bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards a first-principles model of Fermi resonance in the alkyl CH stretch region: Application to 1,2-diphenylethane and 2,2,2-paracyclophane
Authors: Buchanan Evan G. , Dean Jacob C. , Zwier Timothy S. , Sibert Edwin L.
Published: February 2013

The spectroscopy of two flexible hydrocarbons, 1,2-diphenylethane (DPE) and 2,2,2-paracyclophane (TCP) is presented, and a predictive theoretical model for describing the alkyl CH stretch region of these hydrocarbons is developed. Ultraviolet hole-burning spectroscopy identified two isomers of DPE and a single conformation of TCP present in the supersonic jet expansion. Through the analysis of the ground state low-frequency vibronic spectroscopy obtained by dispersed fluorescence, conformational assignments were made for both DPE and TCP. The two isomers of DPE were found to retain the low energy structures of butane, being present in both the gauche and anti structures. TCP forms a C2 symmetric structure, differing from the predicted lower energy C3 conformation by the symmetry of the ethano bridges (−CH2CH2−) linking the phenyl substituents. Resonant ion-dip infrared spectroscopy is used to record single-conformation IR spectra of the two conformers of DPE and the single conformer of TCP in the alkyl CH stretch region and in the mid-IR that covers the CH bend fundamentals. A local mode Hamiltonian that incorporates cubic stretch-bend coupling is developed. Its parameters are obtained from density functional theory methods. Full dimensional calculations are compared to those that use reduced dimensional Hamiltonians in which anharmonic CH stretches and scissor modes are Fermi coupled. Excellent agreement is found. Scale factors of select terms in the reduced dimensional Hamiltonian are determined by fitting the theoretical Hamiltonian to the anti-DPE spectrum. The scaled Hamiltonian is then used to predict successfully structures for the remaining lower symmetry experimentally determined spectra in the alkyl CH stretch region.
Vortical structures of supersonic flow over a delta-wing on a flat plate
Authors: Wang D. P. , Xia Z. X. , Zhao Y. X. , Wang Q. H. , Liu B.
Published: February 2013

Employing the nanoparticle-based planar laser scattering (NPLS), supersonic flow over a delta-winged vortex generator on a flat plate was experimentally investigated in a supersonic quiet wind tunnel at Ma = 2.68. The fine structures of the flow field, shock waves, separation vortices, wake, and boundary layer transition were observed in the NPLS images. According to the time-correlation of the NPLS images and the measurement results of particle image velocimetry, the structural model of the flow field was improved further, and coherent wake structures were observed, which is of significance theoretically and in engineering application.
Microscopic calculation of the free energy cost for activated transport in glass-forming liquids
Authors: Rabochiy Pyotr , Lubchenko Vassiliy
Published: February 2013

Activated transport in liquids—supercooled liquids in particular—occurs via mutual nucleation of alternative, aperiodic minima of the free energy. Xia and Wolynes [Proc. Natl. Acad. Sci. U.S.A. 97, 2990 (2000)10.1073/pnas.97.7.2990] have made a general argument that at temperatures near the ideal glass transition, the surface penalty for this kind of nucleation is largely determined by the temperature and the logarithm of the size of the vibrational fluctuation of rigid molecular units about the local minimum. Here, we independently show how to estimate this surface tension and, hence, the activation barrier for the activated transport for several actual liquids, using their structure factors and knowledge of the finite-frequency elastic constants. In this estimate, the activation free energy, while depending on the configurational entropy, also depends on the elastic modulus as in the “shoving” models. The resulting estimates are however consistent with the estimate provided by Xia and Wolynes' argument near the glass transition and, in addition, reflect the barrier softening effects predicted earlier for fragile substances.
Polymeric photovoltaics with various metallic plasmonic nanostructures
Authors: Zeng Beibei , Gan Qiaoqiang , Kafafi Zakya H. , Bartoli Filbert J.
Published: February 2013

Broadband light absorption enhancement is numerically investigated for the active light harvesting layer of an organic photovoltaic (OPV), which consists of a blend of poly(3-hexylthiophene) (P3HT) and the fullerene derivative [6,6]-phenyl-C61 butyric acid methyl ester (PCBM). Periodic plasmonic nanostructures placed above and below the active layer incorporate Ag, Al, Au, or a combination of two different metals. Three dimensional (3D) full-field electromagnetic simulations are applied to determine the effect of varying the metal employed in the plasmonic nanostructures on the absorption enhancement of the OPV. In addition, the geometric parameters (e.g., film thickness, period, and diameter) of the symmetrically distributed top and bottom metal (Ag, Al, or Au) nanostructures were varied to optimize the device structure and delineate the mechanism(s) leading to the absorption enhancement. A spectrally broadband, polarization-insensitive, and wide-angle absorption enhancement is obtained using a double plasmonic nanostructure and is attributed to the combined excitation of localized and single-interface surface plasmon polariton modes. The total photon absorption of the OPV with the optimized double plasmonic Ag nanostructures was found to be enhanced by as much as 82.8% and 80.4% under normal (0°) and 60° light incidence, respectively.
Identification of long-lived clusters and their link to slow dynamics in a model glass former
Authors: Malins Alex , Eggers Jens , Royall C. Patrick , Williams Stephen R. , Tanaka Hajime
Published: February 2013

