bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear microwave response of a superconducting YBa2Cu3O7−δ microstrip transmission line with a constriction
Authors: Kalenyuk A. A.
Published: March 2009

Microwave power losses IL(Pin) introduced by a superconducting YBa2Cu3O7−δ film microstrip transmission line with a constriction have been investigated experimentally in the temperature range 78–90K. For microwave current flow with amplitude greater than the critical value Ic(rf), losses growing rapidly with increasing input microwave power arise in the line. Hysteresis of the functions IL(Pin) is observed when the microwave power is increased and then decreased. Calculations show that the losses in the line are due to the formation of resistive transverse domains, whose temperature is above the critical value, in the region of the constriction. It is shown that a small constriction consisting of a HTSC film in a microwave transmission line can be regarded as a concentrated nonlinear resistive element, which can be used as basis for building a microwave power limiter.
Pinning and dynamics of vortices in a YBa2Cu3O7−δ crystal with magnetic field orientation near the ab plane: effect of point defects
Authors: Petrusenko Yu. T. , Bondarenko A. V.
Published: March 2009

The change of the pinning force Fp with increasing angle α≡∠H, ab (α<10°) in crystals with different concentration npd of point defects is investigated. For low concentration npd the force Fp decreases monotonically with increasing angle α. However, the functions Fp(α) become nonmonotonic for high concentrations npd. The αmin corresponding to the position of the minimum of Fp(α) decreases with increasing concentration npd. It is shown that the pinning force of a “pancake” vortex increases substantially, while the pinning force of strings increases only negligibly with increasing concentration npd.
Effect of Sn addition on the microstructure and magnetic properties of FePt thin film
Authors: Chun DongWon , Kim SungMan , Kim GyeungHo , Jeung WonYoung
Published: March 2009

An attempt has been made in this study to incorporate an alloying element to lower the order-disorder transformation temperature of Fe–Pt alloy and the effect of Sn addition was investigated for this purpose. The coercivity of the FePtSn film is measured to be about 5000 Oe, whereas that of FePt film is several hundred Oe at the annealing temperature of 300 °C. Therefore, Sn addition is effective to promote the L10 ordering and reduce the ordering temperature of FePt alloy. Analysis of crystal structure by x-ray diffraction reveals that the lattice expansion of cubic FePt phase is induced by Sn addition in as-deposited film. After the annealing from 300 °C to 600 °C, L10 ordered phase is formed in FePtSn films and lattice constant of FePtSn film is approached to pure FePt with increasing annealing temperature up to 600 °C. Difference in solid solubility of Sn between disordered and ordered phase exists and thus excess Sn will diffuse out from ordered FePt L10 phase. Segregated Sn is found at the surface and interfacial region of the ordered FePtSn confirmed by depth profiling of Auger electron spectroscopy. The key role played by Sn addition in FePt alloy is therefore explained by reduction in activation energy for the L10 ordering-disordering transformation through high internal stress in disordered phase induced by supersaturated Sn atoms.
Nonuniform grid algorithm for fast calculation of magnetostatic interactions in micromagnetics
Authors: Livshitz Boris , Boag Amir , Bertram H. Neal , Lomakin Vitaliy
Published: March 2009

A nonuniform grid (NG) algorithm for rapidly computing magnetostatic field for micromagnetic simulations is described. The algorithm relies on spatial NG representation of the potential from the source boxes and local interpolation. Multilevel implementations of the algorithm result in a linear computational complexity with respect to the number of effective magnetic charges and observers. The algorithm is highly adaptive with respect to structure’s geometry, i.e., it becomes automatically faster for low dimensional configurations such as quasiplanar bit patterned medium arrays.
Properties of single crystal Fe1−xGax thin films
Authors: McClure Adam , Albert S. , Jaeger T. , Li H. , Rugheimer P. , Schaefer J. A. , Idzerda Y. U.
Published: March 2009

Molecular beam epitaxy was used to deposit single crystal thin film Fe1−xGax samples on ZnSe buffer layers grown on (001) and (110) single crystal GaAs substrates. The crystal quality of the GaAs surface and each deposited layer was monitored in situ by reflection high energy electron diffraction. The magnetic properties of the samples were characterized by vibrating sample magnetometry and ferromagnetic resonance (FMR). The FMR linewidth increases dramatically with Ga concentration while the cubic anisotropy term K1 switches sign.
Infrared spectroscopy of methanol-hexane liquid mixtures. II. The strength of hydrogen bonding
Authors: Max Jean-Joseph , Chapados Camille
Published: March 2009

