bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of excitation wavelength on the Raman scattering from optical phonons in silicon carbide monofilaments
Authors: Ward Yanling , Young Robert J. , Shatwell Robert A.
Published: July 2007

The Raman spectra of silicon carbide (SiC) monofilaments prepared by the chemical vapor deposition method have been investigated as a function of the excitation wavelength. As the excitation wavelength increases from 442 to 785 nm, significant changes in the Raman spectra from the SiC optical phonons are observed. It was found that Raman spectra excited with a shorter wavelength, are similar to those of bulk crystalline 3C-SiC whereas Raman spectra excited with a longer wavelength show a very broad feature between 600 and 1000 cm−1, similar to that of amorphous SiC. Possible reasons have been discussed to explain the effect of changing excitation wavelength on the line shape of Raman spectra from the SiC monofilaments.
Transport properties of ZnFe2O4−δ thin films
Authors: Marcu Aurelian , Yanagida Takeshi , Nagashima Kazuki , Tanaka Hidekazu , Kawai Tomoji
Published: July 2007

This study presents an experimental investigation on the transport properties of ZnFe2O4−δ (ZFO) thin films to clarify the ambient atmosphere effects on the transport properties by varying the oxygen pressure and the substrate temperature. Previous investigations have demonstrated the significant role of Fe2+ ion concentration due to oxygen vacancies on the transport properties of ZFO. Our systematic investigation suggests that the electrical transport of ZFO thin films is also strongly influenced by structural disorders and vacancies.
Electronic structure and linear optical properties of YAl3(BO3)4
Authors: Wang Yuhua , Wang Lingli , Li Handong
Published: July 2007

The electronic structure and linear optical properties of YAl3(BO3)4 (YAB) crystal are calculated by density functional method with the local-density approximation. An indirect band gap of 6.54eV and a direct gap of 6.91eV at M are obtained for YAB. The calculated total and partial densities of states indicate that the top valence band is constructed from O 2p, B 2s, and B 2p states and the low conduction band mostly consists of Y 4d and B 2p states. The calculated linear optical properties, such as refractive index and absorption spectrum, are in good agreement with experimental values.
Numerical studies of International Linear Collider positron target and optical matching device field effects on beam
Authors: Antipov Sergey , Spentzouris Linda , Liu Wanming , Gai Wei
Published: July 2007

For an International Linear Collider (ILC) undulator-based positron source target configuration, a strong optical matching device (OMD) field is needed inside the target to increase the positron yield (by more than 40%) [Y. K. Batygin, Proceedings of the 2005 ALCPG and ILC Workshops, Snowmas, CO, 14–27 August 2005 (unpublished)] It is also required that the positron target be constantly rotated to reduce thermal and radiation damages. Eddy currents, produced by an OMD field in turn, interact with the magnetic field and produce a drag (stopping) force. This force not only produces heat in the disk but also creates a dipole deflecting field, which affects the beam. Therefore it is important to simulate such a system in detail to design the motor and cooling system and also a correction magnet system. In order to guide the ILC target design, an exact simulation of the spinning disk in a magnetic field is required. In this paper we present a simulation method implemented using COMSOL and compare it with the experimental results recently obtained at Stanford Linear Accelerator Center and Lawrence Livermore National Laboratory. Good agreement between the simulation and the experiment gives confidence in the validity of the method. We give detailed results on the proposed ILC target system, such as parametric studies for reduction of the power required to keep the target spinning. We present simulation results of the induced deflection field and of the reduction of the OMD field effect.
Acoustic limitations on the efficiency of machining by femtosecond laser-induced optical breakdown
Authors: Lee Sanghyun , Bull Joseph L. , Hunt Alan J.
Published: July 2007

The authors find an unexpected strong influence of acoustic phenomena on the efficiency of water-assisted femtosecond laser nanomachining. Analysis of acoustic interactions across a metastable structure of two phase flow in a nanocapillary, predicts acoustic nodes that strongly limit machining efficiency. Strategies for fabrication of high aspect ratio channels (>1000) are identified: increasing the speed of acoustic transmission delays formation of nodes, and can be accomplished by maximizing hydrogen in the gas phase or by varying pressure. These results reveal that laser machining can be strongly limited by acoustic phenomena not previously considered in the analysis of optical breakdown.
Tuning exchange-bias properties by thermal effects in a hard/soft bilayer
Authors: Hauet T. , Mangin S. , Montaigne F. , Borchers J. A. , Henry Y.
Published: July 2007

The effect of temperature on exchange-bias properties of an antiferromagnetically coupled hard/soft bilayer (Tb12Fe88∕Gd40Fe60) is studied. In a similar manner to its cooling field dependence, a continuous transition from a negative to a positive exchange-bias field is observed with increasing temperature. The changes of magnetic configuration responsible for this effect are studied, combining both magnetization and polarized neutron reflectivity measurements. The temperature is found to enhance the exchange-bias training effect as a result of the relaxation of an interface domain wall. The present study demonstrates that both temperature and cooling field may be used to tune the exchange field.
How short-range attractions impact the structural order, self-diffusivity, and viscosity of a fluid
Authors: Krekelberg William P. , Mittal Jeetain , Ganesan Venkat , Truskett Thomas M.
Published: July 2007