We study the relationship between local structural ordering and dynamical heterogeneities in a model glass-forming liquid, the Wahnström mixture. A novel cluster-based approach is used to detect local energy minimum polyhedral clusters and local crystalline environments. A structure-specific time correlation function is then devised to determine their temporal stability. For our system, the lifetime correlation function for icosahedral clusters decays far slower than for those of similarly sized but topologically distinct clusters. Upon cooling, the icosahedra form domains of increasing size and their lifetime increases with the size of the domains. Furthermore, these long-lived domains lower the mobility of neighboring particles. These structured domains show correlations with the slow regions of the dynamical heterogeneities that form on cooling towards the glass transition. Although icosahedral clusters with a particular composition and arrangement of large and small particles are structural elements of the crystal, we find that most icosahedral clusters lack such order in composition and arrangement and thus local crystalline ordering makes only a limited contribution to this process. Finally, we characterize the spatial correlation of the domains of icosahedra by two structural correlation lengths and compare them with the four-point dynamic correlation length. All the length scales increase upon cooling, but in different ways.
Parameter passing between molecular dynamics and continuum models for droplets on solid substrates: The static case
Authors: Tretyakov Nikita , Müller Marcus , Todorova Desislava , Thiele Uwe
Published: February 2013

We study equilibrium properties of polymer films and droplets on a solid substrate employing particle-based simulation techniques (molecular dynamics) and a continuum description. Parameter-passing techniques are explored that facilitate a detailed comparison of the two models. In particular, the liquid-vapor, solid-liquid, and solid-vapor interface tensions, and the Derjaguin or disjoining pressure are determined by molecular dynamics simulations. This information is then introduced into continuum descriptions accounting for (i) the full curvature and (ii) a long-wave approximation of the curvature (thin film model). A comparison of the dependence of the contact angle on droplet size indicates that the theories agree well if the contact angles are defined in a compatible manner.
Density functional theory and global optimization study of SnmPbn clusters (7 ⩽ m + n ⩽ 12, 0 ⩽ m/(m + n) ⩽ 1)
Authors: Orel Slava , Fournier René
Published: February 2013

The global minima of the neutral binary SnmPbn atomic clusters, 7 ⩽ m + n ⩽ 12, of all the possible stoichiometric ratios have been found using tabu search in descriptor space and density functional theory. The effects of spin-orbit coupling on optimized geometries and energies are important. All of the binary clusters form substitution alloys. Apart from the 11-atom case, the pure clusters of the same size have the same ground state geometry. The relative energies of the isomers of a cluster depend on, in order of decreasing importance: the overall geometry; the specific sites occupied by the two atom types; and the degree of segregation. The total cohesive energy difference between the lowest energy homotops is typically on the order of 0.02 eV. The mixing/segregation trends are found to be very different depending on the size of the basis set. Calculations generally overestimate the dipole moments. The trends in calculated dipole moments agree with experiment for the lead-rich clusters, and to a lesser degree, the tin-rich clusters.
Melting of α-Al2O3 and vitrification of the undercooled alumina liquid: Ab initio vibrational calculations and their thermodynamic implications
Authors: Belmonte D. , Ottonello G. , Zuccolini M. Vetuschi
Published: February 2013

We present the results of a computational investigation of the structure-energy and vibrational properties of alumina under various aggregation states (crystalline, glassy, and liquid) with ab initio procedures. IV-fold, V-fold, and VI-fold oxygen-coordinated aluminum monomeric forms in a dielectric continuum with dielectric constant ɛ = 4.575 were investigated through DFT/B3LYP gas-phase calculations coupled with a Polarized Continuum Model approach and those of the periodical structure D63d (R-3c) which leads to the α-Al2O3 polymorph of alumina, when subjected to symmetry operations, were investigated with the same functional within the LCAO approximation and in the framework of Bloch's theorem. Based on the computed energies and vibrational features, an aggregate of the D63d positively charged cluster [Al12O11]14+ contoured by [AlO4]5− units in an approximate 1:3 proportion to achieve neutrality satisfactorily reproduce the heat capacity of the liquid within experimental uncertainty. The glass is seen as a wrong accretionary form induced by fast cooling rates and subjected to steric forces that locally modify the coordination state of the central atom. Cessation of rotational and translational movements, only partly counterbalanced by acoustic sine-wave-dispersed and excess phonons, gives rise to the huge heat-capacity gap observed at the glass transition (∼5.3R). When cooling rates are sufficiently slow, the accretion around the D63d seeds follows the structural constraints and the heat capacity of α-alumina is almost perfectly reproduced by the 27 Einstein oscillators coupled with the 3 acoustic terms and the anharmonic corrections.
Slippage and viscosity predictions in carbon micropores and their influence on CO2 and CH4 transport
Authors: Firouzi Mahnaz , Wilcox Jennifer
Published: February 2013

