bluuebunny/crossref_metadata_2025 huggingface dataset:
Homo-junction ferroelectric field-effect-transistor memory device using solution-processed lithium-doped zinc oxide thin films
Authors: Nayak Pradipta K. , Caraveo-Frescas J. A. , Bhansali Unnat. S. , Alshareef H. N.
Published: June 2012

High performance homo-junction field-effect transistor memory devices were prepared using solution processed transparent lithium-doped zinc oxide thin films for both the ferroelectric and semiconducting active layers. A highest field-effect mobility of 8.7 cm2/Vs was obtained along with an Ion/Ioff ratio of 106. The ferroelectric thin film transistors showed a low sub-threshold swing value of 0.19 V/dec and a significantly reduced device operating voltage (±4 V) compared to the reported hetero-junction ferroelectric transistors, which is very promising for low-power non-volatile memory applications.
Terahertz imaging system using high-Tc superconducting oscillation devices
Authors: Tsujimoto M. , Minami H. , Delfanazari K. , Sawamura M. , Nakayama R. , Kitamura T. , Yamamoto T. , Kashiwagi T. , Hattori T. , Kadowaki K.
Published: June 2012

Microwatt power oscillation devices at sub-terahertz frequency region between 0.3 and 1.0 terahertz (THz) were fabricated from high-Tc superconducting single crystalline Bi2Sr2CaCu2O8+δ and used as a source of the transmission terahertz imaging system. As test examples, terahertz images of coins and a razor blade placed inside the brownish paper envelopes with the spatial resolution of 1 mm are presented. The signal-to-noise ratio exceeds 130 in these images. Using a simple wedge-shaped interferometer and analysing the interference fringe pattern, the wavelength of the terahertz wave is calibrated within 0.1% accuracy. This interferometer also provides a simple method to measure the absorption coefficient of the liquid sample. Two test measurements for distilled water and ethanol are demonstrated and their absorption coefficients are obtained with 99.2% accuracy. This suggests that our terahertz imaging system can be applied to many practical applications, such as biological and biomedical imaging, environmental monitoring, microanalysis of impurities, structure and dynamical analyses of large molecules and ions in solution.
Correlation between quantum conductance and atomic arrangement of atomic-size silver nanowires
Authors: Lagos M. J. , Autreto P. A. S. , Galvao D. S. , Ugarte D.
Published: June 2012

We have studied the effect of thermal effects on the structural and transport response of Ag atomic-size nanowires (NWs) generated by mechanical elongation. Our study involves both time-resolved atomic resolution transmission electron microscopy imaging and quantum conductance measurement using an ultra-high-vacuum mechanically controllable break junction. We have observed drastic changes in conductance and structural properties of Ag nanowires generated at different temperatures (150 and 300 K). By combining electron microscopy images, electronic transport measurements, and quantum transport calculations, we have been able to obtain a consistent correlation between the conductance and structural properties of Ag NWs. In particular, our study has revealed the formation of metastable rectangular rod-like Ag wire (3/3) along the [001] crystallographic direction, whose formation is enhanced. These results illustrate the high complexity of analyzing structural and quantum conductance behaviour of metal atomic-size wires; also, they reveal that it is extremely difficult to compare NW conductance experiments performed at different temperatures due to the fundamental modifications of the mechanical behavior.
Oxidation kinetics of nanoscale copper films studied by terahertz transmission spectroscopy
Authors: Ramanandan Gopika K. P. , Ramakrishnan Gopakumar , Planken Paul C. M.
Published: June 2012

Terahertz (THz) transmission spectroscopy is used to measure the oxidation kinetics of copper thin films evaporated on silicon substrates. The transmission of broadband THz pulses from 1 to 7 THz through the copper film is measured while it gets oxidized at an elevated temperature in ambient air. The change in the transmitted THz electric field is correlated with the growth of the cuprous oxide layer and the decrease in thickness of the copper layer. Oxidation curves were obtained for heating temperatures of 120–150 °C and were found to follow a parabolic rate law. Using the Arrhenius equation, we calculate an activation energy for diffusion of 0.55 eV. By measuring the THz transmission through unoxidized copper layers of several thicknesses, we also measured the optical properties of thin copper films around the percolation threshold thickness of 7 nm. Around the percolation transition, the optical properties of freshly deposited copper thin films are very different from that of copper layers of the same thickness remaining after partial oxidation of thick copper films.
The impact of quantum dots magnetization on spin separation and spin current in a multiple quantum-dot ring in the presence of Rashba spin-orbit coupling
Authors: Faizabadi Edris , Eslami Leila
Published: June 2012

