core samples based on the definition of gas slip effect and in view of different levels of permeability of tight sandstone reservoir. This study inspects a limit pressure of the gas slip effect in tight sandstones and analyzes the characteristic parameter of capillary pressure curves. The experimental results indicate that gas slip effect can be eliminated when the backpressure reaches a limit pressure. When the backpressure exceeds the limit pressure, the measured gas permeability is a relatively stable value whose range is less than 3% for a given core sample. It is also found that the limit pressure increases with the decreasing in permeability and has close relation with pore structure of the core samples. The results have an important influence on correlation study on gas flow in porous medium, and are beneficial to reduce the workload of laboratory experiment. PMID:24379747

  14. Band structure of an electron in a kind of periodic potentials with singularities

    Science.gov (United States)

    Hai, Kuo; Yu, Ning; Jia, Jiangping

    2018-06-01

    Noninteracting electrons in some crystals may experience periodic potentials with singularities and the governing Schrödinger equation cannot be defined at the singular points. The band structure of a single electron in such a one-dimensional crystal has been calculated by using an equivalent integral form of the Schrödinger equation. Both the perturbed and exact solutions are constructed respectively for the cases of a general singular weak-periodic system and its an exactly solvable version, Kronig-Penney model. Any one of them leads to a special band structure of the energy-dependent parameter, which results in an effective correction to the previous energy-band structure and gives a new explanation for forming the band structure. The used method and obtained results could be a valuable aid in the study of energy bands in solid-state physics, and the new explanation may trigger investigation to different physical mechanism of electron band structures.

  15. Preconditioning Filter Bank Decomposition Using Structured Normalized Tight Frames

    Directory of Open Access Journals (Sweden)

    Martin Ehler

    2015-01-01

    Full Text Available We turn a given filter bank into a filtering scheme that provides perfect reconstruction, synthesis is the adjoint of the analysis part (so-called unitary filter banks, all filters have equal norm, and the essential features of the original filter bank are preserved. Unitary filter banks providing perfect reconstruction are induced by tight generalized frames, which enable signal decomposition using a set of linear operators. If, in addition, frame elements have equal norm, then the signal energy is spread through the various filter bank channels in some uniform fashion, which is often more suitable for further signal processing. We start with a given generalized frame whose elements allow for fast matrix vector multiplication, as, for instance, convolution operators, and compute a normalized tight frame, for which signal analysis and synthesis still preserve those fast algorithmic schemes.

  16. Compact electromagnetic bandgap structures for notch band in ultra-wideband applications.

    Science.gov (United States)

    Rotaru, Mihai; Sykulski, Jan

    2010-01-01

    This paper introduces a novel approach to create notch band filters in the front-end of ultra-wideband (UWB) communication systems based on electromagnetic bandgap (EBG) structures. The concept presented here can be implemented in any structure that has a microstrip in its configuration. The EBG structure is first analyzed using a full wave electromagnetic solver and then optimized to work at WLAN band (5.15-5.825 GHz). Two UWB passband filters are used to demonstrate the applicability and effectiveness of the novel EBG notch band feature. Simulation results are provided for two cases studied.

  17. Tunable band structures of polycrystalline graphene by external and mismatch strains

    Institute of Scientific and Technical Information of China (English)

    Jiang-Tao Wu; Xing-Hua Shi; Yu-Jie Wei

    2012-01-01

    Lacking a band gap largely limits the application of graphene in electronic devices.Previous study shows that grain boundaries (GBs) in polycrystalline graphene can dramatically alter the electrical properties of graphene.Here,we investigate the band structure of polycrystalline graphene tuned by externally imposed strains and intrinsic mismatch strains at the GB by density functional theory (DFT) calculations.We found that graphene with symmetrical GBs typically has zero band gap even with large uniaxial and biaxial strain.However,some particular asymmetrical GBs can open a band gap in graphene and their band structures can be substantially tuned by external strains.A maximum band gap about 0.19 eV was observed in matched-armchair GB (5,5) | (3,7) with a misorientation of θ =13° when the applied uniaxial strain increases to 9%.Although mismatch strain is inevitable in asymmetrical GBs,it has a small influence on the band gap of polycrystalline graphene.

  18. Magnetization and spin-polarized conductance of asymmetrically hydrogenated graphene nanoribbons: significance of sigma bands

    International Nuclear Information System (INIS)

    Honda, Syuta; Inuzuka, Kouhei; Inoshita, Takeshi; Ota, Norio; Sano, Nobuyuki

    2014-01-01

    The magnetization and spin transport of asymmetric zigzag-edge graphene nanoribbons, terminated by hydrogen on one edge while unterminated on the other edge, were investigated by a combination of first-principles calculations and a tight-binding approach. At the unterminated edge, a spin-polarized σ edge state of minority spin appears near the Fermi level and contributes to spin transport. This state enters the band gap for ribbon widths of less than 15 chains, dominating the spin-polarized current. This indicates the importance of the σ edge states in the design of spintronic devices using graphene nanoribbons. We also examined the case where the ‘unterminated’ edge is partially terminated by hydrogen. (paper)

  19. First-principles momentum-dependent local ansatz wavefunction and momentum distribution function bands of iron

    International Nuclear Information System (INIS)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-01-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi–Dirac function for the d electrons with e g symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data. (author)

  20. Multi-cavity locally resonant structure with the low frequency and broad band-gaps

    Directory of Open Access Journals (Sweden)

    Jiulong Jiang

    2016-11-01

    Full Text Available A multi-cavity periodic structure with the characteristic of local resonance was proposed in the paper. The low frequency band-gap structure was comparatively analyzed by the finite element method (FEM and electric circuit analogy (ECA. Low frequency band-gap can be opened through the dual influence of the coupling’s resonance in the cavity and the interaction among the couplings between structures. Finally, the influence of the structural factors on the band-gap was analyzed. The results show that the structure, which is divided into three parts equally, has a broader effective band-gap below the frequency of 200 Hz. It is also proved that reducing the interval between unit structures can increase the intensity of the couplings among the structures. And in this way, the width of band-gap would be expanded significantly. Through the parameters adjustment, the structure enjoys a satisfied sound insulation effect below the frequency of 500Hz. In the area of low frequency noise reduction, the structure has a lot of potential applications.

  1. The calculation of deep levels in semiconductors by using a recursion method for super-cells

    International Nuclear Information System (INIS)

    Wong Yongliang.

    1987-01-01

    The paper presents the theory of deep levels in semiconductors, the super-cell approach to the theory of deep level impurities, the calculation of band structure by using the tight-binding method and the recursion method used to study the defects in the presence of lattice relaxation and extended defect complexes. 47 refs

  2. ARPES study of the evolution of band structure and charge density wave properties in RTe3 ( R=Y , La, Ce, Sm, Gd, Tb, and Dy)

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Zahid; Brouet, Veronique; Yang, Wanli; Zhou, Xingjiang; Hussain, Zahid; Moore, R.G.; He, R.; Lu, D. H.; Shen, Z.X.; Laverock, J.; Dugdale, S.B.; Ru, N.; Fisher, R.

    2008-01-16

    We present a detailed angle-resolved photoemission spectroscopy (ARPES) investigation of the RTe3 family, which sets this system as an ideal"textbook" example for the formation of a nesting driven charge density wave (CDW). This family indeed exhibits the full range of phenomena that can be associated to CDWinstabilities, from the opening of large gaps on the best nested parts of Fermi surface (up to 0.4 eV), to the existence of residual metallic pockets. ARPES is the best suited technique to characterize these features, thanks to its unique ability to resolve the electronic structure in k space. An additional advantage of RTe3 is that theband structure can be very accurately described by a simple two dimensional tight-binding (TB) model, which allows one to understand and easily reproduce many characteristics of the CDW. In this paper, we first establish the main features of the electronic structure by comparing our ARPES measurements with the linear muffin-tinorbital band calculations. We use this to define the validity and limits of the TB model. We then present a complete description of the CDW properties and of their strong evolution as a function of R. Using simple models, we are able to reproduce perfectly the evolution of gaps in k space, the evolution of the CDW wave vector with R, and the shape of the residual metallic pockets. Finally, we give an estimation of the CDWinteraction parameters and find that the change in the electronic density of states n (EF), due to lattice expansion when different R ions are inserted, has the correct order of magnitude to explain the evolution of the CDW properties.

  3. Valence band structure of binary chalcogenide vitreous semiconductors by high-resolution XPS

    International Nuclear Information System (INIS)

    Kozyukhin, S.; Golovchak, R.; Kovalskiy, A.; Shpotyuk, O.; Jain, H.

    2011-01-01

    High-resolution X-ray photoelectron spectroscopy (XPS) is used to study regularities in the formation of valence band electronic structure in binary As x Se 100−x , As x S 100−x , Ge x Se 100−x and Ge x S 100−x chalcogenide vitreous semiconductors. It is shown that the highest occupied energetic states in the valence band of these materials are formed by lone pair electrons of chalcogen atoms, which play dominant role in the formation of valence band electronic structure of chalcogen-rich glasses. A well-expressed contribution from chalcogen bonding p electrons and more deep s orbitals are also recorded in the experimental valence band XPS spectra. Compositional dependences of the observed bands are qualitatively analyzed from structural and compositional points of view.

  4. Valence band structure of binary chalcogenide vitreous semiconductors by high-resolution XPS

    Energy Technology Data Exchange (ETDEWEB)

    Kozyukhin, S., E-mail: sergkoz@igic.ras.ru [Russian Academy of Science, Institute of General and Inorganic Chemistry (Russian Federation); Golovchak, R. [Lviv Scientific Research Institute of Materials of SRC ' Carat' (Ukraine); Kovalskiy, A. [Lehigh University, Department of Materials Science and Engineering (United States); Shpotyuk, O. [Lviv Scientific Research Institute of Materials of SRC ' Carat' (Ukraine); Jain, H. [Lehigh University, Department of Materials Science and Engineering (United States)

    2011-04-15

    High-resolution X-ray photoelectron spectroscopy (XPS) is used to study regularities in the formation of valence band electronic structure in binary As{sub x}Se{sub 100-x}, As{sub x}S{sub 100-x}, Ge{sub x}Se{sub 100-x} and Ge{sub x}S{sub 100-x} chalcogenide vitreous semiconductors. It is shown that the highest occupied energetic states in the valence band of these materials are formed by lone pair electrons of chalcogen atoms, which play dominant role in the formation of valence band electronic structure of chalcogen-rich glasses. A well-expressed contribution from chalcogen bonding p electrons and more deep s orbitals are also recorded in the experimental valence band XPS spectra. Compositional dependences of the observed bands are qualitatively analyzed from structural and compositional points of view.

  5. Cooper-pair size and binding energy for unconventional superconducting systems

    Science.gov (United States)

    Dinóla Neto, F.; Neto, Minos A.; Salmon, Octavio D. Rodriguez

    2018-06-01

    The main proposal of this paper is to analyze the size of the Cooper pairs composed by unbalanced mass fermions from different electronic bands along the BCS-BEC crossover and study the binding energy of the pairs. We are considering an interaction between fermions with different masses leading to an inter-band pairing. In addiction to the attractive interaction we have an hybridization term to couple both bands, which in general acts unfavorable for the pairing between the electrons. We get first order phase transitions as the hybridization breaks the Cooper pairs for the s-wave symmetry of the gap amplitude. The results show the dependence of the Cooper-pair size as a function of the hybridization for T = 0 . We also propose the structure of the binding energy of the inter-band system as a function of the two-bands quasi-particle energies.

  6. Structure-Guided Design of an Engineered Streptavidin with Reusability to Purify Streptavidin-Binding Peptide Tagged Proteins or Biotinylated Proteins

    OpenAIRE

    Wu, Sau-Ching; Wong, Sui-Lam

    2013-01-01

    Development of a high-affinity streptavidin-binding peptide (SBP) tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin an...

  7. Shell model description of band structure in 48Cr

    International Nuclear Information System (INIS)

    Vargas, Carlos E.; Velazquez, Victor M.

    2007-01-01

    The band structure for normal and abnormal parity bands in 48Cr are described using the m-scheme shell model. In addition to full fp-shell, two particles in the 1d3/2 orbital are allowed in order to describe intruder states. The interaction includes fp-, sd- and mixed matrix elements

  8. Probing the graphite band structure with resonant soft-x-ray fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Carlisle, J.A.; Shirley, E.L.; Hudson, E.A. [Lawrence Berkeley National Lab., CA (United States)] [and others

    1997-04-01

    Soft x-ray fluorescence (SXF) spectroscopy using synchrotron radiation offers several advantages over surface sensitive spectroscopies for probing the electronic structure of complex multi-elemental materials. Due to the long mean free path of photons in solids ({approximately}1000 {angstrom}), SXF is a bulk-sensitive probe. Also, since core levels are involved in absorption and emission, SXF is both element- and angular-momentum-selective. SXF measures the local partial density of states (DOS) projected onto each constituent element of the material. The chief limitation of SXF has been the low fluorescence yield for photon emission, particularly for light elements. However, third generation light sources, such as the Advanced Light Source (ALS), offer the high brightness that makes high-resolution SXF experiments practical. In the following the authors utilize this high brightness to demonstrate the capability of SXF to probe the band structure of a polycrystalline sample. In SXF, a valence emission spectrum results from transitions from valence band states to the core hole produced by the incident photons. In the non-resonant energy regime, the excitation energy is far above the core binding energy, and the absorption and emission events are uncoupled. The fluorescence spectrum resembles emission spectra acquired using energetic electrons, and is insensitive to the incident photon`s energy. In the resonant excitation energy regime, core electrons are excited by photons to unoccupied states just above the Fermi level (EF). The absorption and emission events are coupled, and this coupling manifests itself in several ways, depending in part on the localization of the empty electronic states in the material. Here the authors report spectral measurements from highly oriented pyrolytic graphite.

  9. Triazole biotin: a tight-binding biotinidase-resistant conjugate.

    Science.gov (United States)

    Germeroth, Anne I; Hanna, Jill R; Karim, Rehana; Kundel, Franziska; Lowther, Jonathan; Neate, Peter G N; Blackburn, Elizabeth A; Wear, Martin A; Campopiano, Dominic J; Hulme, Alison N

    2013-11-28

    The natural amide bond found in all biotinylated proteins has been replaced with a triazole through CuAAC reaction of an alkynyl biotin derivative. The resultant triazole-linked adducts are shown to be highly resistant to the ubiquitous hydrolytic enzyme biotinidase and to bind avidin with dissociation constants in the low pM range. Application of this strategy to the production of a series of biotinidase-resistant biotin-Gd-DOTA contrast agents is demonstrated.

  10. Less-Tight versus Tight Control of Hypertension in Pregnancy

    NARCIS (Netherlands)

    Magee, Laura A.; von Dadelszen, Peter; Rey, Evelyne; Ross, Susan; Asztalos, Elizabeth; Murphy, Kellie E.; Menzies, Jennifer; Sanchez, Johanna; Singer, Joel; Gafni, Amiram; Gruslin, Andrée; Helewa, Michael; Hutton, Eileen; Lee, Shoo K.; Lee, Terry; Logan, Alexander G.; Ganzevoort, Wessel; Welch, Ross; Thornton, Jim G.; Moutquin, Jean-Marie

    2015-01-01

    BACKGROUND The effects of less-tight versus tight control of hypertension on pregnancy complications are unclear. METHODS We performed an open, international, multicenter trial involving women at 14 weeks 0 days to 33 weeks 6 days of gestation who had nonproteinuric preexisting or gestational

  11. Enhancement of phononic band gaps in ternary/binary structure

    International Nuclear Information System (INIS)

    Aly, Arafa H.; Mehaney, Ahmed

    2012-01-01

    Based on the transfer matrix method (TMM) and Bloch theory, the interaction of elastic waves (normal incidence) with 1D phononic crystal had been studied. The transfer matrix method was obtained for both longitudinal and transverse waves by applying the continuity conditions between the consecutive unit cells. Dispersion relations are calculated and plotted for both binary and ternary structures. Also we have investigated the corresponding effects on the band gaps values for the two types of phononic crystals. Furthermore, it can be observed that the complete band gaps are located in the common frequency stop-band regions. Numerical simulations are performed to investigate the effect of different thickness ratios inside each unit cell on the band gap values, as well as unit cells thickness on the central band gap frequency. These phononic band gap materials can be used as a filter for elastic waves at different frequencies values.

  12. Changing optical band structure with single photons

    Science.gov (United States)

    Albrecht, Andreas; Caneva, Tommaso; Chang, Darrick E.

    2017-11-01

    Achieving strong interactions between individual photons enables a wide variety of exciting possibilities in quantum information science and many-body physics. Cold atoms interfaced with nanophotonic structures have emerged as a platform to realize novel forms of nonlinear interactions. In particular, when atoms are coupled to a photonic crystal waveguide, long-range atomic interactions can arise that are mediated by localized atom-photon bound states. We theoretically show that in such a system, the absorption of a single photon can change the band structure for a subsequent photon. This occurs because the first photon affects the atoms in the chain in an alternating fashion, thus leading to an effective period doubling of the system and a new optical band structure for the composite atom-nanophotonic system. We demonstrate how this mechanism can be engineered to realize a single-photon switch, where the first incoming photon switches the system from being highly transmissive to highly reflective, and analyze how signatures can be observed via non-classical correlations of the outgoing photon field.

  13. Structure of the Mr 140,000 growth hormone-dependent insulin-like growth factor binding protein complex: Determination by reconstitution and affinity-labeling

    International Nuclear Information System (INIS)

    Baxter, R.C.; Martin, J.L.

    1989-01-01

    To determine the structure of the high molecular weight, growth hormone-dependent complex between the insulin-like growth factors (IGF-I and IGF-II) and their binding proteins in human serum, we have reconstituted the complex from its purified component proteins and analyzed it by gel electrophoresis and autoradiography after covalent cross-linking. The proteins tested in reconstitution mixtures were an acid-labile Mr 84,000-86,000 glycoprotein doublet (alpha subunit), an acid-stable Mr 47,000-53,000 glycoprotein doublet with IGF-binding activity (BP-53 or beta subunit), and IGF-I or IGF-II (gamma subunit). In incubations containing any one of the three subunits 125I-labeled and the other two unlabeled, identical 125I-labeled alpha-beta-gamma complexes of Mr 140,000 were formed. Minor bands of Mr 120,000 and 90,000 were also seen, thought to represent a partially deglycosylated form of the alpha-beta-gamma complex, and an alpha-gamma complex arising as a cross-linking artifact. When serum samples from subjects of various growth hormone status were affinity-labeled with IGF-II tracer, a growth hormone-dependent Mr 140,000 band was seen, corresponding to the reconstituted alpha-beta-gamma complex. Other growth hormone-dependent labeled bands, of Mr 90,000 (corresponding to alpha-gamma), Mr 55,000-60,000 (corresponding to labeled beta-subunit doublet), and smaller bands of Mr 38,000, 28,000, and 23,000-25,000 (corresponding to labeled beta-subunit degradation products), were also seen in the affinity-labeled serum samples and in the complex reconstituted from pure proteins. All were immunoprecipitable with an anti-BP-53 antiserum. We conclude that the growth hormone-dependent Mr 140,000 IGF-binding protein complex in human serum has three components: the alpha (acid-labile) subunit, the beta (binding) subunit, and the gamma (growth factor) subunit

  14. Predicting nucleic acid binding interfaces from structural models of proteins.

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

  15. Band Gap Properties of Magnetoelectroelastic Grid Structures with Initial Stress

    International Nuclear Information System (INIS)

    Wang Yi-Ze; Li Feng-Ming

    2012-01-01

    The propagation of elastic waves in magnetoelectroelastic grid structures is studied. Band gap properties are presented and the effects of the magnetoelectroelastic coupling and initial stress are considered. Numerical calculations are performed using the plane-wave expansion method. The results show that the band gap width can be tuned by the initial stress. It is hoped that our results will be helpful for designing acoustic filters with magnetoelectroelastic materials and grid structures

  16. High-order harmonic generation from a two-dimensional band structure

    Science.gov (United States)

    Jin, Jian-Zhao; Xiao, Xiang-Ru; Liang, Hao; Wang, Mu-Xue; Chen, Si-Ge; Gong, Qihuang; Peng, Liang-You

    2018-04-01

    In the past few years, harmonic generation in solids has attracted tremendous attention. Recently, some experiments of two-dimensional (2D) monolayer or few-layer materials have been carried out. These studies demonstrated that harmonic generation in the 2D case shows a strong dependence on the laser's orientation and ellipticity, which calls for a quantitative theoretical interpretation. In this work, we carry out a systematic study on the harmonic generation from a 2D band structure based on a numerical solution to the time-dependent Schrödinger equation. By comparing with the 1D case, we find that the generation dynamics can have a significant difference due to the existence of many crossing points in the 2D band structure. In particular, the higher conduction bands can be excited step by step via these crossing points and the total contribution of the harmonic is given by the mixing of transitions between different clusters of conduction bands to the valence band. We also present the orientation dependence of the harmonic yield on the laser polarization direction.

  17. Structure-guided design of an engineered streptavidin with reusability to purify streptavidin-binding peptide tagged proteins or biotinylated proteins.

    Directory of Open Access Journals (Sweden)

    Sau-Ching Wu

    Full Text Available Development of a high-affinity streptavidin-binding peptide (SBP tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin and SBP with streptavidin were explored. Loop3-4 which serves as a mobile lid for the biotin binding pocket in streptavidin is in the closed state with biotin binding. In contrast, this loop is in the open state with SBP binding. Replacement of glycine-48 with a bulkier residue (threonine in this loop selectively reduces the biotin binding affinity (Kd from 4 × 10(-14 M to 4.45 × 10(-10 M without affecting the SBP binding affinity. Introduction of a second mutation (S27A to the first mutein (G48T results in the development of a novel engineered streptavidin SAVSBPM18 which could be recombinantly produced in the functional form from Bacillus subtilis via secretion. To form an intact binding pocket for tight binding of SBP, two diagonally oriented subunits in a tetrameric streptavidin are required. It is vital for SAVSBPM18 to be stably in the tetrameric state in solution. This was confirmed using an HPLC/Laser light scattering system. SAVSBPM18 retains high binding affinity to SBP but has reversible biotin binding capability. The SAVSBPM18 matrix can be applied to affinity purify SBP-tagged proteins or biotinylated molecules to homogeneity with high recovery in a reusable manner. A mild washing step is sufficient to regenerate the matrix which can be reused for multiple rounds. Other applications including development of automated protein purification systems, lab-on-a-chip micro-devices, reusable biosensors, bioreactors and microarrays, and strippable

  18. Structure-guided design of an engineered streptavidin with reusability to purify streptavidin-binding peptide tagged proteins or biotinylated proteins.