Non-equilibrium molecular dynamics simulations of pure carbon dioxide and methane and their equimolar mixtures have been carried out with an external driving force imposed on carbon slit pores to investigate gas slippage and Klinkenberg effects. Simulations were conducted to determine the effect of pore size and exposure to an external potential on the velocity profile and slip-stick boundary conditions. The simulations indicate that molecule-wall collisions influence the velocity profile, which deviates significantly from the Navier-Stokes hydrodynamic prediction for micro- and mesopores. Also, the shape of the velocity profile is found to be independent of the applied pressure gradient in micropores. The results indicate that the velocity profile is uniform for pore sizes less than 2 nm (micropores) where the transport is mainly due to molecular streaming or Knudsen diffusion and, to a lesser extent, molecular diffusion. As pore sizes increase to 10 nm, parabolic profiles are observed due to the reduced interaction of gas molecules with the pore walls. A 3D pore network, representative of porous carbon-based materials, has been generated atomistically using the Voronoi tessellation method. Simulations have been carried out to determine the effect of the pore structure and modeled viscosity on permeability and Klinkenberg parameters. The use of the bulk-phase viscosity for estimating the permeability of CO2 in units of Darcy in a 3D micropore network is not an appropriate assumption as it significantly underestimates the CO2 permeability. On the other hand, since the transport properties of CH4 are less influenced by the pore walls compared with CO2, the use of the bulk-phase CH4 viscosity estimates are a reasonable assumption.
Low-bias electron transport properties of germanium telluride ultrathin films
Authors: Liu Jie , Anantram M. P.
Published: February 2013

The nanometer-scale size-dependent electronic transport properties of crystalline (c-) and amorphous (a-) germanium telluride (GeTe) ultrathin films sandwiched by titanium nitride (TiN) electrodes are investigated using ab initio molecular dynamics, density functional theory, and Green's function calculations. We find that a-GeTe ultrathin films scaled down to about 38 Å (12 atomic layers) still show a band gap and the electrical conductance is mainly due to electron transport via intra-gap states. If the ultrathin films are further scaled, the a-GeTe band gap disappears due to overlap of the two metal induced gap states (MIGS) regions near the TiN electrodes, leading to sharp increase of a-GeTe conductance and significant decrease of c-GeTe/a-GeTe conductance ratio. The c-GeTe/a-GeTe conductance ratio drops below one order of magnitude if the ultrathin films are scaled below about 33 Å, making it difficult to reliably perform read operations in thin film based phase change memory devices. This overlap of the MIGS regions sets up the ultimate scaling limit of phase change memory technology. Our results suggest that the ultimate scaling limit can be pushed to even smaller size, by using phase change material with larger amorphous phase band gap than a-GeTe.
Mid-infrared absorptance of silicon hyperdoped with chalcogen via fs-laser irradiation
Authors: Sher Meng-Ju , Lin Yu-Ting , Winkler Mark T. , Mazur Eric , Pruner Christian , Asenbaum Augustinus
Published: February 2013

Silicon hyperdoped with heavy chalcogen atoms via femtosecond-laser irradiation exhibits strong broadband, sub-bandgap light absorption. Understanding the origin of this absorption could enable applications for hyperdoped-silicon based optoelectronic devices. In this work, we measure absorption to wavelengths up to 14 μm using Fourier transform infrared spectroscopy and study sulfur-, selenium-, and tellurium-hyperdoped Si before and after annealing. We find that absorption in the samples extends to wavelengths as far as 6 μm. After annealing, the absorption spectrum exhibits features that are consistent with free-carrier absorption. Although the surface morphology influences the shape of the absorption curves, the data permit us to place an upper bound on the position of the chalcogen dopant energy levels.
Global current profile effects on the evolution and saturation of magnetic islands
Authors: Poyé A. , Agullo O. , Smolyakov A. , Benkadda S. , Garbet X.
Published: February 2013

The nonlinear evolution of magnetic islands is investigated by means of numerical simulations. The growth and saturation of the island are shown to depend not only on asymptotic tearing mode stability parameter Δ′ but also on the initial global current profile. Presence of the external current sheets leads to the formation of different island state for the same value of Δ′. It is found that the flow vorticity generated by the interacting current sheets is an important feature of nonlocal interactions and nonlocal effects in magnetic islands dynamics.
Development of an identification method of pressure anisotropy based on equilibrium analysis and magnetics
Authors: Asahi Y. , Suzuki Y. , Watanabe K. Y. , Cooper W. A.
Published: February 2013

We evaluate the fluxes measured by the magnetic flux loops installed in LHD by using a three dimensional MHD equilibrium analysis code, ANIMEC, which enable us to directly determine the calibration function between the anisotropic pressure and the measured fluxes for the non-axisymmetric plasmas for the first time. The result indicates that the diamagnetic flux represents a nearly single-valued function of the beta perpendicular with respect to the field, and the saddle loop flux represents a nearly single-valued function of an equally weighted average of the beta values parallel and perpendicular to the field, regardless of the pressure anisotropy or the amount of energetic trapped particles. The values of the beta perpendicular to the field and the equal weighting averaged beta estimated by the single-valued functions (calibration functions) are investigated in order to clarify the magnitude of deviation from those original values, and the range of anisotropy where the beta value evaluated by the magnetic flux measurement is calculated within a 10% error.
Feasibility studies for filament detection in resistively switching SrTiO3 devices by employing grazing incidence small angle X-ray scattering
Authors: Stille S. , Baeumer C. , Krannich S. , Lenser C. , Dittmann R. , Perlich J. , Roth S. V. , Waser R. , Klemradt U.
Published: February 2013

