bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymmetrical linear structures including three-electron hemibonds or other interactions in the (ABA)-type triatomic cations: Ne3+, (He–Ne–He)+, (Ar–Ne–Ar)+, (Ar–O–Ar)+, (He–O–He)+, and (Ar–He–Ar)+
Authors: Sun Xiao-Ying , Li Zhi-Ru , Wu Di , Sun Chia-Chung , Gudowski Serge , Tao Fu-Ming , Janda Kenneth C.
Published: September 2005

By the counterpoise geometry optimization at the level of CCSD(T)∕aug-cc-pVDZ, the asymmetrical linear structures with all the real frequencies were obtained for the triatomic cations of (ABA)+ type: Ne3+, (He–Ne–He)+, (Ar–Ne–Ar)+, (Ar–He–Ar)+, (He–O–He)+, and (Ar–O–Ar)+. The validity of this optimization method is confirmed by comparing with the method of the potential-energy surface for the calculations of Ne3+ and (He–Ne–He)+. Using the molecular-orbital theory, it is found that the interaction within the triatomic cations is dominated by the contribution from the first two atoms while the contribution from the third atom is small. This result is justified as a direct consequence of forming an asymmetrical linear structure. Specifically, four types of interaction within the triatomic cations are identified: three-electron σ-type hemibond, three-electron π-type hemibond, two-electron σ bond, and the attraction between cation and atoms. For Ne3+, (He–Ne–He)+, and (He–O–He)+ clusters, it is shown that the electron correlation effect supports the asymmetry.
IR spectra of N-methylacetamide in water predicted by combined quantum mechanical/molecular mechanical molecular dynamics simulations
Authors: Yang Seongeun , Cho Minhaeng
Published: September 2005

We applied the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulation method in assessing IR spectra of N-methylacetamide and its deuterated form in aqueous solutions. The model peptide is treated at the Austin Model 1 (AM1) level and the induced dipole effects by the solvent are incorporated in fluctuating solute dipole moments, which are calculated using partial charges from Mulliken population analyses without resorting to any available high-level ab initio dipole moment data. Fourier transform of the solute dipole autocorrelation function produces in silico IR spectra, in which the relative peak intensities and bandwidths of major amide bands are quantitatively compatible with experimental results only when both geometric and electronic polarizations of the peptide by the solvent are dealt with at the same quantum-mechanical level. We cast light on the importance of addressing dynamic charge fluctuations of the solute in calculating IR spectra by comparing classical and QM/MM MD simulation results. We propose the adjustable scaling factors for each amide mode to be directly compared with experimental data.
Molecular dissipation phenomena of nanoscopic friction in the heterogeneous relaxation regime of a glass former
Authors: Sills Scott , Gray Tomoko , Overney René M.
Published: September 2005

Nanoscale sliding friction involving a polystyrene melt near its glass transition temperature Tg(373K) exhibited dissipation phenomena that provide insight into the underlying molecular relaxation processes. A dissipative length scale that shows significant parallelism with the size of cooperatively rearranging regions (CRRs) could be experimentally deduced from friction-velocity isotherms, combined with dielectric loss analysis. Upon cooling to ∼10K above Tg, the dissipation length Xd grew from a segmental scale of ∼3Åto2.1nm, following a power-law relationship with the reduced temperature Xd∼TR−ϕ. The resulting ϕ=1.89±0.08 is consistent with growth predictions for the length scale of CRRs in the heterogeneous regime of fragile glass formers. Deviations from the power-law behavior closer to Tg suggest that long-range processes, e.g., the normal mode or ultraslow Fischer modes, may couple with the α relaxation, leading to energy dissipation in domains of tens of nanometers.
Nuclear-electronic orbital nonorthogonal configuration interaction approach
Authors: Skone Jonathan H. , Pak Michael V. , Hammes-Schiffer Sharon
Published: September 2005

The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented. In this framework, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and a mixed nuclear-electronic time-independent Schrödinger equation is solved with molecular orbital techniques. For hydrogen transfer systems, the transferring hydrogen is represented by two basis function centers to allow delocalization of the nuclear wave function. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wave functions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wave functions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between the two delocalized vibronic states. The hydrogen tunneling splittings calculated with the NEO-NOCI approach for the [He–H–He]+ model system with a range of fixed He–He distances are in excellent agreement with NEO-full CI and Fourier grid calculations. These benchmarking calculations indicate that NEO-NOCI is a promising approach for the calculation of delocalized, bilobal hydrogen wave functions and the corresponding hydrogen tunneling splittings.
The onset of chaos in the vibrational dynamics of LiNC∕LiCN
Authors: Arranz F. J. , Benito R. M. , Borondo F.
Published: September 2005

Recent advances in vibrational spectroscopy have greatly enhanced the possibilities of research of highly excited states in molecular systems of moderate size. At sufficiently high level of excitation the correspondence principle holds, and classical mechanical arguments constitute a useful interpretative tool. The corresponding dynamics often become very complex specially in systems with floppy degrees of freedom, and periodic motion plays an important role for its understanding. In this paper, we present a computational procedure to systematically calculate periodic orbits of LiNC∕LiCN with a given symmetry, that has the additional advantage of providing a useful insight into the onset of chaos in this system.
Basis set superposition error in MP2 and density-functional theory: A case of methane-nitric oxide association
Authors: Crespo-Otero Rachel , Montero Luis Alberto , Stohrer Wolf-Dieter , García de la Vega José M.
Published: September 2005