The influence of quantum dot magnetization on electronic spin-dependent transport is investigated through a triple-quantum-dot ring structure in which one of the quantum dots is non-magnetic subjected to the Rashba spin-orbit interaction and the two other ones possess magnetic structure. Evaluated results, based on single particle Green’s function formalism, indicate that the presence of magnetic moment on the quantum dots leads to additional spin-dependent phase factor which affects electronic transport through the system. For both antiferromagnetic and ferromagnetic quantum dots, the system can operate as a spin-splitter but differently; by tuning Rashba spin-orbit strength and in the presence of magnetic flux, respectively. Besides, in the absence of one of the outgoing leads, spin current in the output is calculated and demonstrated that magnetization of quantum dots leads to spin current even in the absence of Rashba spin-orbit effect. Moreover, it is shown that in the presence of Rashba spin orbit interaction, magnetic quantum dots, and magnetic flux, the two terminal system produces a completely tunable spin current.
Three-terminal ferroelectric synapse device with concurrent learning function for artificial neural networks
Authors: Nishitani Y. , Kaneko Y. , Ueda M. , Morie T. , Fujii E.
Published: June 2012

Spike-timing-dependent synaptic plasticity (STDP) is demonstrated in a synapse device based on a ferroelectric-gate field-effect transistor (FeFET). STDP is a key of the learning functions observed in human brains, where the synaptic weight changes only depending on the spike timing of the pre- and post-neurons. The FeFET is composed of the stacked oxide materials with ZnO/Pr(Zr,Ti)O3 (PZT)/SrRuO3. In the FeFET, the channel conductance can be altered depending on the density of electrons induced by the polarization of PZT film, which can be controlled by applying the gate voltage in a non-volatile manner. Applying a pulse gate voltage enables the multi-valued modulation of the conductance, which is expected to be caused by a change in PZT polarization. This variation depends on the height and the duration of the pulse gate voltage. Utilizing these characteristics, symmetric and asymmetric STDP learning functions are successfully implemented in the FeFET-based synapse device by applying the non-linear pulse gate voltage generated from a set of two pulses in a sampling circuit, in which the two pulses correspond to the spikes from the pre- and post-neurons. The three-terminal structure of the synapse device enables the concurrent learning, in which the weight update can be performed without canceling signal transmission among neurons, while the neural networks using the previously reported two-terminal synapse devices need to stop signal transmission for learning.
Propagation of a solitary fission wave
Authors: Osborne A. G. , Recktenwald G. D. , Deinert M. R.
Published: June 2012

Reaction-diffusion phenomena are encountered in an astonishing array of natural systems. Under the right conditions, self stabilizing reaction waves can arise that will propagate at constant velocity. Numerical studies have shown that fission waves of this type are also possible and that they exhibit soliton like properties. Here, we derive the conditions required for a solitary fission wave to propagate at constant velocity. The results place strict conditions on the shapes of the flux, diffusive, and reactive profiles that would be required for such a phenomenon to persist, and this condition would apply to other reaction diffusion phenomena as well. Numerical simulations are used to confirm the results and show that solitary fission waves fall into a bistable class of reaction diffusion phenomena.
Two-step controllable electrochemical etching of tungsten scanning probe microscopy tips
Authors: Khan Yasser , Al-Falih Hisham , Zhang Yaping , Ng Tien Khee , Ooi Boon S.
Published: June 2012

Dynamic electrochemical etching technique is optimized to produce tungsten tips with controllable shape and radius of curvature of less than 10 nm. Nascent features such as “dynamic electrochemical etching” and reverse biasing after “drop-off” are utilized, and “two-step dynamic electrochemical etching” is introduced to produce extremely sharp tips with controllable aspect ratio. Electronic current shut-off time for conventional dc “drop-off” technique is reduced to ∼36 ns using high speed analog electronics. Undesirable variability in tip shape, which is innate to static dc electrochemical etching, is mitigated with novel “dynamic electrochemical etching.” Overall, we present a facile and robust approach, whereby using a novel etchant level adjustment mechanism, 30° variability in cone angle and 1.5 mm controllability in cone length were achieved, while routinely producing ultra-sharp probes.
Source characterization and modeling development for monoenergetic-proton radiography experiments on OMEGA
Authors: Manuel M. J.-E. , Zylstra A. B. , Rinderknecht H. G. , Casey D. T. , Rosenberg M. J. , Sinenian N. , Li C. K. , Frenje J. A. , Séguin F. H. , Petrasso R. D.
Published: June 2012

A monoenergetic proton source has been characterized and a modeling tool developed for proton radiography experiments at the OMEGA [T. R. Boehly et al., Opt. Comm. 133, 495 (1997)]10.1016/S0030-4018(96)00325-2 laser facility. Multiple diagnostics were fielded to measure global isotropy levels in proton fluence and images of the proton source itself provided information on local uniformity relevant to proton radiography experiments. Global fluence uniformity was assessed by multiple yield diagnostics and deviations were calculated to be ∼16% and ∼26% of the mean for DD and D3He fusion protons, respectively. From individual fluence images, it was found that the angular frequencies of ≳50 rad−1 contributed less than a few percent to local nonuniformity levels. A model was constructed using the Geant4 [S. Agostinelli et al., Nuc. Inst. Meth. A 506, 250 (2003)]10.1016/S0168-9002(03)01368-8 framework to simulate proton radiography experiments. The simulation implements realistic source parameters and various target geometries. The model was benchmarked with the radiographs of cold-matter targets to within experimental accuracy. To validate the use of this code, the cold-matter approximation for the scattering of fusion protons in plasma is discussed using a typical laser-foil experiment as an example case. It is shown that an analytic cold-matter approximation is accurate to within ≲10% of the analytic plasma model in the example scenario.
Layer thickness dependent tensile deformation mechanisms in sub-10 nm multilayer nanowires
Authors: Yuan Fuping , Wu Xiaolei
Published: June 2012