We report on fundamental studies of grazing incidence small angle X-ray scattering (GISAXS) on resistively switching SrTiO3 thin film metal-insulator-metal (MIM) devices. Different influence factors on the GISAXS scattering pattern, e.g., surface morphology and top electrode material, were evaluated by simulations and compared with subsequent measurements. Pt top electrodes cause a strong background scattering which covers any information from the underlying SrTiO3 layer. In order to reduce this undesired background scattering, the lighter elements Al and Ti have been used. In case of Ti top electrodes, we observed that a laterally formed structure occurs in the SrTiO3 prior to any electrical treatment, which is consistent with the forming-free properties of the MIM structures. For Al top electrodes, we could detect a significant influence of an electroforming step on the scattered intensity.
Experimental evidence of the atmospheric convective transport contribution to sessile droplet evaporation
Authors: Carle F. , Sobac B. , Brutin D.
Published: February 2013

We investigate the contribution of the natural convective transport in the vapor phase on the evaporation rate of an evaporating sessile droplet. When comparing the experimental data with the quasi-steady diffusion-controlled evaporation model, an increasing deviation with substrate temperature that was attributed to the effect of the natural convection on the vapor field has been recently highlighted. To validate this analysis, we present experimental results obtained with two gravity levels: 1 g and μg. The contribution of the natural convection is analyzed with the Grashof number, and an empirical model is developed combining diffusive and convective transport.
Generating vorticity and magnetic fields in plasmas in general relativity: Spacetime curvature drive
Authors: Asenjo Felipe A. , Mahajan Swadesh M. , Qadir Asghar
Published: February 2013

Using the generally covariant magnetofluid formalism for a hot plasma, a spacetime curvature driven mechanism for generating seed vorticity/magnetic field is presented. The “battery” owes its origin to the interaction between the gravity modified Lorentz factor of the fluid element and the inhomogeneous plasma thermodynamics. The general relativistic drive is evaluated for two simple cases: seed formation in a simplified model of a hot plasma accreting in stable orbits around a Schwarzschild black hole and for particles in free fall near the horizon. Some astrophysical applications are suggested.
Effective charge and effective radius of water droplet in dropwise cluster
Authors: Shavlov A. V. , Romanyuk S. N. , Dzhumandzhi V. A.
Published: February 2013

A particle with large electric charge Z (Z ≫ 1) and radius R0 inserted into plasma is surrounded by a plasma shell, which is stable to weak and short-term external exposures. As a result, during experiments the particle can reveal an effective charge Z* lower than the true one (Z* ≤ Z), and an effective radius R* larger than the true one (R* ≥ R0). The effective electric charge and the effective radius of a water droplet in a dropwise cluster have been calculated using the Poisson-Boltzmann equation. It has been recognized that these parameters are not the function of a droplet's true charge, but are the function of a droplet's true size and the Debye's radius of the plasma. Experimental data on the droplet properties in a dropwise cluster have been explained.
Lower hybrid instability driven by mono-energy α-particles with finite pitch angle spread in a plasma
Authors: Kumar Pawan , Singh Vishwesh , Tripathi V. K.
Published: February 2013

A kinetic formalism of lower hybrid wave instability, driven by mono-energy α-particles with finite pitch angle spread, is developed. The instability arises through cyclotron resonance interaction with high cyclotron harmonics of α-particles. The α-particles produced in D-T fusion reactions have huge Larmor radii (∼10 cm) as compared to the wavelength of the lower hybrid wave, whereas their speed is an order of magnitude smaller than the speed of light in vacuum. As a result, large parallel phase velocity lower hybrid waves, suitable for current drive in tokamak, are driven unstable via coupling to high cyclotron harmonics. The growth rate decreases with increase in pitch angle spread of the beam. At typical electron density of ∼1019 m−3, magnetic field ∼4 Tesla and α-particle concentration ∼0.1%, the large parallel phase velocity lower hybrid wave grows on the time scale of 20 ion cyclotron periods. The growth rate decreases with plasma density.
Ear canal dynamic motion as a source of power for in-ear devices
Authors: Delnavaz Aidin , Voix Jérémie
Published: February 2013

Ear canal deformation caused by temporomandibular joint (jaw joint) activity, also known as “ear canal dynamic motion,” is introduced in this paper as a candidate source of power to possibly recharge hearing aid batteries. The geometrical deformation of the ear canal is quantified in 3D by laser scanning of different custom ear moulds. An experimental setup is proposed to measure the amount of power potentially available from this source. The results show that 9 mW of power is available from a 15 mm3 dynamic change in the ear canal volume. Finally, the dynamic motion and power capability of the ear canal are investigated in a group of 12 subjects.
Cadmium-free copper indium gallium diselenide hybrid solar cells comprising a 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole buffer layer
Authors: Reinhard Manuel , Simon Christoph , Kuhn Johannes , Bürkert Linda , Cemernjak Marco , Dimmler Bernhard , Lemmer Uli , Colsmann Alexander
Published: February 2013