A systematic study of basis set superposition error (BSSE) behavior in H3C–H…[NO] complexes for both –H…N– and –H…O– orientations were carried out using MP2 and density-functional theory with Pople’s [6-31G(d,p),6-311++G(nd,nd), where n=1,2,3, and 6-311++G(3df,3pd)] and Dunning’s augmented correlation consistent basis sets [aug-cc-pVXZ (X=D and T)]. Corrected and uncorrected counterpoise potential-energy surfaces (PESs) were explored and differences obtained between them indicate that reliable optimizations of these molecular interactions must be carried out in a PES free of BSSE, even in the case of large basis sets and popularly used functionals such as B3LYP. Although all basis used could be always considered within a margin of approximation for representing molecular orbitals and show important values of BSSE, 6-311++G(2d,2p) basis set shows the best results in uncorrected PES with respect to the corrected ones. B3LYP functional produces erratic results: complexes appear repulsive and the intermolecular distances are always large, evidencing the lack of a correct dispersive forces treatment in the original parameterization. According to the MP2 results, the –H…N– interactions appear as slightly more stable than those of the –H…O– orientation.
Potential-energy surface for the electronic ground state of NH3 up to 20000cm−1 above equilibrium
Authors: Yurchenko Sergei N. , Zheng Jingjing , Lin Hai , Jensen Per , Thiel Walter
Published: September 2005

Ab initio coupled cluster calculations with single and double substitutions and a perturbative treatment of connected triple excitations [CCSD(T)] with the augmented correlation-consistent polarized valence triple-zeta aug-cc-pVTZ basis at 51 816 geometries provide a six-dimensional potential-energy surface for the electronic ground state of NH3. At 3814 selected geometries, CBS+ energies are obtained by extrapolating the CCSD(T) results for the aug-cc-pVXZ(X=T,Q,5) basis sets to the complete basis set (CBS) limit and adding corrections for core-valence correlation and relativistic effects. CBS** ab initio energies are generated at 51 816 geometries by an empirical extrapolation of the CCSD(T)/aug-cc-pVTZ results to the CBS+ limit. They cover the energy region up to 20000cm−1 above equilibrium. Parametrized analytical functions are fitted through the ab initio points. For these analytical surfaces, vibrational term values and transition moments are calculated by means of a variational program employing a kinetic-energy operator expressed in the Eckart-Sayvetz frame. Comparisons against experiment are used to assess the quality of the generated potential-energy surfaces. A “spectroscopic” potential-energy surface of NH3 is determined by a slight empirical adjustment of the ab initio potential to the experimental vibrational term values. Variational calculations on this refined surface yield rms deviations from experiment of 0.8cm−1 for 24 inversion splittings and 0.4 (3.0)cm−1 for 34 (51) vibrational term values up to 6100 (10300)cm−1.
Dynamic charge fluctuation of endohedral fullerene with coencapsulated Be atom and H2
Authors: Shigeta Yasuteru , Takatsuka Kazuo
Published: September 2005

As one of the typical examples of characteristic reaction field generated in inclusion (enclosure) compounds, the dynamics of an endohedral metallofullerene, (Be+nH2)@C60(n=1,2), is studied with Be atom serving as a test probe. A very large dynamical and thermal fluctuation of electronic state of Be has been found, which is surprising since the highest occupied molecular orbital-lowest unoccupied molecular orbital gap of Be is so wide that such a large fluctuation in a low temperature is never expected. This finding demonstrates one of the special features of endohedral reaction field offered by the fullerene. The physical origin of this phenomenon is analyzed.
Formation of SiCH6-mediated Ge quantum dots with strong field emission properties by ultrahigh vacuum chemical vapor deposition
Authors: Lee S. W. , Chueh Y. L. , Chen L. J. , Chou L. J. , Chen P. S. , Tsai M.-J. , Liu C. W.
Published: September 2005

Pretreatment of silicon surface with SiCH6 was used to modify the Stranski-Krastanow growth mode of Ge on Si(001) at 550°C by ultrahigh vacuum chemical vapor deposition. With the appropriate SiCH6 mediation, the elongated Ge hut clusters can be transformed to highly uniform multifaceted domes with a high Ge composition at the core. These SiCH6-mediated Ge dots have an average diameter and height of 38 and 7 nm, respectively. The modified growth mode for the formation of SiCH6-mediated Ge dots can be attributed to (i) an almost hydrogen-passivated Si surface to limit the nucleation sites for dot formation and (ii) the incorporation of Ge atoms, repelled by the C-rich areas, into the existing Ge dots. The results also demonstrate that SiCH6-mediated dots exhibit the improved field emission characteristics compared to shallow Ge huts.
Determination of the elastic moduli in LiAlO2
Authors: Jachmann Fabian , Pattabiraman M. , Hucho Carsten
Published: September 2005