The study by Fourier transform infrared attenuated total reflectance spectroscopy at 27 °C of methanol (MeOH) and hexane mixtures is presented. In the 0–0.25 and 0.75–1.00 molar fractions, the mixtures form homogeneous solutions, whereas from 0.25 to 0.75, the mixtures are inhomogeneous forming two phases. These mixtures have the near 3300 cm−1 OH stretch band only slightly displaced throughout the whole concentration range indicating very little variation in the H-bonding condition. This result is very different from that of MeOH in CCl4 where the OH stretch bands are scattered in a wide frequency range. Factor analysis applied to the MeOH/hexane spectra gave seven principal factors (one hexane and six methanol factors) and retrieved their principal spectra and abundances. In the inhomogeneous region, the two phase volumes changed inversely with concentration, but their factor compositions are invariable at 1:3 and 3:1 molar ratios. Five of the six principal methanol factors have the O–H and the C–O stretch bands situated near, respectively, 3310 and 1025 cm−1 with little displacement in the whole concentration range. The sixth factor observed at 3654 cm−1 (full width at half height<40 cm−1) was assigned to free methanol OH by Max and Chapados [J. Chem. Phys. 128, 224512 (2008)]. This species concentration is very low but constant at around 0.01M in the methanol range of 0.5–2.5M. The main OH stretch bands (∼3300 cm−1) were simulated with six Gaussian components that were assigned to different hydrogen-bonding situations. These form reverse micelles at low methanol concentrations and micelles at high concentrations that persist in pure methanol. A very different state of affairs exists in MeOH in CCl4 where free OH groups are formed in almost all mixtures except in pure MeOH. Since hexane is a better model of a lipidic milieu than CCl4, the results for MeOH/hexane give a better representation of the fate of alcoholic OH groups in such a milieu.
X-ray diffraction measurements of Mo melting to 119 GPa and the high pressure phase diagram
Authors: Santamaría-Pérez D. , Ross M. , Errandonea D. , Mukherjee G. D. , Mezouar M. , Boehler R.
Published: March 2009

In this paper, we report angle-dispersive X-ray diffraction data of molybdenum melting, measured in a double-sided laser-heated diamond-anvil cell up to a pressure of 119 GPa and temperatures up to 3400 K. The new melting temperatures are in excellent agreement with earlier measurements up to 90 GPa that relied on optical observations of melting and in strong contrast to most theoretical estimates. The X-ray measurements show that the solid melts from the bcc structure throughout the reported pressure range and provide no evidence for a high temperature transition from bcc to a close-packed structure, or to any other crystalline structure. This observation contradicts earlier interpretations of shock data arguing for such a transition. Instead, the values for the Poisson ratios of shock compressed Mo, obtained from the sound speed measurements, and the present X-ray evidence of loss of long-range order suggest that the 210 GPa (∼4100 K) transition in the shock experiment is from the bcc structure to a new, highly viscous, structured melt.
Numerical evaluation of electron repulsion integrals for pseudoatomic orbitals and their derivatives
Authors: Toyoda Masayuki , Ozaki Taisuke
Published: March 2009

A numerical method to calculate the four-center electron-repulsion integrals for strictly localized pseudoatomic orbital basis sets has been developed. Compared to the conventional Gaussian expansion method, this method has an advantage in the ease of combination with O(N) density functional calculations. Additional mathematical derivations are also presented including the analytic derivatives of the integrals with respect to atomic positions and spatial damping of the Coulomb interaction due to the screening effect. In the numerical test for a simple molecule, the convergence up to 10−5 hartree in energy is successfully obtained with a feasible cost of computation.
On the discrepancy between theoretical and experimental thermal stress in chromia oxide films
Authors: Kemdehoundja M. , Grosseau-Poussard J. L. , Dinhut J. F.
Published: March 2009