We present molecular simulation data for viscosity, self-diffusivity, and the local structural ordering of (i) a hard-sphere fluid and (ii) a square-well fluid with short-range attractions. The latter fluid exhibits a region of dynamic anomalies in its phase diagram, where its mobility increases upon isochoric cooling, which is found to be a subset of a larger region of structural anomalies, in which its pair correlations strengthen upon isochoric heating. This “cascade of anomalies” qualitatively resembles that found in recent simulations of liquid water. The results for the hard-sphere and square-well systems also show that the breakdown of the Stokes–Einstein relation upon supercooling occurs for conditions where viscosity and self-diffusivity develop different couplings to the degree of pairwise structural ordering of the liquid. We discuss how these couplings reflect dynamic heterogeneities. Finally, we note that the simulation data suggest how repulsive and attractive glasses may generally be characterized by two distinct levels of short-range structural order.
Advanced gradientlike methods for rigid-body molecular dynamics
Authors: Omelyan Igor P.
Published: July 2007

A novel approach is developed to integrate the equations of motion in many-body systems of interacting rigid polyatomic molecules. It is based on an advanced gradientlike decomposition technique in the presence of translational and orientational degrees of freedom. As a result, a new class of reversible phase-space volume preserving fourth-order algorithms for rotational motion is introduced. Contrary to standard nongradient decomposition integrators, the algorithms derived take into account additional analytically integrable terms in the exponential propagators, while the arising gradients are expressed in terms of forces and torques. This allows one to increase significantly the precision of the integration and, at the same time, reduce the increased computational costs. The optimized second-order integrator is also presented. The gradientlike and optimized algorithms are tested in molecular dynamics simulations of water versus well-established integrators known previously. It is shown that the new algorithms lead to the best efficiency in the rigid-body integration.
Dynamic response and reinforcement mechanism of composites embedded with tetraneedlelike ZnO nanowhiskers
Authors: Cao M. S. , Zhou W. , Shi X. L. , Chen Y. J.
Published: July 2007

A type of glass-fiber reinforced composites was prepared by dispersing tetraneedlelike ZnO nanowhiskers in epoxy matrix. The as-prepared composites exhibited excellent dynamic mechanical properties after the effective dispersion of ZnO nanowhiskers in epoxy. Patulous and fractured reinforcement modes for the composites were proposed. The high strength of composites was attributed to the three dimensional structure of tetraneedlelike ZnO nanowhiskers and the corresponding stress transfer.
Field emission of silicon emitter arrays coated with sol-gel (Ba0.65Sr0.35)1−xLaxTiO3 thin films
Authors: Lu H. , Pan J. S. , Chen X. F. , Zhu W. G.
Published: July 2007

( Ba 0.65 Sr 0.35 ) 1 − x La x TiO 3 (BSLT) thin films with different La concentrations have been deposited on Si field emitter arrays (FEAs) using sol-gel technology for field electron emission applications. The films exhibit the perovskite structure at low La substitution level (x≤0.5) and the pyrochlore phase at high La concentration (x≥0.75). The 30-nm-thick BSLT (x=0.25) thin film has higher crystallinity of perovskite structure in the surface region. An x-ray photoelectron spectroscopy study indicates that the oxygen vacancy concentration decreases with La substitution. With respect to the undoped Ba0.65Sr0.35TiO3 thin film, the Fermi level shifts down for the BSLT sample with x=0.1 ascribed to the decreasing oxygen vacancy concentration, and then shifts up for the BSLT sample with x=0.25 attributed to the increasing La substitution level. In highly doped films with an x value over 0.5, it shifts down again associated with the second pyrochlore phase formation. The best enhancement in field emission is found for the BSLT-coated (x=0.25) Si FEAs due to the improved perovskite structure in the surface region and up-moved Fermi level of the coating.
Development of submillisecond Brillouin spectroscopy with optical beating technique
Authors: Minami Yasuo , Yogi Takeshi , Mitani Shujiro , Sakai Keiji
Published: July 2007

We developed a rapid measurement system for Brillouin scattering spectroscopy, which requires the data acquisition time of only 100 μs. The optical beating detection system was improved to directly observe and accumulate the incoherent signal carrying the information of the power spectrum of the scattered light. The temporal evolution of the mechanical properties of material can be measured with high time resolution. It is also possible to apply it to the light absorbing sample, since the short time radiating of the laser beam does not cause serious temperature change in the sample. The performance was actually demonstrated for the light absorbing material.
Observation of three-photon absorption and saturation of two-photon absorption in amorphous nanolayered Se/As2S3 thin film structures
Authors: Adarsh K. V. , Sangunni K. S. , Sandeep C. S. Suchand , Philip Reji , Kokenyesi S. , Takats V.
Published: July 2007