Copper indium gallium diselenide (CIGS) solar cells are the most efficient thin film photovoltaic devices today. In this work, we investigate CIGS/organic hybrid solar cells comprising a semi-transparent metal top electrode and a wide band gap organic semiconductor as buffer layer. Depositing the organic semiconductor from solution, we fabricate Cd-free solar cells exhibiting about the same efficiency as their counterparts comprising CdS and significantly higher open-circuit voltages as compared to buffer-free devices. Although the organic molecules do not cover the CIGS surface homogeneously, their use enables prolonged charge carrier lifetimes according to impedance spectroscopy measurements.
Optimizing emitter-buffer layer stack thickness for p-type silicon heterojunction solar cells
Authors: Deniz Eygi Zeynep , Das Ujjwal , Hegedus Steven , Birkmire Robert
Published: February 2013

p-type silicon heterojunction solar cells are investigated in terms of doping concentration of emitter a-Si:H(n) layer and thickness of emitter-intrinsic buffer a-Si:H(n/i) layers. Control of doping concentration of the amorphous layer is essential to gain sufficient conductivity and junction potential while avoiding an increase in defect density of the a-Si:H(n) layer. Inserting a-Si:H(i) provides high passivation quality by reducing a-Si:H/c-Si interface recombination and leads to a higher open circuit voltage. Properties and thicknesses of both a-Si:H(n) and a-Si:H(i) have a significant role on the performance of silicon heterojunction cell. In this paper, emitter a-Si:H(n) and buffer a-Si:H(i) layers thicknesses are optimized at the optimum gas phase doping concentration in order to obtain high efficiencies.
Two-surface-plasmon-polariton-absorption based nanolithography
Authors: Li Yunxiang , Liu Fang , Xiao Long , Cui Kaiyu , Feng Xue , Zhang Wei , Huang Yidong
Published: February 2013

We propose and demonstrate the two-surface-plasmon-polariton-absorption (TSPPA), which is a nonlinear effect by absorbing two surface-plasmon-polaritons (SPPs), as well as a nanolithography technique based on TSPPA. The TSPPA effect is verified with the plasmonic interference structure to exclude the possibility of two photon absorption. Benefiting from the short wavelength and the field enhancement of SPP as well as the selective transfer of plasmonic patterns into photoresist induced by TSPPA, resist strips with the linewidth of ∼λ0/11 are achieved by a single illumination on the plasmonic mask with the femtosecond laser for only 15 s, which shows great potential for future large-area nanolithography.
Polarization induced hole doping in graded AlxGa1−xN (x = 0.7 ∼ 1) layer grown by molecular beam epitaxy
Authors: Li Shibin , Zhang Ting , Wu Jiang , Yang Yajie , Wang Zhiming , Wu Zhiming , Chen Zhi , Jiang Yadong
Published: February 2013

Polarization induced hole doping on the order of ∼1018 cm−3 is achieved in linearly graded AlxGa1−xN (x = 0.7 ∼ 1) layer grown by molecular beam epitaxy. Graded AlxGa1−xN and conventional Al0.7Ga0.3N layers grown on AlN are beryllium (Be) doped via epitaxial growth. The hole concentration in graded AlxGa1−xN:Be (x = 0.7 ∼ 1) layers demonstrates that polarization generates hole charges from Be dopant. The Al0.7Ga0.3N layer is not conductive owing to the absence of carriers generated from the Be dopant without the inducement of polarization. Polarization doping provides an approach to high efficiency p-type doping in high Al composition AlGaN.
Systematic study of magnetotransport properties and enhanced low-field magnetoresistance in thin films of La0.67Sr0.33MnO3 + Mg(O)
Authors: Staruch M. , Cantoni C. , Jain M.
Published: February 2013

La, Sr, Mn, and Mg precursors were mixed in stoichiometric ratio 0.67/0.33/1/x with solvent and were spin-coated onto (001) LaAlO3 substrates. X-ray diffraction and elemental mapping of these films indicate that for small addition of Mg precursor, Mg2+ acts as a dopant in La0.67Sr0.33MnO3 phase and for higher concentrations, MgO phase separates out. Curie temperature and metal-insulator transition temperature systematically decrease with increasing molar concentration of Mg(O). Low-field magnetoresistance of films significantly enhanced by Mg addition and for the highest amount of Mg at 10 K, values were −35.5% and −83.2% with 0.5 T and 3 T applied fields, respectively.
Strain relaxation by pitting in AlN thin films deposited by metalorganic chemical vapor deposition
Authors: Bryan I. , Rice A. , Hussey L. , Bryan Z. , Bobea M. , Mita S. , Xie J. , Kirste R. , Collazo R. , Sitar Z.
Published: February 2013

Strain relaxation mechanisms were investigated in epitaxial AlN layers deposited on (0001)-oriented AlN substrates by metalorganic chemical vapor deposition. It was revealed that epitaxial AlN layers under tensile strain can exhibit micro-cracks and nano-pits. A correlation existed between the amount of strain and number of pits in localized areas. Pit densities as high as 1010 cm−2 were observed in areas where the tensile strain reached ∼0.4%, while unstrained areas of the film showed step flow growth. These nano-pits occurred as a strain relaxation mechanism and were not related to intrinsic defects, such as threading dislocations or inversion domains.
Self-contact thin-film organic transistors based on tetramethyltetrathiafulvalene
Authors: Tamura Sumika , Kadoya Tomofumi , Kawamoto Tadashi , Mori Takehiko
Published: February 2013

Carrier injection from organic contacts to tetramethyltetrathiafulvalene (TMTTF) is investigated in the thin-film transistors. When 7,7,8,8-tetracyano-p-quinodimethane (TCNQ) is patterned on a TMTTF film, the resulting (TMTTF)(TCNQ) works as highly conducting source and drain electrodes. Such self-contact transistors, in which the organic material constructing the active layer is selectively transformed to the contacts, have achieved low contact resistance and high performance.
Breaking the acoustic diffraction limit via nonlinear effect and thermal confinement for potential deep-tissue high-resolution imaging
Authors: Yuan Baohong , Pei Yanbo , Kandukuri Jayanth
Published: February 2013