Growth and residual stresses have been determined, thanks to Raman spectroscopy in chromia oxide films thermally grown in air from a Ni33at %Cr alloy between 700 and 900 °C. Due to the good sensibility of the in situ experimental device, the growth stress kinetics even at short oxidation times has been recorded and has been shown to be microstructure sensitive. At different oxidation times, the corresponding residual stress at room temperature has also been investigated and the experimental thermal stress has been deduced. The comparison between the respective magnitudes of stress variations induced by creep relaxation during isothermal oxidation, and by the additional thermal stress occurring upon cooling, has led to the definition of a stress threshold finally proposed to explain the residual stress values and the difference between theoretical and experimental thermal stress components.
Microwave interaction with nonuniform hydrogen gas in carbon nanotubes
Authors: Babaei S. , Babaei Sh.
Published: March 2009

In this paper we study the reflection, absorption, and transmission of microwave from nonuniform hydrogen gas in carbon nanotubes, grown by iron-catalyzed high-pressure carbon monoxide disproportionate (HiPco) process. A discussion on the effect of various hydrogen gas parameters on the reflected power, absorbed power, and transmitted power is presented. The nonuniform hydrogen gas slab is modeled by a series of subslabs. The overall number density profile across the whole slab follows a parabolic function. The total reflected, absorbed, and transmitted powers are then deduced and their functional dependence on the number density, collision frequency, and angle of propagation is studied.
Parametrization of energy gap at the Γ point and outside this point for dilute nitrides: Ga1−yInyNxP1−x and GaNxAs1−x−zPz alloys
Authors: Kudrawiec R.
Published: March 2009

The energy gap at the Γ point and outside this point has been analyzed for Ga1−yInyNxP1−x and GaNxAs1−x−zPz alloys (types I and II quaternary dilute nitrides) within the band anticrossing model [Shan et al., Phys. Rev. Lett. 82, 1221 (1999)] using a method which has been proposed in J. Appl. Phys. 101, 023522 (2007). In this method the well known quadratic formula with a bowing parameter, which is used to calculate the band gap energy for N-free ternary alloys A1−yByC(AC1−zDz), is adopted for N-containing quaternary alloys A1−yByNxC1−x(ANxC1−x−zDz). The binary compounds AC and BC (AC and AD) are replaced by appropriate ANC and BNC (ANC and BND) alloys. The energy gap predictions have been compared with available experimental data. A consistent agreement with the experimental data has been achieved when the optical transitions at the Γ point and outside this point were taken into account.
Convergent beam electron diffraction measurements of relaxation in strained silicon using higher order Laue zone line splitting
Authors: Diercks David , Kaufman Michael , Needleman Alan
Published: March 2009

Convergent beam electron diffraction patterns of silicon from blanket wafers of ∼50 nm Si0.85Ge0.15 on Si and ∼126 nm Si0.79Ge0.21 on Si and from a complementary metal-oxide-semiconductor transistor with recessed Si0.82Ge0.18 stressors were analyzed at zone axes slightly off ⟨110⟩. It was shown that certain higher order Laue zone lines split near the SiGe/Si interfaces, indicating that considerable relaxation occurred during the preparation of the transmission electron microscopy specimens. The variation in splitting as a function of distance from the interface and sample thickness is described. A simple method was used to estimate the relaxation and was compared to behavior predicted by linear elastic finite element modeling of the structures. These methods showed reasonable agreement for the structures that were examined.
Prolonged residence times for particles settling through stratified miscible fluids in the Stokes regime
Authors: Camassa Roberto , Falcon Claudia , Lin Joyce , McLaughlin Richard M. , Parker Richard
Published: March 2009

The behavior of settling particles in stratified fluid is important in a variety of applications, from environmental to medical. We document a phenomenon in which a sphere, when crossing density transitions, slows down substantially in comparison to its settling speed in the bottom denser layer, due to entrainment of buoyant fluid. We present results from an experimental study of the effects of the fluid interface on flight times as well as a theoretical model derived from first principles in the low Reynolds number regimes for stratified miscible fluids. Our work provides a new predictive tool and gives insight into the role of strong stratification in particle settling.
A unimolecular evaporation model for simulating argon condensation flows in direct simulation Monte Carlo
Authors: Zhong Jiaqiang , Moghe Nilesh , Li Zheng , Levin Deborah A.
Published: March 2009