The precise determination of elastic constants of γ-LiAlO2 has recently become important, as this material is being used as a substrate for intensely studied acousto-optical device structures and no values for the elastic moduli have been published to date. The precision of experimentally determined elastic constants hinges significantly on considering the influence of the acoustic transducer on the sound propagation in the system. Therefore, the influence of the transducer is discussed and an approach for corrections is presented. The compressional elastic constants C11 and C33 and the shear constants C12 and C13 of γ-LiAlO2 are determined with an acoustic pulse-echo technique and with sampled-continuous-wave spectroscopy.
Origin of green luminescence in ZnO thin film grown by molecular-beam epitaxy
Authors: Heo Y. W. , Norton D. P. , Pearton S. J.
Published: September 2005

The properties of ZnO films grown by molecular-beam epitaxy are reported. The primary focus was on understanding the origin of deep-level luminescence. A shift in deep-level emission from green to yellow is observed with reduced Zn pressure during the growth. Photoluminescence and Hall measurements were employed to study correlations between deep-level/near-band-edge emission and carrier density. With these results, we suggest that the green emission is related to donor-deep acceptor (Zn vacancy VZn−) and the yellow to donor-deep acceptor (oxygen vacancy, Oi−).
Optical study of magnetostriction in (Bi, Ga)-substituted garnet thin films
Authors: Nistor I. , Mayergoyz I. D. , Rojas R. , Krafft C.
Published: September 2005

The magnetostriction of magnetically diluted (Lu3−xBixFe5−yGayO12) (BiLuIG) thin films grown by epitaxial deposition on (111)-oriented gallium gadolinium garnet substrates was optically studied using the technique based on the bending of samples by an external applied pressure. The real-time optical observations of stripe magnetic domains and their evolution under external applied magnetic fields and applied stresses are reported. The observed changes in the magnetic domain structure are used to infer the magnetostriction coefficient λ111 of garnet films.
Experimental and numerical studies of the effect of phase difference between transport current and perpendicular applied magnetic field on total ac loss in Ag-sheathed (Bi,Pb)2Sr2Ca2Cu3Ox tape
Authors: Nguyen Doan Ngoc , Sastry Pamidi V. P. S. S. , Knoll David C. , Zhang Guomin , Schwartz Justin
Published: September 2005

The effect of phase difference between transport current and perpendicular applied magnetic field, Δφ, on total ac loss in multifilamentary, silver-sheathed (Bi,Pb)2Sr2Ca2Cu3Ox (Bi-2223) superconducting tapes was calculated numerically using Brandt’s equation [Phys. Rev. B 54, 4246 (1996)] and the results were compared with experimental results obtained by the calorimetric method. In the numerical calculations, the superconducting transition was modeled by E-J characteristics represented by a power law. The dependence of critical current density on the n value was taken into account. The dependence of critical current density and n value on applied magnetic field was obtained from experimental data. It was observed that Δφ has a significant effect on the loss behavior of Bi-2223 tapes and depends strongly on the relative values of transport current and applied magnetic field. The effects of Δφ on the individual components of transport loss and magnetization loss were also calculated. Good agreement between the calculated and experimental results is demonstrated.
Crystallization of Al2O3 and its effects on the mechanical properties in TiN∕Al2O3 nanomultilayers
Authors: Wei Lun , Kong Ming , Dong Yunshan , Li Geyang
Published: September 2005

Ti N ∕ Al 2 O 3 nanomultilayers with various Al2O3 layer thicknesses were prepared by multitarget magnetron sputtering method. The composition, growth structures, and mechanical properties of the nanomultilayers were studied by energy dispersive x-ray spectrometry, x-ray diffraction, high-resolution transmission electron microscopy, and nanoindentation. It reveals that when the thickness of Al2O3 layers is small (<∼1.5nm), the cubic TiN layers force Al2O3 to crystallize under the sputtering conditions where the formation of amorphous Al2O3 should be favored, and then the TiN and Al2O3 modulation layers grow coherently and epitaxially. Correspondingly, the hardness and elastic modulus of the multilayers increase abnormally and reach the maximum values of 37.9 and 402GPa, respectively. With the further increase in layer thickness, Al2O3 layers form an amorphous structure and block the coherent growth of the multilayers, and then the hardness and elastic modulus decrease gradually.
Biaxial modulus of fiber-textured cubic polycrystalline films with an arbitrary texture axis [hkl]
Authors: Huang Feng , Weaver Mark L.
Published: September 2005

A simple method to estimate the effective biaxial modulus of cubic polycrystalline films with an arbitrary [hkl] fiber texture is presented. Analytic expressions of the Voigt [Lehrbuch der Kristallphysik (Teubner, Leipzig, 1910)] and the Reuss [Z. Angew. Math. Mech. 9, 49 (1929)] averages of the biaxial modulus are given in terms of the axis orientation [hkl] and single-crystal elastic constants. We then explain why the two averages of the fiber-textured films are identical to the corresponding appropriate biaxial modulus of the constituent grain. Finally, we show that for fiber axes equivalent to [100] or [111], the Voigt and Reuss averages coincide and are identical to the true effective biaxial modulus of the fiber-textured film. For other fiber axes, we further show that the Voigt-Reuss-Hill average of the biaxial modulus is an excellent theoretical estimation.
Adiabatic shear banding instability in bulk metallic glasses
Authors: Dai L. H. , Yan M. , Liu L. F. , Bai Y. L.
Published: September 2005