    Science.gov (United States)

    Wu, Sau-Ching; Wong, Sui-Lam

    2013-01-01

    Development of a high-affinity streptavidin-binding peptide (SBP) tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin and SBP with streptavidin were explored. Loop3-4 which serves as a mobile lid for the biotin binding pocket in streptavidin is in the closed state with biotin binding. In contrast, this loop is in the open state with SBP binding. Replacement of glycine-48 with a bulkier residue (threonine) in this loop selectively reduces the biotin binding affinity (Kd) from 4 × 10(-14) M to 4.45 × 10(-10) M without affecting the SBP binding affinity. Introduction of a second mutation (S27A) to the first mutein (G48T) results in the development of a novel engineered streptavidin SAVSBPM18 which could be recombinantly produced in the functional form from Bacillus subtilis via secretion. To form an intact binding pocket for tight binding of SBP, two diagonally oriented subunits in a tetrameric streptavidin are required. It is vital for SAVSBPM18 to be stably in the tetrameric state in solution. This was confirmed using an HPLC/Laser light scattering system. SAVSBPM18 retains high binding affinity to SBP but has reversible biotin binding capability. The SAVSBPM18 matrix can be applied to affinity purify SBP-tagged proteins or biotinylated molecules to homogeneity with high recovery in a reusable manner. A mild washing step is sufficient to regenerate the matrix which can be reused for multiple rounds. Other applications including development of automated protein purification systems, lab-on-a-chip micro-devices, reusable biosensors, bioreactors and microarrays, and strippable detection agents for

  19. Spin response in LiFeAs and NaFeAs iron-pnictides superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Lochner, Felix; Ahn, Felix; Eremin, Ilya [Ruhr-Universitaet Bochum, Bochum (Germany)

    2016-07-01

    We analyze the spin susceptibility in LiFeAs and NaFeAs by using the ten-orbital tight-binding model that we fitted to the electronic band structure measured by recent ARPES experiments. We identify an effective five-band model for a weak k{sub z}-dependence. Besides we present the bare and RPA-susceptibility and its q{sub z} dependencies to study the magnetic instabilities and estimate the strength of intra-orbital and inter-orbital nesting.

  20. Energy band structure tailoring of vertically aligned InAs/GaAsSb quantum dot structure for intermediate-band solar cell application by thermal annealing process.

    Science.gov (United States)

    Liu, Wei-Sheng; Chu, Ting-Fu; Huang, Tien-Hao

    2014-12-15

    This study presents an band-alignment tailoring of a vertically aligned InAs/GaAs(Sb) quantum dot (QD) structure and the extension of the carrier lifetime therein by rapid thermal annealing (RTA). Arrhenius analysis indicates a larger activation energy and thermal stability that results from the suppression of In-Ga intermixing and preservation of the QD heterostructure in an annealed vertically aligned InAs/GaAsSb QD structure. Power-dependent and time-resolved photoluminescence were utilized to demonstrate the extended carrier lifetime from 4.7 to 9.4 ns and elucidate the mechanisms of the antimony aggregation resulting in a band-alignment tailoring from straddling to staggered gap after the RTA process. The significant extension in the carrier lifetime of the columnar InAs/GaAsSb dot structure make the great potential in improving QD intermediate-band solar cell application.

  1. Studying the hopping parameters of half-Heusler NaAuS using maximally localized Wannier function

    Science.gov (United States)

    Sihi, Antik; Lal, Sohan; Pandey, Sudhir K.

    2018-04-01

    Here, the electronic behavior of half-Heusler NaAuS is studied using PBEsol exchange correlation functional by plotting the band structure curve. These bands are reproduced using maximally localized Wannier function using WANNIER90. Tight-binding bands are nicely matched with density functional theory bands. By fitting the tight-binding model, hopping parameter for NaAuS is obtained by including Na 2s, 2p, Au 6s, 5p, 5d and S 3s, 3p orbitals within the energy interval of -5 to 16 eV around the Fermi level. In present study, hopping integrals for NaAuS are computed for the first primitive unit cell atoms as well as the first nearest neighbor primitive unit cell. The most dominating hopping integrals are found for Na (3s) - S (3s), Na (2px) - S (2px), Au (6s) - S (3px), Au (6s) - S (3py) and Au (6s) - S (3pz) orbitals. The hopping integrals for the first nearest neighbor primitive unit cell are also discussed in this manuscript. In future, these hopping integrals are very important to find the topological invariant for NaAuS compound.

  2. Band Structure and Quantum Confined Stark Effect in InN/GaN superlattices

    DEFF Research Database (Denmark)

    Gorczyca, I.; Suski, T.; Christensen, Niels Egede

    2012-01-01

    InN/GaN superlattices offer an important way of band gap engineering in the blue-green range of the spectrum. This approach represents a more controlled method than the band gap tuning in quantum well systems by application of InGaN alloys. The electronic structures of short-period wurtzite InN/G...... wells and barriers one may tune band gaps over a wide spectral range, which provides flexibility in band gap engineering.......InN/GaN superlattices offer an important way of band gap engineering in the blue-green range of the spectrum. This approach represents a more controlled method than the band gap tuning in quantum well systems by application of InGaN alloys. The electronic structures of short-period wurtzite In......N/GaN(0001) superlattices are investigated, and the variation of the band gap with the thicknesses of the well and the barrier is discussed. Superlattices of the form mInN/nGaN with n ≥ m are simulated using band structure calculations in the Local Density Approximation with a semiempirical correction...

  3. STRUCTURAL FEATURES OF PLANT CHITINASES AND CHITIN-BINDING PROTEINS

    NARCIS (Netherlands)

    BEINTEMA, JJ

    1994-01-01

    Structural features of plant chitinases and chitin-binding proteins are discussed. Many of these proteins consist of multiple domains,of which the chitin-binding hevein domain is a predominant one. X-ray and NMR structures of representatives of the major classes of these proteins are available now,

  4. Emission bands of phosphorus and calculation of band structure of rare earth phosphides

    International Nuclear Information System (INIS)

    Al'perovich, G.I.; Gusatinskij, A.N.; Geguzin, I.I.; Blokhin, M.A.; Torbov, V.I.; Chukalin, V.I.; AN SSSR, Moscow. Inst. Novykh Khimicheskikh Problem)

    1977-01-01

    The method of x-ray emission spectroscopy has been used to investigate the electronic structure of monophosphides of rare-earth metals (REM). The fluorescence K bands of phosphorus have been obtained in LaP, PrP, SmP, GdP, TbP, DyP, HoP, ErP, TmP, YbP, and LuP and also the Lsub(2,3) bands of phosphorus in ErP, TmP, YbP, and LuP. Using the Green function technique involving the muffin-tin potential, the energy spectrum for ErP has been calculated in the single-electron approximation. The hystogram of electronic state distribution N(E) is compared with the experimental K and Lsub(2,3) bands of phosphorus in ErP. The agreement between the main details of N(E) and that of x-ray spectra allows to state that the model used provides a good description of the electron density distribution in crystals of REM monophosphides. In accordance with the character of the N(E) distribution the compounds under study are classified as semimetals or semiconductors with a very narrow forbidden band

  5. Electron states in semiconductor quantum dots

    International Nuclear Information System (INIS)

    Dhayal, Suman S.; Ramaniah, Lavanya M.; Ruda, Harry E.; Nair, Selvakumar V.

    2014-01-01

    In this work, the electronic structures of quantum dots (QDs) of nine direct band gap semiconductor materials belonging to the group II-VI and III-V families are investigated, within the empirical tight-binding framework, in the effective bond orbital model. This methodology is shown to accurately describe these systems, yielding, at the same time, qualitative insights into their electronic properties. Various features of the bulk band structure such as band-gaps, band curvature, and band widths around symmetry points affect the quantum confinement of electrons and holes. These effects are identified and quantified. A comparison with experimental data yields good agreement with the calculations. These theoretical results would help quantify the optical response of QDs of these materials and provide useful input for applications

  6. Chromate Binding and Removal by the Molybdate-Binding Protein ModA.

    Science.gov (United States)

    Karpus, Jason; Bosscher, Michael; Ajiboye, Ifedayo; Zhang, Liang; He, Chuan

    2017-04-04

    Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Band structure of Mgsub(x)Znsub(1-x)Te alloys

    International Nuclear Information System (INIS)

    Laugier, A.; Montegu, B.; Barbier, D.; Chevallier, J.; Guillaume, J.C.; Somogyi, K.

    1980-01-01

    The band structure of Mgsub(x)Znsub(1-x)Te alloys is studied using a double beam wavelength modulated system in first derivative mode. Modulated reflectivity measurements are made from 82 to 300 K within spectral range 2500 to 5400 A. Structures corresponding to the E 0 , E 0 + Δ 0 , E 1 , E 1 + Δ 1 , e 1 and e 1 + Δ 1 critical points are indexed on the basis of existing band calculations for ZnTe. (author)

  8. Band structures and localization properties of aperiodic layered phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yan Zhizhong, E-mail: zzyan@bit.edu.cn [Department of Applied Mathematics, Beijing Institute of Technology, Beijing 100081 (China); Zhang Chuanzeng [Department of Civil Engineering, University of Siegen, D-57078 Siegen (Germany)

    2012-03-15

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  9. Magnon band structure and magnon density in one-dimensional magnonic crystals

    International Nuclear Information System (INIS)

    Qiu, Rong-ke; Huang, Te; Zhang, Zhi-dong

    2014-01-01

    By using Callen's Green's function method and the Tyablikov and Anderson–Callen decoupling approximations, we systematically study the magnon band structure and magnon density perpendicular to the superlattice plane of one-dimensional magnonic crystals, with a superlattice consisting of two magnetic layers with ferromagnetic (FM) or antiferromagnetic (AFM) interlayer exchange coupling. The effects of temperature, interlayer coupling, anisotropy and external magnetic field on the magnon-energy band and magnon density in the K x -direction are investigated in three situations: a) the magnon band of magnetic superlattices with FM interlayer coupling, b) separate and c) overlapping magnon bands of magnetic superlattices with AFM interlayer coupling. In the present work, a quantum approach is developed to study the magnon band structure and magnon density of magnonic crystals and the results are beneficial for the design of magnonic-crystal waveguides or gigahertz-range spin-wave filters. - Highlights: • A quantum approach has been developed to study the magnon band of magnonic crystals. • The separate and overlapping magnon bands of magnetic superlattices are investigated. • The results are beneficial for the design of gigahertz-range spin-wave filters

  10. Magnon band structure and magnon density in one-dimensional magnonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Rong-ke, E-mail: rkqiu@163.com [Shenyang University of Technology, Shenyang 110870 (China); Huang, Te [Shenyang University of Technology, Shenyang 110870 (China); Zhang, Zhi-dong [Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016 (China)

    2014-11-15

    By using Callen's Green's function method and the Tyablikov and Anderson–Callen decoupling approximations, we systematically study the magnon band structure and magnon density perpendicular to the superlattice plane of one-dimensional magnonic crystals, with a superlattice consisting of two magnetic layers with ferromagnetic (FM) or antiferromagnetic (AFM) interlayer exchange coupling. The effects of temperature, interlayer coupling, anisotropy and external magnetic field on the magnon-energy band and magnon density in the K{sub x}-direction are investigated in three situations: a) the magnon band of magnetic superlattices with FM interlayer coupling, b) separate and c) overlapping magnon bands of magnetic superlattices with AFM interlayer coupling. In the present work, a quantum approach is developed to study the magnon band structure and magnon density of magnonic crystals and the results are beneficial for the design of magnonic-crystal waveguides or gigahertz-range spin-wave filters. - Highlights: • A quantum approach has been developed to study the magnon band of magnonic crystals. • The separate and overlapping magnon bands of magnetic superlattices are investigated. • The results are beneficial for the design of gigahertz-range spin-wave filters.

  11. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.

    Directory of Open Access Journals (Sweden)

    Hilal Kazan

    2010-07-01

    Full Text Available Metazoan genomes encode hundreds of RNA-binding proteins (RBPs. These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approaches. We evaluated RNAcontext on recently published in vitro and in vivo RNA affinity selected data and demonstrate that RNAcontext identifies known binding preferences for several control proteins including HuR, PTB, and Vts1p and predicts new RNA structure preferences for SF2/ASF, RBM4, FUSIP1 and SLM2. The predicted preferences for SF2/ASF are consistent with its recently reported in vivo binding sites. RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.

  12. The Controls of Pore-Throat Structure on Fluid Performance in Tight Clastic Rock Reservoir: A Case from the Upper Triassic of Chang 7 Member, Ordos Basin, China

    Directory of Open Access Journals (Sweden)

    Yunlong Zhang

    2018-01-01

    Full Text Available The characteristics of porosity and permeability in tight clastic rock reservoir have significant difference from those in conventional reservoir. The increased exploitation of tight gas and oil requests further understanding of fluid performance in the nanoscale pore-throat network of the tight reservoir. Typical tight sandstone and siltstone samples from Ordos Basin were investigated, and rate-controlled mercury injection capillary pressure (RMICP and nuclear magnetic resonance (NMR were employed in this paper, combined with helium porosity and air permeability data, to analyze the impact of pore-throat structure on the storage and seepage capacity of these tight oil reservoirs, revealing the control factors of economic petroleum production. The researches indicate that, in the tight clastic rock reservoir, largest throat is the key control on the permeability and potentially dominates the movable water saturation in the reservoir. The storage capacity of the reservoir consists of effective throat and pore space. Although it has a relatively steady and significant proportion that resulted from the throats, its variation is still dominated by the effective pores. A combination parameter (ε that was established to be as an integrated characteristic of pore-throat structure shows effectively prediction of physical capability for hydrocarbon resource of the tight clastic rock reservoir.

  13. Collective motions and band structures in A = 60 to 80, even--even nuclei

    International Nuclear Information System (INIS)

    Hamilton, J.H.; Robinson, R.L.; Ramayya, A.V.

    1978-01-01

    Evidence for and the theoretical understanding of the richness of the collective band structures as illustrated by at least seven bands seen in levels of 68 Ge, 74 Se are reviewed. The experimental data on even-even nuclei in the A = 60 to 80 region have now revealed a wide variety of collective bands with different structures. The even parity yrast cascades alone are seen to involve multiple collective structures. In addition to the ground-state bands, strong evidence is presented for both neutron and proton rotation-aligned bands built on the same orbital, (g 9 / 2 ) 2 , in one nucleus. Several other nuclei also show the crossing of RAL bands around the 8 + level in this region. Evidence continues to be strong experimentally and supported theoretically that there is some type of shape transition and shape coexistence occurring now both in the Ge and Se isotopes around N = 40. Negative parity bands with odd and even spins with very collective nature are seen in several nuclei to high spin. These bands seem best understood in the RAL model. Very collective bands with ΔI = 1, extending from 2 + to 9 + are seen with no rotation-alignment. The purity of these bands and their persistence to such high spin establish them as an independent collective mode which is best described as a gamma-type vibration band in a deformed nucleus. In addition to all of the above bands, new bands are seen in 76 Kr and 74 Se. The nature of these bands is not presently known. 56 references

  14. Hubbard-U band-structure methods

    DEFF Research Database (Denmark)

    Albers, R.C.; Christensen, Niels Egede; Svane, Axel

    2009-01-01

    The last decade has seen a large increase in the number of electronic-structure calculations that involve adding a Hubbard term to the local-density approximation band-structure Hamiltonian. The Hubbard term is then determined either at the mean-field level or with sophisticated many......-body techniques such as using dynamical mean-field theory. We review the physics underlying these approaches and discuss their strengths and weaknesses in terms of the larger issues of electronic structure that they involve. In particular, we argue that the common assumptions made to justify such calculations...

  15. Structure of collective bands and deformations in 74,76Kr

    International Nuclear Information System (INIS)

    Tripathy, K.C.; Sahu, R.

    2000-01-01

    The structure of collective bands in 74,76 Kr is studied within the framework of the deformed configuration mixing shell model based on Hartree-Fock states. The active single-particle orbits are 1p 3/2 , 0f 5/2 , 1p 1/2 and 0g 9/2 with 56 Ni as the inert core. A modified Kuo interaction has been used for the above configuration space. The 74 Kr nucleus is found to be the most deformed nucleus among the krypton isotopes which is in agreement with experiment. The deformation is found to decrease for the 76 Kr isotope. The calculated positive- and negative-parity bands agree quite well with the experiment for both the nuclei. A number of excited bands is also predicted. We have also calculated B(E2) values and compared them with available experimental data. The structure of the strongly coupled band built on K = 4 (+) in 76 Kr is also studied. (author)

  16. Photonic band structures in one-dimensional photonic crystals containing Dirac materials

    International Nuclear Information System (INIS)

    Wang, Lin; Wang, Li-Gang

    2015-01-01

    We have investigated the band structures of one-dimensional photonic crystals (1DPCs) composed of Dirac materials and ordinary dielectric media. It is found that there exist an omnidirectional passing band and a kind of special band, which result from the interaction of the evanescent and propagating waves. Due to the interface effect and strong dispersion, the electromagnetic fields inside the special bands are strongly enhanced. It is also shown that the properties of these bands are invariant upon the lattice constant but sensitive to the resonant conditions

  17. The necessity of connection structures in neural models of variable binding.

    Science.gov (United States)

    van der Velde, Frank; de Kamps, Marc

    2015-08-01

    In his review of neural binding problems, Feldman (Cogn Neurodyn 7:1-11, 2013) addressed two types of models as solutions of (novel) variable binding. The one type uses labels such as phase synchrony of activation. The other ('connectivity based') type uses dedicated connections structures to achieve novel variable binding. Feldman argued that label (synchrony) based models are the only possible candidates to handle novel variable binding, whereas connectivity based models lack the flexibility required for that. We argue and illustrate that Feldman's analysis is incorrect. Contrary to his conclusion, connectivity based models are the only viable candidates for models of novel variable binding because they are the only type of models that can produce behavior. We will show that the label (synchrony) based models analyzed by Feldman are in fact examples of connectivity based models. Feldman's analysis that novel variable binding can be achieved without existing connection structures seems to result from analyzing the binding problem in a wrong frame of reference, in particular in an outside instead of the required inside frame of reference. Connectivity based models can be models of novel variable binding when they possess a connection structure that resembles a small-world network, as found in the brain. We will illustrate binding with this type of model with episode binding and the binding of words, including novel words, in sentence structures.

  18. Temperature-induced band shift in bulk γ-InSe by angle-resolved photoemission spectroscopy

    Science.gov (United States)

    Xu, Huanfeng; Wang, Wei; Zhao, Yafei; Zhang, Xiaoqian; Feng, Yue; Tu, Jian; Gu, Chenyi; Sun, Yizhe; Liu, Chang; Nie, Yuefeng; Edmond Turcu, Ion C.; Xu, Yongbing; He, Liang

    2018-05-01

    Indium selenide (InSe) has recently become popular research topics because of its unique layered crystal structure, direct band gap and high electron mobilities. In this work, we have acquired the electronic structure of bulk γ-InSe at various temperatures using angle-resolved photoemission spectroscopy (ARPES). We have also found that as the temperature decreases, the valence bands of γ-InSe exhibit a monotonic shift to lower binding energies. This band shift is attributed to the change of lattice parameters and has been validated by variable temperature X-ray diffraction measurements and theoretical calculations.

  19. Self-consistent, relativistic, ferromagnetic band structure of gadolinium

    International Nuclear Information System (INIS)

    Harmon, B.N.; Schirber, J.; Koelling, D.D.

    1977-01-01

    An initial self-consistent calculation of the ground state magnetic band structure of gadolinium is described. A linearized APW method was used which included all single particle relativistic effects except spin-orbit coupling. The spin polarized potential was obtained in the muffin-tin form using the local spin density approximation for exchange and correlation. The most striking and unorthodox aspect of the results is the position of the 4f spin-down ''bands'' which are required to float just on top of the Fermi level in order to obtain convergence. If the 4f states (l = 3 resonance) are removed from the occupied region of the conduction bands the magnetic moment is approximately .75 μ/sub B//atom; however, as the 4f spin-down states are allowed to find their own position they hybridize with the conduction bands at the Fermi level and the moment becomes smaller. Means of improving the calculation are discussed

  20. The tightly bound nuclei in the liquid drop model

    Science.gov (United States)

    Sree Harsha, N. R.

    2018-05-01

    In this paper, we shall maximise the binding energy per nucleon function in the semi-empirical mass formula of the liquid drop model of the atomic nuclei to analytically prove that the mean binding energy per nucleon curve has local extrema at A ≈ 58.6960, Z ≈ 26.3908 and at A ≈ 62.0178, Z ≈ 27.7506. The Lagrange method of multipliers is used to arrive at these results, while we have let the values of A and Z take continuous fractional values. The shell model that shows why 62Ni is the most tightly bound nucleus is outlined. A brief account on stellar nucleosynthesis is presented to show why 56Fe is more abundant than 62Ni and 58Fe. We believe that the analytical proof presented in this paper can be a useful tool to the instructors to introduce the nucleus with the highest mean binding energy per nucleon.

  1. Two unique ligand-binding clamps of Rhizopus oryzae starch binding domain for helical structure disruption of amylose.

    Directory of Open Access Journals (Sweden)

    Ting-Ying Jiang

    Full Text Available The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21 members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.

