bluuebunny/crossref_metadata_2025 huggingface dataset:
A new numerical approach to dense polymer brushes and surface instabilities
Authors: Romeis D. , Merlitz H. , Sommer J.-U.
Published: January 2012

We present a numerical self-consistent field (SCF) method which describes freely jointed chains of spherical monomers applied to densely grafted polymer brushes. We discuss both the Flory-Huggins model and the Carnahan-Starling equation of state and show the latter being preferable within our model at polymer volume fractions above 10%. We compare the results of our numerical method with data from molecular dynamics (MD) simulations [G.-L. He, H. Merlitz, J.-U. Sommer, and C.-X. Wu, Macromolecules 40, 6721 (2007)] and analytical SCF calculations [P. M. Biesheuvel, W. M. de Vos, and V. M. Amoskov, Macromolecules 41, 6254 (2008)] and obtain close agreement between the density profiles up to high grafting densities. In contrast to prior numerical and analytical studies of densely grafted polymer brushes our method provides detailed information about chain configurations including fluctuation, depletion, and packing effects. Using our model we could study the recently discovered instability of densely grafted polymer brushes with respect to slight variations of individual chain lengths, driven by fluctuation effects [H. Merlitz, G.-L. He, C.-X. Wu, and J.-U. Sommer, Macromolecules 41, 5070 (2008)]. The obtained results are in very close agreement with corresponding MD simulations.
Versatile high-repetition-rate phase-locked chopper system for fast timing experiments in the vacuum ultraviolet and x-ray spectral region
Authors: Plogmaker Stefan , Linusson Per , Eland John H. D. , Baker Neville , Johansson Erik M. J. , Rensmo Håkan , Feifel Raimund , Siegbahn Hans
Published: January 2012

A novel light chopper system for fast timing experiments in the vacuum-ultraviolet (VUV) and x-ray spectral region has been developed. It can be phase-locked and synchronized with a synchrotron radiation storage ring, accommodating repetition rates in the range of ∼8 to ∼120 kHz by choosing different sets of apertures and subharmonics of the ring frequency (MHz range). Also the opening time of the system can be varied from some nanoseconds to several microseconds to meet the needs of a broad range of applications. Adjusting these parameters, the device can be used either for the generation of single light pulses or pulse packages from a microwave driven, continuous He gas discharge lamp or from storage rings which are otherwise often considered as quasi-continuous light sources. This chopper can be utilized for many different kinds of experiments enabling, for example, unambiguous time-of-flight (TOF) multi-electron coincidence studies of atoms and molecules excited by a single light pulse as well as time-resolved visible laser pump x-ray probe electron spectroscopy of condensed matter in the valence and core level region.
The quench rule, Dimits shift, and eigenmode localization by small-scale zonal flows
Authors: Kobayashi Sumire , Rogers Barrett N.
Published: January 2012

We perform gyrokinetic simulations in a simple Z-pinch geometry to study the physics of small scale, entropy-mode-driven zonal flows. The entropy-modes create radial E×B streamers, which become unstable to the Kelvin-Helmholz (KH) instability at the point of nonlinear saturation. Sufficiently close to marginal entropy-mode stability, the break-up of the streamers by the KH mode generates zonal flows that produce a nearly static, low transport state (the Dimits shift). The flows in this state have a preferred, automatically maintained level, typically several times stronger than the quench-rule threshold that sits at a critical point of the linear mode-structure: the radial streamers of the entropy-modes become, at about the preferred shearing rate, radially localized to the regions where the shearing rate of the zonal flows passes through zero. Coincident with the localization, the linear growth rates drop to smaller but usually finite levels.
Rheological measurements of large particles in high shear rate flows
Authors: Koos Erin , Linares-Guerrero Esperanza , Hunt Melany L. , Brennen Christopher E.
Published: January 2012

This paper presents experimental measurements of the rheological behavior of liquid-solid mixtures at moderate Stokes and Reynolds numbers. The experiments were performed in a coaxial rheometer that was designed to minimize the effects of secondary flows. By changing the shear rate, particle size, and liquid viscosity, the Reynolds numbers based on shear rate and particle diameter ranged from 20 to 800 (Stokes numbers from 3 to 90), which is higher than examined in earlier rheometric studies. Prior studies have suggested that as the shear rate is increased, particle-particle collisions also increase resulting in a shear stress that depends non-linearly on the shear rate. However, over the range of conditions that were examined in this study, the shear stress showed a linear dependence on the shear rate. Hence, the effective relative viscosity is independent of the Reynolds and Stokes numbers and a non-linear function of the solid fraction. The present work also includes a series of rough-wall experiments that show the relative effective viscosity is also independent of the shear rate and larger than in the smooth wall experiments. In addition, measurements were made of the near-wall particle velocities, which demonstrate the presence of slip at the wall for the smooth-walled experiments. The depletion layer thickness, a region next to the walls where the solid fraction decreases, was calculated based on these measurements. The relative effective viscosities in the current work are larger than found in low-Reynolds number suspension studies but are comparable with a few granular suspension studies from which the relative effective viscosities can be inferred.
Defect modes in one-dimensional magnetized plasma photonic crystals with a dielectric defect layer
Authors: Qi L. , Yang Z. , Fu T.
Published: January 2012

