bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructure, transport, and acoustic properties of open-cell foam samples: Experiments and three-dimensional numerical simulations
Authors: Perrot Camille , Chevillotte Fabien , Tan Hoang Minh , Bonnet Guy , Bécot François-Xavier , Gautron Laurent , Duval Arnaud
Published: January 2012

This article explores the applicability of numerical homogenization techniques for analyzing transport properties in real foam samples, mostly open-cell, to understand long-wavelength acoustics of rigid-frame air-saturated porous media on the basis of microstructural parameters. Experimental characterization of porosity and permeability of real foam samples are used to provide the scaling of a polyhedral unit-cell. The Stokes, Laplace, and diffusion-controlled reaction equations are numerically solved in such media by a finite element method in three-dimensions; an estimation of the materials’ transport parameters is derived from these solution fields. The frequency-dependent visco-inertial and thermal response functions governing the long-wavelength acoustic wave propagation in rigid-frame porous materials are then determined from generic approximate but robust models and compared to standing wave tube measurements. With no adjustable constant, the predicted quantities were found to be in acceptable agreement with multi-scale experimental data and further analyzed in light of scanning electron micrograph observations and critical path considerations.
Study of thermal and acoustic noise interferences in low stiffness atomic force microscope cantilevers and characterization of their dynamic properties
Authors: Boudaoud Mokrane , Haddab Yassine , Le Gorrec Yann , Lutz Philippe
Published: January 2012

The atomic force microscope (AFM) is a powerful tool for the measurement of forces at the micro/nano scale when calibrated cantilevers are used. Besides many existing calibration techniques, the thermal calibration is one of the simplest and fastest methods for the dynamic characterization of an AFM cantilever. This method is efficient provided that the Brownian motion (thermal noise) is the most important source of excitation during the calibration process. Otherwise, the value of spring constant is underestimated. This paper investigates noise interference ranges in low stiffness AFM cantilevers taking into account thermal fluctuations and acoustic pressures as two main sources of noise. As a result, a preliminary knowledge about the conditions in which thermal fluctuations and acoustic pressures have closely the same effect on the AFM cantilever (noise interference) is provided with both theoretical and experimental arguments. Consequently, beyond the noise interference range, commercial low stiffness AFM cantilevers are calibrated in two ways: using the thermal noise (in a wide temperature range) and acoustic pressures generated by a loudspeaker. We then demonstrate that acoustic noises can also be used for an efficient characterization and calibration of low stiffness AFM cantilevers. The accuracy of the acoustic characterization is evaluated by comparison with results from the thermal calibration.
Saddle-point solutions and grazing bifurcations in an impacting system
Authors: Mason Joanna F. , Piiroinen Petri T.
Published: January 2012

This paper focuses on the intricate relationship between smooth and nonsmooth phenomena in an impacting system. In particular a boundary saddle-point solution, that is born in a nonsmooth fold, is analysed. Accessible boundary saddle-point solutions play a key role in determining the global dynamics of a system and here we will show how grazing bifurcations can affect their existence.
The Biot-Savart operator and electrodynamics on subdomains of the three-sphere
Authors: Parsley Jason
Published: January 2012

We study steady-state magnetic fields in the geometric setting of positive curvature on subdomains of the three-dimensional sphere. By generalizing the Biot-Savart law to an integral operator BS acting on all vector fields, we show that electrodynamics in such a setting behaves rather similarly to Euclidean electrodynamics. For instance, for current J and magnetic field BS(J), we show that Maxwell's equations naturally hold. In all instances, the formulas we give are geometrically meaningful: they are preserved by orientation-preserving isometries of the three-sphere. This article describes several properties of BS: we show it is self-adjoint, bounded, and extends to a compact operator on a Hilbert space. For vector fields that act like currents, we prove the curl operator is a left inverse to BS; thus, the Biot-Savart operator is important in the study of curl eigenvalues, with applications to energy-minimization problems in geometry and physics. We conclude with two examples, which indicate our bounds are typically within an order of magnitude of being sharp.
Vortex dynamics in $\mathbb {R}^4$R4
Authors: Shashikanth Banavara N.
Published: January 2012

The vortex dynamics of Euler's equations for a constant density fluid flow in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^4$\end{document}R4 is studied. Most of the paper focuses on singular Dirac delta distributions of the vorticity two-form ω in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^4$\end{document}R4. These distributions are supported on two-dimensional surfaces termed membranes and are the analogs of vortex filaments in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3$\end{document}R3 and point vortices in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^2$\end{document}R2. The self-induced velocity field of a membrane is shown to be unbounded and is regularized using a local induction approximation. The regularized self-induced velocity field is then shown to be proportional to the mean curvature vector field of the membrane but rotated by 90° in the plane of normals. Next, the Hamiltonian membrane model is presented. The symplectic structure for this model is derived from a general formula for vorticity distributions due to Marsden and Weinstein [“Coadjoint orbits, vortices and Clebsch variables for incompressible fluids,” Physica D 7, 305–323 (1983)10.1016/0167-2789(83)90134-3]. Finally, the dynamics of the four-form ω ∧ ω is examined. It is shown that Ertel's vorticity theorem in \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^3$\end{document}R3, for the constant density case, can be viewed as a special case of the dynamics of this four-form.
Anisotropy of free-carrier absorption and diffusivity in m-plane GaN
Authors: Ščajev P. , Jarašiūnas K. , Özgür Ü. , Morkoç H. , Leach J. , Paskova T.
Published: January 2012