In this letter, a linear instability analysis was performed to highlight the mechanism of formation of adiabatic shear banding instabilities in bulk metallic glasses (BMGs). It is found that this instability is determined by the free volume coalescence-diffusion Deborah number. The most important findings are that both free volume coalescence softening and adiabatic heating softening exert an influence on the formation of adiabatic shear banding instability in BMGs, and higher strain rate promotes the growth of instability. These results are of particular significance in understanding the mechanism of formation of shear bands in BMGs.
On the role of oxygen in the catalysis of C54 titanium disilicide by Ti5Si3 phase
Authors: Ilango S. , Raghavan G. , Kalavathi S. , Panigrahi B. K. , Tyagi A. K.
Published: September 2005

The influence of the native SiO2 in the phase formation sequence of Ti∕Si system has been studied. Furnace annealing of Ti∕Si couples has been investigated by secondary-ion-mass spectrometry, Rutherford backscattering, and glancing incidence x-ray diffraction. The influence of dilute concentration of oxygen at the interface in altering reaction kinetics was studied. These studies reveal that the highly metallic Ti5Si3 phase forms during the intermediate stages of heat treatment. This phase is found to catalyze the direct formation of the low-resistive C54 TiSi2 phase, completely bypassing its polymorphic C49 counterpart. X-ray-diffraction line profile analysis of Bragg peaks indicates that the formation of the C54 phase is accompanied by a reduction in the microstrain. Subsequent annealing results in the complete transformation to TiSi2 with an increase in the average grain size.
Lorentz microscopy and giant magnetoresistance of nanostructured heterogeneous Au–Co alloys
Authors: Zenou V. Y.
Published: September 2005

A detailed Lorentz transmission electron microscopy study of melt-spun Au78Co22 and Au86Co14, and microstructural changes upon annealing, was conducted. The microstructure of the as-cast alloys consisted of small grains with fcc Co precipitates dispersed at the grain boundaries. The interior structures of these grains were Au∕Co lamellar eutectic or very small Co precipitates dispersed in Au matrix, depending on the composition. Up to 10±1at.% Co were dissolved in the Au matrix. This large amount of Co in the Au matrix reduced the mean free path, probably leading to low magnetoresistance values [MR(H=1.45T)=2.4%–2.6%]. Annealing caused precipitation of Co out of the Au matrix and growth of some Co precipitates, which transformed to multidomain particles when exceeded 160–200nm. Annealing at 673K for 1h caused a reduction of MR(H=1.45T) to 0.7%–0.8%, mainly due to growth of Co precipitates. The magnetic and micromagnetic properties were correlated with the microstructural analyses using computer simulations. The Co lamellae and precipitates were single-domain particles and single-domain vortices, respectively.
Morphological evolution and strain relaxation of Ge islands grown on chemically oxidized Si(100) by molecular-beam epitaxy
Authors: Li Qiming , Pattada Belliappa , Brueck Steve R. J. , Hersee Stephen , Han Sang M.
Published: September 2005

We have previously demonstrated that high-quality Ge can be grown on Si by the touchdown process, where chemically oxidized Si is exposed to a Ge molecular beam. The causes of strain relaxation in the Ge epilayer were also proposed and discussed. Herein, we present a detailed analysis on the morphological evolution and strain relaxation of nanoscale Ge islands on SiO2-covered Si in order to identify the mechanisms by which the high-quality epilayer forms. During the touchdown, the Ge seeds are anchored to the underlying Si. This immobility of Ge islands gives rise to a unique bimodal size distribution during coarsening. Three events are observed during coalescence: (1) merging of two small (<10nm) islands largely driven by surface diffusion, (2) merging of a small island and a big island (∼50nm), and (3) merging of two big islands. The coalescence of two small islands is characterized by the formation of twins or stacking faults at the two merging fronts. In contrast, no stacking fault or grain boundary results from the coalescence of large islands, indicating that their coalescence is favorable in achieving high-crystalline quality. For the Ge epilayer, the compressive strain exists mostly within 2nm from the heterojunction, resulting in a fully relaxed Ge epilayer. We attribute the relaxation to three mechanisms: (1) the strain at the junction pad decays below the critical limit within 2nm, a scale exactly comparable with the dimension of individual Ge–Si junction; (2) the remaining SiO2 serves as artificially introduced 60° dislocations; and (3) the intermixing between Ge and Si at the heterojunction reduces the effective lattice mismatch.
Axial segregation in high intensity discharge lamps measured by laser absorption spectroscopy
Authors: Flikweert A. J. , Nimalasuriya T. , Groothuis C. H. J. M. , Kroesen G. M. W. , Stoffels W. W.
Published: September 2005