  2. Empirical pseudo-potential studies on electronic structure

    Indian Academy of Sciences (India)

    Theoretical investigations of electronic structure of quantum dots is of current interest in nanophase materials. Empirical theories such as effective mass approximation, tight binding methods and empirical pseudo-potential method are capable of explaining the experimentally observed optical properties. We employ the ...

  3. Electronic band structure in porous silicon studied by photoluminescence and photoluminescence excitation spectroscopy

    International Nuclear Information System (INIS)

    Lee, Ki-Won; Kim, Young-You

    2004-01-01

    In this research, we used photoluminescence (PL) and photoluminescence excitation (PLE) to visualize the electronic band structure in porous silicon (PS). From the combined results of the PLE measurements at various PL emission energies and the PL measurements under excitation at various PLE absorption energies, we infer that three different electronic band structures, originating from different luminescent origins, give rise to the PL spectrum. Through either thermal activation or diffusive transfer, excited carriers are moved to each of the electronic band structures.

  4. A Compact UWB Band-Pass Filter Using Embedded Circular Slot Structures for Improved Upper Stop-band Performance

    DEFF Research Database (Denmark)

    Shen, Ming; Ren, Jian; Mikkelsen, Jan Hvolgaard

    2016-01-01

    structures into the ring resonator. This is different from conventional designs using cascaded bandstop/low-pass filters for stop-band response suppression, which usually leads to big circuit sizes. And hence the proposed approach can reduce the circuit size significantly. A prototype filter with a compact...... size (13.6 mm×6.75 mm) has been implemented for experimental validation. The measured results show a −3 dB frequency band from 3.4 GHz to 11.7 GHz and > 20 dB upper stop-band suppression from 12.5 GHz to 20GHz....

  5. Topological Classification of Crystalline Insulators through Band Structure Combinatorics

    Science.gov (United States)

    Kruthoff, Jorrit; de Boer, Jan; van Wezel, Jasper; Kane, Charles L.; Slager, Robert-Jan

    2017-10-01

    We present a method for efficiently enumerating all allowed, topologically distinct, electronic band structures within a given crystal structure in all physically relevant dimensions. The algorithm applies to crystals without time-reversal, particle-hole, chiral, or any other anticommuting or anti-unitary symmetries. The results presented match the mathematical structure underlying the topological classification of these crystals in terms of K -theory and therefore elucidate this abstract mathematical framework from a simple combinatorial perspective. Using a straightforward counting procedure, we classify all allowed topological phases of spinless particles in crystals in class A . Employing this classification, we study transitions between topological phases within class A that are driven by band inversions at high-symmetry points in the first Brillouin zone. This enables us to list all possible types of phase transitions within a given crystal structure and to identify whether or not they give rise to intermediate Weyl semimetallic phases.

  6. Solving complex band structure problems with the FEAST eigenvalue algorithm

    Science.gov (United States)

    Laux, S. E.

    2012-08-01

    With straightforward extension, the FEAST eigenvalue algorithm [Polizzi, Phys. Rev. B 79, 115112 (2009)] is capable of solving the generalized eigenvalue problems representing traveling-wave problems—as exemplified by the complex band-structure problem—even though the matrices involved are complex, non-Hermitian, and singular, and hence outside the originally stated range of applicability of the algorithm. The obtained eigenvalues/eigenvectors, however, contain spurious solutions which must be detected and removed. The efficiency and parallel structure of the original algorithm are unaltered. The complex band structures of Si layers of varying thicknesses and InAs nanowires of varying radii are computed as test problems.

  7. Studies on the effect of AgNP binding on α-amylase structure of porcine pancreas and Bacillus subtilis by multi-spectroscopic methods

    International Nuclear Information System (INIS)

    Ernest, Vinita; Sekar, Gajalakshmi; Mukherjee, Amitava; Chandrasekaran, N.

    2014-01-01

    Functionalizing silver nanoparticles (AgNPs) with biomolecules have a number of applications in catalysis, sensing, pharmaceutics and therapy. For the first time, herein we report the interaction of amylase-AgNPs through various spectroscopic techniques. AgNPs are synthesized and characterized by UV–vis spectroscopy, transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). The binding of AgNPs to α-amylase are investigated by UV–vis, fluorescence, circular dichroism and FTIR spectroscopic techniques. Absorption intensity and Stern–Volmer plots confirmed the formation of the ground state complex with AgNPs. The quenching of the intrinsic protein fluorescence in the presence of different concentrations of AgNP was observed. The apparent binding constant (K) and number of binding sites (n) was calculated from the Stern–Volmer plot was found to be 4.92×10 3 , 3.8×10 3 and 1.57, 1.3 for porcine pancreas and Bacillus subtilis α-amylase, respectively. Far-UV CD studies revealed the characteristic dichoric band at 222 nm for α-helical structure was shifted to 215 nm in porcine pancreatic α-amylase upon AgNP binding. Further, structural conformation change with peak shifts and the possible binding residues was confirmed through FTIR spectroscopy. -- Highlights: • AgNPs were synthesized using modified Creighton's method and characterized. • Structural changes analyzed by UV–vis, fluorescence spectroscopy. • CD and FTIR spectra reveal the secondary structure conformation change. • Potential application in food industry

  8. Studies on the effect of AgNP binding on α-amylase structure of porcine pancreas and Bacillus subtilis by multi-spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Ernest, Vinita; Sekar, Gajalakshmi; Mukherjee, Amitava; Chandrasekaran, N., E-mail: nchandrasekaran@vit.ac.in

    2014-02-15

    Functionalizing silver nanoparticles (AgNPs) with biomolecules have a number of applications in catalysis, sensing, pharmaceutics and therapy. For the first time, herein we report the interaction of amylase-AgNPs through various spectroscopic techniques. AgNPs are synthesized and characterized by UV–vis spectroscopy, transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). The binding of AgNPs to α-amylase are investigated by UV–vis, fluorescence, circular dichroism and FTIR spectroscopic techniques. Absorption intensity and Stern–Volmer plots confirmed the formation of the ground state complex with AgNPs. The quenching of the intrinsic protein fluorescence in the presence of different concentrations of AgNP was observed. The apparent binding constant (K) and number of binding sites (n) was calculated from the Stern–Volmer plot was found to be 4.92×10{sup 3}, 3.8×10{sup 3} and 1.57, 1.3 for porcine pancreas and Bacillus subtilis α-amylase, respectively. Far-UV CD studies revealed the characteristic dichoric band at 222 nm for α-helical structure was shifted to 215 nm in porcine pancreatic α-amylase upon AgNP binding. Further, structural conformation change with peak shifts and the possible binding residues was confirmed through FTIR spectroscopy. -- Highlights: • AgNPs were synthesized using modified Creighton's method and characterized. • Structural changes analyzed by UV–vis, fluorescence spectroscopy. • CD and FTIR spectra reveal the secondary structure conformation change. • Potential application in food industry.

  9. Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.

    Science.gov (United States)

    Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R; Stevens, Raymond C

    2010-04-16

    Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-A X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent. Copyright (c) 2010. Published by Elsevier Ltd.

  10. A strategy for increasing the brain uptake of a radioligand in animals: use of a drug that inhibits plasma protein binding

    International Nuclear Information System (INIS)

    Haradahira, Terushi; Zhang, Ming-Rong; Maeda, Jun; Okauchi, Takashi; Kawabe, Kouichi; Kida, Takayo; Suzuki, Kazutoshi; Suhara, Tetsuya

    2000-01-01

    A positron-emitter labeled radioligand for the glycine-binding site of the N-methyl-D-aspartate (NMDA) receptor, [ 11 C]L-703,717, was examined for its ability to penetrate the brain in animals by simultaneous use with drugs having high-affinity separate binding sites on human serum albumin. [ 11 C]L-703,717 has poor blood-brain barrier (BBB) permeability because it binds tightly to plasma proteins. Co-injection of warfarin (50-200 mg/kg), a drug that binds to albumin and resembles L-703,717 in structure, dose-dependently enhanced the penetration by [ 11 C]L-703,717 in mice, resulting in a five-fold increase in the brain radioactivity at 1 min after the injection. Drugs structurally unrelated to L-703,717, salicylate, phenol red, and L-tryptophan, were less effective or ineffective in increasing the uptake of [ 11 C]L-703,717. These results suggest that the simultaneous use of a drug that inhibits the binding of a radioligand to plasma proteins is a useful way to overcome the poor BBB permeability of the radioligand triggered by its tight binding to plasma proteins. In brain distribution studies in rodents, it was found that, after the increase in brain uptake with warfarin, much of the glycine site antagonist accumulates in the cerebellum but its pharmacological specificity did not match the glycine site of NMDA receptors

  11. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  12. Band structure and phonon properties of lithium fluoride at high pressure

    Energy Technology Data Exchange (ETDEWEB)

    Panchal, J. M., E-mail: amitjignesh@yahoo.co.in [Government Engineering College, Gandhinagar 382028, Gujarat (India); Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat (India); Joshi, Mitesh [Government Polytechnic for Girls, Athwagate, Surat395001, Gujarat (India); Gajjar, P. N., E-mail: pngajjar@rediffmail.com [Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat (India)

    2016-05-23

    High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

  13. Band structure and phonon properties of lithium fluoride at high pressure

    International Nuclear Information System (INIS)

    Panchal, J. M.; Joshi, Mitesh; Gajjar, P. N.

    2016-01-01

    High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

  14. Two-dimensional microwave band-gap structures of different ...

    Indian Academy of Sciences (India)

    - stant and/or magnetic permeability (or in particular impedance) are periodic and the propagation of electromagnetic waves is forbidden at certain frequencies when allowed to pass through these structures. This is similar to the electronic band.

  15. Electronic properties and structural phase transition in A4 [M4O4] (A=Li, Na, K and Rb; M=Ag and Cu): A first principles study

    Science.gov (United States)

    Umamaheswari, R.; Yogeswari, M.; Kalpana, G.

    2013-02-01

    Self-consistent scalar relativistic band structure calculations for AMO (A=Li, Na, K and Rb; M=Ag and Cu) compounds have been performed using the tight-binding linear muffin-tin orbital (TB-LMTO) method within the local density approximation (LDA). At ambient conditions, these compounds are found to crystallize in tetragonal KAgO-type structure with two different space group I-4m2 and I4/mmm. Nowadays, hypothetical structures are being considered to look for new functional materials. AMO compounds have stoichiometry similar to eight-electron half-Heusler materials of type I-I-VI which crystallizes in cubic (C1b) MgAgAs-type structure with space group F-43m. For all these compounds, by interchanging the positions of atoms in the hypothetical cubic structure, three phases (α, β and γ) are formed. The energy-volume relation for these compounds in tetragonal KAgO-type structure and cubic α, β and γ phases of related structure have been obtained. Under ambient conditions these compounds are more stable in tetragonal KAgO-type (I4/mmm) structure. The total energies calculated within the atomic sphere approximation (ASA) were used to determine the ground state properties such as equilibrium lattice parameters, c/a ratio, bulk modulus, cohesive energy and are compared with the available experimental results. The results of the electronic band structure calculations at ambient condition show that LiCuO and NaMO are indirect band gap semiconductors whereas KMO and RbMO are direct band gap semiconductors. At high pressure the band gap decreases and the phenomenon of band overlap metallization occur. Also these compounds undergo structural phase transition from tetragonal I-4m2 phase to cubic α-phase and transition pressures were calculated.

  16. Effective Medium Tight-Binding Theory

    OpenAIRE

    Stokbro, Kurt

    1994-01-01

    In this thesis a new model for calculating the total energy of atomic and solid systems is presented. The model is used to study the properties of the Si(100) surface and dislocation dynamics in the diamond structure. For the Si(100) surface the main result is the finding of an incomplete melted state at $1550^0 K$. The studied dislocation is the $90^0$ partial and it is found that the barriers for kink formation and migration are in good accordance with experimental observations. The general...

  17. Volume and surface photoemission from tungsten. I. Calculation of band structure and emission spectra

    DEFF Research Database (Denmark)

    Christensen, N. Egede; Feuerbacher, B.

    1974-01-01

    is obtained from an ad hoc potential based on a Dirac-Slater atomic calculation for the ground-state configuration and with full Slater exchange in the atomic as well as in the crystal potential. The selection of this best potential is justified by comparing the calculated band structure to Fermi...... of states. The present work includes a crude estimate of this surface density of states, which is derived from the bulk band structure by narrowing the d bands according to an effective number of neighbors per surface atom. Estimates of surface relaxation effects are also included.......The electronic energy-band structure of tungsten has been calculated by means of the relativistic-augmented-plane-wave method. A series of mutually related potentials are constructed by varying the electronic configuration and the amount of Slater exchange included. The best band structure...

  18. Analysis of photonic band-gap (PBG) structures using the FDTD method

    DEFF Research Database (Denmark)

    Tong, M.S.; Cheng, M.; Lu, Y.L.

    2004-01-01

    In this paper, a number of photonic band-gap (PBG) structures, which are formed by periodic circuit elements printed oil transmission-line circuits, are studied by using a well-known numerical method, the finite-difference time-domain (FDTD) method. The results validate the band-stop filter...... behavior of these structures, and the computed results generally match well with ones published in the literature. It is also found that the FDTD method is a robust, versatile, and powerful numerical technique to perform such numerical studies. The proposed PBG filter structures may be applied in microwave...

  19. Sub-nanoscale surface ruggedness provides a water-tight seal for exposed regions in soluble protein structure.

    Directory of Open Access Journals (Sweden)

    Erica Schulz

    2010-09-01

    Full Text Available Soluble proteins must maintain backbone hydrogen bonds (BHBs water-tight to ensure structural integrity. This protection is often achieved by burying the BHBs or wrapping them through intermolecular associations. On the other hand, water has low coordination resilience, with loss of hydrogen-bonding partnerships carrying significant thermodynamic cost. Thus, a core problem in structural biology is whether natural design actually exploits the water coordination stiffness to seal the backbone in regions that are exposed to the solvent. This work explores the molecular design features that make this type of seal operative, focusing on the side-chain arrangements that shield the protein backbone. We show that an efficient sealing is achieved by adapting the sub-nanoscale surface topography to the stringency of water coordination: an exposed BHB may be kept dry if the local concave curvature is small enough to impede formation of the coordination shell of a penetrating water molecule. Examination of an exhaustive database of uncomplexed proteins reveals that exposed BHBs invariably occur within such sub-nanoscale cavities in native folds, while this level of local ruggedness is absent in other regions. By contrast, BHB exposure in misfolded proteins occurs with larger local curvature promoting backbone hydration and consequently, structure disruption. These findings unravel physical constraints fitting a spatially dependent least-action for water coordination, introduce a molecular design concept, and herald the advent of water-tight peptide-based materials with sufficient backbone exposure to remain flexible.

  20. Research on the Band Gap Characteristics of Two-Dimensional Phononic Crystals Microcavity with Local Resonant Structure

    Directory of Open Access Journals (Sweden)

    Mao Liu

    2015-01-01

    Full Text Available A new two-dimensional locally resonant phononic crystal with microcavity structure is proposed. The acoustic wave band gap characteristics of this new structure are studied using finite element method. At the same time, the corresponding displacement eigenmodes of the band edges of the lowest band gap and the transmission spectrum are calculated. The results proved that phononic crystals with microcavity structure exhibited complete band gaps in low-frequency range. The eigenfrequency of the lower edge of the first gap is lower than no microcavity structure. However, for no microcavity structure type of quadrilateral phononic crystal plate, the second band gap disappeared and the frequency range of the first band gap is relatively narrow. The main reason for appearing low-frequency band gaps is that the proposed phononic crystal introduced the local resonant microcavity structure. This study provides a good support for engineering application such as low-frequency vibration attenuation and noise control.

  1. Quasiparticle electronic and optical properties of the Si-Sn system

    International Nuclear Information System (INIS)

    Jensen, Rasmus V S; Pedersen, Thomas G; Larsen, Arne N

    2011-01-01

    The Si 1-x Sn x material system is an interesting candidate for an optically active material compatible with Si. Based on density functional theory with quasiparticle corrections we calculate the electronic band structure of zinc-blende SiSn under both compressive and tensile strain. At 2.2% tensile strain the band gap becomes direct with a magnitude of 0.85 eV. We develop an accurate tight-binding parameterization of the electronic structure and calculate the optical properties of SiSn. Furthermore, the silicide SiSn 2 is investigated and found to have metallic character. (paper)

  2. Global structural optimizations of surface systems with a genetic algorithm

    International Nuclear Information System (INIS)

    Chuang, Feng-Chuan

    2005-01-01

    Global structural optimizations with a genetic algorithm were performed for atomic cluster and surface systems including aluminum atomic clusters, Si magic clusters on the Si(111) 7 x 7 surface, silicon high-index surfaces, and Ag-induced Si(111) reconstructions. First, the global structural optimizations of neutral aluminum clusters Al n (n up to 23) were performed using a genetic algorithm coupled with a tight-binding potential. Second, a genetic algorithm in combination with tight-binding and first-principles calculations were performed to study the structures of magic clusters on the Si(111) 7 x 7 surface. Extensive calculations show that the magic cluster observed in scanning tunneling microscopy (STM) experiments consist of eight Si atoms. Simulated STM images of the Si magic cluster exhibit a ring-like feature similar to STM experiments. Third, a genetic algorithm coupled with a highly optimized empirical potential were used to determine the lowest energy structure of high-index semiconductor surfaces. The lowest energy structures of Si(105) and Si(114) were determined successfully. The results of Si(105) and Si(114) are reported within the framework of highly optimized empirical potential and first-principles calculations. Finally, a genetic algorithm coupled with Si and Ag tight-binding potentials were used to search for Ag-induced Si(111) reconstructions at various Ag and Si coverages. The optimized structural models of √3 x √3, 3 x 1, and 5 x 2 phases were reported using first-principles calculations. A novel model is found to have lower surface energy than the proposed double-honeycomb chained (DHC) model both for Au/Si(111) 5 x 2 and Ag/Si(111) 5 x 2 systems

  3. Charge-density-wave instabilities expected in monophosphate tungsten bronzes

    International Nuclear Information System (INIS)

    Canadell, E.; Whangbo, M.

    1991-01-01

    On the basis of tight-binding band calculations, we examined the electronic structures of the tungsten oxide layers found in the monophosphate tungsten bronze (MPTB) phases. The Fermi surfaces of these MPTB phases consist of five well-nested one- and two-dimensional pieces. We calculated the nesting vectors of these Fermi surfaces and discussed the expected charge-density-wave instabilities

  4. Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding

    International Nuclear Information System (INIS)

    Vaezeslami, Soheila; Jia, Xiaofei; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H.

    2008-01-01

    A water network stabilizes the structure of cellular retionic acid binding protein II. The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the α2 helix at its entrance. This chain of interactions acts as a ‘pillar’ that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the α2 helix adopting an altered conformation compared with wild-type CRABPII

  5. Study of multi-quasiparticle band structures in 197Tl using α beam

    International Nuclear Information System (INIS)

    Mukherjee, G.; Nandi, S.; Pai, H.

    2016-01-01

    Study of the multi-quasiparticle (qp) states and the band structures built on them in the neutron deficient Tl nuclei in A ∼ 190 mass region provides useful information on particle-hole interaction in the heavy nuclei. In order to investigate the multi-qp band structures we have studied the excited states in 197 Tl by gamma ray spectroscopy

  6. Effect of van der Waals interactions on the structural and binding properties of GaSe

    Energy Technology Data Exchange (ETDEWEB)

    Sarkisov, Sergey Y., E-mail: sarkisov@mail.tsu.ru [Tomsk State University, Lenin Avenue 36, 634050 Tomsk (Russian Federation); Kosobutsky, Alexey V., E-mail: kosobutsky@kemsu.ru [Tomsk State University, Lenin Avenue 36, 634050 Tomsk (Russian Federation); Kemerovo State University, Krasnaya 6, 650043 Kemerovo (Russian Federation); Shandakov, Sergey D. [Kemerovo State University, Krasnaya 6, 650043 Kemerovo (Russian Federation)

    2015-12-15

    The influence of van der Waals interactions on the lattice parameters, band structure, elastic moduli and binding energy of layered GaSe compound has been studied using projector-augmented wave method within density functional theory. We employed the conventional local/semilocal exchange-correlation functionals and recently developed van der Waals functionals which are able to describe dispersion forces. It is found that application of van der Waals density functionals allows to substantially increase the accuracy of calculations of the lattice constants a and c and interlayer distance in GaSe at ambient conditions and under hydrostatic pressure. The pressure dependences of the a-parameter, Ga–Ga, Ga–Se bond lengths and Ga–Ga–Se bond angle are characterized by a relatively low curvature, while c(p) has a distinct downward bowing due to nonlinear shrinking of the interlayer spacing. From the calculated binding energy curves we deduce the interlayer binding energy of GaSe, which is found to be in the range 0.172–0.197 eV/layer (14.2–16.2 meV/Å{sup 2}). - Highlights: • Effects of van der Waals interactions are analyzed using advanced density functionals. • Calculations with vdW-corrected functionals closely agree with experiment. • Interlayer binding energy of GaSe is estimated to be 14.2–16.2 meV/Å{sup 2}.