We have studied the nonlinear optical properties of nanolayered Se/As2S3 film with a modulation period of 10 nm and a total thickness of 1.15 μm at two [1064 nm (8 ns) and 800 nm (20 ps)] wavelengths using the standard Z-scan technique. Three-photon absorption was observed at off-resonant excitation and saturation of two-photon absorption at quasiresonant excitation. The observation of the saturation of two-photon absorption is because the pulse duration is shorter than the thermalization time of the photocreated carriers in their bands and three-photon absorption is due to high excitation irradiance.
Temperature increment in a current-heated nanowire for current-induced domain wall motion with finite thickness insulator layer
Authors: You Chun-Yeol , Ha Seung-Seok
Published: July 2007

The authors investigate the insulator-layer-thickness-dependent temperature increment in the nanowire for the current-induced domain wall motion. Practically, a finite thickness insulator layer must be placed between the semi-infinite substrate and the metallic nanowire for an electric insulation. Since a good electric insulator is also a thermal insulator, the temperature increment of the nanowire depends on the insulator layer’s thickness. An approximated analytic expression of the insulator thickness dependent temperature increment is obtained by employing the Fourier-transformed Green’s function method, and it is confirmed by the full numerical finite element method. The authors find that the control parameter of the temperature increment is the ratio between the insulator layer’s thickness and the nanowire’s width.
Observation of high permittivity in Ho substituted BaZr0.1Ti0.9O3 ceramics
Authors: Bhaskar Reddy S. , Ramachandra Rao M. S. , Prasad Rao K.
Published: July 2007

The authors observed an extremely high permittivity (∼35000 at TC) in barium zirconate titanate (BaZr0.1Ti0.9O3) ceramics with holmium substitution (1–5mol%) in Ba site. Careful microstructural investigation and energy dispersive spectroscopy analysis of the 1–2mol% of Ho substituted ceramics showed the enrichment of a Ho-phase along the grain boundaries with a composition close to the Ho2Ti2O7 pyrochlore. The formation of Ho rich phase resulted in the Maxwell-Wagner polarization mechanism, which leads to this unusually high permittivity. Ceramics with 3mol% or higher Ho content showed lesser permittivity values compared to 1–2mol%, probably due to the increase in pyrochlore phase. These high dielectric constant ceramics are useful in nanoscale devices.
Correlation between surface composition and luminescence of nanocrystalline silicon particles dispersed in pure water
Authors: Hiruoka Masaki , Sato Keisuke , Hirakuri Kenji
Published: July 2007

The stability of the luminescene of nanocrystalline silicon (nc-Si) particles passivated with a number of different elements, including hydrogen, carbon, and oxygen, has been investigated in pure water. Each sample emitted red light with a peak wavelength in the range of 740–800nm. The intensity of red luminescence decreased after a short period of time when the hydrogen- and/or carbon-passivated samples were immersed in pure water. Further, the peak wavelength concomitantly shifted toward a shorter wavelength. These effects were attributed to the generation of defects (Pb centers), the reduction in particle size due to the desorption of hydrogen and/or carbon atoms, and the replacement of the Si–H and/or Si–C bonds, respectively, with Si-O bonds on the surface of nc-Si particles. On the other hand, the oxygen-passivated samples showed stable luminescence in addition to a slight blueshift of the peak wavelength upon immersion in pure water for 400h. This stability was attributed to the development of stable surface conditions. These results are a strong indication that the stability of luminescence in pure water can be remarkably improved by oxygen passivation on the surface of nc-Si particles.
Dislocation-related optical absorption in plastically deformed GaN
Authors: Hasegawa Hiroki , Kamimura Yasushi , Edagawa Keiichi , Yonenaga Ichiro
Published: July 2007

Optical absorption spectra have been measured for plastically deformed GaN to investigate effects of dislocations. The interband absorption edge has been observed to shift noticeably to lower photon energy by deformation, which has been analyzed based on a model of the Franz-Keldysh effect by the electric fields associated with charged dislocations. This model has satisfactorily reproduced the observed absorption spectra. In a lower energy region, a decrease in free-carrier absorption by deformation has been observed, which is partly attributable to the decrease in carrier concentration by carrier trapping at dislocation states.
High speed atomic force microscope lithography driven by electrostatic interaction
Authors: Ding Lei , Li Yan , Chu Haibin , Li Changqing , Yang Zhaohui , Zhou Weiwei , Tang Zi Kang
Published: July 2007

This letter paper describes a scanning probe lithography method for fabricating patterns of various nanoparticles on SiOx∕Si substrate. The electrostatic interaction resulting from the charge separation caused by the friction between the atomic force microscope (AFM) tip and the substrate was utilized as the driving force for the deposition of nanoparticles. The nanoparticles loaded on the tip were transported onto the substrate as the AFM tip moved at a speed as high as hundreds of μm∕s. This method allows patterning functional inorganic nanoparticles with a deliberate control over the feature size and shape.
Probe-surface interaction mapping in amplitude modulation atomic force microscopy by integrating amplitude-distance and amplitude-frequency curves
Authors: Prokhorov V. V. , Saunin S. A.
Published: July 2007