Using molecular dynamics simulations, the tensile deformation behavior for two types of sub-10 nm multilayer nanowires (NWs) have been investigated. For the structure with interfaces perpendicular to the wire axis, the deformation mechanism is changed from interface crossing by dislocations to interface rotation as the layer thickness is decreasing, causing a significant reduction in yield strength. However, the deformation mechanisms are all accommodated through interface crossing by dislocations regardless of layer thickness for the structure with interfaces parallel to the wire axis. Moreover, the yield strengths in the second structure are found to be controlled by two competing mechanisms: the interface strengthening by increased repulsive force and interface softening by increased dislocation source sites. The sudden stress drop after yielding point in NWs could be explained by the dislocation source-limited hardening mechanism: the more atomic fraction of newly formed stacking faults (SF) after stress drop, the larger normalized stress drop and the larger uniform tensile elongation. For the second structure, the larger total tensile elongation for larger layer thickness could be related to the twinning induced plasticity at the necking position. These findings should have implications for designing functionalized structures and devices in nanoelectromechanical systems.
Direct and indirect electrocaloric measurements on 〈001〉-PbMg1/3Nb2/3O3-30PbTiO3 single crystals
Authors: Goupil Florian Le , Berenov Andrey , Axelsson Anna-Karin , Valant Matjaz , Alford Neil McN.
Published: June 2012

A direct electrocaloric effect (ECE) measurement system, based on a modified-differential scanning calorimeter (DSC), allowing the acquisition of both thermal (ECE, heat capacity) and electrical (P-E loops, leakage current) information simultaneously, was used to analyze 〈001〉-oriented PbMg1/3Nb2/3O3-30PbTiO3 single crystals. Different electric-field-induced phase transitions were identified on direct ECE measurements and confirmed by dielectric measurements. The strongest ECE (ΔTEC = 0.65 K) was measured for an applied electric field E = 10 kV/cm just above the temperature of depolarization. The direct ECE measurements were compared with indirect measurements obtained from dielectric polarization measurements versus electric field and temperature and a very good agreement was found. A region with negative ΔTEC was identified by both direct and indirect measurements. This phenomenon was attributed to the formation of a reversible field-induced phase transition towards a state with a different polar direction.
Bias-dependent impedance model for ionic polymer-metal composites
Authors: Kengne Fotsing Yannick , Tan Xiaobo
Published: June 2012

Ionic polymer-metal composites (IPMCs) are a novel class of soft sensing and actuation materials with promising applications in robotic and biomedical systems. In this paper, we present a model for nonlinear electrical dynamics of IPMC actuators, by applying perturbation analysis on the dynamics-governing partial differential equation (PDE) around a given bias voltage. By approximating the steady-state electric field under the bias with a piecewise linear function, we derive a linear PDE for the perturbed charge dynamics, which has piecewise constant coefficients and coefficients linear in the spatial variable. Through power series expansion, we solve the PDE to get the charge distribution up to any prescribed order. The perturbed electric field and current are subsequently obtained, which result in a bias-dependent impedance model. This model captures the nonlinear nature of the IPMC electrical dynamics and degenerates to the linear model when the bias is zero. The model predicts that, as the bias voltage increases, both the magnitude and the phase delay of the impedance decrease. These trends are quantitatively verified in experiments, where excellent agreement is achieved between the experimental measurements and model predictions.
Microwave heating-induced static magnetic flux penetration in YBa2Cu3O7–δ superconducting thin films
Authors: Kermorvant Julien , Mage Jean-Claude , Marcilhac Bruno , Lemaître Yves , Bobo Jean-François , Jacominus van der Beek Cornelis
Published: June 2012

The magneto-optical imaging technique is used to visualize the penetration of the magnetic induction in YBa2Cu3O7–δ thin films during surface resistance measurements. The in situ surface resistance measurements were performed at 7 GHz using the dielectric resonator method. When only the microwave magnetic field Hrf is applied to the superconductor, no Hrf-induced vortex penetration is observed, even at high rf power. In contrast, in the presence of a constant magnetic field superimposed on Hrf, we observe a progression of the flux front as Hrf is increased. A local thermometry method based on the measurement of the resonant frequency of the dielectric resonator placed on the YBa2Cu3O7–δ thin film shows that the Hrf–induced flux penetration is due to the increase of the film temperature.
Time-resolved photoluminescence properties of CuInS2/ZnS nanocrystals: Influence of intrinsic defects and external impurities
Authors: Komarala Vamsi K. , Xie Chuang , Wang Yongqiang , Xu Jian , Xiao Min
Published: June 2012