Polarization-dependent free-carrier absorption (FCA) in bulk m-plane GaN at 1053 nm revealed approximately 6 times stronger hole-related absorption for E⊥c than for E||c probe polarization both at low and high carrier injection levels. In contrast, FCA at 527 nm was found isotropic at low injection levels due to electron resonant transitions between the upper and lower conduction bands, whereas the anisotropic impact of holes was present only at high injection levels by temporarily blocking electron transitions. Carrier transport was also found to be anisotropic under two-photon excitation, with a ratio of 1.17 for diffusivity perpendicular and parallel to the c-axis.
Intermolecular torsional motion of a π-aggregated dimer probed by two-dimensional electronic spectroscopy
Authors: Seibt Joachim , Eisfeld Alexander
Published: January 2012

The energetic splitting of the two exciton states of a molecular dimer depends strongly on the relative orientation of the monomers with respect to each other. The curvature of the corresponding adiabatic potential energy surfaces can lead to torsional motion of the monomers. It has been suggested recently that this torsional motion could provide a possible relaxation mechanism for the upper state which proceeds via a crossing of the two singly excited state potentials. Another, competing, relaxation mechanism is provided by coupling to the environment, leading to direct exciton relaxation. Here we examine theoretically the combined dynamics of torsional motion and excitonic relaxation for a π-aggregated dimer. Using two-dimensional (2D) spectroscopy, it is shown how torsional motion through a crossing of the adiabatic excitonic potential surfaces could be distinguished from direct relaxation. For the calculations a mixed quantum/classical approach is used, where the torsional motion is treated by an Ehrenfest type of equation, while the excitonic dynamics including dephasing and direct relaxation is described by a quantum master equation.
Theoretical study of photodetachment processes of anionic boron clusters. I. Structure
Authors: Rajagopala Reddy S. , Mahapatra S.
Published: January 2012

Photo-induced electron detachment spectroscopy of anionic boron clusters, \documentclass[12pt]{minimal}\begin{document}${\rm B}_4^{-}$\end{document}B4− and \documentclass[12pt]{minimal}\begin{document}${\rm B}_5^{-}$\end{document}B5−, is theoretically investigated by performing electronic structure calculations and nuclear dynamics simulations. While the electronic potential energy surfaces (\documentclass[12pt]{minimal}\begin{document}$\widetilde{X}^1A_{g}$\end{document}X̃1Ag, \documentclass[12pt]{minimal}\begin{document}$\widetilde{a}^3B_{2u}$\end{document}ã3B2u, \documentclass[12pt]{minimal}\begin{document}$\widetilde{b}^3B_{1u}$\end{document}b̃3B1u, \documentclass[12pt]{minimal}\begin{document}$\widetilde{A}^1B_{2u}$\end{document}Ã1B2u, \documentclass[12pt]{minimal}\begin{document}$\widetilde{c}^3B_{2g}$\end{document}c̃3B2g, and \documentclass[12pt]{minimal}\begin{document}$\widetilde{B}^1B_{2g}$\end{document}B̃1B2g of neutral B4 and \documentclass[12pt]{minimal}\begin{document}$\widetilde{X}^2B_2$\end{document}X̃2B2, \documentclass[12pt]{minimal}\begin{document}$\widetilde{A}^2A_1$\end{document}Ã2A1, \documentclass[12pt]{minimal}\begin{document}$\widetilde{B}^2B_2$\end{document}B̃2B2, \documentclass[12pt]{minimal}\begin{document}$\widetilde{C}^2A_1$\end{document}C̃2A1, \documentclass[12pt]{minimal}\begin{document}$\widetilde{D}^2B_1$\end{document}D̃2B1, and \documentclass[12pt]{minimal}\begin{document}$\widetilde{E}^2A_1$\end{document}Ẽ2A1 of neutral B5) and their coupling surfaces are constructed in this paper, the details of the nuclear dynamics on these electronic states are presented in Paper II. Electronic structure calculations are carried out at the complete active space self-consistent field – multi-reference configuration interaction level of theory employing the correlation consistent polarized valance triple zeta basis set. Using the calculated electronic structure data suitable vibronic Hamiltonians are constructed utilizing a diabatic electronic basis and displacement coordinates of the normal vibrational modes. The theoretical results are discussed in relation to those recorded in recent experiments.
Theoretical study of photodetachment processes of anionic boron clusters. II. Dynamics
Authors: Reddy S. Rajagopala , Mahapatra S.
Published: January 2012