The procedure integrating independent amplitude-distance and amplitude-frequency measurements into a single routine with two variables (frequency and distance) has been developed. The domains of attraction and repulsion regimes of probe-surface interactions are clearly identified on two-dimensional patterns in frequency-distance space due to the stepwise change in a slope of constant amplitude lines and their shear on boundaries. Pattern evolution with the driving amplitude variation was studied, and three characteristic pattern types were selected. The topology of patterns obtained at intermediate drivings indicates that the probe-surface interaction is attractive at large and low cantilever-surface separations being repulsive at intermediate separations.
Photoluminescence of dome and hut shaped Ge(Si) self-assembled islands embedded in a tensile-strained Si layer
Authors: Shaleev M. V. , Novikov A. V. , Yablonskiy A. N. , Drozdov Y. N. , Lobanov D. N. , Krasilnik Z. F. , Kuznetsov O. A.
Published: July 2007

The effect of the growth temperature (Tg) on photoluminescence of Ge(Si) self-assembled islands embedded between tensile-strained Si layers was studied. The observed redshift of the photoluminescence peak of the dome islands with a decrease of Tg from 700to630°C is associated with an increase of Ge content in the islands and with the suppression of smearing of the strained Si layers. The blueshift of the photoluminescence peak with a decrease of Tg from 630to600°C is associated with a change of the type of islands on surface, which is accompanied by a decrease in islands’ height.
Analytical model for island growth in atomic layer deposition using geometrical principles
Authors: Nilsen O. , Mohn C. E. , Kjekshus A. , Fjellvåg H.
Published: July 2007

Island growth has been shown to also occur for atomic layer deposition (ALD) processes. This article presents a relatively simple analytical model using geometrical principles with few independent variables on evolution of thickness and roughness in island-dominated ALD processes. The model is well suited for the fitting of experimental data to extract parameters such as density of islands and growth rate. It allows islands of various shapes, but most of the attention here is devoted to cone and hemispherical shaped islands in a hexagonal grid on a flat substrate. For a selection of cases, exact analytical expressions are derived. The model shows that it is possible to reproduce the growth characteristics of substrate-inhibited growth of both types 1 and 2 with a suitable choice of functional form of the islands. Finally it is compared with previously advanced models describing substrate-inhibited growth.
Synthesis of band-gap-reduced p-type ZnO films by Cu incorporation
Authors: Ahn Kwang-Soon , Deutsch Todd , Yan Yanfa , Jiang Chun-Sheng , Perkins Craig L. , Turner John , Al-Jassim Mowafak
Published: July 2007

p -type ZnO thin films with significantly reduced band gaps were synthesized by heavy Cu incorporation at room temperature and followed by postdeposition annealing at 500°C in air for 2h. All the films were synthesized by rf magnetron sputtering on F-doped tin oxide-coated glass. The p-type conductivity was confirmed by Mott-Schottky plots and illuminated I-V analysis. The Cu+1 acceptor states (at substitutional sites) and their band-gap reduction were demonstrated by UV-visible absorption and x-ray excited valence band measurements.
Magnetic anisotropy in arrays of Ni, CoFeB, and Ni/Cu nanowires
Authors: Carignan Louis-Philippe , Lacroix Christian , Ouimet Alexandre , Ciureanu Mariana , Yelon Arthur , Ménard David
Published: July 2007

An effective field model based on intrawire and interwire dipolar interactions has been developed in order to describe the magnetic anisotropy in arrays of homogeneous and multilayer nanowires. Variable angle ferromagnetic resonance (FMR) and vibrating sample magnetometry (VSM) characterization techniques were used to determine the effective interaction field acting on Ni, CoFeB, and Ni/Cu nanowires. FMR spectra are well described by a rigid magnetization model and VSM data are in rough agreement with a mean longitudinal field model. FMR and VSM values of the effective fields are mutually consistent and in fair agreement with the values calculated with the model. The results show that the anisotropy of our arrays is strongly dominated by the dipolar interactions.
Lifetime measurements on collector optics from Xe and Sn extreme ultraviolet sources
Authors: Srivastava S. N. , Thompson K. C. , Antonsen E. L. , Qiu H. , Spencer J. B. , Papke D. , Ruzic D. N.
Published: July 2007

Next generation lithography to fabricate smaller and faster chips will use extreme ultraviolet (EUV) light sources with emission at 13.5nm. A challenging problem in the development of this technology is the lifetime of collector optics. Mirror surfaces are subjected to harsh debris fluxes of plasma in the form of ions, neutrals, and other radiation, which can damage the surface and degrade reflectivity. This manuscript presents the measurement of debris ion fluxes and energies in absolute units from Xe and Sn EUV sources using a spherical sector ion energy analyzer. Experimentally measured erosion on Xe exposed samples is in good agreement with predicted erosion. This result allows prediction of erosion using measured ion fluxes in experiment. Collector optic lifetime is then calculated for Xe and Sn sources without debris mitigation. Lifetime is predicted as 6h for Xe EUV sources and 34h for Sn EUV sources. This result allows calculation of expected collector optic lifetimes, which can be an important tool in optimizing source operation for high volume manufacturing.
Bulk FePt-based nanocomposite magnets with enhanced exchange coupling
Authors: Rong Chuan-Bing , Nandwana Vikas , Poudyal Narayan , Liu J. Ping , Kozlov Mikhail E. , Baughman Ray H. , Ding Yong , Wang Zhong Lin
Published: July 2007