Photoluminescence (PL) lifetime studies of CuInS2 nanocrystals (NCs) are carried out after synthesizing core-shell and compositionally variant structures using time-resolved PL spectroscopy. Long-lived excited state decay times are observed for the NCs, and decay times are very much dependent on the size of the CuInS2 NCs. The emission bands are attributed to the surface (shorter PL lifetime) and defect (longer PL lifetime) related trap states, respectively. The decay dynamics of the CuInS2 NC’s excited-state carriers is very sensitive to the surface, intrinsic defects, and extrinsic impurities. The observed large Stokes shifts and broad PL spectra also reveal the involvement of the defect-related trapping sites in the emission process.
Conductivity of nanosecond discharges in nitrogen and sulfur hexafluoride studied by particle-in-cell simulations
Authors: Levko D. , Tz. Gurovich V. , Krasik Ya. E.
Published: June 2012

The conductivity of the discharge gap during the nanosecond high-voltage pulsed discharge in nitrogen and sulfur hexafluoride is studied using particle-in-cell numerical simulations. It is shown that the conductivity in different locations of the cathode-anode gap is not uniform and that the conductivity is determined by both the runaway and the plasma electrons. In addition, it is shown that runaway electrons generated prior to the virtual cathode formation pre-ionize the discharge gap, which makes it conductive.
Bandgap engineering of ZnSnP2 for high-efficiency solar cells
Authors: Scanlon David O. , Walsh Aron
Published: June 2012

ZnSnP2, an absorber material for solar cells, transitions from an ordered chalcopyrite to a disordered sphalerite structure at high temperatures. We investigate the electronic structure of both phases, combining a screened hybrid density functional with the special quasi-random structure method. We predict a bandgap reduction of 0.95 eV between the ordered and fully disordered materials. Experimental reports are consistent with partial disorder. Tuning of the order parameter would lead to a family of ZnSnP2 phases with bandgaps ranging from 0.75 eV to 1.70 eV, thus providing graded solar cell absorbers from a single material system.
Reduced spin transfer torque switching current density with non-collinear polarizer layer magnetization in magnetic multilayer systems
Authors: You Chun-Yeol
Published: June 2012

Through micromagnetic simulations, it was found that the spin transfer torque (STT) switching current density is reduced with non-collinear polarizer layer magnetization. The dependence of the switching current density on the polarizer layer magnetization angle was investigated, and a typical magnetic tunneling junction structure with an exchange biased synthetic ferrimagnetic polarizer layers was considered. The easy axis of the polarizer layer was varied through controlling the exchange bias field direction in the ellipse cross-section nano-pillar structures. It was found that the switching current density was reduced by 39% when the exchange bias field was 10° from the long axis of the ellipse without the perpendicular STT. When the effect of the perpendicular STT was included, the switching current reductions were general for the non-collinear polarizer layer.
Sulfur-mediated palladium catalyst immobilized on a GaAs surface
Authors: Shimoda M. , Konishi T. , Nishiwaki N. , Yamashita Y. , Yoshikawa H.
Published: June 2012

We present a hard x-ray photoelectron spectroscopy study on the preparation process of palladium catalyst immobilized on an S-terminated GaAs(100) surface. It is revealed that Pd(II) species are reduced on the GaAs surface and yield Pd nanoparticles during the process of Pd immobilization and the subsequent heat treatment. A comparison with the results on GaAs without S-termination suggests that the reduction of Pd is promoted by hydroxy groups during the Pd immobilization and by S during the heat treatment.
Surface plasmon polariton model of high-spatial frequency laser-induced periodic surface structure generation in silicon
Authors: Straub M. , Afshar M. , Feili D. , Seidel H. , König K.
Published: June 2012

In recent years, high-spatial frequency laser-induced surfaces structures have been generated in a large variety of dielectrics. In silicon subwavelength ripples, some of which featured periodicities below 100 nm, were formed using ultrafast lasers. We demonstrate for Si(100) surfaces that generation of a dense electron-hole plasma in the focal spot of ultrashort-pulsed laser light followed by massive excitation of plasma waves provides an explanation for the formation of such high-spatial frequency surface structures. The applied Drude-like model includes carrier-carrier collisions and is in excellent agreement with the experimentally observed ripple period.
Magnetic states and optical properties of single-layer carbon-doped hexagonal boron nitride
Authors: Park Hyoungki , Wadehra Amita , Wilkins John W. , Castro Neto Antonio H.
Published: June 2012

We show that carbon-doped hexagonal boron nitride (h-BN) has extraordinary properties with many possible applications. We demonstrate that the substitution-induced impurity states, associated with carbon atoms, and their interactions dictate the electronic structure and properties of C-doped h-BN. Furthermore, we show that stacking of localized impurity states in small C clusters embedded in h-BN forms a set of discrete energy levels in the wide gap of h-BN. The electronic structures of these C clusters have a plethora of applications in optics, magneto-optics, and opto-electronics.
A new architecture for solar cells involving a metal bridge deposited between active TiO2 particles
Authors: Saehana Sahrul , Arifin Pepen , Khairurrijal  , Abdullah Mikrajuddin
Published: June 2012