Photodetachment bands of anionic boron clusters, Bn (n = 4,5) are theoretically examined here. The model Hamiltonians developed through extensive ab initio quantum chemistry calculations in Paper I are employed for the required nuclear dynamics study. While the precise location of vibronic lines and progression of vibrational modes within a given electronic band is derived from time-independent quantum mechanical studies, the broadband spectral envelopes and the nonradiative decay rate of electronic states are calculated by propagating wave packets in a time-dependent quantum mechanical framework. The theoretical results are in good accord with the experiment to a large extent. The discrepancies between the two can be partly attributed to the inadequate energy resolution of the experimental results and also to the neglect of dynamic spin-orbit interactions and computational difficulty related with detachment channels involving multi-electron transitions in the theoretical formalism.
Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method
Authors: Dora Amar , Bryjko Lilianna , van Mourik Tanja , Tennyson Jonathan
Published: January 2012

R-matrix calculations on electron collisions with the purine bases found in DNA and RNA (i.e., adenine and guanine) are presented. Resonant anion states of these systems are identified by employing different approximation levels of ab initio theoretical methods, such as the static exchange, the static exchange plus polarization, and the close-coupling methods. The results are compared with other available calculations and experiments. All of these ab initio approximations, which we refer to as a scattering “model,” give four shape resonances of 2A′′ (π) symmetry within the energy range of 10 eV for both molecules. For adenine, the most sophisticated method, the close-coupling model, gives two very narrow 2A′ (σ) symmetry Feshbach-type resonances at energies above 5 eV. Quantitative results for the total elastic and electronic excitation cross sections are also presented.
Quantum-Hall plateau−plateau transition in top-gated epitaxial graphene grown on SiC (0001)
Authors: Shen T. , Neal A. T. , Bolen M. L. , Gu J. J. , Engel L. W. , Capano M. A. , Ye P. D.
Published: January 2012

We investigate the low-temperature magneto-transport properties of monolayer epitaxial graphene films formed on the Si-face of semi-insulating 4 H−SiC substrates by a high-temperature sublimation process. A high-k top-gate on the epitaxial graphene is realized by inserting a fully oxidized nanometer-thin aluminum film as a seeding layer, followed by an atomic layer deposition process. At low temperatures, the devices demonstrate a strong field effect by the top gate with an on/off ratio of ∼7 and an electron mobility up to ∼3250 cm2/Vs. After the observation of the half-integer quantum-Hall effect for monolayer epitaxial graphene films, detailed magneto-transport measurements have been carried out including varying densities, temperatures, magnetic fields, and currents. We study the width of the distinguishable quantum-Hall plateau to plateau transition (Landau level index n = 0 to n = 1) as temperature (T) and current are varied. For both gate voltage and magnetic field sweeps and T > 10 K, the transition width goes as T−κ with exponent k ∼ 0.42. This universal scaling exponent agrees well with those found in III−V heterojunctions with short-range alloy disorders and in exfoliated graphene.
Electrochemical strain microscopy with blocking electrodes: The role of electromigration and diffusion
Authors: Morozovska A. N. , Eliseev E. A. , Kalinin S. V.
Published: January 2012

Electrochemical strains are a ubiquitous feature of solid state ionic devices ranging from ion batteries and fuel cells to electroresistive and memristive memories. Recently, we proposed a scanning probe microscopy (SPM) based approach, referred as electrochemical strain microscopy (ESM), for probing local ionic flows and electrochemical reactions in solids based on bias-strain coupling. In ESM, the sharp SPM tip concentrates the electric field in a small (10–50 nm) region of material, inducing interfacial electrochemical processes and ionic flows. The resultant electrochemical strains are determined from dynamic surface displacement and provide information on local electrochemical functionality. Here, we analyze image formation mechanism in ESM for a special case of mixed electronic-ionic conductor with blocking tip electrode, and determine frequency dependence of response, role of diffusion and electromigration effects, and resolution and detection limits.
Freezing lines of colloidal Yukawa spheres. I. A Rogers-Young integral equation study
Authors: Gapinski Jacek , Nägele Gerhard , Patkowski Adam
Published: January 2012