High intensity discharge lamps have a high efficiency. These lamps contain rare-earth additives (in our case dysprosium iodide) which radiate very efficiently. A problem is color separation in the lamp because of axial segregation of the rare-earth additives, caused by diffusion and convection. Here two-dimensional atomic dysprosium density profiles are measured by means of laser absorption spectroscopy; the order of magnitude of the density is 1022m−3. The radially resolved atomic density measurements show a hollow density profile. In the outer parts of the lamp molecules dominate, while the center is depleted of dysprosium atoms due to ionization. From the axial profiles the segregation parameter is determined. It is shown that the lamp operates on the right-hand side of the Fischer curve [J. Appl. Phys. 47, 2954 (1976)], i.e., a larger convection leads to less segregation.
Metal-adlayer-stabilized ZnO(0001) surfaces: Toward a new growth mode for oxides
Authors: Northrup J. E. , Neugebauer J.
Published: September 2005

First-principles total energy calculations were performed for clean and In-rich ZnO(0001) surfaces. The calculations indicate that Zn adlayers themselves are not energetically favorable, but that In can form a stable adlayer in Zn-rich conditions. This result opens the possibility that In may serve as a surfactant for the growth of ZnO.
Ultraviolet lasing from optically pumped BeMgZnSe quantum-well laser structures
Authors: Niiyama Yuuki , Murata Tomoyuki , Watanabe Masahiro
Published: September 2005

We achieved lasing of an optically pumped ultraviolet BeMgZnSe-based quantum-well laser grown closely lattice matched to a GaP substrate. A laser emission wavelength of 373 nm at 13 K was observed. The threshold excitation power density was 0.415MW∕cm2 at 13 K. In addition, we have demonstrated lasing up to 130 K. This indicates that the BeMgZnSe compound is promising as a new candidate for ultraviolet (UV) laser diodes, which possess potential application for UV optoelectronic integrated circuits UV-OEICs on silicon substrates.
Quantum dot emitters in two-dimensional photonic crystals of macroporous silicon
Authors: Richter Stefan , Steinhart Martin , Hofmeister Herbert , Zacharias Margit , Gösele Ulrich , Gaponik Nikolai , Eychmüller Alexander , Rogach Andrey L. , Wendorff Joachim H. , Schweizer Stefan L. , von Rhein Andreas , Wehrspohn Ralf B.
Published: September 2005

We report on the incorporation of semiconductor quantum dots as internal emitters into two-dimensional photonic crystals of macroporous silicon. For this purpose we prepared composite nanotubes within the pores consisting of quantum dots embedded in a polymeric matrix. A spectral modification of the emission by the surrounding photonic crystal is demonstrated for mercury telluride quantum dots when the emission coincides with the photonic band gap of the Si photonic crystal.
Near-field spectroscopy of bimodal size distribution of InAs∕AlGaAs single quantum dots
Authors: Yu Young-Jun , Jeong In-Taek , Woo Jong-Chun , Jhe Wonho
Published: September 2005

We report on high-resolution photoluminescence (PL) spectroscopy of size distribution of InAs∕AlGaAs quantum dots (QDs) by using a near-field scanning optical microscope (NSOM). The double-peaked distribution of PL spectra is clearly observed, which is associated with the bimodal size distribution of single QDs. In particular, the size difference of single QDs, represented by the doublet spectral distribution, is directly observed by the NSOM images of PL.
Ferroelectric (Pb,Sr)TiO3 epitaxial thin films on (001) MgO for room temperature high-frequency tunable microwave elements
Authors: Liu S. W. , Weaver J. , Yuan Z. , Donner W. , Chen C. L. , Jiang J. C. , Meletis E. I. , Chang W. , Kirchoefer S. W. , Horwitz J. , Bhalla A.
Published: September 2005

Ferroelectric Pb0.35Sr0.65TiO3 (PSTO) thin films were grown on (001) MgO by using pulsed laser deposition. Microstructure studies from x-ray diffraction and electron microscopy indicate that the as-grown PSTO films have excellent single crystal quality and good epitaxial behavior with their c-axis oriented perpendicular to the plane of the films. The interface relationships between the PSTO films and MgO were determined to be [100]PSTO∕∕[100]MgO and (001)PSTO∕∕(001)MgO. The high frequency dielectric property measurements (up to 20 GHz) reveal that the as-grown films have a high dielectric constant value above 1420 and very large dielectric tunability above 34% at room temperature. These results suggest that the as-grown PSTO thin films on MgO are a good candidate for developing room-temperature high-frequency tunable microwave elements.
Dislocation-induced nonuniform interfacial reactions of Ti∕Al∕Mo∕Au ohmic contacts on AlGaN∕GaN heterostructure
Authors: Wang Liang , Mohammed Fitih M. , Adesida Ilesanmi
Published: September 2005

Transmission electron microscopy (TEM) is utilized to elucidate the postannealing interfacial microstructure of Ti∕Al∕Mo∕Au metallization with AlGaN∕GaN heterostructures to gain insight into the formation mechanism of low-resistance ohmic contacts. The reaction between the metal and the AlGaN layer does not proceed uniformly. Localized penetration through the AlGaN layer beyond the two-dimensional electron gas (2DEG) is observed while partial consumption of the AlGaN layer is noted in other areas. Analytical TEM analyses confirm that the main reaction product is TiN. A correlation between the appearance of TiN islands and threading dislocations is observed. Threading dislocations serve as short-circuit diffusion channels, and are responsible for the nonuniform reaction. TiN islands have a large total area of intimate contact with the 2DEG, and since no tunneling of electron through the AlGaN is required, a low-resistance ohmic contact is obtained.
Theoretical study of environmental dependence of oxygen vacancy formation in CeO2
Authors: Jiang Yong , Adams James B. , van Schilfgaarde Mark , Sharma Renu , Crozier Peter A.
Published: September 2005