The efficiency of titanium dioxide (TiO2)-based film solar cells fabricated by combined spray and electroplating methods was improved by forming metal bridges in the pores between TiO2 nanoparticles. The interfaces between TiO2 nanoparticles and metal bridges formed Schottky contacts, which minimized recombination of electron-hole pairs and increased electron transfer. A maximum efficiency of 4.38% was achieved for cells plated at 50 mA and 55 °C. This efficiency is higher than that reported for solar cells with a similar structure [Saehana et al., AIP Conf. Proc. 1284, 154 (2010); 1415, 163 (2011); IJBAS/IJENS 11, 15 (2011)]. We also identified that both current and temperature influence the morphology of the metal bridges and efficiency of the solar cell.
Anti-reflection coating for nitrogen-vacancy optical measurements in diamond
Authors: Yeung T. K. , Le Sage D. , Pham L. M. , Stanwix P. L. , Walsworth R. L.
Published: June 2012

We realize anti-reflection (AR) coatings for optical excitation and fluorescence measurements of nitrogen-vacancy (NV) color centers in bulk diamond by depositing quarter-wavelength thick silica layers on the diamond surface. These AR coatings improve NV-diamond optical measurements by reducing optical reflection at the diamond-air interface from ≈17% to ≈2%, which allows more effective NV optical excitation and more efficient detection of NV fluorescence. We also show that diamond AR coatings eliminate standing-wave interference patterns of excitation laser intensity within bulk diamond, and thereby greatly reduce spatial variations in NV fluorescence, which can degrade spatially resolved magnetic field sensing using NV centers.
Proposal of an optical nonvolatile switch utilizing surface plasmon antenna resonance controlled by giant magnetoresistance
Authors: Ogasawara Takeshi , Kuwatsuka Haruhiko , Hasama Toshifumi , Ishikawa Hiroshi
Published: June 2012

We propose an operating principle for an optical nonvolatile switch utilizing surface plasmon antenna resonance controlled by giant magnetoresistance. The optical spectra of an array of nanoscale dipole antennas composed of Co/Cu multilayers with parallel and anti-parallel magnetization alignments were estimated by a first-principle calculation and a finite difference time domain electromagnetic field analysis. The extinction efficiency changed more than 40% in the infrared region due to the magnetization alignment, demonstrating its promise as a nonvolatile optical switch.
Spatial configuration and technology strategy of China’s green coal-electricity system
Authors: Ma Tieju , Chi Chunjie
Published: June 2012

Although China is doing much on developing alternative energies, coal will still be the main energy resource for China in the near to medium term. Developing a green coal-electricity system in China is very important for reduction of carbon emissions and local air pollutants, while satisfying China’s rapidly growing electricity demand. This paper first reviews the advancement in optimization models with endogenous technological change and spatial energy systems modeling. Then, present situation and technology strategy of coal-electricity industry in China are analyzed. Three interweaved issues are identified for the development of China’s green coal-electricity system. It can be concluded that the future integration of spatial data with MESSAGE model is vital for the analysis of China’s coal-electricity system. It will be helpful to study optimal spatial configuration and technology development strategies for the development of a green coal-electricity system in China.
Plasmon enhanced resonant defect absorption in thin a-Si:H n-i-p devices
Authors: Lükermann F. , Heinzmann U. , Stiebig H.
Published: June 2012

By embedding silver nanoparticles (Ag NPs) of approximately 20 nm diameter inside the intrinsic layer of thin hydrogenated amorphous silicon (a-Si:H) n-i-p devices, a photocurrent is measured for photon energies below the a-Si:H bandgap. This is attributed to the excitation of charge carriers from defect states created by the incorporation of the Ag inside the silicon network. The defect location inside the strong electromagnetic fields close to the resonant absorbing NPs enables high transition rates. This is a proof of concept for the use of the impurity photovoltaic effect in a-Si:H devices.
The wavelength dependent photovoltaic effects caused by two different mechanisms in carbon nanotube film/CuO nanowire array heterodimensional contacts
Authors: Xu Jia , Sun Jia-Lin , Wei Jinquan , Xu Jinliang
Published: June 2012

Hetrodimensional contacts were fabricated by coating double-walled carbon nanotube (CNT) films on CuO nanowire arrays. Wavelength dependent photovoltaic effects by irradiating the devices with 405, 532, and 1064 nm lasers were observed. Two possible mechanisms responsible for the observed results were discussed. Photoexcitations within CuO nanowires and Schottky barriers in the heterojunctions dominate the photovoltaics in the 405 and 532 nm cases. For the 1064 nm case, the photovoltaic is the result of the excitation within the CNTs and of the heterodimensionality effect. Control experiments on CNT film/CuO granular film hetrodimensional contacts further show the relationship between these two mechanisms.
Note: Automatic mass-flow configuration method for evaluating turbomolecular pump performance
Authors: Hsieh Fan-Chun , Su Yu-Jen , Lin Bing-Hong , Liu Da-Ren , Chen Fong-Zhi
Published: June 2012