High density bulk FePt/Fe3Pt nanocomposite magnets have been prepared by high-pressure warm compaction of chemically synthesized FePt and Fe3O4 nanoparticles. It is found that the density increases with the compaction pressure and temperature. Density of the bulk samples up to 95% theoretical value has been obtained while the nanostructured morphology is retained. It is also observed that a high pressure expedites the FePt phase transition from the disordered face-centered-cubic structure to the L10 structure, leading to the phase transition temperature in the compacts one hundred degrees lower than usual. This phase transition in turn facilitates the consolidation of the compacts. Magnetic characterizations showed that interphase exchange coupling is enhanced upon the compaction. Post-annealing of the compacts results in further improved magnetic performance of the compacts owing to interface modification. Energy products up to 16.3 MG Oe of the isotropic bulk nanocomposite magnets have been achieved, which is significantly higher than the theoretical limit for fully dense single-phase FePt magnets.
Low energy stable plasma calibration facility
Authors: Frederick-Frost K. M. , Lynch K. A.
Published: July 2007

We have designed and fabricated a low energy plasma calibration facility for testing and calibration of rocket-borne charged-particle detectors and for the investigation of plasma sheath formation in an environment with ionospheric plasma energies, densities, and Debye lengths. We describe the vacuum system and associated plasma source, which was modified from a Naval Research Laboratory design [Bowles et al. Rev. Sci. Instrum. 67, 455 (1996)]. Mechanical and electrical modifications to this cylindrical microwave resonant source are outlined together with a different method of operating the magnetron that achieves a stable discharge. This facility produces unmagnetized plasmas with densities from 1×103∕cm3to6×105∕cm3, electron temperatures from 0.1to1.7eV, and plasma potentials from 0.5to8V depending on varying input microwave power and neutral gas flow. For the range of input microwave power explored (350–600W), the energy density of the plasma remains constant because of an inverse relationship between density and temperature. This relationship allows a wide range of Debye lengths (0.3–8.4cm) to be investigated, which is ideal for simulating the ionospheric plasma sheaths we explore.
Detecting dynamic signals of ideally ordered nanohole patterned disk media fabricated using nanoimprint lithography
Authors: Oshima Hirotaka , Kikuchi Hideyuki , Nakao Hiroshi , Itoh Ken-ichi , Kamimura Takuya , Morikawa Takeshi , Matsumoto Koji , Umada Takahiro , Tamura Hiroaki , Nishio Kazuyuki , Masuda Hideki
Published: July 2007

The authors have fabricated ideally ordered alumina nanohole patterned disk media via anodic oxidation and nanoimprint lithography with a thermoplastic resist. The ordered arrays of alumina nanoholes with 100nm pitch, filled with Co by electrodeposition, were created over a macroscopically large area on a hard-disk substrate using these industrially applicable nanofabrication technologies. Stable flight of a perpendicular magnetic head above the media and perpendicular magnetic anisotropy of the Co nanopillars enable high-speed dynamic magnetic recording and playback. Dynamic periodic signals that matched the nanopillar periodicity were clearly observed after writing bit patterns, showing alternate reversal of magnetization of the nanopillars.
No bias pi cell using a dual alignment layer with an intermediate pretilt angle
Authors: Kim Jong Bok , Kim Kyung Chan , Ahn Han Jin , Hwang Byoung Har , Kim Jong Tae , Jo Sung Jin , Kim Chang Su , Baik Hong Koo , Choi Chu Ji , Jo Min Kyoung , Kim Youn Sang , Park Jin Seol , Kang Daeseung
Published: July 2007

The authors fabricated a no-bias pi cell using a dual alignment layer with an intermediate pretilt angle via a rubbing. In the dual alignment layer system, the competition between crest region favoring the vertical alignment and trough region favoring planar alignment made it possible to achieve various pretilt angles, and adjusted pretilt angle from 90° to 20° with rubbing. In addition, as the intermediate pretilt angle plays a role in eliminating the activation energy and thus allowing formation of the initial bend state in pi cell fabrication, this approach achieved a no-bias pi cell for a liquid crystal display with both low power consumption and fast response.
Application of weak ferromagnetic BiFeO3 films as the photoelectrode material under visible-light irradiation
Authors: Chen X. Y. , Yu T. , Gao F. , Zhang H. T. , Liu L. F. , Wang Y. M. , Li Z. S. , Zou Z. G. , Liu J.-M.
Published: July 2007