Our recently developed ultrasound-switchable fluorescence (USF) imaging technique showed that it was feasible to conduct high-resolution fluorescence imaging in a centimeter-deep turbid medium. Because the spatial resolution of this technique highly depends on the ultrasound-induced temperature focal size (UTFS), minimization of UTFS becomes important for further improving the spatial resolution USF technique. In this study, we found that UTFS can be significantly reduced below the diffraction-limited acoustic intensity focal size via nonlinear acoustic effects and thermal confinement by appropriately controlling ultrasound power and exposure time, which can be potentially used for deep-tissue high-resolution imaging.
Stability of flowing open fluidic channels
Authors: Tan Jue Nee , Alan Tuncay , Neild Adrian
Published: February 2013

Open fluidic systems have a distinct advantage over enclosed channels in that the fluids exposed nature makes for easy external interaction, this finds uses in introduction of samples by adding liquid droplets or from the surrounding gaseous medium. This work investigates flowing open channels and films, which can potentially make use of the open section of the system as an external interface, before bringing the sample into an enclosed channel. Clearly, in this scenario a key factor is the stability of the flowing open fluid. The open channels investigated include a straight open channel defined by a narrow strip of solid surface, the edges of which allow large contact angle hysteresis, and a wider structure allowing for multiple inputs and outputs. A model is developed for fluid flow, and the findings used to describe the process of failure in both cases.
Strong enhancement of Eu+3 luminescence in europium-implanted GaN by Si and Mg codoping
Authors: Mishra J. K. , Langer T. , Rossow U. , Shvarkov S. , Wieck A. , Hangleiter A.
Published: February 2013

A strong enhancement of Eu3+ luminescence in europium-implanted GaN samples is obtained by codoping with silicon (Si) and magnesium (Mg), simultaneously. The Eu3+ intensity in the 5D0 to 7F2 transition region is found to be 30 times higher compared to europium-implanted undoped GaN. The major contribution to this overall enhancement is due a weak peak present only in europium-implanted Mg-doped GaN at 2.0031 eV (618.9 nm) which is strongly enhanced by codoping both Mg and Si. The excitation process of europium ions is proposed to take place through a donor-acceptor pair related energy transfer mechanism.
Surviving the Turbulent Future
Authors: Amin Ash
Published: February 2013

In neoliberal societies, the future is increasingly being cast as unpredictable and dangerous, reason to fashion new ways of managing hazard and risk. In the process, a culture based on providing comprehensive risk avoidance and protection from an authorised centre is being displaced by one in which the authorities, experts, and publics are expected to work in concert to do the best they can to resist adversity. Two emerging keywords are preparedness and resilience, intended to strengthen the human capacity to anticipate, resist, and recover from adversity. Building on an earlier critique of the neoliberal calculus of risk mitigation, this paper turns to the machinery of urban maintenance and to the trysts of embedded welfare democracy to propose a counterposition. In recognising the entanglements between humans and nonhumans in the management of urban unpredictability and emergency, and also the settlements of social contract between state and citizen in social democracies such as Sweden, the paper both redefines and displaces ideas of risk management through human resilience.
Crops for a future climate
Authors: Gleadow Roslyn , Johnson Alexander , Tausz Michael
Published: February 2013

The papers in this special issue were mainly derived from sessions at the International Botanical Congress in July 2011 in Melbourne, and at the ComBio meeting in Cairns, September 2011. They make contributions towards one of the most burning issues we face today: increasing sustainable crop production to provide sufficient high quality food to feed an ever increasing global human population, all in the face of climate change. Plant and crop science will have a major part in ensuring that agricultural production can meet these multiple demands. Contributions in this volume go beyond raising issues and highlighting potential effects of climate change factors, but also point out ways to better adapt to the inevitable.
Functional consequences of sequence variation in the pheromone biosynthetic gene
pgFAR
for
Ostrinia
moths
Authors: Lassance Jean-Marc , Liénard Marjorie A. , Antony Binu , Qian Shuguang , Fujii Takeshi , Tabata Jun , Ishikawa Yukio , Löfstedt Christer
Published: February 2013

Pheromones are central to the mating systems of a wide range of organisms, and reproductive isolation between closely related species is often achieved by subtle differences in pheromone composition. In insects and moths in particular, the use of structurally similar components in different blend ratios is usually sufficient to impede gene flow between taxa. To date, the genetic changes associated with variation and divergence in pheromone signals remain largely unknown. Using the emerging model system
Ostrinia
, we show the functional consequences of mutations in the protein-coding region of the pheromone biosynthetic fatty-acyl reductase gene
pgFAR
. Heterologous expression confirmed that
pgFAR
orthologs encode enzymes exhibiting different substrate specificities that are the direct consequences of extensive nonsynonymous substitutions. When taking natural ratios of pheromone precursors into account, our data reveal that pgFAR substrate preference provides a good explanation of how species-specific ratios of pheromone components are obtained among
Ostrinia
species. Moreover, our data indicate that positive selection may have promoted the observed accumulation of nonsynonymous amino acid substitutions. Site-directed mutagenesis experiments substantiate the idea that amino acid polymorphisms underlie subtle or drastic changes in pgFAR substrate preference. Altogether, this study identifies the reduction step as a potential source of variation in pheromone signals in the moth genus
Ostrinia
and suggests that selection acting on particular mutations provides a mechanism allowing pheromone reductases to evolve new functional properties that may contribute to variation in the composition of pheromone signals.
Prosodic marking of narrow focus across varieties of South African English
Authors: Zerbian Sabine
Published: February 2013