  7. Mapping small molecule binding data to structural domains.

    Science.gov (United States)

    Kruger, Felix A; Rostom, Raghd; Overington, John P

    2012-01-01

    Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes

  8. Two band superconductivity for MgB{sub 2}: T{sub c} and isotope exponent {alpha} as a function of the carrier number n and the role of the center of the band

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Nunez, J J [Lab. SUPERCOMP, Departamento de Fisica - FACYT - UC, Valencia (Venezuela) and Abdus Salam International Centre for Theoretical Physics, Trieste (Italy); Schmidt, A A [Departamento de Matematica, UFSM, Santa Maria, RS (Brazil); Bianconi, A [Physics Department, Universita di Roma, Rome (Italy); Perali, A [Physics Department, University of Camerino, Camerino - MC (Italy)

    2005-08-15

    We study a two band superconducting, assuming that we have two tight binding bands, {epsilon}{sub 2}(k-vector) = {epsilon}{sub 2}{sup (0)} - t{sub 2}[cos(k{sub x}) + cos(k{sub y}) + s{sub 2} cos(k{sub z})] - {mu} and {epsilon}{sub 3}(k-vector) {epsilon}{sub 3}{sup (0)} - t{sub 3} [cos(k{sub x}) + cos(k{sub y})+s{sub 3} cos(k{sub z})] - {mu}. We solve the two gap equations at T = T{sub c} and calculate T{sub c} x n and {mu} x n for various values of pairing interaction, V, and Debye frequency, {omega}{sub D}. Also, from an expression developed in a previous paper by two of the present authors, we calculate {alpha} x n, where n is the number of carriers per site per band and {alpha} is the isotope exponent. We take only interband scattering, V, as a first approach. We find that in order to have superconductivity (T{sub c} {ne} 0), large values of V are necessary. Also, for V/{omega}{sub D} > 1, we obtain {alpha} > 1.00 and for V/{omega}{sub D}>1.00, the isotope exponent becomes less than 1. (author)

  9. Theoretical study of the influence of the electric field on the electronic properties of armchair boron nitride nanoribbon

    Science.gov (United States)

    Chegel, Raad; Behzad, Somayeh

    2014-11-01

    We have investigated the electronic properties of A-BNNRs in the external electric field using third nearest neighbor tight binding approximation including edge effects. We found that the dependence of on-site energy to the external electric field for edge atoms and center part atoms is different. By comparing the band structure in the different fields, several differences are clearly seen such as modification of energy dispersions, creation of additional band edge states and band gap reduction. By increasing the electric field the band gap reduces linearly until reaches zero and BNNRs with larger width are more sensitive than small ones. All changes in the band structure are directly reflected in the DOS spectrum. The numbers and the energies of the DOS peaks are dependent on the electric field strength.

  10. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  11. Activator Protein-1: redox switch controlling structure and DNA-binding

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Zhou; Machius, Mischa; Nestler, Eric J.; Rudenko, Gabby (Texas-MED); (Icahn)

    2017-09-07

    The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a ‘redox switch’ centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the ‘OFF’ state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins.

  12. Structural Analysis of Botulinum Neurotoxin Type G Receptor Binding

    Energy Technology Data Exchange (ETDEWEB)

    Schmitt, John; Karalewitz, Andrew; Benefield, Desire A.; Mushrush, Darren J.; Pruitt, Rory N.; Spiller, Benjamin W.; Barbieri, Joseph T.; Lacy, D. Borden (Vanderbilt); (MCW)

    2010-10-19

    Botulinum neurotoxin (BoNT) binds peripheral neurons at the neuromuscular junction through a dual-receptor mechanism that includes interactions with ganglioside and protein receptors. The receptor identities vary depending on BoNT serotype (A-G). BoNT/B and BoNT/G bind the luminal domains of synaptotagmin I and II, homologous synaptic vesicle proteins. We observe conditions under which BoNT/B binds both Syt isoforms, but BoNT/G binds only SytI. Both serotypes bind ganglioside G{sub T1b}. The BoNT/G receptor-binding domain crystal structure provides a context for examining these binding interactions and a platform for understanding the physiological relevance of different Syt receptor isoforms in vivo.

  13. Lam'e Instantons

    OpenAIRE

    Dunne, Gerald V.; Rao, Kumar

    1999-01-01

    We perform a precise analytic test of the instanton approximation by comparing the exact band spectrum of the periodic Lam\\'e potential to the tight-binding, instanton and WKB approximations. The instanton result gives the correct leading behavior in the semiclassical limit, while the tight-binding approximation does even better. WKB is off by an overall factor of $\\sqrt{e/\\pi}$.

  14. Electronic band structure of magnetic bilayer graphene superlattices

    International Nuclear Information System (INIS)

    Pham, C. Huy; Nguyen, T. Thuong; Nguyen, V. Lien

    2014-01-01

    Electronic band structure of the bilayer graphene superlattices with δ-function magnetic barriers and zero average magnetic flux is studied within the four-band continuum model, using the transfer matrix method. The periodic magnetic potential effects on the zero-energy touching point between the lowest conduction and the highest valence minibands of pristine bilayer graphene are exactly analyzed. Magnetic potential is shown also to generate the finite-energy touching points between higher minibands at the edges of Brillouin zone. The positions of these points and the related dispersions are determined in the case of symmetric potentials.

  15. Band structure and optical properties of opal photonic crystals

    OpenAIRE

    Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

    2005-01-01

    A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order...

  16. Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2

    Directory of Open Access Journals (Sweden)

    Yan Li

    2015-04-01

    Full Text Available Cyclin-dependent kinase 2 (CDK2 is a crucial regulator of the eukaryotic cell cycle. However it is well established that monomeric CDK2 lacks regulatory activity, which needs to be aroused by its positive regulators, cyclins E and A, or be phosphorylated on the catalytic segment. Interestingly, these activation steps bring some dynamic changes on the 3D-structure of the kinase, especially the activation segment. Until now, in the monomeric CDK2 structure, three binding sites have been reported, including the adenosine triphosphate (ATP binding site (Site I and two non-competitive binding sites (Site II and III. In addition, when the kinase is subjected to the cyclin binding process, the resulting structural changes give rise to a variation of the ATP binding site, thus generating an allosteric binding site (Site IV. All the four sites are demonstrated as being targeted by corresponding inhibitors, as is illustrated by the allosteric binding one which is targeted by inhibitor ANS (fluorophore 8-anilino-1-naphthalene sulfonate. In the present work, the binding mechanisms and their fluctuations during the activation process attract our attention. Therefore, we carry out corresponding studies on the structural characterization of CDK2, which are expected to facilitate the understanding of the molecular mechanisms of kinase proteins. Besides, the binding mechanisms of CDK2 with its relevant inhibitors, as well as the changes of binding mechanisms following conformational variations of CDK2, are summarized and compared. The summary of the conformational characteristics and ligand binding mechanisms of CDK2 in the present work will improve our understanding of the molecular mechanisms regulating the bioactivities of CDK2.

  17. Pb chains on ordered Si(3 3 5) surface

    International Nuclear Information System (INIS)

    Kisiel, M.; Skrobas, K.; Zdyb, R.; Mazurek, P.; Jalochowski, M.

    2007-01-01

    The electronic band structure of the Si(3 3 5)-Au surface decorated with Pb atoms was studied with angle resolved photoelectron spectroscopy (ARPES) in ultra high vacuum (UHV) conditions. The photoemission spectra were measured in two perpendicular directions, along and across the steps. In the direction parallel to the step edges the ARPES spectra show strongly dispersive electron energy band while in the perpendicular direction there is no electronic dispersion at all. This confirms one-dimensional character of the system. The theoretical band dispersion calculated within a tight-binding model was fitted to that obtained from the experiment

  18. Band gaps from the Tran-Blaha modified Becke-Johnson approach: A systematic investigation

    Science.gov (United States)

    Jiang, Hong

    2013-04-01

    The semi-local Becke-Johnson (BJ) exchange-correlation potential and its modified form proposed by Tran and Blaha (TB-mBJ) have attracted a lot of interest recently because of the surprisingly accurate band gaps they can deliver for many semiconductors and insulators. In this work, we have investigated the performance of the TB-mBJ potential for the description of electronic band structures in a comprehensive set of semiconductors and insulators. We point out that a perturbative use of the TB-mBJ potential can give overall better results. By investigating a set of IIB-VI and III-V semiconductors, we point out that although the TB-mBJ approach can describe the band gap of these materials quite well, the binding energies of semi-core d-states in these materials deviate strongly from experiment. The difficulty of the TB-mBJ potential to describe the localized states is likely the cause for the fact that the electronic band structures of Cu2O and La2O3 are still poorly described. Based on these observations, we propose to combine the TB-mBJ approach with the Hubbard U correction for localized d/f states, which is able to provide overall good descriptions for both the band gaps and semi-core states binding energies. We further apply the approach to calculate the band gaps of a set of Ti(IV)-oxides, many of which have complicated structures so that the more advanced methods like GW are expensive to treat directly. An overall good agreement with experiment is obtained, which is remarkable considering its little computational efforts compared to GW.

  19. Structural and Functional Changes in the Tight Junctions of Asymptomatic and Serology-negative First-degree Relatives of Patients With Celiac Disease.

    Science.gov (United States)

    Mishra, Asha; Prakash, Shyam; Sreenivas, Vishnubhatla; Das, Taposh K; Ahuja, Vineet; Gupta, Siddhartha D; Makharia, Govind K

    2016-08-01

    Ten to 15% of first-degree relatives (FDRs) of celiac disease (CeD) patients develop CeD. Although intestinal barrier functions (intestinal permeability) are abnormal in the subset of serology-negative FDRs, what leads to the abnormal barrier function is not known. To study the ultrastructure and functions of tight junctions in serology-negative FDRs of CeD patients. The intestinal permeability was measured in 97 asymptomatic and anti-tissue transglutaminase antibody (anti-tTG Ab)-negative FDRs (using the lactulose mannitol ratio) and in 75 controls. The ultrastructure of tight junctions using transmission electron microscopy, and the expression of key tight junction proteins (claudin-2, claudin-3, occludin, JAM-A, and ZO-1) and zonulin using real-time PCR and immunohistochemistry were assessed in anti-tTG Ab-negative, HLA-DQ2/-DQ8-positive FDRs having normal villi and in disease controls. In addition, the serum zonulin level was measured in 172 anti-tTG Ab-negative FDRs and 198 controls. The intestinal permeability was significantly increased in FDRs than in controls. Ultrastructural abnormalities such as dilatation of the tight junction (P=0.004) and loss of the pentalaminar structure (P=0.001) were more common in FDRs than in disease controls. There was significant underexpression of tight junction proteins ZO-1 (P=0.040) and occludin (P=0.041) in FDRs. There was no significant difference in the serum zonulin level between FDRs and controls (P=0.154). Even asymptomatic, anti-tTG-Ab-negative FDRs with a normal villous histology have both ultrastructural and functional abnormalities in tight junctions. These findings are indirect evidence of the presence of tight junction abnormalities before the onset of the disease and may have therapeutic implications.

  20. High gradient test of X-band accelerating structure at GLCTA

    International Nuclear Information System (INIS)

    Watanabe, K.; Higo, T.; Hayano, H.; Terunuma, N.; Saeki, T.; Kudo, N.; Sanuki, T.; Seuhara, T.

    2004-01-01

    GLCTA (Global Linear Collider Test Accelerator) is the high power test facility for X-band acceleration. We have installed an X-band 60cm structure in April 2004 and have been processing it for more than 3 months. Now it is under test on long-term operation. We report here the installation process and high power test result to date. (author)

  1. A tool for calculating binding-site residues on proteins from PDB structures

    Directory of Open Access Journals (Sweden)

    Hu Jing

    2009-08-01

    Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

  2. Band structures in two-dimensional phononic crystals with periodic Jerusalem cross slot

    Science.gov (United States)

    Li, Yinggang; Chen, Tianning; Wang, Xiaopeng; Yu, Kunpeng; Song, Ruifang

    2015-01-01

    In this paper, a novel two-dimensional phononic crystal composed of periodic Jerusalem cross slot in air matrix with a square lattice is presented. The dispersion relations and the transmission coefficient spectra are calculated by using the finite element method based on the Bloch theorem. The formation mechanisms of the band gaps are analyzed based on the acoustic mode analysis. Numerical results show that the proposed phononic crystal structure can yield large band gaps in the low-frequency range. The formation mechanism of opening the acoustic band gaps is mainly attributed to the resonance modes of the cavities inside the Jerusalem cross slot structure. Furthermore, the effects of the geometrical parameters on the band gaps are further explored numerically. Results show that the band gaps can be modulated in an extremely large frequency range by the geometry parameters such as the slot length and width. These properties of acoustic waves in the proposed phononic crystals can potentially be applied to optimize band gaps and generate low-frequency filters and waveguides.

  3. Band structure and optical properties of opal photonic crystals

    Science.gov (United States)

    Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

    2005-07-01

    A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order planes (corresponding to the excitation of photonic modes in the crystal). Reflectance measurements on artificial opals made of self-assembled polystyrene spheres are analyzed according to the theoretical scheme and give evidence of diffraction by higher-order crystalline planes in the photonic structure.

  4. Experimental Studies of W-Band Accelerator Structures at High Field

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Marc E

    2001-02-09

    A high-gradient electron accelerator is desired for high-energy physics research, where frequency scalings of breakdown and trapping of itinerant beamline particles dictates operation of the accelerator at short wavelengths. The first results of design and test of a high-gradient mm-wave linac with an operating frequency at 91.392 GHz (W-band) are presented. A novel approach to particle acceleration is presented employing a planar, dielectric lined waveguide used for particle acceleration. The traveling wave fields in the planar dielectric accelerator (PDA) are analyzed for an idealized structure, along with a circuit equivalent model used for understanding the structure as a microwave circuit. Along with the W-band accelerator structures, other components designed and tested are high power rf windows, high power attenuators, and a high power squeeze-type phase shifter. The design of the accelerator and its components where eased with the aide of numerical simulations using a finite-difference electromagnetic field solver. Manufacturing considerations of the small, delicate mm-wave components and the steps taken to reach a robust fabrication process are detailed. These devices were characterized under low power using a two-port vector network analyzer to verify tune and match, including measurements of the structures' fields using a bead-pull. The measurements are compared with theory throughout. Addition studies of the W-band structures were performed under high power utilizing a 11.424 GHz electron linac as a current source. Test results include W-band power levels of 200 kW, corresponding to fields in the PDA of over 20 MV/m, a higher gradient than any collider. Planar accelerator devices naturally have an rf quadrupole component of the accelerating field. Presented for the first time are the measurements of this effect.

  5. Study of band structure in 78,80Sr using Triaxial Projected Shell Model

    International Nuclear Information System (INIS)

    Behera, N.; Naik, Z.; Bhat, G.H.; Sheikh, J.A.; Palit, R.; Sun, Y.

    2017-01-01

    The purpose of present work is to carry out a systematic study of the yrast-band and gamma-band structure for the even-even 78-80 Sr nuclei using Triaxial Projected Shell Model (TPSM) approach. These nuclei were chosen because 78 Sr has well developed side band(unassigned configuration) and 80 Sr has well developed band observed experimentally

  6. Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

    DEFF Research Database (Denmark)

    Link, Todd M; Valentin-Hansen, Poul; Brennan, Richard G

    2009-01-01

    (A) RNA, A(15). The structure reveals a unique RNA binding mechanism. Unlike uridine-containing sequences, which bind to the "proximal" face, the poly(A) tract binds to the "distal" face of Hfq using 6 tripartite binding motifs. Each motif consists of an adenosine specificity site (A site), which......Hfq is a small, highly abundant hexameric protein that is found in many bacteria and plays a critical role in mRNA expression and RNA stability. As an "RNA chaperone," Hfq binds AU-rich sequences and facilitates the trans annealing of small RNAs (sRNAs) to their target mRNAs, typically resulting...... in the down-regulation of gene expression. Hfq also plays a key role in bacterial RNA decay by binding tightly to polyadenylate [poly(A)] tracts. The structural mechanism by which Hfq recognizes and binds poly(A) is unknown. Here, we report the crystal structure of Escherichia coli Hfq bound to the poly...

  7. Bulk band structure of Bi2Te3

    DEFF Research Database (Denmark)

    Michiardi, Matteo; Aguilera, Irene; Bianchi, Marco

    2014-01-01

    -electron full-potential linearized augmented-plane-wave (FLAPW) formalism, fully taking into account spin-orbit coupling. Quasiparticle effects produce significant changes in the band structure of Bi2Te3 when compared to LDA. Experimental and calculated results are compared in the spectral regions where...

  8. On the mechanism of sulfite activation of chloroplast thylakoid ATPase and the relation of ADP tightly bound at a catalytic site to the binding change mechanism

    International Nuclear Information System (INIS)

    Du, Z.; Boyer, P.D.

    1990-01-01

    Washed chloroplast thylakoid membranes upon exposure to [ 3 H]ADP retain in tightly bound [ 3 H]ADP on a catalytic site of the ATP synthase. The presence of sufficient endogenous or added Mg 2+ results in an enzyme with essentially no ATPase activity. Sulfite activates the ATPase, and many molecules of ATP per synthase can be hydrolyzed before most of the bound [ 3 H]ADP is released, a result interpreted as indicating that the ADP is not bound at a site participating in catalysis by the sulfite-activated enzyme. The authors present evidence that this is not the case. The Mg 2+ - and ADP-inhibited enzyme when exposed to MgATP and 20-100 mM sulfite shows a lag of about 1 min at 22 degree C and of about 15 s at 37 degree C before reaching the same steady-state rate as attained with light-activated ATPase that has not been inhibited by Mg 2+ and ADP. The lag is not eliminated if the enzyme is exposed to sulfite prior to MgATP addition, indicating that ATPase turnover is necessary for the activation. The release of most of the bound [ 3 H]ADP parallels the onset of ATPase activity, although some [ 3 H]ADP is not released even with prolonged catalytic turnover and may be on poorly active or inactive enzyme or at noncatalytic sites. The results are consistent with most of the tightly bound [ 3 H]ADP being at a catalytic site and being replaced as this Mg 2+ - and ADP-inhibited site regains equivalent participation with other catalytic sites on the activated enzyme. The sulfite activation can be explained by sulfite combination at a P i binding site of the enzyme-ADP-Mg 2+ complex to give a form more readily activated by ATP binding at an alternative site

  9. Structural-Diagenetic Controls on Fracture Opening in Tight Gas Sandstone Reservoirs, Alberta Foothills

    Science.gov (United States)

    Ukar, Estibalitz; Eichhubl, Peter; Fall, Andras; Hooker, John

    2013-04-01

    In tight gas reservoirs, understanding the characteristics, orientation and distribution of natural open fractures, and how these relate to the structural and stratigraphic setting are important for exploration and production. Outcrops provide the opportunity to sample fracture characteristics that would otherwise be unknown due to the limitations of sampling by cores and well logs. However, fractures in exhumed outcrops may not be representative of fractures in the reservoir because of differences in burial and exhumation history. Appropriate outcrop analogs of producing reservoirs with comparable geologic history, structural setting, fracture networks, and diagenetic attributes are desirable but rare. The Jurassic to Lower Cretaceous Nikanassin Formation from the Alberta Foothills produces gas at commercial rates where it contains a network of open fractures. Fractures from outcrops have the same diagenetic attributes as those observed in cores fractures relative to fold cores, hinges and limbs, 2) compare the distribution and attributes of fractures in outcrop vs. core samples, 3) estimate the timing of fracture formation relative to the evolution of the fold-and-thrust belt, and 4) estimate the degradation of fracture porosity due to postkinematic cementation. Cathodoluminescence images of cemented fractures in both outcrop and core samples reveal several generations of quartz and ankerite cement that is synkinematic and postkinematic relative to fracture opening. Crack-seal textures in synkinematic quartz are ubiquitous, and well-developed cement bridges abundant. Fracture porosity may be preserved in fractures wider than ~100 microns. 1-D scanlines in outcrop and core samples indicate fractures are most abundant within small parasitic folds within larger, tight, mesoscopic folds. Fracture intensity is lower away from parasitic folds; intensity progressively decreases from the faulted cores of mesoscopic folds to their forelimbs, with lowest intensities within

  10. Scaling Universality between Band Gap and Exciton Binding Energy of Two-Dimensional Semiconductors

    Science.gov (United States)

    Jiang, Zeyu; Liu, Zhirong; Li, Yuanchang; Duan, Wenhui

    2017-06-01

    Using first-principles G W Bethe-Salpeter equation calculations and the k .p theory, we unambiguously show that for two-dimensional (2D) semiconductors, there exists a robust linear scaling law between the quasiparticle band gap (Eg) and the exciton binding energy (Eb), namely, Eb≈Eg/4 , regardless of their lattice configuration, bonding characteristic, as well as the topological property. Such a parameter-free universality is never observed in their three-dimensional counterparts. By deriving a simple expression for the 2D polarizability merely with respect to Eg, and adopting the screened hydrogen model for Eb, the linear scaling law can be deduced analytically. This work provides an opportunity to better understand the fantastic consequence of the 2D nature for materials, and thus offers valuable guidance for their property modulation and performance control.

  11. A strategy for increasing the brain uptake of a radioligand in animals: use of a drug that inhibits plasma protein binding

    Energy Technology Data Exchange (ETDEWEB)

    Haradahira, Terushi E-mail: terushi@nirs.go.jp; Zhang, Ming-Rong; Maeda, Jun; Okauchi, Takashi; Kawabe, Kouichi; Kida, Takayo; Suzuki, Kazutoshi; Suhara, Tetsuya

    2000-05-01

    A positron-emitter labeled radioligand for the glycine-binding site of the N-methyl-D-aspartate (NMDA) receptor, [{sup 11}C]L-703,717, was examined for its ability to penetrate the brain in animals by simultaneous use with drugs having high-affinity separate binding sites on human serum albumin. [{sup 11}C]L-703,717 has poor blood-brain barrier (BBB) permeability because it binds tightly to plasma proteins. Co-injection of warfarin (50-200 mg/kg), a drug that binds to albumin and resembles L-703,717 in structure, dose-dependently enhanced the penetration by [{sup 11}C]L-703,717 in mice, resulting in a five-fold increase in the brain radioactivity at 1 min after the injection. Drugs structurally unrelated to L-703,717, salicylate, phenol red, and L-tryptophan, were less effective or ineffective in increasing the uptake of [{sup 11}C]L-703,717. These results suggest that the simultaneous use of a drug that inhibits the binding of a radioligand to plasma proteins is a useful way to overcome the poor BBB permeability of the radioligand triggered by its tight binding to plasma proteins. In brain distribution studies in rodents, it was found that, after the increase in brain uptake with warfarin, much of the glycine site antagonist accumulates in the cerebellum but its pharmacological specificity did not match the glycine site of NMDA receptors.