By using transfer matrix method, properties of one-dimensional magnetized plasma photonic crystals with a dielectric defect layer are studied. Results show that several defect modes appear within the photonic band gaps; periodic number and collision frequency only affect transmission magnitude of the defect modes; the external magnetic field and incident angle control both the transmission magnitude and frequency of the defect modes; thickness and dielectric constant of the defect layer determine both the number and frequency of the defect modes. This phenomenon may be useful in designing of narrow band filters or multi-channel filters.
A nano-cheese-cutter to directly measure interfacial adhesion of freestanding nano-fibers
Authors: Wang Xin , Najem Johnny F. , Wong Shing-Chung , Wan Kai-tak
Published: January 2012

A nano-cheese-cutter is fabricated to directly measure the adhesion between two freestanding nano-fibers. A single electrospun fiber is attached to the free end of an atomic force microscope cantilever, while a similar fiber is similarly prepared on a mica substrate in an orthogonal direction. External load is applied to deform the two fibers into complementary V-shapes, and the force measurement allows the elastic modulus to be determined. At a critical tensile load, “pull-off” occurs when the adhering fibers spontaneously detach from each other, yielding the interfacial adhesion energy. Loading-unloading cycles are performed to investigate repeated adhesion-detachment and surface degradation.
The effect of a hydrostatic pressure induced phase transformation on the unipolar electrical response of Nb modified 95/5 lead zirconate titanate
Authors: Valadez J. C. , Sahul R. , Alberta E. , Hackenberger W. , Lynch C. S.
Published: January 2012

Niobium doped lead zirconate titanate (95/5 NbPZT) undergoes a hydrostatic pressure induced ferroelectric rhombohedral to antiferroelectric orthorhombic phase transformation (FE-AFE). This work reports on the experimental characterization of the large field dielectric response to unipolar electric field as it passes through the forward and reverse FE-AFE transformations. The poled ceramic was hydrostatically depoled by driving the FE-AFE phase transformation and stress-strain and stress-electric displacement responses were measured. After this initial characterization, specimens of 95/5 NbPZT were subjected to unipolar electric field loading at different hydrostatic pressure levels. Electric field was varied from zero to 1 MV/m at a series of fixed pressure levels between zero and 550 MPa. This resulted in minor hysteresis loops with the area inside the loops dependent on both pressure and electric field amplitude. Two different slopes were taken from the D-E loops, identified as the small field and large field slopes. Each changed with pressure and displayed distinct jumps at the forward and reverse FE-AFE phase transformations. The area within the loops in the ferroelectric regime, attributed to domain wall motion, increased as pressure was increased and dropped abruptly as the material passed through the pressure induced phase transformation.
Entropic uncertainty relations and the stabilizer formalism
Authors: Niekamp Sönke , Kleinmann Matthias , Gühne Otfried
Published: January 2012

Entropic uncertainty relations express the quantum mechanical uncertainty principle by quantifying uncertainty in terms of entropy. Central questions include the derivation of lower bounds on the total uncertainty for given observables, the characterization of observables that allow strong uncertainty relations, and the construction of such relations for the case of several observables. We demonstrate how the stabilizer formalism can be applied to these questions. We show that the Maassen–Uffink entropic uncertainty relation is tight for the measurement in any pair of stabilizer bases. We compare the relative strengths of variance-based and various entropic uncertainty relations for dichotomic anticommuting observables.
Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals
Authors: Tsuchiizu Masahisa , Omori Yukiko , Suzumura Yoshikazu , Bonnet Marie-Laure , Robert Vincent
Published: January 2012

From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.
Flow and mixing characteristics of an elevated pulsating transverse jet
Authors: Huang Rong F. , Hsu Ching M.
Published: January 2012

Flow-evolution processes as well as the penetration, spread, and dispersion characteristics of elevated pulsating transverse jets were studied experimentally in a wind tunnel. Jet pulsations were induced by means of acoustic excitation. Streak pictures of the smoke-flow patterns, illuminated by a laser-light sheet in the median plane, were recorded by a high-speed digital camera. A hot-wire anemometer was used to digitize instantaneous velocities of instabilities in the flow. Penetration height and spread width were obtained through a binary edge identification technique. Tracer-gas concentrations were measured to provide information on jet dispersions and trajectories. Three characteristic flow modes (synchronized flapping jet, transition, and synchronized shear-layer vortices) were identified in the domain of the jet-to-crossflow momentum-flux ratio and the excitation Strouhal number. At low excitation Strouhal numbers, the jet column near the tube exit flapped back-and-forth periodically at the excitation frequency and induced large up-down motions of the deflected jet. The penetration, spread, and dispersion of the jet increased drastically compared with the non-excited jet because the up-down oscillating motions of the deflected jet transformed the axial momentum into oscillating lateral momentum. Forcing the jet into the transition and synchronized shear-layer vortices regimes caused the vortices to appear along the upwind shear layer of the deflected jet. Under these conditions, the penetration, spread, and dispersion of the jet presented insignificant increases because the entrainment effect induced by the shear-layer vortices was not as large as that produced by the jet oscillating motions in the synchronized flapping jet regime.
Reordering orbitals of semiconductor multi-shell quantum dot-quantum well heteronanocrystals
Authors: Şahin Mehmet , Nizamoglu Sedat , Yerli Ozan , Volkan Demir Hilmi
Published: January 2012