Using the Rogers-Young (RY) integral equation scheme for the static structure factor combined with the one-phase Hansen-Verlet (HV) freezing rule, we study the equilibrium structure and two-parameter freezing lines of colloidal particles with Yukawa-type pair interactions representing charge-stabilized silica spheres suspended in dimethylformamide (DMF). Results are presented for a vast range of concentrations, salinities and effective charges covering particles with masked excluded-volume interactions. The freezing lines were obtained for the low-charge and high-charge solutions of the static structure factor, for various two-parameter sets of experimentally accessible system parameters. All RY-HV based freezing lines can be mapped on a universal fluid-solid coexistence line in good agreement with computer simulation predictions. The RY-HV calculations extend the freezing lines obtained in earlier simulations to a broader parameter range. The experimentally observed fluid-bcc-fluid reentrant transition of charged silica spheres in DMF can be explained using the freezing lines obtained in this work.
Nonspherical model density matrices for Rung 3.5 density functionals
Authors: Janesko Benjamin G. , Aguero Austin
Published: January 2012

“Rung 3.5” exchange-correlation functionals for Kohn-Sham density functional theory depend linearly on the nonlocal one-particle density matrix of the noninteracting Kohn-Sham reference system. Rung 3.5 functionals also require a semilocal model for the one-particle density matrix. This work presents new model density matrices for Rung 3.5 functionals. The resulting functionals give reasonable predictions for total energies, molecular thermochemistry and kinetics, odd-electron bonds, and conjugated polymer bandgaps. Global-hybrid-like combinations of semilocal and Rung 3.5 exchange, and empirical density matrix models, also show promise.
Phonon-mediated path-interference in electronic energy transfer
Authors: Hossein-Nejad Hoda , Olaya-Castro Alexandra , Scholes Gregory D.
Published: January 2012

We present a formalism to quantify the contribution of path-interference in phonon-mediated electronic energy transfer. The transfer rate between two molecules is computed by considering the quantum mechanical amplitudes associated with pathways connecting the initial and final sites. This includes contributions from classical pathways, but also terms arising from interference of different pathways. We treat the vibrational modes coupled to the molecules as a non-Markovian harmonic oscillator bath, and investigate the correction to transfer rates due to the lowest-order interference contribution. We show that depending on the structure of the harmonic bath, the correction due to path-interference may have a dominant vibrational or electronic character, and can make a notable contribution to the transfer rate in the steady state.
Reference molecules for nonlinear optics: A joint experimental and theoretical investigation
Authors: Castet Frédéric , Bogdan Elena , Plaquet Aurélie , Ducasse Laurent , Champagne Benoît , Rodriguez Vincent
Published: January 2012

Hyper-Rayleigh scattering (HRS) experiments and quantum chemical calculations are combined to investigate the second-order nonlinear optical responses of a series of reference molecules, namely, carbon tetrachloride, chloroform, trichloroacetonitrile, acetonitrile, and dichloromethane. The multipolar decomposition of the first hyperpolarizability tensor through the use of the spherical harmonics formalism is employed to highlight the impact of the symmetry of the molecular scatterers on their nonlinear optical responses. It is demonstrated that HRS is a technique of choice to probe the molecular symmetry of the compounds. Coupled-cluster calculations performed at the coupled-cluster level with singles, doubles, and perturbative triples in combination with highly extended basis sets and including environment effects by using the polarizable continuum model qualitatively reproduce the molecular first hyperpolarizabilities and depolarization ratios of the molecular scatterers.
Note: Molecular dynamics studies of high-density amorphous ice: Influence of long-range Coulomb interactions
Authors: Seidl Markus , Karsai Ferenc , Loerting Thomas , Zifferer Gerhard
Published: January 2012

Making use of isothermal-isobaric molecular dynamics high-density amorphous ice is simulated at a pressure of 0.3 GPa. Heating/cooling cycles are performed in the temperature range 80 K–300 K. Analysis of quantities like density, total energy, and mobility give clear evidence for a glass-to-liquid transition. However, raw data as well as the observed glass transition temperatures Tg are not only dependent on the force field used but in addition on the treatment of Coulomb interactions (group based cut-off or long-range terms by Ewald summation). Nevertheless, all models indicate that high-density amorphous ices may indeed be low-temperature proxies of ultraviscous high-density liquids.
Coaxing graphene to be piezoelectric
Authors: Chandratre Swapnil , Sharma Pradeep
Published: January 2012

Several exotic characteristics and properties have made graphene a well-studied material from both a basic science viewpoint as well as tantalizing applications ranging from nanoelectronics, gas separation membranes to ultracapacitors. Graphene, however, is non-piezoelectric. This is obvious when graphene is in its metallic or semi-metallic state. However, even when graphene is in dielectric form—which can be engineered through porosity or by using nanoribbons—graphene is non-piezoelectric due to its centrosymmetric crystal structure. Using quantum mechanical calculations, we show that merely by creating holes of the right symmetry, graphene can be coaxed to act as a piezoelectric. We find that certain specifically tailored porous graphene sheets can “acquire” piezoelectricity coefficient that is nearly 72% of the well-known piezoelectric (quartz) or 36% of boron nitride nanotubes.
Quantum dynamics of proton migration in H2O dications: H2+ formation on ultrafast timescales
Authors: Garg Manish , Tiwari Ashwani K. , Mathur Deepak
Published: January 2012