Bi Fe O 3 films prepared by pulsed laser deposition on Pt∕TiO2∕SiO2∕Si substrates were studied as photoelectrode for water splitting. Under visible-light irradiation, the photocurrent intensity of the polycrystalline BiFeO3 film was found to double that of the amorphous one in a three-electrode cell. The incident photon to current conversion efficiency for the polycrystalline BiFeO3 electrode was approximately 16% at 350nm and 7% at 530nm at 1.5V (versus saturated calomel electrode). The ferromagnetism of the amorphous BiFeO3 film was an order of magnitude weaker than that of the polycrystalline one, supporting the “size effect” explanation for magnetic origin.
Electromagnetomechanical coupling characteristics of plastoferrites
Authors: Brosseau Christian , NDong Wilfried , Castel Vincent , Youssef Jamal Ben , Vidal Alain
Published: July 2007

The impetus of this work was to investigate the electromagnetic and tensile properties of several commercially available plastoferrites (PFs) at ambient conditions. The approach involved selection of a set of PFs and measuring their complex effective permittivity ε=ε′−jε″ and permeability μ=μ′−jμ″ under uniaxial stress at microwave frequencies (0.1–4.5GHz) and room temperature. We analyze the ε and μ spectra for tensilely strained PFs up to 3%. Comparing our experimental ε data against several dielectric relaxational behaviors, we find that the main physics cannot be understood with a single relaxation mechanism. We then go on to consider the magnetic permeability spectra in the microwave range of frequencies and show that an appropriate magnetization mechanism is given by the gyromagnetic spin resonance mechanism. We use a combination of Bruggeman mean field analysis and Landau-Lifshitz-Gilbert modeling to reproduce the experimental bimodal line-shape characteristics of the effective complex magnetic permeability. These findings are discussed in light of the polydispersity in size of the ferrite gains contained in the PFs. The vibrating sample magnetometry investigations of the static magnetization are found to be consistent with this modeling. In addition, the analysis shows also how magnetized PFs respond to electromagnetic waves, and we evaluate the hysteretic behaviors of ε and μ. More importantly we show that the ε and μ measurements under stress can be explained in terms of a Gaussian molecular network model in the limit of low stress. The present results have important applications in magnetoactive smart composite materials, e.g., flexible circuit technology in the electronics industry (sensors, actuators, and micromechanical systems), functionalized artificial skin, and muscles for robotic applications.
Competition between excitons and exciplexes: Experiments on multilayered organic light emitting diodes
Authors: Castellani M. , Berner D.
Published: July 2007

The electronic processes responsible for charge transport and electroluminescence in multilayered organic light emitting diodes (OLEDs) are very sensitive to the properties of the organic heterojunction. In particular, the height of the energy barrier affects the way in which electrons and holes meet at the heterojunction, the way in which the barrier is crossed, and the probability for photon creation. We investigate these aspects experimentally using a family of OLED devices in which different hole transporting materials are used in otherwise identical device architectures to vary the interfacial hole barrier over a wide energy range. We find that the quantum efficiency of the device is maximum for low-energy barriers and drops for high barrier values where a redshifted electroluminescence spectrum is observed. This shift is attributed to exciplex generation at the heterojunction. The contributions of exciton and exciplex annihilation in radiative and nonradiative channels to the charge flow within the heterojunction region are separated and quantified.
Electrically switchable nonreciprocal transmission of plasmonic nanorods with liquid crystal
Authors: Evans P. R. , Wurtz G. A. , Hendren W. R. , Atkinson R. , Dickson W. , Zayats A. V. , Pollard R. J.
Published: July 2007

The electro-optic response of a cell consisting of a thin layer of liquid crystal deposited onto gold nanorods embedded in thin film alumina with a transparent top electrode has been investigated. For p-polarized light incident from the liquid crystal side, the extinction peak associated with the nanorod longitudinal plasmon resonance is completely suppressed. The peak could be recovered by applying an external electric field parallel to the long axis of the nanorods. No extinction peak suppression is observed when the light was incident from the nanorod side of the cell. The effect is explained by polarization properties of liquid crystal.
Micropatterning metal electrode of organic light emitting devices using rapid polydimethylsiloxane lift-off
Authors: Yu Jennifer , Bulović Vladimir
Published: July 2007

The authors demonstrate a subtractive stamping technique for patterning metal electrodes of organic light emitting devices. Patterning is achieved by placing a relief patterned polydimethylsiloxane stamp in contact with a planar metal electrode film and subsequently peeling off the stamp. A fast peel rate increases the weak adhesion energy of the stamp to the metal so that no surface treatment, pressure, or temperature control is necessary to lift-off the metal film in contact with the stamp. Patterning is dependent on metal film thickness, geometry of the features, and peel direction of stamp release. The minimum feature size patterned is 13μm wide stripes within <1μm in-plane edge roughness and 0.1μm height transition region of the patterned edge.
Multicontact measurements of a superconducting Sn nanowire
Authors: Lucot D. , Pierre F. , Mailly D. , Yu-Zhang K. , Michotte S. , de Menten de Horne F. , Piraux L.
Published: July 2007