Based on self-consistent computational modeling of quantum dot-quantum well (QDQW) heteronanocrystals, we propose and demonstrate that conduction-electron and valence-hole orbitals can be reordered by controlling shell thicknesses, unlike widely known core/shell quantum dots (QDs). Multi-shell nanocrystals of CdSe/ZnS/CdSe, which exhibit an electronic structure of 1s-1p-2s-2p-1d-1f for electrons and 1s-1p-2s-2p-1d-2d for holes using thin ZnS and CdSe shells (each with two monolayers), lead to 1s-2s-1p-1d-1f-2p electron-orbitals and 1s-2s-1p-1d-2p-1f hole orbitals upon increasing the shell thicknesses while keeping the same core. This is characteristically different from the only CdSe core and CdSe/ZnS core/shell QDs, both exhibiting only 1s-1p-1d-2s-1f-2p ordering for electrons and holes.
A fractal permeability model for gas flow through dual-porosity media
Authors: Zheng Qian , Yu Boming
Published: January 2012

The dual-porosity medium, i.e., a matrix porous medium coupled with fractured networks, extensively exists in fissured rocks, natural gas reservoirs, and other natural underground reservoirs or in resolving subsurface contamination problems. This work investigates gas permeability through matrix porous media embedded with randomly distributed fractal-like tree networks. The analytical expression for gas permeability in dual-porosity media is derived based on both the pore size of matrix and the mother channel diameter of embedded fractal-like tree networks having fractal distribution. It is found that gas permeability is a function of structural parameters (the fractal dimensions for pore area and tortuous capillaries, porosity and the maximum diameter of matrix, the length ratio, the diameter ratio, the branching levels and angle of the embedded networks) for dual-porosity media. The proposed model does not contain any empirical constant. The model predictions are compared with the available experimental data and simulating results, a fair agreement among them is found. The influences of geometrical parameters on the gas permeability in the media are also analyzed.
Decreasing high ion energy during transition in pulsed inductively coupled plasmas
Authors: Agarwal Ankur , Stout Phillip J. , Banna Samer , Rauf Shahid , Collins Ken
Published: January 2012

Pulsed RF plasmas sustained in electronegative gas mixtures are increasingly being employed for plasma etching at future technological nodes. During the plasma transition from the afterglow to the active-glow, ion energies at the wafer can substantially increase due to the high voltage required to deposit bias power into few electrons. These high energy ions, albeit few, increase the possibility of ion bombardment damage and are, therefore, detrimental to the etching process. Strategies to decrease the high ion energies during transition are investigated using a two-dimensional computational plasma model. Results for poly-Si etch in an Ar/Cl2 gas mixture indicate that the high ion energies can be reduced by offsetting the bias pulse from the source pulse with minimal impact on the etch depth rates.
n-ZnO:N/p-Si nanowire photodiode prepared by atomic layer deposition
Authors: Kang Hyemin , Park Jusang , Choi Taejin , Jung Hanearl , Lee Kwang H. , Im Seongil , Kim Hyungjun
Published: January 2012

Core-shell p-n junction diode was fabricated using the atomic layer deposition (ALD) of ZnO on p-Si nanowire (NW) array prepared by electroless etching method. I-V measurements have shown that the carrier concentrations in ALD ZnO for both of the core-shell and planar diodes are effectively controlled by nitrogen doping to a proper level to form rectifying junction. Responsivity of the core-shell device was about 0.98 A/W at 660 nm, which is significantly improved compared to planar device. The superior sensitivity of core-shell structure is attributed to the effective carrier separation and collection originating from the characteristic of core-shell NWs full depletion.
Defect configurations of high-k cations in germanium
Authors: Chroneos A. , Dimoulas A.
Published: January 2012

At germanium/high-k interfaces cations and oxygen interstitials can diffuse into the germanium substrate. Here we employ density functional theory calculations to investigate the interaction of a range of such cations (Al, Y, Zr, Nb, La, and Hf) with intrinsic defects and oxygen in germanium. It is predicted that high-k cations strongly bind with lattice vacancies, oxygen interstitials, and A-centers. The implications for microelectronic device performance are discussed.
Effect of point defects on band-gap properties in diamond structure photonic crystals
Authors: Dai Wei , Wang Hong , Chen Shibin , Li Dichen , Zhou Di
Published: January 2012