In previous work, a cluster evaporation model was derived from the classical nucleation theory (CNT) to simulate condensation in free expanding plumes using the direct simulation Monte Carlo (DSMC) method. However, the use of a CNT evaporation model, especially in a low temperature environment, is problematic because macroparameters such as cluster surface tension and vapor saturation pressure are not physical for small cluster sizes. In this work, we propose a kinetic based evaporation model obtained from unimolecular dissociation theory (UDT) to model argon cluster evaporation processes in a free expanding plume. The UDT argon cluster evaporation model has been directly verified by molecular dynamics and quasiclassical trajectory simulations. It is found that although there is about one order of magnitude difference in the CNT and UDT evaporation rates, these two theories predict similar cluster evaporation rate trends as a function of cluster size and temperature. The verified new UDT evaporation model, as well as the previous CNT model, are applied to a free expanding argon condensation plume simulated with DSMC. The simulation results show that although there are some differences in cluster number density and average cluster size using the CNT and UDT evaporation models, the condensation onset conditions and Rayleigh scattering intensity for both models agree reasonably well with experimental data.
Complex non-Markovian effect on time-dependent quantum transport
Authors: Zheng Xiao , Luo JunYan , Jin Jinshuang , Yan YiJing
Published: March 2009

Transient electronic dynamics of a single-lead double-quantum-dot system is significantly affected by intrasystem or lead-mediated interdot coupling. Unique occupancy-state transition features are distinguished in the response current spectrum, due to the presence of irreducible frequency-dependent correlation functions. The complex non-Markovian effects are demonstrated numerically by implementing the exact theory, based on the hierarchical equations of motion for the reduced dynamics of quantum transport systems. They are expected to play a prevalent and nontrivial role in the quantum dynamics of realistic nanoelectronic devices.
Epitaxial ZnO films on (111) Si substrates with Sc2O3 buffer layers
Authors: Guo W. , Katz M. B. , Nelson C. T. , Heeg T. , Schlom D. G. , Liu B. , Che Y. , Pan X. Q.
Published: March 2009

Epitaxial (0001) ZnO films were grown on (111) Si substrates using epitaxial (111) Sc2O3 buffer layers. The quality of the ZnO epilayers is manifested by a Hall mobility of 77 cm2/V s at room temperature, x-ray diffraction rocking curve full widths at half maximum of 300–400 arc sec, and optical properties comparable to ZnO single crystals. Transmission electron microscopy studies reveal that a thin layer of SiOx was formed at the Sc2O3/Si interface not during the Sc2O3 growth, but during the growth of the ZnO films. The thermal-mismatch induced residual strain in the films causes an energy shift of the exciton resonances in the photoluminescence spectrum. The redshifts are smaller than those of GaN films, indicating that the optical properties of ZnO are less strain sensitive.
Comparison of photoexcited p-InAs THz radiation source with conventional thermal radiation sources
Authors: Smith M. L. , Mendis R. , Vickers R. E. M. , Lewis R. A.
Published: March 2009

P -type InAs excited by ultrashort optical pulses has been shown to be a strong emitter of terahertz radiation. In a direct comparison between a p-InAs emitter and conventional thermal radiation sources, we demonstrate that under typical excitation conditions p-InAs produces more radiation below 1.2 THz than a globar. By treating the globar as a blackbody emitter we calibrate a silicon bolometer which is used to determine the power of the p-InAs emitter. The emitted terahertz power was found to be 98±10 nW in this experiment.
Simultaneous deposition of diamondlike carbon films on both surfaces of aluminum substrate by electrochemical technique
Authors: Li R. S. , Zhou M. , Pan X. J. , Zhang Z. X. , Lu B. A. , Wang T. , Xie E. Q.
Published: March 2009

By electrolysis of the N,N-dimethylformamide solution, an attempt was made to simultaneously deposit diamondlike carbon (DLC) films on both surfaces of an aluminum (Al) substrate. Raman spectra showed that the structures of the DLC film were uniform. The thickness distribution of the film was 260–300 nm. A simple model of the sustaining mechanism was proposed for simultaneous electrodeposition of the DLC film on both surfaces of conductive substrates. The simultaneous formation of the DLC film on both surfaces of the Al substrate showed a possibility in the three-dimensional deposition of DLC films on complex conductive substrates.
Synchronization of a spiral by a circularly polarized electric field in reaction-diffusion systems
Authors: Chen Jiang-Xing , Zhang Hong , Li You-Quan
Published: March 2009