Density functional methods were used to study the environmental dependence of O vacancy formation in CeO2. It was found that an O vacancy in the 2+ charged state has the lowest formation energy for a wide range of Fermi energies (EF) from 0 to ∼1.9eV, while a neutral vacancy becomes the most stable at higher EF values. The O vacancy formation energy can be strongly affected by temperature (T) and the partial pressure of oxygen (PO2). The effect of T and PO2 on the equilibrium compositions of reduced ceria (CeO2−x) was also calculated and showed qualitative agreement with gravimetric experiments.
Dielectric relaxation properties of perovskite-pyrochlore biphase ceramics
Authors: Hsiao Yu-Jen , Chang Yen-Hwei , Fang Te-Hua , Chang Yee-Shin
Published: September 2005

The structure and dielectric relaxation properties of (1−x)NaNbO3-xBiCrO3(0.1⩽x⩽0.5) composite ceramics with perovskite-pyrochlore biphase were studied. The coexistence of cubic perovskite and a cubic pyrochlore structure was characterized. A lack of mutual solubility between the two phases was observed. Biphase ceramics with x=0.3 exhibited dielectric relaxation behavior with a diffuse-like phase transition. Pyrochlore-rich biphase ceramics with x=0.4 exhibit dielectric relaxor-like behavior. The biphase ceramics have high dielectric constants, because of the reorientation of the dipoles and the formation of barrier layers at the grain boundaries.
Supplementation of Acacia mearnsii tannins decreases methanogenesis and urinary nitrogen in forage-fed sheep
Authors: Carulla J. E. , Kreuzer M. , Machmüller A. , Hess H. D.
Published: September 2005

The objective of this experiment was to assess the effects of a partial replacement of ryegrass (Lolium perenne) by red clover (Trifolium pratense) or alfalfa (Medicago sativa) supplemented with 0 or 41 g Acacia mearnsii extract (containing 0.615 g/g condensed tannins)/kg dietary dry matter on nitrogen turnover and methane release by sheep, using the respiration chamber technique. Across all variables, there was no significant interaction between basal diet and tannin supplementation. The partial replacement of the grass by the legumes remained without effect on the amounts of nitrogen excreted through faeces or urine. Nitrogen and energy utilisation was lower (P < 0.05) with ryegrass–alfalfa than with ryegrass alone, and methane release (kJ/MJ gross energy intake) was higher (P < 0.05) with ryegrass–red clover than with ryegrass alone. Tannin supplementation decreased (P < 0.05) ruminal ammonia concentration and urinary nitrogen excretion without affecting body nitrogen and energy retention, and reduced (P < 0.001) methane release by 13% on average. The results suggest that supplemented Acacia mearnsii tannins can be useful in mitigating methane and potential gaseous nitrogen emissions, whereas a replacement of grass by legumes obviously shows no advantage in this respect.
Spatial assessment of the physiological status of wheat crops as affected by water and nitrogen supply using infrared thermal imagery
Authors: Rodriguez D. , Sadras V. O. , Christensen L. K. , Belford R.
Published: September 2005

This work addresses the need for meaningful spatial indices of the physiological condition of field crops for site-specific management and variable rate application in precision agriculture. Precision agriculture is designed to target crop inputs according to within-field requirements to increase profitability while protecting the environment. The objectives of this work were to (a) develop a canopy physiological stress index with spatial resolution commensurate with the needs of site-specific management, and (b) test the physiological meaning of this index by exploring its association with key processes and variables at leaf and crop levels. We report results from a single-year field experiment where different levels of irrigation, wheat crop density, and nitrogen supply were applied to increase the expression of within-season variability. We defined a canopy stress index (CSI) as the difference between canopy (Tc), and air temperature (Ta), normalised by vapour pressure deficit (VPD): CSI = (Tc – Ta)/VPD. A novel method to extract canopy temperatures (Tc) from complex digital thermal images was developed, thus allowing for the spatial characterisation of CSI. CSI is expected to be positive and high if the capacity of the canopy to dissipate heat is reduced as when stomata close. CSI accounted for 80% of the variation in growth rate and yield, compared with 46–49% explained by the normalised difference vegetation index (NDVI). Most of the variation in crop response variables was related to water supply. The physiological meaning of this index was reinforced by its significant association with gas exchange variables measured at the leaf-level. The potential for the use of digital thermal imaging in precision agriculture is discussed.
Growth and seed yield of lentil (Lens culinaris Medikus) genotypes of West Asian and South Asian origin and crossbreds between the two under rainfed conditions in Nepal
Authors: Shrestha R. , Siddique K. H. M. , Turner N. C. , Turner D. W. , Berger J. D.
Published: September 2005