Three dimensional diamond structure photonic crystals (PCs) with point defects fabricated by rapid prototyping and gel casting with alumina were studied at microwave frequencies. The sphere, ellipsoid, and cylinder point defects were introduced in the PCs first and it was found that the localization of electromagnetic wave is the strongest in ellipsoid point defect photonic crystals. Then, the size change of the ellipsoid point defect was studied to find out the optimal size. When the size of the ellipsoid point defect is close to one unit cell, the Q factor, which represents the localization intensity of the electromagnetic wave, will be the biggest. Based on the optimal size of ellipsoid point defect, more ellipsoid point defects were introduced into one diamond PC structure. Three point defect resonant modes were found in a photonic crystal with three ellipsoid point defects and the distance between each defect was twice of the lattice constant. A guided band was observed in the forbidden band gap in a photonic crystal with five ellipsoid point defects, in which the distance between each defect was of one lattice constant.
Influence of surface bow on reconstruction on 2-inch SiC (0001) wafer
Authors: Zhu Ming-Xing , Chen Yi , Shi Biao , Liu Xue-Chao , Chang Shao-Hui , Yan Cheng-Feng , Yang Jian-Hua , Shi Er-Wei
Published: January 2012

The step morphologies of a gas-etched 2-in. 6H-SiC (0001) wafer are investigated by the atomic force microscope. Due to the concave surface induced by bow, undulation surface morphologies were observed in the edge region. In the upside and downside region of the center along the 〈112¯0〉 miscut direction, ripples and bimodal steps are observed, respectively. In the other edge regions, a complex pattern of waves enveloped in microsteps was formed. The complex reorganized surface morphology is discussed by the viewpoint of the two or three-dimensional phase separation. Compared to the regular unit cell high steps, the formalism of waved surface is interpreted by competing free energy curve through changes in surface structure faceting, where the step separated at a specific orientation and favor to match to surface reconstruction with unit cell high steps.
Improved photoresponse of InAs/GaAs quantum dot infrared photodetectors by using GaAs1−xSbx strain reducing layer
Authors: Huang Chia-Tze , Chen Yu-Cheng , Lee Si-Chen
Published: January 2012

The effect of a GaAs1−xSbx strain reducing layer on the performance of InAs/GaAs quantum-dot infrared photodetectors was investigated. The results suggest that increasing Sb composition x from 0 to 0.2 leads to an enhanced peak response and a pronounced narrowing of the band width of the spectral response from 3.3 to 1.5 μm. For a photodetector with GaAs0.8Sb0.2 strain reducing layer, the best responsivity obtained is 533 mA/W, which is 380 times higher than that without strain reducing layer. In addition, the operating temperature increases from 50 to 90 K when increasing Sb composition from 0 to 0.2.
Ultra-broad spontaneous emission and modal gain spectrum from a hybrid quantum well/quantum dot laser structure
Authors: Chen S. M. , Zhou K. J. , Zhang Z. Y. , Childs D. T. D. , Hugues M. , Ramsay A. J. , Hogg R. A.
Published: January 2012

We propose and demonstrate a hybrid quantum well/quantum dot structure to enhance the gain and spontaneous emission bandwidth of a quantum dot active region. A single quantum well is introduced into a multi-layer stack of quantum dots, spectrally positioned to cancel the losses due to the second excited state of the dots. As a result, the modal gain at room temperature is extended to 300 nm, covering the wavelength range of 1100-1400 nm, and spontaneous emission has a 250 nm, 3 dB linewidth from 1080-1335 nm, of interest to short-haul telecom and optical coherence tomography applications.
Numerical analysis on the effects of bandgap energy and polarization of electron blocking layer in near-ultraviolet light-emitting diodes
Authors: Kuo Yen-Kuang , Chen Yu-Han , Chang Jih-Yuan , Tsai Miao-Chan
Published: January 2012

The influences of bandgap energy and polarization of the electron blocking layer (EBL) in near-ultraviolet light-emitting diodes (NUV LEDs) are systematically investigated. Design curves for the output power of NUV LEDs as a function of bandgap energy and polarization of EBL are provided. The simulation results show that, when the bandgap of the EBL increases, the polarization and polarization-induced charge increase accordingly. Both mechanisms have opposite effects for the EBL in confining electrons. The NUV LEDs with an EBL of large bandgap or small polarization have improved performance due to the enhanced efficiency of electron confining and hole injection.
Hexagonal-based pyramid void defects in GaN and InGaN
Authors: Yankovich A. B. , Kvit A. V. , Li X. , Zhang F. , Avrutin V. , Liu H. Y. , Izyumskaya N. , Özgür Ü. , Morkoç H. , Voyles P. M.
Published: January 2012