Multicontact transport measurements were performed on a superconducting tin nanowire to probe its local properties and especially the formation of phase-slip centers (PSCs). We find that normal metal contacts strongly disturb the behavior of the nanowire. In particular, they provide an efficient escape way for the energy dissipated at the PSC and thereby limit its size. We were able to observe PSC at 30mK with an associated relaxation time typical to that of the inelastic scattering time for bulk normal tin.
Interaction of electron irradiation with nitrogen-related deep levels in InGaAsN
Authors: Khan Aurangzeb , Gou J. , Imazumi M. , Yamaguchi M.
Published: July 2007

The authors present an investigation of 1MeV electron irradiation-induced defects in p-InGaAsN and their impact on nitrogen-related defects. A hitherto existing nitrogen-related electron trap E1 (0.20eV) shows a significant increase in concentration after 1MeV electron irradiation. In addition, 1MeV electron irradiation induced a hole trap H1 at energy of about 0.75eV above the valence band. Isothermal annealing analysis indicates that E1 is a complex defect involving an interstitial or a substitutional atom in combination with some other defect, whose concentration is enhanced by irradiation. A correlation exists between the recovery of free carrier concentration and recovery of the E1 center to preradiation concentrations, which indicates the possibility of the E1 as an acceptorlike center.
Development of a direct three-dimensional biomicrofabrication concept based on electrospraying a custom made siloxane sol
Authors: Sullivan Alice C. , Jayasinghe Suwan N.
Published: July 2007

We demonstrate here the discovery of a unique and direct three-dimensional biomicrofabrication concept possessing the ability to revolutionize the jet-based fabrication arena. Previous work carried out on similar jet-based approaches have been successful in fabricating only vertical wall/pillar-structures by the controlled deposition of stacked droplets. However, these advanced jet-techniques have not been able to directly fabricate self-supporting arches/links (without molds or reaction methods) between adjacent structures (walls or pillars). Our work reported here gives birth to a unique type of jet determined by high intensity electric fields, which is derived from a specially formulated siloxane sol. The sol studied here has been chosen for its attractive properties (such as an excellent cross-linking nature as well as the ability to polymerize via polycondensation on deposition to its biocompatability), which promotes direct forming of biostructures with nanometer (<50 nm) sized droplets in three dimensions. We foresee that this direct three-dimensional biomicrofabrication jet technique coupled with a variety of formulated sols having focused and enhanced functionality will be explored throughout the physical and life sciences.
Eye Movements in Drawing Simple Lines
Authors: Tchalenko John
Published: July 2007

As part of an investigation into real-world drawing, eye movements and eye – hand interactions have been recorded for twenty subjects of varying drawing experience drawing simple straight and curved lines and a square. Two modes of eye — hand behaviour were observed. In the first, named ‘close pursuit’, fixations closely followed the pencil with a sequence of small saccades. In the second, named ‘target locking’, a stable fixation was made on the end-point of the line throughout the entire drawing action. Depending on subject and type of line, close pursuit, target locking, or a combination of these modes was used regardless of previous drawing experience. The results are discussed in terms of the role of the eye in the control of the movement trajectory of the hand.
Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics
Authors: Wu Song , Yang Jie , Wu Rongling
Published: July 2007

Motivation: Functional mapping has proven to be powerful for characterizing quantitative trait loci (QTL) that control complex dynamic traits. More recently, functional mapping has been extended to identify the host QTL responsible for HIV dynamics by incorporating a parametric bi-exponential function for earlier stages of viral load trajectories. However, existing functional mapping cannot be used to map long-term HIV dynamics because no mathematical functions are available for later stages of HIV dynamic changes.

Results: We derived a statistical model for functional mapping of dynamic QTL through characterizing HIV load trajectories during a long-term period semiparametrically. The new model was constructed within the maximum likelihood framework and implemented with the EM-simplex algorithm. It allows for the test of differences in the genetic control of short- and long-term HIV dynamics and the characterization of the effects of viral-host genome interaction. Extensive simulation studies have been performed to test the statistical behavior of this model. The new model will provide an important tool for genetic and genomic studies of human complex diseases like HIV/AIDS and their pathological progression.

Availability: Available on request from the corresponding author.

Contact: rwu@stat.ufl.edu
Learning to extract relations for protein annotation
Authors: Kim Jee-Hyub , Mitchell Alex , Attwood Teresa K. , Hilario Melanie
Published: July 2007

Motivation: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real-world scenarios such as in the biomedical domain. In this article, we describe an IE system that requires only sentences labelled according to their relevance or not to a given topic by domain experts.

Results: We applied our system to meet the annotation needs of a well-known protein family database; the results show that our IE system can annotate proteins with a set of extracted relations by learning relations and IE rules for disease, function and structure from only relevant and irrelevant sentences.

Contact: jee.kim@cui.unige.ch
Polyploids, genome halving and phylogeny
Authors: Sankoff David , Zheng Chunfang , Zhu Qian
Published: July 2007

Motivation: Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in the same phylogeny.

Results: We propose a framework for solving this difficulty by integrating the rearrangement median and genome halving algorithms. Though the framework is general, some problems remain open. We implement a heuristic solution to the prototypical case of a tree with one tetraploid and two diploid genomes, and apply it to study the evolution of cereals and of yeast.