Irradiation of isolated water molecules by few-cycle pulses of intense infrared laser light can give rise to ultrafast rearrangement resulting in formation of the H2+ ion. Such unimolecular reactions occur on the potential energy surface of the H2O2+ dication that is accessed when peak laser intensities in the 1015 W cm−2 range and pulse durations as short as 9–10 fs are used; ion yields of ∼1.5% relative to the H2O+ ion are measured. We also study such reactions by means of time-dependent wavepacket dynamics on an ab initio potential energy surface of the dication and show that a proton, generated from O–H bond rupture, migrates towards the H-atom, and forms vibrationally excited H2+ in a well-defined spatial zone.
Photon recycling effect on electroluminescent refrigeration
Authors: Lee Kuan-Chen , Yen Shun-Tung
Published: January 2012

We study electroluminescent refrigeration in an AlGaAs/GaAs double heterostructure by a self-consistent calculation with photon recycling considered. To gain insight, we investigate the influence of the recycling on the carrier density and the current components due to various recombination mechanisms in the device under different bias voltages. The photon recycling is a feedback process, which behaves as an internal source of generating electron-hole pairs in the active region and causes an effective feedback current to compensate the driving current from the external source. Consequently, it reduces the driving current, improves the external quantum efficiency, and loosens the requirement on the photon extraction efficiency for refrigeration. For the device with a 1 μm GaAs active layer operating at 300 K, the minimum required extraction efficiency is less than 20% if the trapped photons are completely recycled and remains a feasible value of 45% if the recycling efficiency is 90%, which is not difficult to achieve. In addition, photon recycling eases the problem of the drastic deterioration of the cooling power and the external efficiency as the extraction efficiency reduces. These results reveal a good possibility of realizing electroluminescent refrigeration in semiconductors.
A theoretical investigation on photocatalytic oxidation on the TiO2 surface
Authors: Suzuki Satoshi , Tsuneda Takao , Hirao Kimihiko
Published: January 2012

The TiO2 photocatalytic oxidation mechanism was theoretically investigated by using long-range corrected time-dependent density functional theory (LC-TDDFT) with a cluster model of the anatase TiO2(001) surface. We found that LC-TDDFT with the cluster model quantitatively reproduces the photoexcitations of the TiO2 surface by calculating the electronic spectra of a clean TiO2 surface and one with oxygen defects. We calculated the electronic spectra of a molecularly adsorbed TiO2 surface for the adsorptions of phenol, methanol, and methane molecules as typical organic molecules. We obtained the surprising result that the main peak of the phenol-adsorbed TiO2 surface, which overlaps with the main peak of the clean TiO2 surface, corresponds to charge transfers from the phenol molecule to the TiO2 surface. This indicates that the TiO2 photocatalytic oxidation proceeds through direct charge transfer excitation from the substrate molecules to the TiO2 surface. In contrast, we found slight and no charge transfer for methanol and methane adsorption, respectively, in agreement with the experimental findings for their reactivities. In light of these results, we propose a new mechanism for heterogeneous TiO2 photocatalytic oxidations.
Direct evidence of type II band alignment in ZnO nanorods/poly(3-hexylthiophene) heterostructures
Authors: Chan M. H. , Chen J. Y. , Lin T. Y. , Chen Y. F.
Published: January 2012

The emission from ZnO nanorods/poly(3-hexylthiophene) (P3HT) heterostructures with type II band alignment has been investigated. The additional emission due to the formation of the heterojunction around 950 nm has been found and attributed to the type II transition related to the recombination of electrons in conduction band of ZnO and holes in highest occupied molecular orbital band of P3HT. The consistency of excitation power density dependent photoluminescence (PL) spectra with the theoretical prediction offers a firm evidences for the type II transition. In addition, lifetime of P3HT measured by time-resolved PL also strongly supports that the infrared light indeed arises from the type II transition. Our results shown here provide the first direct evidence of the type II band alignment in ZnO nanorods/P3HT heterostructure, which should be very useful for the realization of underpinned mechanism of the developed optoelectronic devices.
Single-photon emitters based on epitaxial isolated InP/InGaP quantum dots
Authors: Ugur Asli , Kremling Stefan , Hatami Fariba , Höfling Sven , Worschech Lukas , Forchel Alfred , Ted Masselink W.
Published: January 2012