We report a void defect in gallium nitride (GaN) and InGaN, revealed by aberration-corrected scanning transmission electron microscopy (STEM). The voids are pyramids with symmetric hexagonal {0001} base facets and {101¯1} side facets. Each pyramid void has a dislocation at the peak of the pyramid, which continues up along the [0001] growth direction to the surface. Some of the dislocations are hexagonal open core screw dislocations with {101¯0} side facets, varying lateral widths, and varying degrees of hexagonal symmetry. STEM electron energy loss spectroscopy spectrum imaging showed a large C concentration inside the void and on the void surfaces. There is also a larger C concentration in the GaN (or InGaN) below the void than above the void. We propose that inadvertent carbon deposition during metal organic chemical vapor deposition growth acts as a mask, stopping the GaN deposition locally, which in combination with lateral overgrowth, creates a void. Subsequent layers of GaN deposited around the C covered region create the overhanging {101¯1} facets, and the meeting of the six {101¯1} facets at the pyramid’s peak is not perfect, resulting in a dislocation.
Temperature dependence of microwave voltage emission associated to spin-transfer induced vortex oscillation in magnetic tunnel junction
Authors: Bortolotti P. , Dussaux A. , Grollier J. , Cros V. , Fukushima A. , Kubota H. , Yakushiji K. , Yuasa S. , Ando K. , Fert A.
Published: January 2012

The temperature dependence of a vortex-based nano-oscillator induced by spin transfer torque (STVO) in magnetic tunnel junctions (MTJ) is considered. We obtain emitted signals with large output power and good signal coherence. Due to the reduced non-linearities compared to the uniform magnetization case, we first observe a linear decrease of linewidth with decreasing temperature. However, this expected behavior no longer applies at lower temperature and a bottom limit of the linewidth is measured.
Effect of uni-axial strain on THz/far-infrared response of graphene
Authors: Kim JooYoun , Lee Chul , Bae Sukang , Jin Kim Sang , Soo Kim Keun , Hee Hong Byung , Choi E. J.
Published: January 2012

We present polarized optical transmission study of uniaxially strained large scale graphene in THz/far-infrared (IR) frequency region. Graphene was supported on stretchable polyethylene substrate and they were elongated up to 20% (ΔL/Lo = 0.2) by applying tensile force. For the IR light polarized along the strain direction (EIR//strain), the optical conductivity σ1(ω) of graphene changes from Drude response into strongly non-Drude-like behavior with a peak formed at finite energy ∼10 meV. In contrast, the coherent Drude conductivity is preserved along the direction perpendicular to the strain (EIR⊥strain). Possible origin of the strain-induced non-Drude σ1(ω)-behavior is discussed.
Electric resonance-rectifier circuit for renewable energy conversion
Authors: Boström C. , Ekergård B. , Leijon M.
Published: January 2012

Variable speed generators are used more frequently for converting the energy from renewable energy sources to electric energy. The power production form a variable speed generator is dependent on the electrical damping of the generator. In this paper, a resonance circuit connected to a direct driven linear generator used for wave energy utilization is investigated. At resonance, the electrical damping in the generator increases which results in an increased power production. The results show that resonance can be achieved with the suggested circuit.
Boron-oxygen defect in Czochralski-silicon co-doped with gallium and boron
Authors: Forster M. , Fourmond E. , Rougieux F. E. , Cuevas A. , Gotoh R. , Fujiwara K. , Uda S. , Lemiti M.
Published: January 2012

We study the boron-oxygen defect in Si co-doped with gallium and boron with the hole density 10 times higher than the boron concentration. Instead of the linear dependence of the defect density on the hole density observed in boron and phosphorus compensated silicon, we find a proportionality to the boron concentration. This indicates the participation of substitutional, rather than interstitial, boron in the defect complex. The measured defect formation rate constant is proportional to the hole density squared, which gives credit to latent defect models against defect reactions limited by the diffusion and trapping of oxygen dimers by boron atoms.
Enhanced carrier injection in pentacene thin-film transistors by inserting a MoO3-doped pentacene layer
Authors: Wang Zhaokui , Waqas Alam Mir , Lou Yanhui , Naka Shigeki , Okada Hiroyuki
Published: January 2012

We report on the enhanced carrier injection in pentacene thin-film transistors with a thin MoO3-doped pentacene layer between pentacene semiconductor and the source-drain electrodes. Device performance including drain current, field effect mobility, and threshed voltage are improved by employing a MoO3-doped pentacene thin layer. The barrier height at the Au/pentacene interface is lowered from 0.12 to 0.05 eV after inserting a MoO3-doped pentacene thin layer between them. The reduced barrier height is attributed to the formation of a good contact between MoO3-doped pentacene and Au owing to smoothed surface morphology of pentancene and suitable band bending by MoO3 doping.
Giant, voltage-actuated deformation of a dielectric elastomer under dead load
Authors: Huang Jiangshui , Li Tiefeng , Chiang Foo Choon , Zhu Jian , Clarke David R. , Suo Zhigang
Published: January 2012