This paper reports on an elicited production study which investigates prosodic marking of narrow focus in modified noun phrases in varieties of South African English. The acoustic analysis of fundamental frequency, intensity, and duration in narrow focus is presented and discussed. The results suggest that these three acoustic parameters are manipulated differently in narrow focus in the varieties of English as a Second Language as compared to General South African English. The article compares the results to what is known about prosodic marking of information structure in other varieties of English as a Second Language and underlines the necessity of carefully controlled data in the investigation of phonological and phonetic variation in varieties of English.
Quotatives down under
Authors: Rodríguez Louro Celeste
Published: February 2013

The English quotative system (featuring forms such as say, think, zero, go, all and be like used in direct speech reproduction and thought) has been the subject of vigorous, in-depth sociolinguistic investigation, particularly in the past two decades. However, with the notable exception of Winter’s (2002) study of quotative be like in the speech of Melbourne adolescents, the Australian English quotative system remains virtually uncharted. I address this gap in the literature by offering a quantitative sociolinguistic analysis of the quotative system of Perth English, investigating to what extent linguistic (grammatical person, content of quote and tense) and social (age and sex) variables are implicated in the use of be like. My results stem from 32.5 hours (325 096 words) of spontaneous narratives of personal experience recorded with 47 speakers in Perth in 2011 and evince an overwhelming increase in the use of be like particularly amongst the youngest speakers — as compared to Winter’s (2002) findings for Melbourne in the late 1990s. Multivariate analysis using Goldvarb X (Sankoff, Tagliamonte and Smith 2005) indicates that — although some constraints like the favouring effect of first person subjects behave similarly across the generations and are in line with other Englishes — Australian be like is subject to different constraints across generations of young speakers. Pre-adolescent and adolescent girls are active agents of language change by upping be like’s frequency and its use with the historical present in narratives. Young adults are steady users of be like in historical present contexts but the significant effect of sex has reversed: it is young male adults — rather than women — who favour be like in this cohort. The findings are in line with trends noted in the literature on English quotation elsewhere and point once again to the irrevocable link between system-internal forces and social factors as speakers move through life.
Moduli of parabolic connections on curves and the Riemann-Hilbert correspondence
Authors: Inaba Michi-aki
Published: February 2013

Let

(
C
,

t

)

(C,\mathbf {t})

(

t

=
(

t
1

,
…
,

t
n

)

\mathbf {t}=(t_1,\ldots ,t_n)

) be an

n
n

-pointed smooth projective curve of genus

g
g

and take an element

λ
=
(

λ
j

(
i
)

)
∈

C

n
r

\boldsymbol {\lambda }=(\lambda ^{(i)}_j)\in \mathbf {C}^{nr}

such that

−

∑

i
,
j

λ
j

(
i
)

=
d
∈

Z

-\sum _{i,j}\lambda ^{(i)}_j=d\in \mathbf {Z}

. For a weight

α
\boldsymbol {\alpha }

, let

M
C

α

(

t

,
λ
)

M_C^{\boldsymbol {\alpha }}(\mathbf {t},\boldsymbol {\lambda })

be the moduli space of

α
\boldsymbol {\alpha }

-stable

(

t

,
λ
)

(\mathbf {t},\boldsymbol {\lambda })

-parabolic connections on

C
C

and let

R

P
r

(
C
,

t

)

a

RP_r(C,\mathbf {t})_{\mathbf {a}}

be the moduli space of representations of the fundamental group

π
1

(
C
∖
{

t
1

,
…
,

t
n

}
,
∗
)

\pi _1(C\setminus \{t_1,\ldots ,t_n\},*)

with the local monodromy data

a

\mathbf {a}

for a certain

a

∈

C

n
r

\mathbf {a}\in \mathbf {C}^{nr}

. Then we prove that the morphism
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="bold upper R bold upper H colon upper M Subscript upper C Superscript bold-italic alpha Baseline left-parenthesis bold t comma bold-italic lamda right-parenthesis right-arrow upper R upper P Subscript r Baseline left-parenthesis upper C comma bold t right-parenthesis Subscript bold a Baseline">

R
H

:

M
C

α

(

t

,
λ
)
→
R

P
r

(
C
,

t

)

a

\mathbf {RH}:M_C^{\boldsymbol {\alpha }}(\mathbf {t},\boldsymbol {\lambda })\rightarrow RP_r(C,\mathbf {t})_{\mathbf {a}}

determined by the Riemann-Hilbert correspondence is a proper surjective bimeromorphic morphism. As a corollary, we prove the geometric Painlevé property of the isomonodromic deformation defined on the moduli space of parabolic connections.
A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing
Authors: Zhang Yu
Published: February 2013

Motivation: Next-generation sequencing (NGS) technologies have enabled whole-genome discovery and analysis of genetic variants in many species of interest. Individuals are often sequenced at low coverage for detecting novel variants, phasing haplotypes and inferring population structures. Although several tools have been developed for SNP and genotype calling in NGS data, haplotype phasing is often done separately on the called genotypes.