Quantum dots as single-photon sources have several advantages, such as emitting light over a broad spectral range and being photostable. Quantum dots with densities as low as 1 dot/μm2 have been achieved using ultra-low-rate epitaxy and single-dot emission measured without apertures or post-growth processing. Both excitionic and biexcitonic emissions are observed from single dots created in this way, appearing as doublets with a fine-structure splitting of 320 μeV. The polarization of the split states is also investigated. Hanbury Brown-Twiss correlation measurements for the excitonic emission under cw excitation show anti-bunching behavior with an autocorrelation value of g(2)(0) = 0.2.
Metalorganic chemical vapor deposition of N-polar GaN films on vicinal SiC substrates using indium surfactants
Authors: Won Dongjin , Weng Xiaojun , Redwing Joan M.
Published: January 2012

The effect of indium surfactants on the growth of N-polar GaN films on vicinal C-face SiC substrates by metalorganic chemical vapor deposition was investigated. Triangular hillocks formed on the surface of N-polar GaN without indium, resulting in a rough surface. When indium surfactants were introduced during GaN growth, the surface roughness was reduced from 18.1 to 3.5 nm over a 20 × 20 μm2 area. The photoluminescence characteristics of N-polar GaN film were also improved because of a reduction of carbon caused by the presence of indium, demonstrating that indium is a useful surfactant in the growth of N-polar GaN.
Top-gate thin-film transistors based on GaN channel layer
Authors: Chen Rongsheng , Zhou Wei , Sing Kwok Hoi
Published: January 2012

Gallium nitride (GaN) thin films were utilized as active channel layer to produce top-gate n-type thin-film transistors (TFTs). GaN thin films with wurtzite structure were deposited by reactive DC magnetron sputtering technique at room temperature using liquid gallium target. The GaN TFTs exhibit good electrical performance such as field effect mobility of 1 cm2/Vs, threshold voltage of −0.4 V, on/off current ratio of 105, and subthreshold swing of 0.8 V/decade.
Reduced leakage current, enhanced ferroelectric and dielectric properties in (Ce,Fe)-codoped Na0.5Bi0.5TiO3 film
Authors: Yang C. H. , Hu G. D. , Wu W. B. , Wu H. T , Yang F. , Lu Z. Y. , Wang L.
Published: January 2012

Na0.5Bi0.5TiO3 (NBT), Ce-doped NBT (NBTCe), Fe-doped NBT (NBTFe), and (Ce,Fe)-codoped NBT (NBTCeFe) thin films were fabricated on LaNiO3(100)/Si substrates by metal organic decomposition. The leakage current density of NBTCeFe at 500 kV/cm is reduced by approximately two orders of magnitude by reducing the density of oxygen vacancies and forming the defect complexes, compared with NBT film. Enhanced ferroelectricity is achieved in NBTCeFe with a large remanent polarization of 24 μC/cm2 due to the reduced leakage current, extra A-site vacancies, and lattice distortion. The NBTCeFe also exhibits a dielectric constant of 585 and dielectric loss of 0.05 at 10 kHz.
Ohmic contacts to n-type germanium with low specific contact resistivity
Authors: Gallacher K. , Velha P. , Paul D. J. , MacLaren I. , Myronov M. , Leadley D. R.
Published: January 2012

A low temperature nickel process has been developed that produces Ohmic contacts to n-type germanium with specific contact resistivities down to (2.3 ± 1.8) × 10−7 Ω-cm2 for anneal temperatures of 340 °C. The low contact resistivity is attributed to the low resistivity NiGe phase which was identified using electron diffraction in a transmission electron microscope. Electrical results indicate that the linear Ohmic behaviour of the contact is attributed to quantum mechanical tunnelling through the Schottky barrier formed between the NiGe alloy and the heavily doped n-Ge.
Study on erosion mechanism of graphite electrode in two-electrode spark gap switch
Authors: Zeng Han , Lin Fuchang , Cai Li , Li Lee , Zhou Zhengyang , Qi Xiangdong
Published: January 2012

In a high-powered single pulse system, the graphite electrode is better than other common metal electrodes for high energy transfer and pulse discharge. In this paper, the erosion mechanism of graphite electrode is investigated with the thermodynamics theory and the experimental results. Based on a simplified mathematical model, the graphite electrode erosion process of high-powered spark gap switch is also analyzed. The analysis results show that the relationship of the graphite electrode erosion and the charge transfer is linear, which is accordant with the experimental results.
Charge transport in dual-gate organic field-effect transistors
Authors: Brondijk J. J. , Spijkman M. , Torricelli F. , Blom P. W. M. , de Leeuw D. M.
Published: January 2012

The charge carrier distribution in dual-gate field-effect transistors is investigated as a function of semiconductor thickness. A good agreement with 2-dimensional numerically calculated transfer curves is obtained. For semiconductor thicknesses larger than the accumulation width, two spatially separated channels are formed. The cross-over from accumulation into depletion of the two channels in combination with a carrier density dependent mobility causes a shoulder in the transfer characteristics. A semiconducting monolayer has only a single channel. The charge carrier density, and consequently the mobility, are virtually constant and change monotonically with applied gate biases, leading to transfer curves without a shoulder.
Suppressing RF breakdown of powerful backward wave oscillator by field redistribution
Authors: Song W. , Sun J. , Song Z. M. , Chen C. H. , Shao H. , Zhang Y. C.
Published: January 2012