  12. Photo field emission spectroscopy of the tantalum band structure

    International Nuclear Information System (INIS)

    Kleint, Ch.; Radon, T.

    1978-01-01

    Photo field emission (PFE) currents of clean and barium covered tantalum tips have been measured with single lines of the mercury arc spectrum and phase-sensitive detection. Field strength and work function were determined from Fowler-Nordheim plots of the FE currents. Shoulders in the PFE current-voltage characteristics could be correlated to transitions in the band structure of tantalum according to a recently proposed two-step PFE model. A comparison with the relativistic calculations of Mattheiss and the nonrelativistic bands of Petroff and Viswanathan shows that Mattheiss' bands are more appropriate. Beside direct transitions several nondirect transitions from the different features composing the upper two density of states maxima below the Fermi edge of tantalum have been found. (Auth.)

  13. The structure of collective bands in 72Ge

    International Nuclear Information System (INIS)

    Tripathy, K.C.; Sahu, R.

    1999-01-01

    In recent years, extensive experimental studies of nuclei in the mass region A=80 have led to exciting discoveries of large ground state deformations, coexistence of shapes, band crossings, rapid variations of structure with changing nucleon numbers etc. A theoretical study of 72 Ge is presented

  14. Design for maximum band-gaps in beam structures

    DEFF Research Database (Denmark)

    Olhoff, Niels; Niu, Bin; Cheng, Gengdong

    2012-01-01

    This paper aims to extend earlier optimum design results for transversely vibrating Bernoulli-Euler beams by determining new optimum band-gap beam structures for (i) different combinations of classical boundary conditions, (ii) much larger values of the orders n and n-1 of adjacent upper and lower...

  15. High Power Test of an X-Band Slotted-IRIS Accelerator Structure at NLCTA

    International Nuclear Information System (INIS)

    Doebert, S.; Fandos, R.; Grudiev, A.; Heikkinen, S.; Rodriquez, J.A.; Taborelli, M.; Wuensch, W.; Adolphsen, Chris E.; Laurent, L.

    2007-01-01

    The CLIC study group at CERN has built two X-band HDS (hybrid damped structure) accelerating structures for high-power testing in NLCTA at SLAC. These accelerating structures are novel with respect to their rf- design and their fabrication technique. The eleven-cell constant impedance structures, one made out of copper and one out of molybdenum, are assembled from clamped high-speed milled quadrants. They feature the same heavy higher-order-mode damping as nominal CLIC structures achieved by slotted irises and radial damping waveguides for each cell. The X-band accelerators are exactly scaled versions of structures tested at 30 GHz in the CLIC test facility, CTF3. The results of the X-band tests are presented and compared to those at 30 GHz to determine frequency scaling, and are compared to the extensive copper data from the NLC structure development program to determine material dependence and make a basic validation of the HDS design

  16. Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

    Science.gov (United States)

    Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

  17. MicroRNA-target binding structures mimic microRNA duplex structures in humans.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    Full Text Available Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In this work, we consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. We have analyzed thousands of such structure pairs and found many of them share high structural similarity. Therefore, we conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient--the microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. We have developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. Our software and methods can be utilized in the other RNA secondary structure comparisons as well.

  18. Chain-Branching Control of the Atomic Structure of Alkanethiol-Based Gold–Sulfur Interfaces

    DEFF Research Database (Denmark)

    Wang, Yun; Chi, Qijin; Zhang, Jingdong

    2011-01-01

    Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111......): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling...

  19. Purification and characterization of cGMP binding protein-phosphodiesterase from rat lung

    International Nuclear Information System (INIS)

    Francis, S.H.; Walseth, T.F.; Corbin, J.D.

    1986-01-01

    The cGMP binding protein-phosphodiesterase (cG-BPP) with a phosphodiesterase specific activity of 7 μM/min/mg has been purified from rat lung by sequential chromatography on DEAE-cellulose, Blue-Sepharose, zinc chelate affinity adsorbent and HPLC-DEAE. Migration of the major band on SDS-PAGE corresponds to a MW of ∼93,000. Both cGMP phosphodiesterase activity and cGMP binding from the HPLC-DEAE profile correlate with this band. Since the authors previous work has determined the native MW to be ∼177,000, this suggests a dimeric structure comprised of two 93,000 MW subunits for the rat lung cG-BPP. At low cGMP concentrations, cGMP binding is stimulated ∼20-fold by histone and ∼5-fold by 3-isobutyl-1-methylxanthine(IBMX). The purified protein has one component of cGMP dissociation with a rate constant of 0.045/min. Photolysis of the purified protein in the presence of 32 P-cGMP labels the 93,000 MW band and this labeling is increased by IBMX, indicating that the 93,000 MW band is a subunit of the cGMP-BPP. This implies that the enzyme preparation is nearly homogeneous, a conclusion also supported by a minimum [ 3 H]-cGMP binding stoichiometry of 0.5 mol per 93,000 subunit. An additional protein band with a MW of ∼90,000 also occurs in these preparations which exhibits behavior similar to the 93,000 MW protein. N 2 -Hexyl-cGMP inhibits phosphodiesterase activity by competing with cGMP for hydrolysis at the catalytic site but not at the binding site. N 2 -Hexyl cGMP actually increases cGMP binding. This provides the first evidence that cGMP binding is increased by compounds hydrolyzed at the catalytic site. This interaction between the binding and phosphodiesterase sites could be important in the regulation of the functions of these sites in vivo

  20. Activator Protein-1: redox switch controlling structure and DNA-binding.

    Science.gov (United States)

    Yin, Zhou; Machius, Mischa; Nestler, Eric J; Rudenko, Gabby

    2017-11-02

    The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a 'redox switch' centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the 'OFF' state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Band structures of 4f and 5f materials studied by angle-resolved photoelectron spectroscopy.

    Science.gov (United States)

    Fujimori, Shin-ichi

    2016-04-20

    Recent remarkable progress in angle-resolved photoelectron spectroscopy (ARPES) has enabled the direct observation of the band structures of 4f and 5f materials. In particular, ARPES with various light sources such as lasers (hν ~ 7 eV) or high-energy synchrotron radiations (hν >/~ 400 eV) has shed light on the bulk band structures of strongly correlated materials with energy scales of a few millielectronvolts to several electronvolts. The purpose of this paper is to summarize the behaviors of 4f and 5f band structures of various rare-earth and actinide materials observed by modern ARPES techniques, and understand how they can be described using various theoretical frameworks. For 4f-electron materials, ARPES studies of CeMIn5(M = Rh, Ir, and Co) and YbRh2Si2 with various incident photon energies are summarized. We demonstrate that their 4f electronic structures are essentially described within the framework of the periodic Anderson model, and that the band-structure calculation based on the local density approximation cannot explain their low-energy electronic structures. Meanwhile, electronic structures of 5f materials exhibit wide varieties ranging from itinerant to localized states. For itinerant U5f compounds such as UFeGa5, their electronic structures can be well-described by the band-structure calculation assuming that all U5f electrons are itinerant. In contrast, the band structures of localized U5f compounds such as UPd3 and UO2 are essentially explained by the localized model that treats U5f electrons as localized core states. In regards to heavy fermion U-based compounds such as the hidden-order compound URu2Si2, their electronic structures exhibit complex behaviors. Their overall band structures are generally well-explained by the band-structure calculation, whereas the states in the vicinity of EF show some deviations due to electron correlation effects. Furthermore, the electronic structures of URu2Si2 in the paramagnetic and hidden-order phases are

  2. Effect of Γ-X band mixing on the donor binding energy in a Quantum Wire

    Science.gov (United States)

    Vijaya Shanthi, R.; Jayakumar, K.; Nithiananthi, P.

    2015-02-01

    To invoke the technological applications of heterostructure semiconductors like Quantum Well (QW), Quantum Well Wire (QWW) and Quantum Dot (QD), it is important to understand the property of impurity energy which is responsible for the peculiar electronic & optical behavior of the Low Dimensional Semiconductor Systems (LDSS). Application of hydrostatic pressure P>35kbar drastically alters the band offsets leading to the crossover of Γ band of the well & X band of the barrier resulting in an indirect transition of the carrier and this effect has been studied experimentally and theoretically in a QW structure. In this paper, we have investigated the effect of Γ-X band mixing due to the application of hydrostatic pressure in a GaAs/AlxGa1-xAs QWW system. The results are presented and discussed for various widths of the wire.

  3. Atomistic tight-binding theory of excitonic splitting energies in CdX(X = Se, S and Te)/ZnS core/shell nanocrystals

    Science.gov (United States)

    Sukkabot, Worasak; Pinsook, Udomsilp

    2017-01-01

    Using the atomistic tight-binding theory (TB) and a configuration interaction description (CI), we numerically compute the excitonic splitting of CdX(X = Se, S and Te)/ZnS core/shell nanocrystals with the objective to explain how types of the core materials and growth shell thickness can provide the detailed manipulation of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting, beneficial for the active application of quantum information. To analyze the splitting of the excitonic states, the optical band gaps, ground-state wave function overlaps and atomistic electron-hole interactions tend to be numerically demonstrated. Based on the atomistic computations, the single-particle and excitonic gaps are mainly reduced with the increasing ZnS shell thickness owing to the quantum confinement. In the range of the higher to lower energies, the order of the single-particle gaps is CdSe/ZnS, CdS/ZnS and CdTe/ZnS core/shell nanocrystals, while one of the excitonic gaps is CdS/ZnS, CdSe/ZnS and CdTe/ZnS core/shell nanocrystals because of the atomistic electron-hole interaction. The strongest electron-hole interactions are mainly observed in CdSe/ZnS core/shell nanocrystals. In addition, the computational results underline that the energies of the dark-dark (DD), dark-bright (DB) and bright-bright (BB) excitonic splitting are generally reduced with the increasing ZnS growth shell thickness as described by the trend of the electron-hole exchange interaction. The high-to-low splitting of the excitonic states is demonstrated in CdSe/ZnS, CdTe/ZnS and CdS/ZnS core/shell nanocrystals because of the fashion in the electron-hole exchange interaction and overlaps of the electron-hole wave functions. As the resulting calculations, it is expected that CdS/ZnS core/shell nanocrystals are the best candidates to be the source of entangled photons. Finally, the comprehensive information on the excitonic splitting can enable the use of suitable core

  4. 8-band and 14-band kp modeling of electronic band structure and material gain in Ga(In)AsBi quantum wells grown on GaAs and InP substrates

    Energy Technology Data Exchange (ETDEWEB)

    Gladysiewicz, M.; Wartak, M. S. [Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw (Poland); Department of Physics and Computer Science, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5 (Canada); Kudrawiec, R. [Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw (Poland)

    2015-08-07

    The electronic band structure and material gain have been calculated for GaAsBi/GaAs quantum wells (QWs) with various bismuth concentrations (Bi ≤ 15%) within the 8-band and 14-band kp models. The 14-band kp model was obtained by extending the standard 8-band kp Hamiltonian by the valence band anticrossing (VBAC) Hamiltonian, which is widely used to describe Bi-related changes in the electronic band structure of dilute bismides. It has been shown that in the range of low carrier concentrations n < 5 × 10{sup 18 }cm{sup −3}, material gain spectra calculated within 8- and 14-band kp Hamiltonians are similar. It means that the 8-band kp model can be used to calculate material gain in dilute bismides QWs. Therefore, it can be applied to analyze QWs containing new dilute bismides for which the VBAC parameters are unknown. Thus, the energy gap and electron effective mass for Bi-containing materials are used instead of VBAC parameters. The electronic band structure and material gain have been calculated for 8 nm wide GaInAsBi QWs on GaAs and InP substrates with various compositions. In these QWs, Bi concentration was varied from 0% to 5% and indium concentration was tuned in order to keep the same compressive strain (ε = 2%) in QW region. For GaInAsBi/GaAs QW with 5% Bi, gain peak was determined to be at about 1.5 μm. It means that it can be possible to achieve emission at telecommunication windows (i.e., 1.3 μm and 1.55 μm) for GaAs-based lasers containing GaInAsBi/GaAs QWs. For GaInAsBi/Ga{sub 0.47}In{sub 0.53}As/InP QWs with 5% Bi, gain peak is predicted to be at about 4.0 μm, i.e., at the wavelengths that are not available in current InP-based lasers.

  5. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.; Qian, Zhaohui; Holmes, Kathryn V.; Li, Fang (Cornell); (UMM-MED); (Colorado)

    2011-09-28

    Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.

  6. Tight junctions and human diseases.

    Science.gov (United States)

    Sawada, Norimasa; Murata, Masaki; Kikuchi, Keisuke; Osanai, Makoto; Tobioka, Hirotoshi; Kojima, Takashi; Chiba, Hideki

    2003-09-01

    Tight junctions are intercellular junctions adjacent to the apical end of the lateral membrane surface. They have two functions, the barrier (or gate) function and the fence function. The barrier function of tight junctions regulates the passage of ions, water, and various macromolecules, even of cancer cells, through paracellular spaces. The barrier function is thus relevant to edema, jaundice, diarrhea, and blood-borne metastasis. On the other hand, the fence function maintains cell polarity. In other words, tight junctions work as a fence to prevent intermixing of molecules in the apical membrane with those in the lateral membrane. This function is deeply involved in cancer cell biology, in terms of loss of cell polarity. Of the proteins comprising tight junctions, integral membrane proteins occludin, claudins, and JAMs have been recently discovered. Of these molecules, claudins are exclusively responsible for the formation of tight-junction strands and are connected with the actin cytoskeleton mediated by ZO-1. Thus, both functions of tight junctions are dependent on the integrity of the actin cytoskeleton as well as ATP. Mutations in the claudin14 and the claudin16 genes result in hereditary deafness and hereditary hypomagnesemia, respectively. Some pathogenic bacteria and viruses target and affect the tight-junction function, leading to diseases. In this review, the relationship between tight junctions and human diseases is summarized.

  7. Effect of pressure on the structural properties and electronic band structure of GaSe

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, U.; Olguin, D.; Syassen, K. [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany); Cantarero, A. [Department of Materials Sciences, University of Valencia, 46000 Burjasot (Spain); Hanfland, M. [European Synchrotron Radiation Facility, BP 220, 38043 Grenoble (France)

    2007-01-15

    The structural properties of GaSe have been investigated up to 38 GPa by monochromatic X-ray diffraction. The onset of the phase transition from the {epsilon}-GaSe to a disordered NaCl-type structural motif is observed near 21 GPa. Using the experimentally determined lattice parameters of the layered {epsilon}-phase as input, constrained ab-initio total energy calculations were performed in order to optimize the internal structural parameters at different pressures. The results obtained for the nearest-neighbor Ga-Se distance agree with those derived from recent EXAFS measurements. In addition, information is obtained on the changes of Ga-Ga and Se-Se bond lengths which were not accessible to a direct experimental determination yet. Based on the optimized structural parameters, we report calculations of band gap changes of {epsilon}-GaSe under pressure. The optical response and electronic band structure of the metallic high-pressure phase of GaSe are discussed briefly. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  8. Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA.

    Directory of Open Access Journals (Sweden)

    Justina C Wolters

    2010-04-01

    Full Text Available The ABC transporter OpuA from Lactococcus lactis transports glycine betaine upon activation by threshold values of ionic strength. In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC was characterized.The binding of glycine betaine to purified OpuA and OpuAC (K(D = 4-6 microM did not show any salt dependence or cooperative effects, in contrast to the transport activity. OpuAC is highly specific for glycine betaine and the related proline betaine. Other compatible solutes like proline and carnitine bound with affinities that were 3 to 4 orders of magnitude lower. The low affinity substrates were not noticeably transported by membrane-reconstituted OpuA. OpuAC was crystallized in an open (1.9 A and closed-liganded (2.3 A conformation. The binding pocket is formed by three tryptophans (Trp-prism coordinating the quaternary ammonium group of glycine betaine in the closed-liganded structure. Even though the binding site of OpuAC is identical to that of its B. subtilis homolog, the affinity for glycine betaine is 4-fold higher.Ionic strength did not affect substrate binding to OpuA, indicating that regulation of transport is not at the level of substrate binding, but rather at the level of translocation. The overlap between the crystal structures of OpuAC from L.lactis and B.subtilis, comprising the classical Trp-prism, show that the differences observed in the binding affinities originate from outside of the ligand binding site.

  9. Development of constraint algorithm for the number of electrons in molecular orbitals consisting mainly 4f atomic orbitals of rare-earth elements and its introduction to tight-binding quantum chemical molecular dynamics method

    International Nuclear Information System (INIS)

    Endou, Akira; Onuma, Hiroaki; Jung, Sun-ho

    2007-01-01

    Our original tight-binding quantum chemical molecular dynamics code, Colors', has been successfully applied to the theoretical investigation of complex materials including rare-earth elements, e.g., metal catalysts supported on a CeO 2 surface. To expand our code so as to obtain a good convergence for the electronic structure of a calculation system including a rare-earth element, we developed a novel algorithm to provide a constraint condition for the number of electrons occupying the selected molecular orbitals that mainly consist of 4f atomic orbitals of the rare-earth element. This novel algorithm was introduced in Colors. Using Colors, we succeeded in obtaining the classified electronic configurations of the 4f atomic orbitals of Ce 4+ and reduced Ce ions in a CeO 2 bulk model with one oxygen defect, which makes it difficult to obtain a good convergence using a conventional first-principles quantum chemical calculation code. (author)

  10. Band structure, band offsets, substitutional doping, and Schottky barriers of bulk and monolayer InSe

    Science.gov (United States)

    Guo, Yuzheng; Robertson, John

    2017-09-01

    We present a detailed study of the electronic structure of the layered semiconductor InSe. We calculate the band structure of the monolayer and bulk material using density functional theory, hybrid functionals, and G W . The band gap of the monolayer InSe is calculated to be 2.4 eV in screened exchange hybrid functional, close to the experimental photoluminescence gap. The electron affinities and band offsets are calculated for vertical stacked-layer heterostructures, and are found to be suitable for tunnel field effect transistors (TFETs) in combination with WS e2 or similar. The valence-band edge of InSe is calculated to lie 5.2 eV below the vacuum level, similar to that for the closed shell systems HfS e2 or SnS e2 . Hence InSe would be suitable to act as a p -type drain in the TFET. The intrinsic defects are calculated. For Se-rich layers, the Se adatom (interstitial) is found to be the most stable defect, whereas for In-rich layers, the Se vacancy is the most stable for the neutral state. Antisites tend to have energies just above those of vacancies. The Se antisite distorts towards a bond-breaking distortion as in the EL2 center of GaAs. Both substitutional donors and acceptors are calculated to be shallow, and effective dopants. They do not reconstruct to form nondoping configurations as occurs in black phosphorus. Finally, the Schottky barriers of metals on InSe are found to be strongly pinned by metal induced gap states (MIGS) at ˜0.5 eV above the valence-band edge. Any interfacial defects would lead to a stronger pinning at a similar energy. Overall, InSe is an effective semiconductor combining the good features of 2D (lack of dangling bonds, etc.) with the good features of 3D (effective doping), which few others achieve.

  11. Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

    Science.gov (United States)

    Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

    2008-02-01

    In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.

  12. Exact solution of corner-modified banded block-Toeplitz eigensystems

    International Nuclear Information System (INIS)

    Cobanera, Emilio; Alase, Abhijeet; Viola, Lorenza; Ortiz, Gerardo

    2017-01-01

    Motivated by the challenge of seeking a rigorous foundation for the bulk-boundary correspondence for free fermions, we introduce an algorithm for determining exactly the spectrum and a generalized-eigenvector basis of a class of banded block quasi-Toeplitz matrices that we call corner-modified . Corner modifications of otherwise arbitrary banded block-Toeplitz matrices capture the effect of boundary conditions and the associated breakdown of translational invariance. Our algorithm leverages the interplay between a non-standard, projector-based method of kernel determination (physically, a bulk-boundary separation) and families of linear representations of the algebra of matrix Laurent polynomials. Thanks to the fact that these representations act on infinite-dimensional carrier spaces in which translation symmetry is restored, it becomes possible to determine the eigensystem of an auxiliary projected block-Laurent matrix. This results in an analytic eigenvector Ansatz , independent of the system size, which we prove is guaranteed to contain the full solution of the original finite-dimensional problem. The actual solution is then obtained by imposing compatibility with a boundary matrix , whose shape is also independent of system size. As an application, we show analytically that eigenvectors of short-ranged fermionic tight-binding models may display power-law corrections to exponential behavior, and demonstrate the phenomenon for the paradigmatic Majorana chain of Kitaev. (paper)

  13. Anion-induced reconstitution of a self-assembling system to express a chloride-binding Co10L15 pentagonal prism.

    Science.gov (United States)

    Riddell, Imogen A; Smulders, Maarten M J; Clegg, Jack K; Hristova, Yana R; Breiner, Boris; Thoburn, John D; Nitschke, Jonathan R

    2012-09-01

    Biochemical systems are adaptable, capable of reconstitution at all levels to achieve the functions associated with life. Synthetic chemical systems are more limited in their ability to reorganize to achieve new functions; they can reconfigure to bind an added substrate (template effect) or one binding event may modulate a receptor's affinity for a second substrate (allosteric effect). Here we describe a synthetic chemical system that is capable of structural reconstitution on receipt of one anionic signal (perchlorate) to create a tight binding pocket for another anion (chloride). The complex, barrel-like structure of the chloride receptor is templated by five perchlorate anions. This second-order templation phenomenon allows chemical networks to be envisaged that express more complex responses to chemical signals than is currently feasible.

  14. Electronic structure of the misfit layer compound (SnS)(1.20)TiS2 : Band structure calculations and photoelectron spectra

    NARCIS (Netherlands)

    Fang, CM; deGroot, RA; Wiegers, GA; Haas, C

    1996-01-01

    In order to understand the electronic structure of the incommensurate misfit layer compound (SnS)(1.20)TiS2 we carried out an ab initio band structure calculation in the supercell approximation. The band structure is compared with that of the components 1T-TiS2 and hypothetical SnS with a similar

  15. Electronic structure of the misfit layer compound (SnS)1.20TiS2 : band structure calculations and photoelectron spectra

    NARCIS (Netherlands)

    Fang, C.M.; Groot, R.A. de; Wiegers, G.A.; Haas, C.