An automatic mass-flow configuration method is presented for the evaluation of turbomolecular pump performance. This configuration method is used to obtain an effective mass-flow rate. In addition, the throughput, inlet pressure, and compression ratio are evaluated. The throughput increases with the mass-flow rate. Moreover, the compression ratio increases almost linearly with the outlet pressure for mass-flow rates from 2.97 × 10−9 to 3.96 × 10−7 kg/s. Finally, empirical correlations are proposed for the throughput and inlet pressure.
Oxygen migration induced resistive switching effect and its thermal stability in W/TaOx/Pt structure
Authors: Chen C. , Song C. , Yang J. , Zeng F. , Pan F.
Published: June 2012

We investigate the resistive switching mechanism and the thermal stability in room temperature-fabricated nonvolatile memory consisting of W/TaOx/Pt. By comparing the chemical bonding of Ta 4f between high and low resistance states at W/TaOx and TaOx/Pt interfaces, the switching mechanism is confirmed to be dominated by the oxygen ions drift in the TaOx film. Besides, it is demonstrated that the resistive switching behavior is still dynamic and the resistance can be maintained at temperature as high as 510 K. We found that the resistive switching behavior of TaOx film exhibits little degradation even after annealed at 1273 K.
Thermocoalescence of microdroplets in a microfluidic chamber
Authors: Luong Trung-Dung , Nguyen Nam-Trung , Sposito Alex
Published: June 2012

Droplet coalescence plays an important role in droplet-based microfluidics. This letter reports the phenomenon of thermocoalescence of two droplets in a chamber with a microheater. An integrated resistive sensor allows the measurement of heating temperature. The merging process was investigated at different flow rates. Experimental results showed that the droplet slows down at increasing temperature and eventually merges with the subsequent droplet. Coalescence occurs at a critical heating temperature. The letter discusses the relationship between droplet velocity, critical merging temperature, and flow rates.
Fabrication of solution-processed hydrogenated amorphous silicon single-junction solar cells
Authors: Masuda Takashi , Sotani Naoya , Hamada Hiroki , Matsuki Yasuo , Shimoda Tatsuya
Published: June 2012

Hydrogenated amorphous silicon solar cells were fabricated using solution-based processes. All silicon layers of the p-i-n junction were stacked by a spin-cast method using doped and non-doped polydihydrosilane solutions. Further, a hydrogen-radical treatment under vacuum conditions was employed to reduce spin density in the silicon films. Following this treatment, the electric properties of the silicon films were improved, and the power conversion efficiency of the solar cells was also increased from 0.01% to 0.30%–0.51% under the AM-1.5G (100 mW/cm2) illumination conditions.
Semiconductor ring lasers coupled by a single waveguide
Authors: Coomans W. , Gelens L. , Van der Sande G. , Mezosi G. , Sorel M. , Danckaert J. , Verschaffelt G.
Published: June 2012

We experimentally and theoretically study the characteristics of semiconductor ring lasers bidirectionally coupled by a single bus waveguide. This configuration has, e.g., been suggested for use as an optical memory and as an optical neural network motif. The main results are that the coupling can destabilize the state in which both rings lase in the same direction, and it brings to life a state with equal powers at both outputs. These are both undesirable for optical memory operation. Although the coupling between the rings is bidirectional, the destabilization occurs due to behavior similar to an optically injected laser system.
Epitaxial growth and capacitance-voltage characteristics of BiFeO3/CeO2/yttria-stabilized zirconia/Si(001) heterostructure
Authors: Hu Zhongqiang , Li Meiya , Zhu Yongdan , Pu Shizhou , Liu Xiaolian , Sebo Bobby , Zhao Xingzhong , Dong Shuxiang
Published: June 2012

We report the epitaxial growth of multiferroic BiFeO3 (BFO) film on Si(001) substrate by pulsed laser deposition using CeO2/yttria-stabilized zirconia (YSZ) as buffer layers. The epitaxial relationships of the films were BFO(001)/CeO2(001)/YSZ(001)/Si(001) for out-of-plane and [110]BFO‖[100]CeO2‖[100]YSZ‖[100]Si for in-plane, respectively. Capacitance-voltage characteristics of a Pt/BFO/CeO2/YSZ/p-Si capacitor exhibited clockwise hysteresis loops with a large memory window of 2.5 V at sweeping voltages of ±16 V. Both the high and low capacitance values showed no obvious degradation after 104 s. The improved retention property was attributed to the use of high-k CeO2/YSZ insulating layers that effectively eliminated the charge trapping in the heterostructure.
Genetic and functional analyses implicate the
NUDT11
,
HNF1B
, and
SLC22A3
genes in prostate cancer pathogenesis
Authors: Grisanzio Chiara , Werner Lillian , Takeda David , Awoyemi Bisola C. , Pomerantz Mark M. , Yamada Hiroki , Sooriakumaran Prasanna , Robinson Brian D. , Leung Robert , Schinzel Anna C. , Mills Ian , Ross-Adams Helen , Neal David E. , Kido Masahito , Yamamoto Toshihiro , Petrozziello Gillian , Stack Edward C. , Lis Rosina , Kantoff Philip W. , Loda Massimo , Sartor Oliver , Egawa Shin , Tewari Ashutosh K. , Hahn William C. , Freedman Matthew L.
Published: June 2012