An over mode method for suppressing the RF breakdown on metal surface of resonant reflector cavity in powerful backward wave oscillator is investigated. It is found that the electric field is redistributed and electron emission is restrained with an over longitudinal mode cavity. Compared with the general device, a frequency band of about 5 times wider and a power capacity of at least 1.7 times greater are obtained. The results were verified in an X-band high power microwave generation experiment with the output power near 4 gigawatt.
Effect of annealing on the temperature-dependent dielectric properties of LaAlO3 at terahertz frequencies
Authors: Zou Xingquan , He Mi , Springer Daniel , Lee Dongwook , Nair Saritha K. , Ann Cheong Siew , Wu Tom , Panagopoulos C. , Talbayev D. , Chia Elbert E. M.
Published: January 2012

We present THz conductivity of LaAlO3 (LAO) as a function of temperature and annealing, using terahertz time-domain spectroscopy (THz-TDS). We observed that, after annealing, spectral weight redistribution occurs, such that the real conductivity σ1(ω) changed from a featureless and almost frequency-independent spectrum, into one where peaks occur near the phonon frequencies. These phonon frequencies increase with increasing temperature. We attribute the appearance of these absorption peaks to the diffusion and relocation of oxygen vacancies. The dielectric functions of annealed LAO are well fitted with the Drude-Lorentz model.
Determinants of Producers' Participation in Agricultural Cooperatives: Evidence from Northern China
Authors: Zheng Shi , Wang Zhigang , Awokuse Titus O.
Published: January 2012

Agricultural producer cooperatives are of great significance to the development of agricultural productivity and can provide improved economic welfare benefits to farmers. However, such organizations have not been well‐developed in China. While China's new Cooperatives Law of 2007 has generated interest among scholars, very few empirical analyses have focused on the role of cooperatives in China's agricultural sector. The main objective of this study is to investigate the determinants of farmers' perception and their decision to participate in cooperatives, using a unique dataset from recently collected survey data of farming households in China's Jilin Province. The empirical results from probit and logit regression models suggest that educational attainment, risk comfort level, farm expansion, operational costs, geographic location and crop types are significant factors that influence producers' perception of cooperatives, as well as their participation behavior.
Robust rank aggregation for gene list integration and meta-analysis
Authors: Kolde Raivo , Laur Sven , Adler Priit , Vilo Jaak
Published: January 2012

Motivation: The continued progress in developing technological platforms, availability of many published experimental datasets, as well as different statistical methods to analyze those data have allowed approaching the same research question using various methods simultaneously. To get the best out of all these alternatives, we need to integrate their results in an unbiased manner. Prioritized gene lists are a common result presentation method in genomic data analysis applications. Thus, the rank aggregation methods can become a useful and general solution for the integration task.

Results: Standard rank aggregation methods are often ill-suited for biological settings where the gene lists are inherently noisy. As a remedy, we propose a novel robust rank aggregation (RRA) method. Our method detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene. The underlying probabilistic model makes the algorithm parameter free and robust to outliers, noise and errors. Significance scores also provide a rigorous way to keep only the statistically relevant genes in the final list. These properties make our approach robust and compelling for many settings.

Availability: All the methods are implemented as a GNU R package RobustRankAggreg, freely available at the Comprehensive R Archive Network http://cran.r-project.org/.

Contact:  vilo@ut.ee

Supplementary information  Supplementary data are available at Bioinformatics online.
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins
Authors: Hayat Sikander , Elofsson Arne
Published: January 2012

Motivation: Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important.

Results: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task.

Availability: BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/. The datasets used for training and evaluations are also available from this site.

Contact:  arne@bioinfo.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Roundup 2.0: enabling comparative genomics for over 1800 genomes
Authors: DeLuca Todd F. , Cui Jike , Jung Jae-Yoon , St. Gabriel Kristian Che , Wall Dennis P.
Published: January 2012

Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available.

Availability:  http://roundup.hms.harvard.edu

Contact:  dpwall@hms.harvard.edu; todd_deluca@hms.harvard.edu
nEASE: a method for gene ontology subclassification of high-throughput gene expression data
Authors: Chittenden Thomas W. , Howe Eleanor A. , Taylor Jennifer M. , Mar Jessica C. , Aryee Martin J. , Gómez Harold , Sultana Razvan , Braisted John , Nair Sarita J. , Quackenbush John , Holmes Chris
Published: January 2012

Summary: High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline.

Availability: nEASE is implemented within the Multiple Experiment Viewer software package available at http://www.tm4.org/mev.