    1996-01-01

    In order to understand the electronic structure of the incommensurate misfit layer compound (SnS)1.20TiS2 we carried out an ab initio band structure calculation in the supercell approximation. The band structure is compared with that of the components 1T-TiS2 and hypothetical SnS with a similar

  16. Cherenkov oscillator operating at the second band gap of leakage waveguide structures

    Directory of Open Access Journals (Sweden)

    Kyu-Ha Jang

    2016-10-01

    Full Text Available An electromagnetic wave source operating around second band gaps of metallic grating structures is presented. The considered metallic grating structures are not perfect periodic but inhomogeneously structured within a period to have a second band gap where the wavelength is equal to the period of the structures. The radiation mechanism by an electron beam in the structures is different from the well-known Smith-Purcell radiation occurring in perfect periodic grating structures. That is, the radiating wave has a single frequency and the radiation is unidirectional. When the energy of the electron beam is synchronized at the standing wave point in the dispersion curves, strong interaction happens and coherent radiation perpendicular to the grating surface is generated with relatively lower starting oscillation current.

  17. The band gap variation of a two dimensional binary locally resonant structure in thermal environment

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2017-01-01

    Full Text Available In this study, the numerical investigation of thermal effect on band gap dynamical characteristic for a two-dimensional binary structure composed of aluminum plate periodically filled with nitrile rubber cylinder is presented. Initially, the band gap of the binary structure variation trend with increasing temperature is studied by taking the softening effect of thermal stress into account. A breakthrough is made which found the band gap being narrower and shifting to lower frequency in thermal environment. The complete band gap which in higher frequency is more sensitive to temperature that it disappears with temperature increasing. Then some new transformed models are created by changing the height of nitrile rubber cylinder from 1mm to 7mm. Simulations show that transformed model can produce a wider band gap (either flexure or complete band gap. A proper forbidden gap of elastic wave can be utilized in thermal environment although both flexure and complete band gaps become narrower with temperature. Besides that, there is a zero-frequency flat band appearing in the first flexure band, and it becomes broader with temperature increasing. The band gap width decreases trend in thermal environment, as well as the wider band gap induced by the transformed model with higher nitrile rubber cylinder is useful for the design and application of phononic crystal structures in thermal environment.

  18. Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding.

    Science.gov (United States)

    Huang, Kai-Fa; Liaw, Su-Sen; Huang, Wei-Lin; Chia, Cho-Yun; Lo, Yan-Chung; Chen, Yi-Ling; Wang, Andrew H-J

    2011-04-08

    Aberrant pyroglutamate formation at the N terminus of certain peptides and proteins, catalyzed by glutaminyl cyclases (QCs), is linked to some pathological conditions, such as Alzheimer disease. Recently, a glutaminyl cyclase (QC) inhibitor, PBD150, was shown to be able to reduce the deposition of pyroglutamate-modified amyloid-β peptides in brain of transgenic mouse models of Alzheimer disease, leading to a significant improvement of learning and memory in those transgenic animals. Here, we report the 1.05-1.40 Å resolution structures, solved by the sulfur single-wavelength anomalous dispersion phasing method, of the Golgi-luminal catalytic domain of the recently identified Golgi-resident QC (gQC) and its complex with PBD150. We also describe the high-resolution structures of secretory QC (sQC)-PBD150 complex and two other gQC-inhibitor complexes. gQC structure has a scaffold similar to that of sQC but with a relatively wider and negatively charged active site, suggesting a distinct substrate specificity from sQC. Upon binding to PBD150, a large loop movement in gQC allows the inhibitor to be tightly held in its active site primarily by hydrophobic interactions. Further comparisons of the inhibitor-bound structures revealed distinct interactions of the inhibitors with gQC and sQC, which are consistent with the results from our inhibitor assays reported here. Because gQC and sQC may play different biological roles in vivo, the different inhibitor binding modes allow the design of specific inhibitors toward gQC and sQC.

  19. Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

    Science.gov (United States)

    Ahmed, Aqeel; Smith, Richard D; Clark, Jordan J; Dunbar, James B; Carlson, Heather A

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Comparison and fit of the two and six band k.p models for the band edge structure of Pbsub(1-x)Snsub(x)Te

    International Nuclear Information System (INIS)

    Weissman, Y.

    1975-10-01

    The band edge structure of Pbsub(1-x)Snsub(x)Te is derived in detail using a two band ellipsoidal model and compared with a more rigorous calculation based on six bands. A quantitative comparison is made for two values of the energy gap, corresponding to the cases where x=0 and x=0.17. It was found that, for the occupied states in nondegenerate materials, both models are practically equivalent. Discrepancies may occur only in high degeneracies or deep inversion layers. The agreement between both models was significantly improved by introducing an effective energy gap in the two band model. It is suggested that the use of the effective energy gap may improve the agreement between the two band model and experiment whenever the details of the band edge structure enter the interpretation of the experimental results. (author)

  1. Modeling of full-Heusler alloys within tight-binding approximation: Case study of Fe2MnAl

    Science.gov (United States)

    Azhar, A.; Majidi, M. A.; Nanto, D.

    2017-07-01

    Heusler alloys have been known for about a century, and predictions of magnetic moment values using Slater-Pauling rule have been successful for many such materials. However, such a simple counting rule has been found not to always work for all Heusler alloys. For instance, Fe2CuAl has been found to have magnetic moment of 3.30 µB per formula unit although the Slater-Pauling rule suggests the value of 2 µB. On the other hand, a recent experiment shows that a non-stoichiometric Heusler compound Fe2Mn0.5Cu0.5Al possesses magnetic moment of 4 µB, closer to the Slater-Pauling prediction for the stoichiometric compound. Such discrepancies signify that the theory to predict the magnetic moment of Heusler alloys in general is still far from being complete. Motivated by this issue, we propose to do a theoretical study on a full-Heusler alloy Fe2MnAl to understand the formation of magnetic moment microscopically. We model the system by constructing a density-functional-theory-based tight-binding Hamiltonian and incorporating Hubbard repulsive as well as spin-spin interactions for the electrons occupying the d-orbitals. Then, we solve the model using Green's function approach, and treat the interaction terms within the mean-field approximation. At this stage, we aim to formulate the computational algorithm for the overall calculation process. Our final goal is to compute the total magnetic moment per unit cell of this system and compare it with the experimental data.

  2. Efficacy of pulmonary artery banding in patients with uneventricular defects

    Directory of Open Access Journals (Sweden)

    Ю. С. Синельников

    2015-10-01

    Full Text Available Long-term results where evaluated for different methods of pulmonary artery banding (PAB in 25 patients with univentricular congenital heart defects with used three methods. Hospital mortality was 8%. Second stage palliation was performed in 61% of patients. More tight PA banding in patients with univentriclar gave opportunity to perform 2nd stage of operation in 100% of patients, decrease complications and mortality rate, modify pulmonary circulation effectively.

  3. ELECTRONIC-STRUCTURE OF THE MISFIT-LAYER COMPOUND (SNS)(1.17)NBS2 DEDUCED FROM BAND-STRUCTURE CALCULATIONS AND PHOTOELECTRON-SPECTRA

    NARCIS (Netherlands)

    FANG, CM; ETTEMA, ARHF; HAAS, C; WIEGERS, GA; VANLEUKEN, H; DEGROOT, RA

    1995-01-01

    In order to understand the electronic structure of the misfit-layer compound (SnS)(1.17)NbS2 we carried out an ab initio band-structure calculation of the closely related commensurate compound (SnS)(1.20)NbS2. The band structure is compared with calculations for NbS2 and for hypothetical SnS with

  4. Results from the CLIC X-Band Structure Test Program at NLCTA

    International Nuclear Information System (INIS)

    Adolphsen, C.

    2009-01-01

    As part of a SLAC-CERN-KEK collaboration on high gradient X-band structure research, several prototype structures for the CLIC linear collider study have been tested using two of the high power (300 MW) X-band rf stations in the NLCTA facility at SLAC. These structures differ in terms of their fabrication (brazed disks and clamped quadrants), gradient profile (amount by which the gradient increases along the structure, which optimizes efficiency and maximizes sustainable gradient) and HOM damping (use of slots or waveguides to rapidly dissipate dipole mode energy). The CLIC goal in the next few years is to demonstrate the feasibility of a CLIC-ready baseline design and to investigate alternatives that could increase efficiency. This paper summarizes the high gradient test results from NLCTA in support of this effort.

  5. Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

    Science.gov (United States)

    Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

    2016-08-05

    The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Doping-dependent quasiparticle band structure in cuprate superconductors

    NARCIS (Netherlands)

    Eder, R; Ohta, Y.; Sawatzky, G.A

    1997-01-01

    We present an exact diagonalization study of the single-particle spectral function in the so-called t-t'-t ''-J model in two dimensions. As a key result, we find that hole doping leads to a major reconstruction of the quasiparticle band structure near (pi,0): whereas for the undoped system the

  7. Energy Band Gap Dependence of Valley Polarization of the Hexagonal Lattice

    Science.gov (United States)

    Ghalamkari, Kazu; Tatsumi, Yuki; Saito, Riichiro

    2018-02-01

    The origin of valley polarization of the hexagonal lattice is analytically discussed by tight binding method as a function of energy band gap. When the energy gap decreases to zero, the intensity of optical absorption becomes sharp as a function of k near the K (or K') point in the hexagonal Brillouin zone, while the peak intensity at the K (or K') point keeps constant with decreasing the energy gap. When the dipole vector as a function of k can have both real and imaginary parts that are perpendicular to each other in the k space, the valley polarization occurs. When the dipole vector has only real values by selecting a proper phase of wave functions, the valley polarization does not occur. The degree of the valley polarization may show a discrete change that can be relaxed to a continuous change of the degree of valley polarization when we consider the life time of photo-excited carrier.

  8. Evidence of ion intercalation mediated band structure modification and opto-ionic coupling in lithium niobite

    Science.gov (United States)

    Shank, Joshua C.; Tellekamp, M. Brooks; Doolittle, W. Alan

    2015-01-01

    The theoretically suggested band structure of the novel p-type semiconductor lithium niobite (LiNbO2), the direct coupling of photons to ion motion, and optically induced band structure modifications are investigated by temperature dependent photoluminescence. LiNbO2 has previously been used as a memristor material but is shown here to be useful as a sensor owing to the electrical, optical, and chemical ease of lithium removal and insertion. Despite the high concentration of vacancies present in lithium niobite due to the intentional removal of lithium atoms, strong photoluminescence spectra are observed even at room temperature that experimentally confirm the suggested band structure implying transitions from a flat conduction band to a degenerate valence band. Removal of small amounts of lithium significantly modifies the photoluminescence spectra including additional larger than stoichiometric-band gap features. Sufficient removal of lithium results in the elimination of the photoluminescence response supporting the predicted transition from a direct to indirect band gap semiconductor. In addition, non-thermal coupling between the incident laser and lithium ions is observed and results in modulation of the electrical impedance.

  9. Evidence of ion intercalation mediated band structure modification and opto-ionic coupling in lithium niobite

    International Nuclear Information System (INIS)

    Shank, Joshua C.; Tellekamp, M. Brooks; Doolittle, W. Alan

    2015-01-01

    The theoretically suggested band structure of the novel p-type semiconductor lithium niobite (LiNbO 2 ), the direct coupling of photons to ion motion, and optically induced band structure modifications are investigated by temperature dependent photoluminescence. LiNbO 2 has previously been used as a memristor material but is shown here to be useful as a sensor owing to the electrical, optical, and chemical ease of lithium removal and insertion. Despite the high concentration of vacancies present in lithium niobite due to the intentional removal of lithium atoms, strong photoluminescence spectra are observed even at room temperature that experimentally confirm the suggested band structure implying transitions from a flat conduction band to a degenerate valence band. Removal of small amounts of lithium significantly modifies the photoluminescence spectra including additional larger than stoichiometric-band gap features. Sufficient removal of lithium results in the elimination of the photoluminescence response supporting the predicted transition from a direct to indirect band gap semiconductor. In addition, non-thermal coupling between the incident laser and lithium ions is observed and results in modulation of the electrical impedance

  10. Effect of pore structure on the seepage characteristics of tight sandstone reservoirs: A case study of Upper Jurassic Penglaizhen Fm reservoirs in the western Sichuan Basin

    Directory of Open Access Journals (Sweden)

    Liqiang Sima

    2017-01-01

    Full Text Available Tight sandstone reservoirs are characterized by complex pore structures and strong heterogeneity, and their seepage characteristics are much different from those of conventional sandstone reservoirs. In this paper, the tight sandstone reservoirs of Upper Jurassic Penglaizhen Fm in western Sichuan Basin were analyzed in terms of their pore structures by using the data about physical property, mercury injection and nuclear magnetic resonance (NMR tests. Then, the seepage characteristics and the gas–water two-phase migration mechanisms and distribution of tight sandstone reservoirs with different types of pore structures in the process of hydrocarbon accumulation and development were simulated by combining the relative permeability experiment with the visual microscopic displacement model. It is shown that crotch-like viscous fingering occurs in the process of gas front advancing in reservoirs with different pore structures. The better the pore structure is, the lower the irreducible water saturation is; the higher the gas-phase relative permeability of irreducible water is, the more easily the gas reservoir can be developed. At the late stage of development, the residual gas is sealed in reservoirs in the forms of bypass, cutoff and dead end. In various reservoirs, the interference between gas and water is stronger, so gas and water tends to be produced simultaneously. The sealed gas may reduce the production rate of gas wells significantly, and the existence of water phase may reduce the gas permeability greatly; consequently, the water-bearing low-permeability tight sandstone gas reservoirs reveal serious water production, highly-difficult development and low-recovery percentage at the late stage, which have adverse impacts on the effective production and development of gas wells.

  11. The use of Wannier function in the calculations of band structure of covalent crystals

    International Nuclear Information System (INIS)

    Lu Dong; Yang Guang

    1985-10-01

    A variational procedure has been used to build up Wannier functions to study the energy bands of diamond, silicon and α-tin. For the case of silicon the Wannier function, density of charge and band structure are calculated self-consistently and a simple method in a non-self-consistent way has been used to compute the band structure of diamond, silicon and α-tin. The method seems to be effective to describe the electronic properties of covalent crystals. (author)

  12. Measurement of valence band structure in arbitrary dielectric films

    International Nuclear Information System (INIS)

    Uhm, Han S.; Choi, Eun H.

    2012-01-01

    A new way of measuring the band structure of various dielectric materials using the secondary electron emission from Auger neutralization of ions is introduced. The first example of this measurement scheme is the magnesium oxide (MgO) films with respect to the application of the films in the display industries. The density of state in the valence bands of MgO film and MgO film with a functional layer (FL) deposited over a dielectric surface reveals that the density peak of film with a FL is considerably less than that of film, thereby indicating a better performance of MgO film with functional layer in display devices. The second example of the measurement is the boron-zinc oxide (BZO) films with respect to the application of the films to the development of solar cells. The measurement of density of state in BZO film suggests that a high concentration of boron impurity in BZO films may enhance the transition of electrons and holes through the band gap from the valence to the conduction band in zinc oxide crystals; thereby improving the conductivity of the film. Secondary electron emission by the Auger neutralization of ions is highly instrumental for the determination of the density of states in the valence band of dielectric materials.

  13. Band gap of corundumlike α -Ga2O3 determined by absorption and ellipsometry

    Science.gov (United States)

    Segura, A.; Artús, L.; Cuscó, R.; Goldhahn, R.; Feneberg, M.

    2017-07-01

    The electronic structure near the band gap of the corundumlike α phase of Ga2O3 has been investigated by means of optical absorption and spectroscopic ellipsometry measurements in the ultraviolet (UV) range (400-190 nm). The absorption coefficient in the UV region and the imaginary part of the dielectric function exhibit two prominent absorption thresholds with wide but well-defined structures at 5.6 and 6.3 eV which have been ascribed to allowed direct transitions from crystal-field split valence bands to the conduction band. Excitonic effects with large Gaussian broadening are taken into account through the Elliott-Toyozawa model, which yields an exciton binding energy of 110 meV and direct band gaps of 5.61 and 6.44 eV. The large broadening of the absorption onset is related to the slightly indirect character of the material.

  14. Structural and binding studies of a C-type galactose-binding lectin from Bothrops jararacussu snake venom.

    Science.gov (United States)

    Sartim, Marco A; Pinheiro, Matheus P; de Pádua, Ricardo A P; Sampaio, Suely V; Nonato, M Cristina

    2017-02-01

    BJcuL is a snake venom galactoside-binding lectin (SVgalL) isolated from Bothrops jararacussu and is involved in a wide variety of biological activities including triggering of pro-inflammatory response, disruption of microbial biofilm structure and induction of apoptosis. In the present work, we determined the crystallographic structure of BJcuL, the first holo structure of a SVgalL, and introduced the fluorescence-based thermal stability assay (Thermofluor) as a tool for screening and characterization of the binding mechanism of SVgalL ligands. BJcuL structure revealed the existence of a porous and flexible decameric arrangement composed of disulfide-linked dimers related by a five-fold symmetry. Each monomer contains the canonical carbohydrate recognition domain, a calcium ion required for BJcuL lectinic activity and a sodium ion required for protein stabilization. BJcuL thermostability was found to be induced by calcium ion and galactoside sugars which exhibit hyperbolic saturation profiles dependent on ligand concentration. Serendipitously, the gentamicin group of aminoglycoside antibiotics (gAGAs) was also identified as BJcuL ligands. On contrast, gAGAs exhibited a sigmoidal saturation profile compatible with a cooperative mechanism of binding. Thermofluor, hemagglutination inhibition assay and molecular docking strategies were used to identify a distinct binding site in BJcuL localized at the dimeric interface near the fully conserved intermolecular Cys86-Cys86 disulfide bond. The hybrid approach used in the present work provided novel insights into structural behavior and functional diversification of SVgaLs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Quantum spin Hall insulator BiXH (XH = OH, SH) monolayers with a large bulk band gap.

    Science.gov (United States)

    Hu, Xing-Kai; Lyu, Ji-Kai; Zhang, Chang-Wen; Wang, Pei-Ji; Ji, Wei-Xiao; Li, Ping

    2018-05-16

    A large bulk band gap is critical for the application of two-dimensional topological insulators (TIs) in spintronic devices operating at room temperature. On the basis of first-principles calculations, we predict BiXH (X = OH, SH) monolayers as TIs with an extraordinarily large bulk gap of 820 meV for BiOH and 850 meV for BiSH, and propose a tight-binding model considering spin-orbit coupling to describe the electronic properties of BiXH. These large gaps are entirely due to the strong spin-orbit interaction related to the pxy orbitals of the Bi atoms of the honeycomb lattice. The orbital filtering mechanism can be used to understand the topological properties of BiXH. The XH groups simply remove one branch of orbitals (pz of Bi) and reduce the trivial 6-band lattice into a 4-band, which is topologically non-trivial. The topological characteristics of BiXH monolayers are confirmed by nonzero topological invariant Z2 and a single pair of gapless helical edge states in the bulk gap. Owing to these features, the BiXH monolayers of the large-gap TIs are an ideal platform to realize many exotic phenomena and fabricate new quantum devices working at room temperature.

  16. QUANTITATIVE ANALYSIS OF BANDED STRUCTURES IN DUAL-PHASE STEELS

    Directory of Open Access Journals (Sweden)

    Benoit Krebs

    2011-05-01

    Full Text Available Dual-Phase (DP steels are composed of martensite islands dispersed in a ductile ferrite matrix, which provides a good balance between strength and ductility. Current processing conditions (continuous casting followed by hot and cold rolling generate 'banded structures' i.e., irregular, parallel and alternating bands of ferrite and martensite, which are detrimental to mechanical properties and especially for in-use properties. We present an original and simple method to quantify the intensity and wavelength of these bands. This method, based on the analysis of covariance function of binary images, is firstly tested on model images. It is compared with ASTM E-1268 standard and appears to be more robust. Then it is applied on real DP steel microstructures and proves to be sufficiently sensitive to discriminate samples resulting from different thermo-mechanical routes.

  17. Quasiparticle semiconductor band structures including spin-orbit interactions.

    Science.gov (United States)

    Malone, Brad D; Cohen, Marvin L

    2013-03-13

    We present first-principles calculations of the quasiparticle band structure of the group IV materials Si and Ge and the group III-V compound semiconductors AlP, AlAs, AlSb, InP, InAs, InSb, GaP, GaAs and GaSb. Calculations are performed using the plane wave pseudopotential method and the 'one-shot' GW method, i.e. G(0)W(0). Quasiparticle band structures, augmented with the effects of spin-orbit, are obtained via a Wannier interpolation of the obtained quasiparticle energies and calculated spin-orbit matrix. Our calculations explicitly treat the shallow semicore states of In and Ga, which are known to be important in the description of the electronic properties, as valence states in the quasiparticle calculation. Our calculated quasiparticle energies, combining both the ab initio evaluation of the electron self-energy and the vector part of the pseudopotential representing the spin-orbit effects, are in generally very good agreement with experimental values. These calculations illustrate the predictive power of the methodology as applied to group IV and III-V semiconductors.

  18. Band structure in Platinum nuclei (A ∼ 182)

    International Nuclear Information System (INIS)

    Popescu, D.G.