Far greater voltage-actuated deformation is achievable for a dielectric elastomer under equal-biaxial dead load than under rigid constraint usually employed. Areal strains of 488% are demonstrated. The dead load suppresses electric breakdown, enabling the elastomer to survive the snap-through electromechanical instability. The breakdown voltage is found to increase with the voltage ramp rate. A nonlinear model for viscoelastic dielectric elastomers is developed and shown to be consistent with the experimental observations.
Effect of an electron blocking layer on the piezoelectric field in InGaN/GaN multiple quantum well light-emitting diodes
Authors: Lee Dong-Yul , Han Sang-Heon , Lee Dong-Ju , Wook Lee Jeong , Kim Dong-Joon , Sun Kim Young , Kim Sung-Tae
Published: January 2012

We report the effect of an electron blocking layer (EBL) on the piezoelectric field in InGaN/GaN multiple quantum well light-emitting diodes (LEDs). Electric-field-dependent ER measurements showed an enhanced piezoelectric field in LEDs with a p-AlGaN EBL compared with LEDs without EBL. In contrast, LEDs with a p-AlGaN EBL exhibited reduced blueshift and a sublinear increase of full width at half maximum in EL spectra at low current densities. These behaviors can be explained by the strong localization of injected carriers in dominant InGaN regions due to an increase of the piezoelectric field by subsequent growing EBL.
Variable range hopping in TiO2 insulating layers for oxide electronic devices
Authors: Zhao Y. L. , Lv W. M. , Liu Z. Q. , Zeng S. W. , Motapothula M. , Dhar S. , Ariando  , Wang Q. , Venkatesan T.
Published: January 2012

TiO2 thin films are of importance in oxide electronics, e.g., Pt/TiO2/Pt for memristors and Co-TiO2/TiO2/Co-TiO2 for spin tunneling devices. When such structures are deposited at a variety of oxygen pressures, how does TiO2 behave as an insulator? We report the discovery of an anomalous resistivity minimum in a TiO2 film at low pressure (not strongly dependent on deposition temperature). Hall measurements rule out band transport and in most of the pressure range the transport is variable range hopping (VRH) though below 20 K it was difficult to differentiate between Mott and Efros-Shklovskii's (ES) mechanism. Magnetoresistance (MR) of the sample with lowest resistivity was positive at low temperature (for VRH) but negative above 10 K indicating quantum interference effects.
Perceived stigma and social risk of HIV testing and disclosure among Iranian-Australians living in the Sydney metropolitan area
Authors: Hosseinzadeh Hassan , Hossain Syeda Zakia , Bazargan-Hejazi Shahrzad
Published: January 2012

Background
Fear of being stigmatised is a major social risk for seeking help in the HIV/AIDS arena. However, little is known about the social perceptions that people hold about the disease. This study explores the level of perceived stigma and its effect on the social risk of HIV testing and disclosure among Iranian-Australians immigrants living in the Sydney metropolitan area. Methods: A total of 236 Iranian-Australians immigrants aged 20–65 years participated in this cross-sectional study. Results: The majority of respondents (73.3%) perceived that HIV-infected people face a great deal of or some stigma. Participants were concerned about being stigmatised if they tested positive or were known to be HIV-positive in the future. A significant majority expressed that such concerns would affect their decision-making related to HIV testing and disclosure. Females were more likely to perceive HIV/AIDS stigma. Multiple regression analyses showed that perceived HIV/AIDS stigma could explain 28.6% of the variance in social risk of HIV testing and disclosure (B = 0.89, β = 0.53, P < 0.0001) and 24.6% of the variance in decision-making related to HIV testing and disclosure (B = 0.62, β = 0.49, P < 0.0001) after controlling for sociodemographic factors. Time since migration (predictive power of 4.8–6.78%) strongly influenced the associations. Conclusions: If social stigma is left unaddressed, individuals would be reluctant to undertake HIV testing or disclose their HIV status if tested positive. Further attempts are needed to change the current social construction of HIV/AIDS among Iranians-Australians living in Sydney.
Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion
Authors: Ahmad Basir , Chen Yujie , Lapidus Lisa J.
Published: January 2012

We hypothesize that the first step of aggregation of disordered proteins, such as α-synuclein, is controlled by the rate of backbone reconfiguration. When reconfiguration is fast, bimolecular association is not stable, but as reconfiguration slows, association is more stable and subsequent aggregation is faster. To investigate this hypothesis, we have measured the rate of intramolecular diffusion in α-synuclein, a protein involved in Parkinson’s disease, under solvent conditions that accelerate or decelerate aggregation. Using the method of tryptophan-cysteine (Trp-Cys) quenching, the rate of intramolecular contact is measured in four different loops along the chain length. This intrinsically disordered protein is highly diffusive at low temperature at neutral pH, when aggregation is slow, and compacts and diffuses more slowly at high temperature or low pH, when aggregation is rapid. Diffusion also slows with the disease mutation A30P. This work provides unique insights into the earliest steps of α-synuclein aggregation pathway and should provide the basis for the development of drugs that can prevent aggregation at the initial stage.
Probing chelation motifs in HIV integrase inhibitors
Authors: Agrawal Arpita , DeSoto Jamie , Fullagar Jessica L. , Maddali Kasthuraiah , Rostami Shahrzad , Richman Douglas D. , Pommier Yves , Cohen Seth M.
Published: January 2012