Nineteen diverse lentil genotypes, 8 originating from South Asia, 6 from West Asia, and 5 crossbreds using parents from South Asia and West Asia (or other Mediterranean environments), were evaluated for growth, phenology, yield, and yield components at Khumaltar in the mid-hill region of Nepal. Additionally, dry matter production, partitioning, root growth and water use of 8 selected genotypes from the 3 groups were measured at key phenological stages. The seed yield of the West Asian genotypes was only 330 kg/ha, whereas the South Asian genotypes produced a mean seed yield of 1270 kg/ha. The crossbreds had a significantly (P = 0.05) greater seed yield (1550 kg/ha) than the South Asian genotypes. The high seed yield of both the South Asian and crossbred genotypes was associated with rapid ground cover, early flowering and maturity, a long reproductive period, a greater number of seeds and pods, high total dry matter, greater harvest index, and high water use efficiency. West Asian genotypes, on the other hand, flowered 43 days later, matured 15 days later, and had a shorter reproductive period (by 22 days) than the crossbred and South Asian genotypes. The 23% greater seed yield in the crossbreds compared with the South Asian genotypes was the result of a similar increase in seed size (weight per seed).
There were no significant differences in total root length (mean 4.7 km/m2), root dry matter (mean 95.5 g/m2), or water use among the 3 groups during the major part of the growing period. There was a significant difference in total water use due to the longer growing season of the West Asian genotype ILL 7983 and its ability to use late-season rainfall. Maximum water use efficiencies for seed yield of 7.0 kg/ha.mm and for above-ground dry matter of 18.9 kg/ha.mm were comparable with those reported in India and the Mediterranean environments of south-western Australia and Syria.
The struggle to exploit non-additive variation
Authors: Walsh Bruce
Published: September 2005

Whereas animal breeders largely focus on improvement using additive genetic variance, inbreeding and asexual reproduction allow plant breeders to at least partially exploit non-additive genetic variance as well. We briefly review various approaches used by breeders to exploit dominance and epistatic variance, discuss their constraints and limitations, and examine what (if anything) can be done to improve our ability to further use often untapped genetic variation.
Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models
Authors: van Eeuwijk Fred A. , Malosetti Marcos , Yin Xinyou , Struik Paul C. , Stam Piet
Published: September 2005

To study the performance of genotypes under different growing conditions, plant breeders evaluate their germplasm in multi-environment trials. These trials produce genotype × environment data. We present statistical models for the analysis of such data that differ in the extent to which additional genetic, physiological, and environmental information is incorporated into the model formulation. The simplest model in our exposition is the additive 2-way analysis of variance model, without genotype × environment interaction, and with parameters whose interpretation depends strongly on the set of included genotypes and environments. The most complicated model is a synthesis of a multiple quantitative trait locus (QTL) model and an eco-physiological model to describe a collection of genotypic response curves. Between those extremes, we discuss linear-bilinear models, whose parameters can only indirectly be related to genetic and physiological information, and factorial regression models that allow direct incorporation of explicit genetic, physiological, and environmental covariables on the levels of the genotypic and environmental factors. Factorial regression models are also very suitable for the modelling of QTL main effects and QTL × environment interaction. Our conclusion is that statistical and physiological models can be fruitfully combined for the study of genotype × environment interaction.
Gene-to-phenotype models and complex trait genetics
Authors: Cooper Mark , Podlich Dean W. , Smith Oscar S.
Published: September 2005

The premise that is explored in this paper is that in some cases, in order to make progress in the design of molecular breeding strategies for complex traits, we will need a theoretical framework for quantitative genetics that is grounded in the concept of gene-networks. We seek to develop a gene-to-phenotype (G→P) modelling framework for quantitative genetics that explicitly deals with the context-dependent gene effects that are attributed to genes functioning within networks, i.e. epistasis, gene × environment interactions, and pleiotropy. The E(NK) model is discussed as a starting point for building such a theoretical framework for complex trait genetics. Applying this framework to a combination of theoretical and empirical G→P models, we find that although many of the context-dependent effects of genetic variation on phenotypic variation can reduce the rate of genetic progress from breeding, it is possible to design molecular breeding strategies for complex traits that on average will outperform phenotypic selection. However, to realise these potential advantages, empirical G→P models of the traits will need to take into consideration the context-dependent effects that are a consequence of epistasis, gene × environment interactions, and pleiotropy. Some promising G→P modelling directions are discussed.
Flowering time control: gene network modelling and the link to quantitative genetics
Authors: Welch Stephen M. , Dong Zhanshan , Roe Judith L. , Das Sanjoy
Published: September 2005

Flowering is a key stage in plant development that initiates grain production and is vulnerable to stress. The genes controlling flowering time in the model plant Arabidopsis thaliana are reviewed. Interactions between these genes have been described previously by qualitative network diagrams. We mathematically relate environmentally dependent transcription, RNA processing, translation, and protein–protein interaction rates to resultant phenotypes. We have developed models (reported elsewhere) based on these concepts that simulate flowering times for novel A. thaliana genotype–environment combinations. Here we draw 12 contrasts between genetic network (GN) models of this type and quantitative genetics (QG), showing that both have equal contributions to make to an ideal theory. Physiological dominance and additivity are examined as emergent properties in the context of feed-forwards networks, an instance of which is the signal-integration portion of the A. thaliana flowering time network. Additivity is seen to be a complex, multi-gene property with contributions from mass balance in transcript production, the feed-forwards structure itself, and downstream promoter reaction thermodynamics. Higher level emergent properties are exemplified by critical short daylength (CSDL), which we relate to gene expression dynamics in rice (Oryza sativa). Next to be discussed are synergies between QG and GN relating to the quantitative trait locus (QTL) mapping of model coefficients. This suggests a new verification test useful in GN model development and in identifying needed updates to existing crop models. Finally, the utility of simple models is evinced by 80 years of QG theory and mathematical ecology.
Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems
Authors: Hammer Graeme L. , Chapman Scott , van Oosterom Erik , Podlich Dean W.
Published: September 2005