Results: We propose a dynamic Bayesian Markov model (DBM) for simultaneous genotype calling and haplotype phasing in low-coverage NGS data of unrelated individuals. Our method is fully probabilistic that produces consistent inference of genotypes, haplotypes and recombination probabilities. Using data from the 1000 Genomes Project, we demonstrate that DBM not only yields more accurate results than some popular methods, but also provides novel characterization of haplotype structures at the individual level for visualization, interpretation and comparison in downstream analysis. DBM is a powerful and flexible tool that can be applied to many sequencing studies. Its statistical framework can also be extended to accommodate broader scopes of data.

Availability and implementation:  http://stat.psu.edu/∼yuzhang/software/dbm.tar

Contact:  yuzhang@stat.psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Early Exposure to General Anesthesia Disturbs Mitochondrial Fission and Fusion in the Developing Rat Brain
Authors: Boscolo Annalisa , Milanovic Desanka , Starr John A. , Sanchez Victoria , Oklopcic Azra , Moy Laurie , Ori C Carlo , Erisir Alev , Jevtovic-Todorovic Vesna
Published: February 2013

Background:

General anesthetics induce apoptotic neurodegeneration in the developing mammalian brain. General anesthesia (GA) also causes significant disturbances in mitochondrial morphogenesis during intense synaptogenesis. Mitochondria are dynamic organelles that undergo remodeling via fusion and fission. The fine balance between these two opposing processes determines mitochondrial morphometric properties, allowing for their regeneration and enabling normal functioning. As mitochondria are exquisitely sensitive to anesthesia-induced damage, we examined how GA affects mitochondrial fusion/fission.

Methods:

Seven-day-old rat pups received anesthesia containing a sedative dose of midazolam followed by a combined nitrous oxide and isoflurane anesthesia for 6 h.

Results:

GA causes 30% upregulation of reactive oxygen species (n = 3–5 pups/group), accompanied by a 2-fold downregulation of an important scavenging enzyme, superoxide dismutase (n = 6 pups/group). Reactive oxygen species upregulation is associated with impaired mitochondrial fission/fusion balance, leading to excessive mitochondrial fission. The imbalance between fission and fusion is due to acute sequestration of the main fission protein, dynamin-related protein 1, from the cytoplasm to mitochondria, and its oligomerization on the outer mitochondrial membrane. These are necessary steps in the formation of the ring-like structures that are required for mitochondrial fission. The fission is further promoted by GA-induced 40% downregulation of cytosolic mitofusin-2, a protein necessary for maintaining the opposing process, mitochondrial fusion (n = 6 pups/group).

Conclusions:

Early exposure to GA causes acute reactive oxygen species upregulation and disturbs the fine balance between mitochondrial fission and fusion, leading to excessive fission and disturbed mitochondrial morphogenesis. These effects may play a causal role in GA-induced developmental neuroapoptosis.
Importance of Addressing Anxiety in Youth With Functional Abdominal Pain
Authors: Cunningham Natoshia R. , Lynch‐Jordan Anne , Mezoff Adam G. , Farrell Michael K. , Cohen Mitchell B. , Kashikar‐Zuck Susmita
Published: February 2013

Functional abdominal pain (FAP) is a common pediatric disorder associated with impairment in functioning that may persist for the long term. Anxiety is common in youth with FAP, and may be an important factor in predicting youth who are at greatest risk for increased impairment because of pain symptoms. In this article, we examine the relation between anxiety and impairment in youth with FAP. Furthermore, we explore various biopsychosocial factors (eg, neurobiological substrates, coping strategies, social factors) that may be implicated in the relation among FAP, anxiety, and increased impairment. Finally, we propose physician guidelines for screening and treatment of youth with FAP and co‐occurring anxiety. Youth with FAP and co‐occurring anxiety may benefit from cognitive‐behavioral therapy in the context of multidisciplinary care.
A vitamin B
12
transporter in
Mycobacterium tuberculosis
Authors: Gopinath Krishnamoorthy , Venclovas Česlovas , Ioerger Thomas R. , Sacchettini James C. , McKinney John D. , Mizrahi Valerie , Warner Digby F.
Published: February 2013

Vitamin B
12
-dependent enzymes function in core biochemical pathways in
Mycobacterium tuberculosis
, an obligate pathogen whose metabolism
in vivo
is poorly understood. Although
M. tuberculosis
can access vitamin B
12
in vitro
, it is uncertain whether the organism is able to scavenge B
12
during host infection. This question is crucial to predictions of metabolic function, but its resolution is complicated by the absence in the
M. tuberculosis
genome of a direct homologue of BtuFCD, the only bacterial B
12
transport system described to date. We applied genome-wide transposon mutagenesis to identify
M. tuberculosis
mutants defective in their ability to use exogenous B
12
. A small proportion of these mapped to
Rv1314c
, identifying the putative PduO-type ATP : co(I)rrinoid adenosyltransferase as essential for B
12
assimilation. Most notably, however, insertions in
Rv1819c
dominated the mutant pool, revealing an unexpected function in B
12
acquisition for an ATP-binding cassette (ABC)-type protein previously investigated as the mycobacterial BacA homologue. Moreover, targeted deletion of
Rv1819c
eliminated the ability of
M. tuberculosis
to transport B
12
and related corrinoids
in vitro
. Our results establish an alternative to the canonical BtuCD-type system for B
12
uptake in
M. tuberculosis
, and elucidate a role in B
12
metabolism for an ABC protein implicated in chronic mycobacterial infection.