A series of HIV integrase (HIV-1 IN) inhibitors were synthesized to evaluate the role of the metal-binding group (MBG) in this class of metalloenzyme inhibitors. A total of 21 different raltegravir-chelator derivative (RCD) compounds were prepared that differed only in the nature of the MBG. These IN strand-transfer inhibitors (INSTIs) were evaluated in vitro in cell-free enzyme activity assays, and the in vitro results were further validated in cell culture experiments. All of the active compounds showed selective inhibition of the strand-transfer reaction over 3′-processing, suggesting a common mode of action with raltegravir. The results of the in vitro activity suggest that the nature of the MBG donor atoms, the overall MBG structure, and the specific arrangement of the MBG donor atom triad are essential for obtaining maximal HIV-1 IN inhibition. At least two compounds (RCD-4, RCD-5) containing a hydroxypyrone MBG were found to display superior strand-transfer inhibition when compared to an abbreviated analogue of raltegravir (RCD-1). By isolating and examining the role of the MBG in a series of INSTIs, we have identified a scaffold (hydroxypyrones) that may provide access to a unique class of HIV-1 IN inhibitors, and may help overcome rising raltegravir resistance.
The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family
Authors: Smith Paul , Wang Li Kai , Nair Pravin A. , Shuman Stewart
Published: January 2012

Pnkp is the end-healing and end-sealing component of an RNA repair system present in diverse bacteria from ten different phyla. To gain insight to the mechanism and evolution of this repair system, we determined the crystal structures of the ligase domain of
Clostridium thermocellum
Pnkp in three functional states along the reaction pathway: apoenzyme, ligase•ATP substrate complex, and covalent ligase-AMP intermediate. The tertiary structure is composed of a classical ligase nucleotidyltransferase module that is embellished by a unique α-helical insert module and a unique C-terminal α-helical module. Structure-guided mutational analysis identified active site residues essential for ligase adenylylation. Pnkp defines a new RNA ligase family with signature structural and functional properties.
Human ovarian cancer stem/progenitor cells are stimulated by doxorubicin but inhibited by Mullerian inhibiting substance
Authors: Meirelles Katia , Benedict Leo Andrew , Dombkowski David , Pepin David , Preffer Frederic I. , Teixeira Jose , Tanwar Pradeep Singh , Young Robert H. , MacLaughlin David T. , Donahoe Patricia K. , Wei Xiaolong
Published: January 2012

Women with late-stage ovarian cancer usually develop chemotherapeutic-resistant recurrence. It has been theorized that a rare cancer stem cell, which is responsible for the growth and maintenance of the tumor, is also resistant to conventional chemotherapeutics. We have isolated from multiple ovarian cancer cell lines an ovarian cancer stem cell-enriched population marked by CD44, CD24, and Epcam (3+) and by negative selection for Ecadherin (Ecad−) that comprises less than 1% of cancer cells and has increased colony formation and shorter tumor-free intervals in vivo after limiting dilution. Surprisingly, these cells are not only resistant to chemotherapeutics such as doxorubicin, but also are stimulated by it, as evidenced by the significantly increased number of colonies in treated 3+Ecad− cells. Similarly, proliferation of the 3+Ecad− cells in monolayer increased with treatment, by either doxorubicin or cisplatin, compared with the unseparated or cancer stem cell-depleted 3−Ecad+ cells. However, these cells are sensitive to Mullerian inhibiting substance (MIS), which decreased colony formation. MIS inhibits ovarian cancer cells by inducing G1 arrest of the 3+Ecad− subpopulation through the induction of cyclin-dependent kinase inhibitors. 3+Ecad− cells selectively expressed LIN28, which colocalized by immunofluorescence with the 3+ cancer stem cell markers in the human ovarian carcinoma cell line, OVCAR-5, and is also highly expressed in transgenic murine models of ovarian cancer and in other human ovarian cancer cell lines. These results suggest that chemotherapeutics may be stimulative to cancer stem cells and that selective inhibition of these cells by treating with MIS or targeting LIN28 should be considered in the development of therapeutics.
Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data
Authors: Li Yihan , Ghosh Debashis
Published: January 2012

Motivation: There is now a large literature on statistical methods for the meta-analysis of genomic data from multiple studies. However, a crucial assumption for performing many of these analyses is that the data exhibit small between-study variation or that this heterogeneity can be sufficiently modelled probabilistically.