One of the central goals of human genetics is to discover the genes and pathways driving human traits. To date, most of the common risk alleles discovered through genome-wide association studies (GWAS) map to nonprotein-coding regions. Because of our relatively poorer understanding of this part of the genome, the functional consequences of trait-associated variants pose a considerable challenge. To identify the genes through which risk loci act, we hypothesized that the risk variants are regulatory elements. For each of 12 known risk polymorphisms, we evaluated the correlation between risk allele status and transcript abundance for all annotated protein-coding transcripts within a 1-Mb interval. A total of 103 transcripts were evaluated in 662 prostate tissue samples [normal (
n
= 407) and tumor (
n
= 255)] from 483 individuals [European Americans (
n
= 233), Japanese (
n
= 127), and African Americans (
n
= 123)]. In a pooled analysis, 4 of the 12 risk variants were strongly associated with five transcripts (
NUDT11
,
MSMB
,
NCOA4
,
SLC22A3
, and
HNF1B
) in histologically normal tissue (
P
≤ 0.001). Although associations were also observed in tumor tissue, they tended to be more attenuated. Previously, we showed that
MSMB
and
NCOA4
participate in prostate cancer pathogenesis. Suppressing the expression of
NUDT11
,
SLC22A3
, and
HNF1B
influences cellular phenotypes associated with tumor-related properties in prostate cancer cells. Taken together, the data suggest that these transcripts contribute to prostate cancer pathogenesis.
Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin
Authors: Meyer Danilo , Neumann Piotr , Koers Eline , Sjuts Hanno , Lüdtke Stefan , Sheldrick George M. , Ficner Ralf , Tittmann Kai
Published: June 2012

Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 Å resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than
π
-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms.
Autonomous Patterns and Scientific Realism
Authors: Brading Katherine
Published: June 2012

Taking Bogen and Woodward's discussion of data and phenomena as his starting point, McAllister presents a challenge to scientific realism. I discuss this challenge and offer a suggestion for how the scientific realist could respond to both its epistemic and ontological aspects. In so doing, I urge that the scientific realist should not reject ontological pluralism from the start, but should seek to explore versions of scientific realism that leave open the possibility of certain kinds of pluralist ontology. I investigate the available options (in terms of foundationalism, reductionism, and universalism) and use a law-constitutive approach to offer a strategy for the scientific realist who is open-minded about ontological pluralism.
ChromoHub: a data hub for navigators of chromatin-mediated signalling
Authors: Liu Lihua , Zhen Xi Ting , Denton Emily , Marsden Brian D. , Schapira Matthieu
Published: June 2012

Summary: The rapidly increasing research activity focused on chromatin-mediated regulation of epigenetic mechanisms is generating waves of data on writers, readers and erasers of the histone code, such as protein methyltransferases, bromodomains or histone deacetylases. To make these data easily accessible to communities of research scientists coming from diverse horizons, we have created ChromoHub, an online resource where users can map on phylogenetic trees disease associations, protein structures, chemical inhibitors, histone substrates, chromosomal aberrations and other types of data extracted from public repositories and the published literature. The interface can be used to define the structural or chemical coverage of a protein family, highlight domain architectures, interrogate disease relevance or zoom in on specific genes for more detailed information. This open-access resource should serve as a hub for cell biologists, medicinal chemists, structural biologists and other navigators that explore the biology of chromatin signalling.

Availability:  http://www.thesgc.org/chromohub/.

Contact:  matthieu.schapira@utoronto.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome
Authors: Jeggari Ashwini , Marks Debora S , Larsson Erik
Published: June 2012

Summary: Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell, long non-coding RNAs (lncRNAs) have only recently started to emerge as abundant regulators of cell physiology, and their functions may be diverse. A small number of studies describe interactions between small and lncRNAs, with lncRNAs acting either as inhibitory decoys or as regulatory targets of microRNAs, but such interactions are still poorly explored. To facilitate the study of microRNA–lncRNA interactions, we implemented miRcode: a comprehensive searchable map of putative microRNA target sites across the complete GENCODE annotated transcriptome, including 10 419 lncRNA genes in the current version.