    1991-01-01

    In this thesis, the author studies the band structure in Platinum nuclei and has divided his work in 5 parts: in the first, the author makes a general presentation of nucleus physics with a high angular momentum and introduces to the deformed nucleus notion -axial, triaxial or mixing of different deformations. The notion of form co-existence will be used to interpret the experimental results. In the second part, the author describes the detection means which have been used to make measurements. An abstract of theoretical notions, usefull for the understanding of fusion-evaporation reaction is presented. The author explains the details, performances and different modes of using of 'Chateau de cristal' and others used spectrometers. In the third part, the author presents all experimental data. He has effected γ coincidence measurements for Pt, Au and Ir nuclei. In the fourth part, for a classical analysis or an interpretation in the frame of cranking model the author presents theoretical models which are adapted at the study of high spin states and band structures

  19. Cobalt uptake and binding in human red blood cells

    DEFF Research Database (Denmark)

    Simonsen, Lars Ole; Brown, Anthony M; Harbak, Henrik

    2011-01-01

    of cobalt, and also from the initial slope of the cobalt buffering curve. The cobalt accumulation is similar in fed and ATP-depleted cells. The buffering curve for [Co(T)](c) can be fitted by a Michaelis type function with B(max)=24 mmol (l cells)(-1) and half-saturation at 240 µM [Co(2+)](c). The tracer...... reversibly bound, being releasable by excess extracellular EGTA in the presence of A23187, and partly tightly bound, remaining in the cells even at high ionophore concentrations. The tightly bound fraction builds up over time, and is larger and develops earlier in fed cells compared to ATP-depleted cells......-migrate with hemoglobin in Sephadex column chromatography of a lysate of (57)Co-loaded cells. (57)Co also co-migrates with hemoglobin when added to a lysate of unlabeled cells or to a solution of purified hemoglobin, in both cases with a time-dependent development of tight binding. Cobalt is known to bind to the globin...

  20. Band structures of two dimensional solid/air hierarchical phononic crystals

    International Nuclear Information System (INIS)

    Xu, Y.L.; Tian, X.G.; Chen, C.Q.

    2012-01-01

    The hierarchical phononic crystals to be considered show a two-order “hierarchical” feature, which consists of square array arranged macroscopic periodic unit cells with each unit cell itself including four sub-units. Propagation of acoustic wave in such two dimensional solid/air phononic crystals is investigated by the finite element method (FEM) with the Bloch theory. Their band structure, wave filtering property, and the physical mechanism responsible for the broadened band gap are explored. The corresponding ordinary phononic crystal without hierarchical feature is used for comparison. Obtained results show that the solid/air hierarchical phononic crystals possess tunable outstanding band gap features, which are favorable for applications such as sound insulation and vibration attenuation.

  1. Band structures of two dimensional solid/air hierarchical phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y.L.; Tian, X.G. [State Key Laboratory for Mechanical Structure Strength and Vibration, Xi' an Jiaotong University, Xi' an 710049 (China); Chen, C.Q., E-mail: chencq@tsinghua.edu.cn [Department of Engineering Mechanics, AML and CNMM, Tsinghua University, Beijing 100084 (China)

    2012-06-15

    The hierarchical phononic crystals to be considered show a two-order 'hierarchical' feature, which consists of square array arranged macroscopic periodic unit cells with each unit cell itself including four sub-units. Propagation of acoustic wave in such two dimensional solid/air phononic crystals is investigated by the finite element method (FEM) with the Bloch theory. Their band structure, wave filtering property, and the physical mechanism responsible for the broadened band gap are explored. The corresponding ordinary phononic crystal without hierarchical feature is used for comparison. Obtained results show that the solid/air hierarchical phononic crystals possess tunable outstanding band gap features, which are favorable for applications such as sound insulation and vibration attenuation.

  2. Electronic structure and transport properties of hydrogenated graphene and graphene nanoribbons

    Energy Technology Data Exchange (ETDEWEB)

    Choe, D H; Bang, Junhyeok; Chang, K J, E-mail: kchang@kaist.ac.kr [Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of)

    2010-12-15

    The band gap opening is one of the important issues in applications of graphene and graphene nanoribbons (GNRs) to nanoscale electronic devices. As hydrogen strongly interacts with graphene and creates short-range disorder, the electronic structure is significantly modified by hydrogenation. Based on first-principles and tight-binding calculations, we investigate the electronic and transport properties of hydrogenated graphene and GNRs. In disordered graphene with low doses of H adsorbates, the low-energy states near the neutrality point are localized, and the degree of localization extends to high-energy states with increasing adsorbate density. To characterize the localization of eigenstates, we examine the inverse participation ratio and find that the localization is greatly enhanced for the defect levels, which are accumulated around the neutrality point. Our calculations support the previous result that even with a low dose of H adsorbates, graphene undergoes a metal-insulator transition. In GNRs, relaxations of the edge C atoms play a role in determining the edge structure and the hydrocarbon conformation at low and high H concentrations, respectively. In disordered nanoribbons, we find that the energy states near the neutrality point are localized and conductances through low-energy channels decay exponentially with sample size, similar to disordered graphene. For a given channel energy, the localization length tends to decrease as the adsorbate density increases. Moreover, the energy range of localization exceeds the intrinsic band gap.

  3. The quasiparticle band structure of zincblende and rocksalt ZnO.

    Science.gov (United States)

    Dixit, H; Saniz, R; Lamoen, D; Partoens, B

    2010-03-31

    We present the quasiparticle band structure of ZnO in its zincblende (ZB) and rocksalt (RS) phases at the Γ point, calculated within the GW approximation. The effect of the p-d hybridization on the quasiparticle corrections to the band gap is discussed. We compare three systems, ZB-ZnO which shows strong p-d hybridization and has a direct band gap, RS-ZnO which is also hybridized but includes inversion symmetry and therefore has an indirect band gap, and ZB-ZnS which shows a weaker hybridization due to a change of the chemical species from oxygen to sulfur. The quasiparticle corrections are calculated with different numbers of valence electrons in the Zn pseudopotential. We find that the Zn(20+) pseudopotential is essential for the adequate treatment of the exchange interaction in the self-energy. The calculated GW band gaps are 2.47 eV and 4.27 eV respectively, for the ZB and RS phases. The ZB-ZnO band gap is underestimated compared to the experimental value of 3.27 by ∼ 0.8 eV. The RS-ZnO band gap compares well with the experimental value of 4.5 eV. The underestimation for ZB-ZnO is correlated with the strong p-d hybridization. The GW band gap for ZnS is 3.57 eV, compared to the experimental value of 3.8 eV.

  4. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

    Energy Technology Data Exchange (ETDEWEB)

    Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

    2014-06-01

    The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

  5. Calcium binding in α-amylases: An X-ray diffraction study at 2.1-angstrom resolution of two enzymes from Aspergillus

    International Nuclear Information System (INIS)

    Boel, E.; Jensen, V.J.; Petersen, S.B.; Thim, L.; Woldike, H.F.; Brady, L.; Brzozowski, AM.; Derewenda, Z.; Dodson, G.G.; Swift, H.

    1990-01-01

    X-ray diffraction analysis (at 2.1-angstrom resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding around the active site) contains a tightly bound Ca 2+ with an unusually high number of eight ligands. A secondary binding site was identified at the bottom of the substrate binding cleft; it involves the residues presumed to play a catalytic role (Asp206 and Glu230). This explains the inhibitory effect of calcium observed at higher concentrations. Neutral Aspergillus oryzae (TAKA) α-amylase was also refined in a new crystal at 2.1-angstrom resolution. The structure of this homologous (over 80%) enzyme and addition kinetic studies support all the structural conclusions regarding both calcium-binding sites

  6. Valley-dependent band structure and valley polarization in periodically modulated graphene

    Science.gov (United States)

    Lu, Wei-Tao

    2016-08-01

    The valley-dependent energy band and transport property of graphene under a periodic magnetic-strained field are studied, where the time-reversal symmetry is broken and the valley degeneracy is lifted. The considered superlattice is composed of two different barriers, providing more degrees of freedom for engineering the electronic structure. The electrons near the K and K' valleys are dominated by different effective superlattices. It is found that the energy bands for both valleys are symmetric with respect to ky=-(AM+ξ AS) /4 under the symmetric superlattices. More finite-energy Dirac points, more prominent collimation behavior, and new crossing points are found for K' valley. The degenerate miniband near the K valley splits into two subminibands and produces a new band gap under the asymmetric superlattices. The velocity for the K' valley is greatly renormalized compared with the K valley, and so we can achieve a finite velocity for the K valley while the velocity for the K' valley is zero. Especially, the miniband and band gap could be manipulated independently, leading to an increase of the conductance. The characteristics of the band structure are reflected in the transmission spectra. The Dirac points and the crossing points appear as pronounced peaks in transmission. A remarkable valley polarization is obtained which is robust to the disorder and can be controlled by the strain, the period, and the voltage.

  7. A theoretical inquiry into the question of W and Ta (100) atomic structures

    International Nuclear Information System (INIS)

    Treglia, G.; Spanjaard, D.

    1983-01-01

    In spite of the very large number of experiments (LEED, AES, UPS, MeV He + scattering, work function, FIM) carried out on W (100), no structural model consistent with all the data has been proposed yet: in particular, the question of the reconstruction thermally induced when the sample is cooled below room temperature remains a puzzling problem. Furthermore, from a theoretical point of view, no definitive answer has been given. Actually, either the mechanism invoked for the reconstruction is too weak, or some contributions are omitted or calculated without sufficient care. The surface energy of W (100) is computed taking into account the band term treated in the tight binding approximation, a pairwise repulsive potential of the Born-Mayer type and the electronic correlation contribution obtained from a perturbation treatment of the Hubbard model in the band limit. This energy is then fully minimised with respect to all coordinates of surface atoms, keeping all atoms neutral for any displace,ment. It is found that the unreconstructed surface is the most stable at T = 0 K and discuss this unexpected result. A similar calculation for Ta (100) leads to opposite conclusions. (author)

  8. Engineering the electronic band structures of novel cubic structured germanium monochalcogenides for thermoelectric applications

    Science.gov (United States)

    Ul Haq, Bakhtiar; AlFaify, S.; Ahmed, R.; Butt, Faheem K.; Laref, A.; Goumri-Said, Souraya; Tahir, S. A.

    2018-05-01

    Germanium mono-chalcogenides have received considerable attention for being a promising replacement for the relatively toxic and expensive chalcogenides in renewable and sustainable energy applications. In this paper, we explore the potential of the recently discovered novel cubic structured (π-phase) GeS and GeSe for thermoelectric applications in the framework of density functional theory coupled with Boltzmann transport theory. To examine the modifications in their physical properties, the across composition alloying of π-GeS and π-GeSe (such as π-GeS1-xSex for x =0, 0.25, 0.50, 0.75, and 1) has been performed that has shown important effects on the electronic band structures and effective masses of charge carriers. An increase in Se composition in π-GeS1-xSex has induced a downward shift in their conduction bands, resulting in the narrowing of their energy band gaps. The thermoelectric coefficients of π-GeS1-xSex have been accordingly influenced by the evolution of the electronic band structures and effective masses of charge carriers. π-GeS1-xSex features sufficiently larger values of Seebeck coefficients, power factors and figures of merit (ZTs), which experience further improvement with an increase in temperature, revealing their potential for high-temperature applications. The calculated results show that ZT values equivalent to unity can be achieved for π-GeS1-xSex at appropriate n-type doping levels. Our calculations for the formation enthalpies indicate that a π-GeS1-xSex alloying system is energetically stable and could be synthesized experimentally. These intriguing characteristics make π-GeS1-xSex a promising candidate for futuristic thermoelectric applications in energy harvesting devices.

  9. Evidence of ion intercalation mediated band structure modification and opto-ionic coupling in lithium niobite

    Energy Technology Data Exchange (ETDEWEB)

    Shank, Joshua C.; Tellekamp, M. Brooks; Doolittle, W. Alan, E-mail: alan.doolittle@ece.gatech.edu [Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    2015-01-21

    The theoretically suggested band structure of the novel p-type semiconductor lithium niobite (LiNbO{sub 2}), the direct coupling of photons to ion motion, and optically induced band structure modifications are investigated by temperature dependent photoluminescence. LiNbO{sub 2} has previously been used as a memristor material but is shown here to be useful as a sensor owing to the electrical, optical, and chemical ease of lithium removal and insertion. Despite the high concentration of vacancies present in lithium niobite due to the intentional removal of lithium atoms, strong photoluminescence spectra are observed even at room temperature that experimentally confirm the suggested band structure implying transitions from a flat conduction band to a degenerate valence band. Removal of small amounts of lithium significantly modifies the photoluminescence spectra including additional larger than stoichiometric-band gap features. Sufficient removal of lithium results in the elimination of the photoluminescence response supporting the predicted transition from a direct to indirect band gap semiconductor. In addition, non-thermal coupling between the incident laser and lithium ions is observed and results in modulation of the electrical impedance.

  10. Estimating tropical forest structure using LIDAR AND X-BAND INSAR

    Science.gov (United States)

    Palace, M. W.; Treuhaft, R. N.; Keller, M. M.; Sullivan, F.; Roberto dos Santos, J.; Goncalves, F. G.; Shimbo, J.; Neumann, M.; Madsen, S. N.; Hensley, S.

    2013-12-01

    Tropical forests are considered the most structurally complex of all forests and are experiencing rapid change due to anthropogenic and climatic factors. The high carbon stocks and fluxes make understanding tropical forests highly important to both regional and global studies involving ecosystems and climate. Large and remote areas in the tropics are prime targets for the use of remotely sensed data. Radar and lidar have previously been used to estimate forest structure, with an emphasis on biomass. These two remote sensing methods have the potential to yield much more information about forest structure, specifically through the use of X-band radar and waveform lidar data. We examined forest structure using both field-based and remotely sensed data in the Tapajos National Forest, Para, Brazil. We measured multiple structural parameters for about 70 plots in the field within a 25 x 15 km area that have TanDEM-X single-pass horizontally and vertically polarized radar interferometric data. High resolution airborne lidar were collected over a 22 sq km portion of the same area, within which 33 plots were co-located. Preliminary analyses suggest that X-band interferometric coherence decreases by about a factor of 2 (from 0.95 to 0.45) with increasing field-measured vertical extent (average heights of 7-25 m) and biomass (10-430 Mg/ha) for a vertical wavelength of 39 m, further suggesting, as has been observed at C-band, that interferometric synthetic aperture radar (InSAR) is substantially more sensitive to forest structure/biomass than SAR. Unlike InSAR coherence versus biomass, SAR power at X-band versus biomass shows no trend. Moreover, airborne lidar coherence at the same vertical wavenumbers as InSAR is also shown to decrease as a function of biomass, as well. Although the lidar coherence decrease is about 15% more than the InSAR, implying that lidar penetrates more than InSAR, these preliminary results suggest that X-band InSAR may be useful for structure and

  11. Monolithic dual-band HgCdTe infrared detector structure

    CSIR Research Space (South Africa)

    Parish, G

    1997-07-01

    Full Text Available A monolithic HgCdTe photoconductive device structure is presented that is suitable for dual-band optically registered infrared photodetection in the two atmospheric transmission windows of 3-5 mu m and 8-12 mu m, which correspond to the mid...

  12. Band Structure Analysis of La0.7Sr0.3MnO3 Perovskite Manganite Using a Synchrotron

    Directory of Open Access Journals (Sweden)

    Hong-Sub Lee

    2015-01-01

    Full Text Available Oxide semiconductors and their application in next-generation devices have received a great deal of attention due to their various optical, electric, and magnetic properties. For various applications, an understanding of these properties and their mechanisms is also very important. Various characteristics of these oxides originate from the band structure. In this study, we introduce a band structure analysis technique using a soft X-ray energy source to study a La0.7Sr0.3MnO3 (LSMO oxide semiconductor. The band structure is formed by a valence band, conduction band, band gap, work function, and electron affinity. These can be determined from secondary electron cut-off, valence band spectrum, O 1s core electron, and O K-edge measurements using synchrotron radiation. A detailed analysis of the band structure of the LSMO perovskite manganite oxide semiconductor thin film was established using these techniques.

  13. Metal-like Band Structures of Ultrathin Si {111} and {112} Surface Layers Revealed through Density Functional Theory Calculations.

    Science.gov (United States)

    Tan, Chih-Shan; Huang, Michael H

    2017-09-04

    Density functional theory calculations have been performed on Si (100), (110), (111), and (112) planes with tunable number of planes for evaluation of their band structures and density of states profiles. The purpose is to see whether silicon can exhibit facet-dependent properties derived from the presence of a thin surface layer having different band structures. No changes have been observed for single to multiple layers of Si (100) and (110) planes with a consistent band gap between the valence band and the conduction band. However, for 1, 2, 4, and 5 Si (111) and (112) planes, metal-like band structures were obtained with continuous density of states going from the valence band to the conduction band. For 3, 6, and more Si (111) planes, as well as 3 and 6 Si (112) planes, the same band structure as that seen for Si (100) and (110) planes has been obtained. Thus, beyond a layer thickness of five Si (111) planes at ≈1.6 nm, normal semiconductor behavior can be expected. The emergence of metal-like band structures for the Si (111) and (112) planes are related to variation in Si-Si bond length and bond distortion plus 3s and 3p orbital electron contributions in the band structure. This work predicts possession of facet-dependent electrical properties of silicon with consequences in FinFET transistor design. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Theoretical study of band structure of odd-mass {sup 115,117}I isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Dhanvir, E-mail: singh1472phy@gmail.com; Kumar, Amit, E-mail: akbcw2@gmail.com; Sharma, Chetan, E-mail: chetan24101985@gmail.com [Research Scholar, Department of Physics and Electronics, University of Jammu, Jammu-180006 (India); Singh, Suram, E-mail: suramsingh@gmail.com [Assistant Professor, Department of Physics, Govt. Degree College, Kathua-184101 (India); Bharti, Arun, E-mail: arunbharti-2003@yahoo.co.in [Professor, Department of Physics and Electronics, University of Jammu, Jammu-180006 (India)

    2016-05-06

    By using the microscopic approach of Projected Shell Model (PSM), negative-parity band structures of odd mass neutron-rich {sup 115,117}I nuclei have been studied with the deformed single-particle states generated by the standard Nilsson potential. For these isotopes, the band structures have been analyzed in terms of quasi-particles configurations. The phenomenon of back bending in moment of inertia is also studied in the present work.

  15. Density functional study of graphene antidot lattices: Roles of geometrical relaxation and spin

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Pedersen, Thomas Garm; Brandbyge, Mads

    2009-01-01

    thereof. We find from DFT that all structures investigated have band gaps ranging from 0.2 to 1.5 eV. Band gap sizes and general trends are well captured by DFTB with band gaps agreeing within about 0.2 eV even for very small structures. A combination of the two methods is found to offer a good trade...... properties. In this work, we perform calculations of the band structure for various hydrogen-passivated hole geometries using both spin-polarized density functional theory (DFT) and DFT based tight-binding (DFTB) and address the importance of relaxation of the structures using either method or a combination......-off between computational cost and accuracy. Both methods predict nondegenerate midgap states for certain antidot hole symmetries. The inclusion of spin results in a spin-splitting of these states as well as magnetic moments obeying the Lieb theorem. The local-spin texture of both magnetic and nonmagnetic...

  16. Density Functional Theory Calculations Revealing Metal-like Band Structures for Ultrathin Ge {111} and {211} Surface Layers.

    Science.gov (United States)

    Tan, Chih-Shan; Huang, Michael Hsuan-Yi

    2018-05-21

    To find out if germanium should also possess facet-dependent electrical conductivity properties, surface state density functional theory (DFT) calculations were performed on 1-6 layers of Ge (100), (110), (111), and (211) planes. Tunable Ge (100) and (110) planes always present the same semiconducting band structure with a band gap of 0.67 eV expected of bulk germanium. In contrast, 1, 2, 4, and 5 layers of Ge (111) and (211) plane models show metal-like band structures with continuous density of states (DOS) throughout the entire band. For 3 and 6 layers of Ge (111) and (211) plane models, the normal semiconducting band structure was obtained. The plane layers with metal-like band structures also show Ge-Ge bond length deviations and bond distortions, as well as significantly different 4s and 4p frontier orbital electron count and their relative percentages integrated over the valence and conduction bands from those of the semiconducting state. These differences should contribute to strikingly dissimilar band structures. The calculation results suggest observation of facet-dependent electrical conductivity properties of germanium materials, and transistors made of germanium may also need to consider the facet effects with shrinking dimensions approaching 3 nm. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. [Strangulation of the penis with a rubber band : a case report].

    Science.gov (United States)

    Sekii, Yosuke; Katayama, Kinzou; Hayashi, Takuji; Kamoto, Akihito; Kakuta, Youiti; Mori, Naoki; Yoshioka, Toshiaki

    2013-06-01

    We report a case of strangulation of the penis with a rubber band. A 68-year-old man visited our hospital for treatment of a markedly swollen penis. Physical examination revealed one rubber band tightly coiled around the penis. The rubeer band was soon removed, gangrene of the penis continued. A high fever, chills and hypotension were recognized. Sepsis was presumed, and administration of antibiotics was started. Microbiologic cultures revealed streptococcus agalactiae in blood. Since his general condition did not improve, we performed partial penectomy. After the surgery, he showed complete recovery.

  18. Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2)

    International Nuclear Information System (INIS)

    Marr, Eric; Tardie, Mark; Carty, Maynard; Brown Phillips, Tracy; Wang, Ing-Kae; Soeller, Walt; Qiu, Xiayang; Karam, George

    2006-01-01

    The crystal structure of human adipocyte lipid-binding protein (aP2) with a bound palmitate is reported at 1.5 Å resolution. Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 Å resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity

  19. Infrared absorption, multiphonon processes and time reversal effect on Si and Ge band structure

    International Nuclear Information System (INIS)

    Kunert, H.W.; Machatine, A.G.J.; Malherbe, J.B.; Barnas, J.; Hoffmann, A.; Wagner, M.R.