Results: In this article, we propose ‘assumption weighting’, which exploits a weighted hypothesis testing framework proposed by Genovese et al. to incorporate tests of between-study variation into the meta-analysis context. This methodology is fast and computationally simple to implement. Several weighting schemes are considered and compared using simulation studies. In addition, we illustrate application of the proposed methodology using data from several high-profile stem cell gene expression datasets.

Availability:  http://works.bepress.com/debashis_ghosh/50/

Contact:  ghoshd@psu.edu
Literature mining of host–pathogen interactions: comparing feature-based supervised learning and language-based approaches
Authors: Thieu Thanh , Joshi Sneha , Warren Samantha , Korkin Dmitry
Published: January 2012

Motivation: In an infectious disease, the pathogen's strategy to enter the host organism and breach its immune defenses often involves interactions between the host and pathogen proteins. Currently, the experimental data on host–pathogen interactions (HPIs) are scattered across multiple databases, which are often specialized to target a specific disease or host organism. An accurate and efficient method for the automated extraction of HPIs from biomedical literature is crucial for creating a unified repository of HPI data.

Results: Here, we introduce and compare two new approaches to automatically detect whether the title or abstract of a PubMed publication contains HPI data, and extract the information about organisms and proteins involved in the interaction. The first approach is a feature-based supervised learning method using support vector machines (SVMs). The SVM models are trained on the features derived from the individual sentences. These features include names of the host/pathogen organisms and corresponding proteins or genes, keywords describing HPI-specific information, more general protein–protein interaction information, experimental methods and other statistical information. The language-based method employed a link grammar parser combined with semantic patterns derived from the training examples. The approaches have been trained and tested on manually curated HPI data. When compared to a naïve approach based on the existing protein–protein interaction literature mining method, our approaches demonstrated higher accuracy and recall in the classification task. The most accurate, feature-based, approach achieved 66–73% accuracy, depending on the test protocol.

Availability: Both approaches are available through PHILM web-server: http://korkinlab.org/philm.html

Contact:  korkin@korkinlab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Functional microRNA targets in protein coding sequences
Authors: Reczko Martin , Maragkakis Manolis , Alexiou Panagiotis , Grosse Ivo , Hatzigeorgiou Artemis G.
Published: January 2012

Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.

Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3′-untranslated regions (3′-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3′-UTR target sites. Further analysis indicates that genes with shorter 3′-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3′-UTR.

Availability: The results of DIANA-microT-CDS are available at www.microrna.gr/microT-CDS

Contact:  hatzigeorgiou@fleming.gr; reczko@fleming.gr

Supplementary information:  Supplementary data are available at Bioinformatics online.
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots
Authors: Seetin Matthew G. , Mathews David H.
Published: January 2012

Motivation: Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important.

Results: TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods.

Availability: The program is available for download under an open-source license as part of the RNAstructure package at: http://rna.urmc.rochester.edu.

Contact:  david_mathews@urmc.rochester.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genotype calling from next-generation sequencing data using haplotype information of reads
Authors: Zhi Degui , Wu Jihua , Liu Nianjun , Zhang Kui
Published: January 2012

Motivation: Low coverage sequencing provides an economic strategy for whole genome sequencing. When sequencing a set of individuals, genotype calling can be challenging due to low sequencing coverage. Linkage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy. Current LD-based methods use read counts or genotype likelihoods at individual potential polymorphic sites (PPSs). Reads that span multiple PPSs (jumping reads) can provide additional haplotype information overlooked by current methods.

Results: In this article, we introduce a new Hidden Markov Model (HMM)-based method that can take into account jumping reads information across adjacent PPSs and implement it in the HapSeq program. Our method extends the HMM in Thunder and explicitly models jumping reads information as emission probabilities conditional on the states of adjacent PPSs. Our simulation results show that, compared to Thunder, HapSeq reduces the genotyping error rate by 30%, from 0.86% to 0.60%. The results from the 1000 Genomes Project show that HapSeq reduces the genotyping error rate by 12 and 9%, from 2.24% and 2.76% to 1.97% and 2.50% for individuals with European and African ancestry, respectively. We expect our program can improve genotyping qualities of the large number of ongoing and planned whole genome sequencing projects.

Contact:  dzhi@ms.soph.uab.edu; kzhang@ms.soph.uab.edu

Availability: The software package HapSeq and its manual can be found and downloaded at www.ssg.uab.edu/hapseq/.

Supplementary information:  Supplementary data are available at Bioinformatics online.
vHOG, a multispecies vertebrate ontology of homologous organs groups
Authors: Niknejad Anne , Comte Aurélie , Parmentier Gilles , Roux Julien , Bastian Frederic B. , Robinson-Rechavi Marc
Published: January 2012

Motivation: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species.

Results: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available.

Availability and implementation: vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites.

Contact:  bgee@isb-sib.ch; frederic.bastian@unil.ch