Availability:  http://www.mircode.org

Contact:  erik.larsson@gu.se

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Accelerated protein structure comparison using TM-score-GPU
Authors: Hung Ling-Hong , Samudrala Ram
Published: June 2012

Motivation: Accurate comparisons of different protein structures play important roles in structural biology, structure prediction and functional annotation. The root-mean-square-deviation (RMSD) after optimal superposition is the predominant measure of similarity due to the ease and speed of computation. However, global RMSD is dependent on the length of the protein and can be dominated by divergent loops that can obscure local regions of similarity. A more sophisticated measure of structure similarity, Template Modeling (TM)-score, avoids these problems, and it is one of the measures used by the community-wide experiments of critical assessment of protein structure prediction to compare predicted models with experimental structures. TM-score calculations are, however, much slower than RMSD calculations. We have therefore implemented a very fast version of TM-score for Graphical Processing Units (TM-score-GPU), using a new and novel hybrid Kabsch/quaternion method for calculating the optimal superposition and RMSD that is designed for parallel applications. This acceleration in speed allows TM-score to be used efficiently in computationally intensive applications such as for clustering of protein models and genome-wide comparisons of structure.

Results: TM-score-GPU was applied to six sets of models from Nutritious Rice for the World for a total of 3 million comparisons. TM-score-GPU is 68 times faster on an ATI 5870 GPU, on average, than the original CPU single-threaded implementation on an AMD Phenom II 810 quad-core processor.

Availability and implementation: The complete source, including the GPU code and the hybrid RMSD subroutine, can be downloaded and used without restriction at http://software.compbio.washington.edu/misc/downloads/tmscore/. The implementation is in C++/OpenCL.

Contact:  ram@compbio.washington.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Topology of functional networks predicts physical binding of proteins
Authors: Saraç Ömer Sinan , Pancaldi Vera , Bähler Jürg , Beyer Andreas
Published: June 2012

Motivation: It has been recognized that the topology of molecular networks provides information about the certainty and nature of individual interactions. Thus, network motifs have been used for predicting missing links in biological networks and for removing false positives. However, various different measures can be inferred from the structure of a given network and their predictive power varies depending on the task at hand.

Results: Herein, we present a systematic assessment of seven different network features extracted from the topology of functional genetic networks and we quantify their ability to classify interactions into different types of physical protein associations. Using machine learning, we combine features based on network topology with non-network features and compare their importance of the classification of interactions. We demonstrate the utility of network features based on human and budding yeast networks; we show that network features can distinguish different sub-types of physical protein associations and we apply the framework to fission yeast, which has a much sparser known physical interactome than the other two species. Our analysis shows that network features are at least as predictive for the tasks we tested as non-network features. However, feature importance varies between species owing to different topological characteristics of the networks. The application to fission yeast shows that small maps of physical interactomes can be extended based on functional networks, which are often more readily available.

Availability and implementation: The R-code for computing the network features is available from www.cellularnetworks.org

Contacts:  andreas.beyer@biotec.tu-dresden.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality
Authors: Szalay-Bekő Máté , Palotai Robin , Szappanos Balázs , Kovács István A. , Papp Balázs , Csermely Péter
Published: June 2012

Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.

Availability: The plug-in and its user guide can be downloaded freely from: http://www.linkgroup.hu/modules.php.

Contact:  csermely.peter@med.semmelweis-univ.hu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Left ventricular systolic dysfunction associated with pulmonary hypertension riociguat trial (LEPHT): rationale and design
Authors: Ghio Stefano , Bonderman Diana , Felix Stephan B. , Ghofrani Hossein A. , Michelakis Evangelos D. , Mitrovic Veselin , Oudiz Ronald J. , Frey Reiner , Roessig Lothar , Semigran Marc J.
Published: June 2012

Aims

Pulmonary hypertension (PH) due to systolic left ventricular dysfunction (PH‐sLVD) frequently complicates heart failure (HF), and greatly worsens the prognosis of patients with sLVD, but as yet has no approved treatment. The LEPHT study aims to characterize the haemodynamic profile, safety, tolerability, and pharmacokinetic profile of riociguat (BAY 63‐2521), an oral stimulator of soluble guanylate cyclase, in patients with PH‐sLVD.

Methods and results

This 16‐week, phase IIb, randomized, placebo‐controlled, double‐blind study enrols patients with PH‐sLVD, defined as left ventricular ejection fraction (LVEF) ≤40% and mean pulmonary arterial pressure (PAPmean) ≥25 mmHg at rest. Patients using optimized HF medication will receive placebo or riociguat 0.5 mg, 1 mg, or up to 2 mg three times daily. The dose will be titrated for 8 weeks, based on systolic blood pressure and well‐being, followed by 8 weeks of treatment at a stable dose. The primary efficacy variable is PAPmean, while secondary efficacy endpoints include LVEF, exercise capacity, quality of life, and other haemodynamic and echocardiographic measurements. Safety and pharmacokinetics will also be assessed. After the 16‐week study, patients will have the opportunity to be treated with riociguat in a long‐term extension phase.

Conclusion

The LEPHT study will provide valuable information on the haemodynamic, echocardiographic, and preliminary clinical effects of riociguat in patients with PH‐sLVD.

Trial registration

NCT01065454