    2008-01-01

    We have examined the effect of Time Reversal Symmetry (TRS) on vibrational modes and on the electronic band structure of Si and Ge. Most of the primary non-interacting modes are not affected by TRS. Only phonons originating from high symmetry lines S and A of the Brillouin Zone (BZ) indicate extra degeneracy. Selection rules for some two and three phonons originating from high symmetry lines are determined. The states of electrons and holes described by electronic band structure due to spin-inclusion are assigned by spinor representations of the double space group. Inclusion of the TRS into the band structure results in extra degeneracy of electrons and holes, and therefore optical selection rules suppose to be modified

  20. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  1. X-BAND LINEAR COLLIDER R and D IN ACCELERATING STRUCTURES THROUGH ADVANCED COMPUTING

    International Nuclear Information System (INIS)

    Li, Z

    2004-01-01

    This paper describes a major computational effort that addresses key design issues in the high gradient accelerating structures for the proposed X-band linear collider, GLC/NLC. Supported by the US DOE's Accelerator Simulation Project, SLAC is developing a suite of parallel electromagnetic codes based on unstructured grids for modeling RF structures with higher accuracy and on a scale previously not possible. The new simulation tools have played an important role in the R and D of X-Band accelerating structures, in cell design, wakefield analysis and dark current studies

  2. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

    Science.gov (United States)

    Parca, Luca; Ferré, Fabrizio; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2013-07-01

    Nucleos is a web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing nucleotide modules, namely the nucleobase, carbohydrate and phosphate. Structural features, clustering and conservation are used to filter and score the predictions. The predicted nucleotide modules are then joined to build whole nucleotide-binding sites, which are ranked by their score. The server takes as input either the PDB code of the query protein structure or a user-submitted structure in PDB format. The output of Nucleos is composed of ranked lists of predicted nucleotide-binding sites divided by nucleotide type (e.g. ATP-like). For each ranked prediction, Nucleos provides detailed information about the score, the template structure and the structural match for each nucleotide module composing the nucleotide-binding site. The predictions on the query structure and the template-binding sites can be viewed directly on the web through a graphical applet. In 98% of the cases, the modules composing correct predictions belong to proteins with no homology relationship between each other, meaning that the identification of brand-new nucleotide-binding sites is possible using information from non-homologous proteins. Nucleos is available at http://nucleos.bio.uniroma2.it/nucleos/.

  3. On the mechanism of sulfite activation of chloroplast thylakoid ATPase and the relation of ADP tightly bound at a catalytic site to the binding change mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Du, Z.; Boyer, P.D. (Univ. of California, Los Angeles (USA))

    1990-01-16

    Washed chloroplast thylakoid membranes upon exposure to ({sup 3}H)ADP retain in tightly bound ({sup 3}H)ADP on a catalytic site of the ATP synthase. The presence of sufficient endogenous or added Mg{sup 2+} results in an enzyme with essentially no ATPase activity. Sulfite activates the ATPase, and many molecules of ATP per synthase can be hydrolyzed before most of the bound ({sup 3}H)ADP is released, a result interpreted as indicating that the ADP is not bound at a site participating in catalysis by the sulfite-activated enzyme. The authors present evidence that this is not the case. The Mg{sup 2+}- and ADP-inhibited enzyme when exposed to MgATP and 20-100 mM sulfite shows a lag of about 1 min at 22{degree}C and of about 15 s at 37{degree}C before reaching the same steady-state rate as attained with light-activated ATPase that has not been inhibited by Mg{sup 2+} and ADP. The lag is not eliminated if the enzyme is exposed to sulfite prior to MgATP addition, indicating that ATPase turnover is necessary for the activation. The release of most of the bound ({sup 3}H)ADP parallels the onset of ATPase activity, although some ({sup 3}H)ADP is not released even with prolonged catalytic turnover and may be on poorly active or inactive enzyme or at noncatalytic sites. The results are consistent with most of the tightly bound ({sup 3}H)ADP being at a catalytic site and being replaced as this Mg{sup 2+}- and ADP-inhibited site regains equivalent participation with other catalytic sites on the activated enzyme. The sulfite activation can be explained by sulfite combination at a P{sub i} binding site of the enzyme-ADP-Mg{sup 2+} complex to give a form more readily activated by ATP binding at an alternative site.

  4. Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.

    Science.gov (United States)

    Li, Kunhua; Fielding, Elisha N; Condurso, Heather L; Bruner, Steven D

    2017-07-01

    The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket. The key residues implicated in dioxygen trafficking were studied to probe the process of binding, activation and chemistry. The results support the proposed chemistry and provide insight into the general mechanism of dioxygen binding and activation.

  5. Ischemic preconditioning enhances integrity of coronary endothelial tight junctions

    International Nuclear Information System (INIS)

    Li, Zhao; Jin, Zhu-Qiu

    2012-01-01

    Highlights: ► Cardiac tight junctions are present between coronary endothelial cells. ► Ischemic preconditioning preserves the structural and functional integrity of tight junctions. ► Myocardial edema is prevented in hearts subjected to ischemic preconditioning. ► Ischemic preconditioning enhances translocation of ZO-2 from cytosol to cytoskeleton. -- Abstract: Ischemic preconditioning (IPC) is one of the most effective procedures known to protect hearts against ischemia/reperfusion (IR) injury. Tight junction (TJ) barriers occur between coronary endothelial cells. TJs provide barrier function to maintain the homeostasis of the inner environment of tissues. However, the effect of IPC on the structure and function of cardiac TJs remains unknown. We tested the hypothesis that myocardial IR injury ruptures the structure of TJs and impairs endothelial permeability whereas IPC preserves the structural and functional integrity of TJs in the blood–heart barrier. Langendorff hearts from C57BL/6J mice were prepared and perfused with Krebs–Henseleit buffer. Cardiac function, creatine kinase release, and myocardial edema were measured. Cardiac TJ function was evaluated by measuring Evans blue-conjugated albumin (EBA) content in the extravascular compartment of hearts. Expression and translocation of zonula occludens (ZO)-2 in IR and IPC hearts were detected with Western blot. A subset of hearts was processed for the observation of ultra-structure of cardiac TJs with transmission electron microscopy. There were clear TJs between coronary endothelial cells of mouse hearts. IR caused the collapse of TJs whereas IPC sustained the structure of TJs. IR increased extravascular EBA content in the heart and myocardial edema but decreased the expression of ZO-2 in the cytoskeleton. IPC maintained the structure of TJs. Cardiac EBA content and edema were reduced in IPC hearts. IPC enhanced the translocation of ZO-2 from cytosol to cytoskeleton. In conclusion, TJs occur in

  6. Ischemic preconditioning enhances integrity of coronary endothelial tight junctions

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhao [Department of Pharmaceutical Sciences, College of Pharmacy, South Dakota State University, Brookings, SD 57007 (United States); Jin, Zhu-Qiu, E-mail: zhu-qiu.jin@sdstate.edu [Department of Pharmaceutical Sciences, College of Pharmacy, South Dakota State University, Brookings, SD 57007 (United States)

    2012-08-31

    Highlights: Black-Right-Pointing-Pointer Cardiac tight junctions are present between coronary endothelial cells. Black-Right-Pointing-Pointer Ischemic preconditioning preserves the structural and functional integrity of tight junctions. Black-Right-Pointing-Pointer Myocardial edema is prevented in hearts subjected to ischemic preconditioning. Black-Right-Pointing-Pointer Ischemic preconditioning enhances translocation of ZO-2 from cytosol to cytoskeleton. -- Abstract: Ischemic preconditioning (IPC) is one of the most effective procedures known to protect hearts against ischemia/reperfusion (IR) injury. Tight junction (TJ) barriers occur between coronary endothelial cells. TJs provide barrier function to maintain the homeostasis of the inner environment of tissues. However, the effect of IPC on the structure and function of cardiac TJs remains unknown. We tested the hypothesis that myocardial IR injury ruptures the structure of TJs and impairs endothelial permeability whereas IPC preserves the structural and functional integrity of TJs in the blood-heart barrier. Langendorff hearts from C57BL/6J mice were prepared and perfused with Krebs-Henseleit buffer. Cardiac function, creatine kinase release, and myocardial edema were measured. Cardiac TJ function was evaluated by measuring Evans blue-conjugated albumin (EBA) content in the extravascular compartment of hearts. Expression and translocation of zonula occludens (ZO)-2 in IR and IPC hearts were detected with Western blot. A subset of hearts was processed for the observation of ultra-structure of cardiac TJs with transmission electron microscopy. There were clear TJs between coronary endothelial cells of mouse hearts. IR caused the collapse of TJs whereas IPC sustained the structure of TJs. IR increased extravascular EBA content in the heart and myocardial edema but decreased the expression of ZO-2 in the cytoskeleton. IPC maintained the structure of TJs. Cardiac EBA content and edema were reduced in IPC hearts. IPC

  7. Phosphorus Binding Sites in Proteins: Structural Preorganization and Coordination

    DEFF Research Database (Denmark)

    Gruber, Mathias Felix; Greisen, Per Junior; Junker, Märta Caroline

    2014-01-01

    to individual structures that bind to phosphate groups; here, we investigate a total of 8307 structures obtained from the RCSB Protein Data Bank (PDB). An analysis of the binding site amino acid propensities reveals very characteristic first shell residue distributions, which are found to be influenced...... by the characteristics of the phosphorus compound and by the presence of cobound cations. The second shell, which supports the coordinating residues in the first shell, is found to consist mainly of protein backbone groups. Our results show how the second shell residue distribution is dictated mainly by the first shell...

  8. Structure of Drosophila Oskar reveals a novel RNA binding protein

    Science.gov (United States)

    Yang, Na; Yu, Zhenyu; Hu, Menglong; Wang, Mingzhu; Lehmann, Ruth; Xu, Rui-Ming

    2015-01-01

    Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix–fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3′UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3′UTRs, and provide structural insights into a novel protein–RNA interaction motif involving a hydrolase-related domain. PMID:26324911

  9. An open-structure sound insulator against low-frequency and wide-band acoustic waves

    Science.gov (United States)

    Chen, Zhe; Fan, Li; Zhang, Shu-yi; Zhang, Hui; Li, Xiao-juan; Ding, Jin

    2015-10-01

    To block sound, i.e., the vibration of air, most insulators are based on sealed structures and prevent the flow of the air. In this research, an acoustic metamaterial adopting side structures, loops, and labyrinths, arranged along a main tube, is presented. By combining the accurately designed side structures, an extremely wide forbidden band with a low cut-off frequency of 80 Hz is produced, which demonstrates a powerful low-frequency and wide-band sound insulation ability. Moreover, by virtue of the bypass arrangement, the metamaterial is based on an open structure, and thus air flow is allowed while acoustic waves can be insulated.

  10. Band structures of phononic crystal composed of lattices with different periodic constants

    International Nuclear Information System (INIS)

    Hu, Jia-Guang; Xu, Wen

    2014-01-01

    With a square lattice mercury and water system being as the model, the band structures of nesting and compound phononic crystals with two different lattice constants were investigated using the method of the supercell plane wave expansion. It was observed that large band gaps can be achieved in low frequency regions by adjusting one of the lattice constants. Meanwhile, effects similar to interstitial impurity defects can be achieved with the increase of lattice constant of the phononic crystal. The corresponding defect modes can be stimulated in band gaps. The larger the lattice constant, the stronger the localization effect of defect modes on the wave. In addition, the change of the filling fraction of impurity exerts great influence on the frequency and localization of defect modes. Furthermore, the change of the position of impurity has notable influence on the frequency of defect modes and their localization. However, the geometry structure and orientation of impurity have little effect on the frequency of defect modes and their localization in the band gap.

  11. Solution structure of the 45-residue ATP-binding peptide of adenylate kinase as determined by 2-D NMR, FTIR, and CD spectroscopy

    International Nuclear Information System (INIS)

    Fry, D.C.; Byler, D.M.; Susi, H.; Brown, E.M.; Kuby, S.A.; Mildyan, A.S.

    1986-01-01

    In the X-ray structure of adenylate kinase residues 1-45 exist as 47% α-helix, 29% β-structure (strands and turns) and 24% coil. The solution structure of a synthetic peptide corresponding to residues 1-45, which constitutes the MgATP binding site was studied by 3 independent spectroscopic methods. Globularity of the peptide was shown by its broad NMR resonances which narrow upon denaturation, and by its ability to bind MgATP with similar affinity and conformation as the intact enzyme does. COSY and NOESY NMR methods at 250 and 500 MHz reveal proximities among NH, Cα, and Cβ protons indicative of >20% α-helix, and >20% β-structure. Correlation of regions of secondary structure with the primary sequence by 2D NMR indicates at least one α-helix (res. 23 to 29) and two β-strands (res. 12 to 15 and 34 to 38). The broad amide I band in the deconvoluted FTIR spectrum could be fit as the sum of 4 peaks due to specific secondary structures, yielding ≤=45% α-helix, ≤=40% β-structure and ≥=15% coil. The CD spectrum, from 185-250 nm, interpreted with a 3-parameter basis set, yielded 20 +/- 5% α=helix, and ≤=20% β-structure. The solution structure of peptide 1-45 thus approximates that of residues 1-45 in the crystal

  12. Electrical properties and band structures of Pb1-x Snx Te alloys

    International Nuclear Information System (INIS)

    Ocio, Miguel

    1972-01-01

    Both p type alloys Pb 0.72 Sn 0.28 Te and Pb 0.53 Sn 0.47 Te have been studied in the present work. The main obtained results are the following: the materials have a two-valence band structure, the first band following non-parabolic Cohen's dispersion law; at low temperatures, carriers are scattered by ionized impurities; the Coulomb potentials being screened almost completely, impurities act like neutral centers. At room temperature, scattering by acoustic modes can explain lattice mobility behavior; reversing of the thermo-power, for samples with carrier densities of about 10 20 cm -3 , is possibly due to inter-band scattering between both valence bands; a very simple picture of the band parameters variations as a function of alloy fraction is suggested. (author) [fr

  13. Triple photonic band-gap structure dynamically induced in the presence of spontaneously generated coherence

    International Nuclear Information System (INIS)

    Gao Jinwei; Bao Qianqian; Wan Rengang; Cui Cuili; Wu Jinhui

    2011-01-01

    We study a cold atomic sample coherently driven into the five-level triple-Λ configuration for attaining a dynamically controlled triple photonic band-gap structure. Our numerical calculations show that three photonic band gaps with homogeneous reflectivities up to 92% can be induced on demand around the probe resonance by a standing-wave driving field in the presence of spontaneously generated coherence. All these photonic band gaps are severely malformed with probe reflectivities declining rapidly to very low values when spontaneously generated coherence is gradually weakened. The triple photonic band-gap structure can also be attained in a five-level chain-Λ system of cold atoms in the absence of spontaneously generated coherence, which however requires two additional traveling-wave fields to couple relevant levels.

  14. SINGLE-BAND, TRIPLE-BAND, OR MULTIPLE-BAND HUBBARD MODELS

    NARCIS (Netherlands)

    ESKES, H; SAWATZKY, GA

    1991-01-01

    The relevance of different models, such as the one-band t-J model and the three-band Emery model, as a realistic description of the electronic structure of high-T(c) materials is discussed. Starting from a multiband approach using cluster calculations and an impurity approach, the following

  15. Electronic structure of the copper oxides: Band picture versus correlated behavior

    Energy Technology Data Exchange (ETDEWEB)

    Pickett, W E; Cohen, R E; Singh, D [Naval Research Lab., Washington, DC (USA); Krakauer, H [Coll. of William and Mary, Williamsburg, VA (USA)

    1989-12-01

    In the 2 1/2 years since the discovery of the high temperature superconducting copper oxides, a great deal has been learned from experiment about their behavior. From the theoretical side, there continues to be developments both within the band picture and from the model Hamiltonian viewpoint emphasizing correlations. In this paper we discuss briefly these complementary viewpoints in relation to certain of the experimental data. Due to our background in the band structure area, we approach the discussion by evaluating which phenomena can be (or has been) accounted for by the standard band approach, and point out which properties appear to require more intricate treatments of correlation. (orig.).

  16. Band structure and optical properties of sinusoidal superlattices: ZnSe1-xTex

    International Nuclear Information System (INIS)

    Yang, G.; Lee, S.; Furdyna, J. K.

    2000-01-01

    This paper examines the band structure and optical selection rules in superlattices with a sinusoidal potential profile. The analysis is motivated by the recent successful fabrication of high quality ZnSe 1-x Te x superlattices in which the composition x varies sinusoidally along the growth direction. Although the band alignment in the ZnSe 1-x Te x sinusoidal superlattices is staggered (type II), they exhibit unexpectedly strong photoluminescence, thus suggesting interesting optical behavior. The band structure of such sinusoidal superlattices is formulated in terms of the nearly-free-electron (NFE) approximation, in which the superlattice potential is treated as a perturbation. The resulting band structure is unique, characterized by a single minigap separating two wide, free-electron-like subbands for both electrons and holes. Interband selection rules are derived for optical transitions involving conduction and valence-band states at the superlattice Brillouin-zone center, and at the zone edge. A number of transitions are predicted due to wave-function mixing of different subband states. It should be noted that the zone-center and zone-edge transitions are especially easy to distinguish in these superlattices because of the large width of the respective subbands. The results of the NFE approximation are shown to hold surprisingly well over a wide range of parameters, particularly when the period of the superlattice is short. (c) 2000 The American Physical Society

  17. Relativistic band-structure calculations for electronic properties of actinide dioxides

    International Nuclear Information System (INIS)

    Maehira, Takahiro; Hotta, Takashi

    2007-01-01

    Energy band structures of actinide dioxides AnO 2 (An=Th, U, Np, and Pu) are investigated by a relativistic linear augmented-plane-wave method with the exchange-correlation potential in a local density approximation (LDA). It is found in common that the energy bands in the vicinity of the Fermi level are mainly due to the hybridization between actinide 5f and oxygen 2p electrons. By focusing on the crystalline electric field states, we point out the problem in the application of the LDA to AnO 2

  18. Structural determination of functional units of the nucleotide binding domain (NBD94 of the reticulocyte binding protein Py235 of Plasmodium yoelii.

    Directory of Open Access Journals (Sweden)

    Ardina Grüber

    2010-02-01

    Full Text Available Invasion of the red blood cells (RBC by the merozoite of malaria parasites involves a large number of receptor ligand interactions. The reticulocyte binding protein homologue family (RH plays an important role in erythrocyte recognition as well as virulence. Recently, it has been shown that members of RH in addition to receptor binding may also have a role as ATP/ADP sensor. A 94 kDa region named Nucleotide-Binding Domain 94 (NBD94 of Plasmodium yoelii YM, representative of the putative nucleotide binding region of RH, has been demonstrated to bind ATP and ADP selectively. Binding of ATP or ADP induced nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94, and directly impacted on the RBC binding ability of RH.In order to find the smallest structural unit, able to bind nucleotides, and its coupling module, the hinge region, three truncated domains of NBD94 have been generated, termed NBD94(444-547, NBD94(566-663 and NBD94(674-793, respectively. Using fluorescence correlation spectroscopy NBD94(444-547 has been identified to form the smallest nucleotide binding segment, sensitive for ATP and ADP, which became inhibited by 4-Chloro-7-nitrobenzofurazan. The shape of NBD94(444-547 in solution was calculated from small-angle X-ray scattering data, revealing an elongated molecule, comprised of two globular domains, connected by a spiral segment of about 73.1 A in length. The high quality of the constructs, forming the hinge-region, NBD94(566-663 and NBD94(674-793 enabled to determine the first crystallographic and solution structure, respectively. The crystal structure of NBD94(566-663 consists of two helices with 97.8 A and 48.6 A in length, linked by a loop. By comparison, the low resolution structure of NBD94(674-793 in solution represents a chair-like shape with three architectural segments.These structures give the first insight into how nucleotide binding impacts on the overall structure of RH and demonstrates the

  19. Electronic structure of SnS deduced from photoelectron spectra and band-structure calculations

    NARCIS (Netherlands)

    Ettema, A.R.H.F.; Groot, R.A. de; Haas, C.; Turner, T.S.

    1992-01-01

    SnS is a layer compound with a phase transition from a high-temperature β phase to a low-temperature α phase with a lower symmetry. Ab initio band-structure calculations are presented for both phases. The calculations show that the charge distributions in the two phases are very similar. However,

  20. Electronic band structures of binary skutterudites

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Banaras [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Aliabad, H.A. Rahnamaye [Department of Physics, Hakim Sabzevari University, Sabzevar (Iran, Islamic Republic of); Saifullah [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Jalali-Asadabadi, S. [Department of Physics, Faculty of Science, University of Isfahan (UI), 81744 Isfahan (Iran, Islamic Republic of); Khan, Imad [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan); Ahmad, Iftikhar, E-mail: ahma5532@gmail.com [Center for Computational Materials Science, University of Malakand, Chakdara (Pakistan); Department of Physics, University of Malakand, Chakdara (Pakistan)

    2015-10-25

    The electronic properties of complex binary skutterudites, MX{sub 3} (M = Co, Rh, Ir; X = P, As, Sb) are explored, using various density functional theory (DFT) based theoretical approaches including Green's Function (GW) as well as regular and non-regular Tran Blaha modified Becke Jhonson (TB-mBJ) methods. The wide range of calculated bandgap values for each compound of this skutterudites family confirm that they are theoretically as challenging as their experimental studies. The computationally expensive GW method, which is generally assume to be efficient in the reproduction of the experimental bandgaps, is also not very successful in the calculation of bandgaps. In this article, the issue of the theoretical bandgaps of these compounds is resolved by reproducing the accurate experimental bandgaps, using the recently developed non-regular TB-mBJ approach, based on DFT. The effectiveness of this technique is due to the fact that a large volume of the binary skutterudite crystal is empty and hence quite large proportion of electrons lie outside of the atomic spheres, where unlike LDA and GGA which are poor in the treatment of these electrons, this technique properly treats these electrons and hence reproduces the clear electronic picture of these compounds. - Highlights: • Theoretical and experimental electronic band structures of binary skutterudites are reviewed. • The literature reveals that none of the existing theoretical results are consistent with the experiments. • GW, regular and non-regular TB-mBJ methods are used to reproduce the correct results. • The GW and regular TB-mBJ results are better than the available results in literature. • However, non-regular TB-mBJ reproduces the correct experimental band structures.