Contact:  cholmes@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mining and evaluation of molecular relationships in literature
Authors: Senger Christian , Grüning Björn A. , Erxleben Anika , Döring Kersten , Patel Hitesh , Flemming Stephan , Merfort Irmgard , Günther Stefan
Published: January 2012

Motivation: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.

Results:  prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise ‘heat-maps’ and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug–protein relationships showed that up to 69% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific.

Availability: The web-application is available at http://prolific.pharmaceutical-bioinformatics.de and a web service at http://www.pharmaceutical-bioinformatics.de/prolific/soap/prolific.wsdl.

Contact:  stefan.guenther@pharmazie.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Application of canonical correlation analysis for identifying viral integration preferences
Authors: Gumus Ergun , Kursun Olcay , Sertbas Ahmet , Ustek Duran
Published: January 2012

Motivation: Gene therapy aims at using viral vectors for attaching helpful genetic code to target genes. Therefore, it is of great importance to develop methods that can discover significant patterns around viral integration sites. Canonical correlation analysis is an unsupervised statistical tool that is used to describe the relations between two related views of the same semantic object, which fits well for identifying such salient patterns.

Results: Proposed method is demonstrated on a sequence dataset obtained from a study on HIV-1 preferred integration regions. The subsequences on the left and right sides of the integration points are given to the method as the two views, and statistically significant relations are found between sequence-driven features derived from these two views, which suggest that the viral preference must be the factor responsible for this correlation. We found that there are significant correlations at x=5 indicating a palindromic behavior surrounding the viral integration site, which complies with the previously reported results.

Availability: Developed software tool is available at http://ce.istanbul.edu.tr/bioinformatics/hiv1/

Contact:  egumus@istanbul.edu.tr
Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems
Authors: Shackell Nancy L. , Bundy Alida , Nye Janet A. , Link Jason S.
Published: January 2012

Shackell, N. L., Bundy, A., Nye, J. A., and Link, J. S. 2012. Common large-scale responses to climate and fishing across Northwest Atlantic ecosystems. – ICES Journal of Marine Science, 69: 151–152. Investigating whether there were common biological responses to climate and fishing across seven Northwest Atlantic ecosystems, a minimum/maximum autocorrelation factor analysis of biological indicators for each region revealed a common primary multivariate trend of a rapid change during the 1980s and early 1990s. There was a strong common pattern in the biological indicators responsible for the primary multivariate temporal trend in the five more northerly regions: an increase in the abundance of phytoplankton, an increase in biomass at mid-trophic levels, and a decline in predatory groundfish size. The common associations between patterns and drivers were fishing indices and the Atlantic Multidecadal Oscillation, but all associations weakened when co-varying drivers were held constant. The results are consistent with known long-term effects of intense fishing, such as a decline in average fish size and changes in species composition. Less fishing pressure has allowed some regions to recover to former predatory biomass levels since the late 1990s, but the bulk of the biomass consists of fewer species. However, fishing was not the only driver, and a more mechanistic understanding of how the climate affects lower trophic levels is needed to contextualize climate effects in heavily fished ecosystems.
Evaluation of Risk Factors for Bleeding After Liver Biopsy in Children
Authors: Westheim Birgitte H. , Østensen Anniken B. , Aagenæs Ingegerd , Sanengen Truls , Almaas Runar
Published: January 2012

Objectives:

Acetylsalicylic acid is used in liver‐transplanted children to prevent thrombosis of the hepatic artery. We evaluated whether acetylsalicylic acid and other risk factors were associated with bleeding after percutaneous liver biopsy.

Methods:

Medical charts, laboratory results, imaging studies, and anesthesia charts of 275 ultrasound‐guided liver biopsy procedures in 190 children were reviewed. A total of 178 biopsies were performed on native livers and 97 on transplanted livers.

Results:

Three major and 28 minor bleeding incidents were found. The mortality rate was 0%. Acetylsalicylic acid had been given the last 5 days before 55 of the biopsy procedures and no increased risk of bleeding was found (odds ratio 0.96 [0.37–2.26]; P = 1.00). Low‐molecular‐weight heparin and biopsies from focal lesions were risk factors for bleeding complications. Acute liver failure was associated with increased risk for major complications (odds ratio 26.1 [3.3–205]; P = 0.01) and was a risk factor for major bleeding. Postbiopsy ultrasound the day after the procedure (n = 266 [96% of 275 biopsies]) revealed minor bleeding after 7.1% of the biopsies and after 2.6% of the ultrasounds revealed unsuspected bleeding, but none of these required intervention.

Conclusions:

Ultrasound‐guided liver biopsy in children is a procedure with a low rate of major complications and a high rate of minor bleeding not requiring intervention. Treatment with low‐dose acetylsalicylic acid did not increase bleeding incidence or total complication rate. Low‐molecular‐weight heparin and biopsies from focal lesions were risk factors for bleeding complications. Routine ultrasound the day after the procedure did not change handling of the patients.