Contact: sankoff@uottawa.ca
Spectrum: joint bayesian inference of population structure and recombination events
Authors: Sohn Kyung-Ah , Xing Eric P.
Published: July 2007

Motivation: While genetic properties such as linkage disequilibrium (LD) and population structure are closely related under a common inheritance process, the statistical methodologies developed so far mostly deal with LD analysis and structural inference separately, using specialized models that do not capture their statistical and genetic relationships. Also, most of these approaches ignore the inherent uncertainty in the genetic complexity of the data and rely on inflexible models built on a closed genetic space. These limitations may make it difficult to infer detailed and consistent structural information from rich genomic data such as populational single nucleotide polymorphisms (SNP) profiles.

Results: We propose a new model-based approach to address these issues through joint inference of population structure and recombination events under a non-parametric Bayesian framework; we present Spectrum, an efficient implementation based on our new model. We validated Spectrum on simulated data and applied it to two real SNP datasets, including single-population Daly data and the four-population HapMap data. Our method performs well relative to LDhat 2.0 in estimating the recombination rates and hotspots on these datasets. More interestingly, it generates an ancestral spectrum for representing population structures which not only displays sub-structure based on population founders but also reveals details of the genetic diversity of each individual. It offers an alternative view of the population structures to that offered by Structure 2.1, which ignores chromosome-level mutation and recombination with respect to founders.

Contact: epxing@cs.cmu.edu
Cotranslational protein folding—fact or fiction?
Authors: Deane Charlotte M. , Dong Mingqiang , Huard Fabien P.E. , Lance Braddon K. , Wood Graham R.
Published: July 2007

Motivation: Experimentalists have amassed extensive evidence over the past four decades that proteins appear to fold during production by the ribosome. Protein structure prediction methods, however, do not incorporate this property of folding. A thorough study to find the fingerprint of such sequential folding is the first step towards using it in folding algorithms, so assisting structure prediction.

Results: We explore computationally the existence of evidence for cotranslational folding, based on large sets of experimentally determined structures in the PDB. Our perspective is that cotranslational folding is the norm, but that the effect is masked in most classes. We show that it is most evident in α/β proteins, confirming recent findings. We also find mild evidence that older proteins may fold cotranslationally. A tool is provided for determining, within a protein, where cotranslation is most evident.

Contact: gwood@efs.mq.edu.au
Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
Authors: Mayrose Itay , Doron-Faigenboim Adi , Bacharach Eran , Pupko Tal
Published: July 2007

Codon evolutionary models are widely used to infer the selection forces acting on a protein. The non-synonymous to synonymous rate ratio (denoted by Ka/Ks) is used to infer specific positions that are under purifying or positive selection. Current evolutionary models usually assume that only the non-synonymous rates vary among sites while the synonymous substitution rates are constant. This assumption ignores the possibility of selection forces acting at the DNA or mRNA levels. Towards a more realistic description of sequence evolution, we present a model that accounts for among-site-variation of both synonymous and non-synonymous substitution rates. Furthermore, we alleviate the widespread assumption that positions evolve independently of each other. Thus, possible sources of bias caused by random fluctuations in either the synonymous or non-synonymous rate estimations at a single site is removed. Our model is based on two hidden Markov models that operate on the spatial dimension: one describes the dependency between adjacent non-synonymous rates while the other describes the dependency between adjacent synonymous rates. The presented model is applied to study the selection pressure across the HIV-1 genome. The new model better describes the evolution of all HIV-1 genes, as compared to current codon models. Using both simulations and real data analyses, we illustrate that accounting for synonymous rate variability and dependency greatly increases the accuracy of Ka/Ks estimation and in particular of positively selected sites. Finally, we discuss the applicability of the developed model to infer the selection forces in regulatory and overlapping regions of the HIV-1 genome.

Contact: talp@post.tau.ac.il
Translation initiation site prediction on a genomic scale: beauty in simplicity
Authors: Saeys Yvan , Abeel Thomas , Degroeve Sven , Van de Peer Yves
Published: July 2007

Motivation: The correct identification of translation initiation sites (TIS) remains a challenging problem for computational methods that automatically try to solve this problem. Furthermore, the lion's share of these computational techniques focuses on the identification of TIS in transcript data. However, in the gene prediction context the identification of TIS occurs on the genomic level, which makes things even harder because at the genome level many more pseudo-TIS occur, resulting in models that achieve a higher number of false positive predictions.

Results: In this article, we evaluate the performance of several ‘simple’ TIS recognition methods at the genomic level, and compare them to state-of-the-art models for TIS prediction in transcript data. We conclude that the simple methods largely outperform the complex ones at the genomic scale, and we propose a new model for TIS recognition at the genome level that combines the strengths of these simple models. The new model obtains a false positive rate of 0.125 at a sensitivity of 0.80 on a well annotated human chromosome (chromosome 21). Detailed analyses show that the model is useful, both on its own and in a simple gene prediction setting.

Availability: Datafiles and a web interface for the StartScan program are available at http://bioinformatics.psb.ugent.be/supplementary_data/

Contact: yvan.saeys@psb.ugent.be