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits—phenology, osmotic adjustment, transpiration efficiency, stay-green—and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location–season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.
A label-free immunosensor array using single-chain antibody fragments
Authors: Backmann Natalija , Zahnd Christian , Huber Francois , Bietsch Alexander , Plückthun Andreas , Lang Hans-Peter , Güntherodt Hans-Joachim , Hegner Martin , Gerber Christoph
Published: September 2005

We report a microcantilever-based immunosensor operated in static deflection mode with a performance comparable with surface plasmon resonance, using single-chain Fv (scFv) antibody fragments as receptor molecules. As a model system scFv fragments with specificity to two different antigens were applied. We introduced a cysteine residue at the C terminus of each scFv construct to allow covalent attachment to gold-coated sensor interfaces in directed orientation. Application of an array enabled simultaneous deflection measurements of sensing and reference cantilevers. The differential deflection signal revealed specific antigen binding and was proportional to the antigen concentration in solution. Using small, oriented scFv fragments as receptor molecules we increased the sensitivity of microcantilevers to ≈1 nM.
Conversion of nicotine to nornicotine in
Nicotiana tabacum
is mediated by CYP82E4, a cytochrome P450 monooxygenase
Authors: Siminszky Balazs , Gavilano Lily , Bowen Steven W. , Dewey Ralph E.
Published: September 2005

Nornicotine is a secondary tobacco alkaloid that is produced by the N-demethylation of nicotine. Nornicotine production and accumulation in tobacco are undesirable because nornicotine serves as the precursor in the synthesis of the well characterized carcinogen
N
′-nitrosonornicotine during the curing and processing of tobacco. Although nornicotine is typically a minor alkaloid in tobacco plants, in many tobacco populations a high percentage of individuals can be found that convert a substantial proportion of the nicotine to nornicotine during leaf senescence and curing. We used a microarray-based strategy to identify genes that are differentially regulated between closely related tobacco lines that accumulate either nicotine (nonconverters) or nornicotine (converters) as the predominant alkaloid in the cured leaf. These experiments led to the identification of a small number of closely related cytochrome P450 genes, designated the
CYP82E2
family, whose collective transcript levels were consistently higher in converter versus nonconverter tobacco lines. RNA interference-induced silencing of the
CYP82E2
gene family suppressed the synthesis of nornicotine in strong converter plants to levels similar to that observed in nonconverter individuals. Although each of the six identified members of the P450 family share >90% nucleotide sequence identity, sense expression of three selected isoforms revealed that only one (
CYP82E4v1
) was involved in the conversion of nicotine to nornicotine. Yeast expression analysis revealed that CYP82E4v1 functions as a nicotine demethylase. Identification of the gene(s) responsible for nicotine demethylation provides a potentially powerful tool toward efforts to minimize nornicotine levels, and thereby
N
′-nitrosonornicotine formation, in tobacco products.
Phospho-dependent binding of the clathrin AP2 adaptor complex to GABA
A
receptors regulates the efficacy of inhibitory synaptic transmission
Authors: Kittler Josef T. , Chen Guojun , Honing Stephan , Bogdanov Yury , McAinsh Kristina , Arancibia-Carcamo I. Lorena , Jovanovic Jasmina N. , Pangalos Menelas N. , Haucke Volker , Yan Zhen , Moss Stephen J.
Published: September 2005

The efficacy of synaptic inhibition depends on the number of γ-aminobutyric acid type A receptors (GABA
A
Rs) expressed on the cell surface of neurons. The clathrin adaptor protein 2 (AP2) complex is a critical regulator of GABA
A
R endocytosis and, hence, surface receptor number. Here, we identify a previously uncharacterized atypical AP2 binding motif conserved within the intracellular domains of all GABA
A
R β subunit isoforms. This AP2 binding motif (KTHLRRRSSQLK in the β3 subunit) incorporates the major sites of serine phosphorylation within receptor β subunits, and phosphorylation within this site inhibits AP2 binding. Furthermore, by using surface plasmon resonance, we establish that a peptide (pepβ3) corresponding to the AP2 binding motif in the GABA
A
R β3 subunit binds to AP2 with high affinity only when dephosphorylated. Moreover, the pepβ3 peptide, but not its phosphorylated equivalent (pepβ3-phos), enhanced the amplitude of miniature inhibitory synaptic current and whole cell GABA
A
R current. These effects of pepβ3 on GABA
A
R current were occluded by inhibitors of dynamin-dependent endocytosis supporting an action of pepβ3 on GABA
A
R endocytosis. Therefore phospho-dependent regulation of AP2 binding to GABA
A
Rs provides a mechanism to specify receptor cell surface number and the efficacy of inhibitory synaptic transmission.