Synchronization of a spiral by a circularly polarized electric field (CPEF) in reaction-diffusion systems is investigated since they both possess rotation symmetry. It is found that spirals in different regimes (including rigidly rotating, meandering, and drifting spirals) can be forced to be rigidly rotating ones by CPEFs. Moreover, the rotational frequency of the entrained spiral is found to be synchronized with the frequency of the electric field in a ratio of 1:1.
Quantitative characterization of solid state phases by secondary neutral mass spectrometry
Authors: Oechsner H. , Getto R. , Kopnarski M.
Published: March 2009

The quantitative determination of chemical solid phases by secondary neutral mass spectrometry (SNMS) based on the quantitative character of this technique is described and demonstrated for several thin film structures. The intermetallic phases in a Ni–Zn coating on Fe are shown to be achieved directly from the concentration ratios determined by SNMS. When correlating the local elemental concentration tupels with the corresponding phase fractions by a matrix equation, the determination of chemical solid phase depth profiles becomes possible. This is exemplified by the detection of temperature induced chemical phases in Ni and Ti/Si films on SiC substrates.
High-quality Schottky contacts to n-InGaN alloys prepared for photovoltaic devices
Authors: Chen D. J. , Huang Y. , Liu B. , Xie Z. L. , Zhang R. , Zheng Y. D. , Wei Y. , Narayanamurti V.
Published: March 2009

Large-area Au∕Pt∕n-In0.2Ga0.8N Schottky contacts have been fabricated for photovoltaic devices. The current transport mechanisms of the Schottky contacts to n-In0.2Ga0.8N with different background carrier concentrations are investigated. The thermionic emission is a dominating current transport mechanism at the Pt∕n-InGaN interface in a low background carrier concentration sample, while the defect-assisted tunneling current and trap-related recombination current play important roles in high background carrier concentration samples. The Schottky diode fabricated using the low background carrier concentration sample gives much better Schottky barrier characteristics and exhibits a three to four order of magnitude higher spectral responsivity and a larger rejection ratio in comparison with those fabricated using the high background carrier concentration samples.
Room-temperature Coulomb oscillation of a proton dot in Ni–Nb–Zr–H glassy alloys with nanofarad capacitance
Authors: Fukuhara Mikio , Inoue Akihisa
Published: March 2009

A dc-induced voltage oscillation was observed at room temperature in (Ni36Nb24Zr40)90.1H9.9 glassy alloy ribbons of about 1 mm width and 30 μm thickness and an electrode distance of 20 mm. The I-V characteristic provided evidence of the Coulomb staircase at ∼300 K, suggesting the existence of macroscopic proton dot tunneling along the Zr(Nb)–H–◻–H–Zr(Nb) atomic bond array, where ◻ is the vacancy barrier among clusters. The frequency decreased remarkably with increasing capacitance (C) and resistance (R) at room temperature. Thus the (Ni36Nb24Zr40)90.1H9.9 glassy alloy can be regarded as a dc/ac converting device with a large number of nanofarad capacitance.
Numerical analysis of ac loss in bifilar stacks and coils of ion beam assisted deposition YBCO coated conductors
Authors: Nguyen Doan N. , Ashworth Stephen P. , Willis Jeffrey O.
Published: March 2009

In this paper we present a finite element model using the commercial COMSOL® software package for calculating the ac loss in bifilar stacks of high temperature superconducting tape. In the model, the current-voltage relationship characterizing the superconducting properties is assumed to follow a power law. The calculations were performed for infinite bifilar stacks with different values of layer-to-layer separation D. With appropriate settings for the boundary conditions, the numerical results agree well with the analytical data obtained from a recently proposed model [J. R. Clem, Phys. Rev. B 77, 134506 (2008)]. The numerical approach was also used to investigate the end effects in a bifilar stack to answer the following question: how many layers away from the end of a stack are required before the environment of a given layer is identical to that in an infinite stack? We find that the answer to this question depends strongly on the value of D. Based on this study, a model for calculating the ac loss in bifilar noninductively wound coils with a finite number of turns is proposed.
Rapid prototyping encapsulation for polymer light-emitting lasers
Authors: Persano Luana , Camposeo Andrea , Del Carro Pompilio , Solaro Pierpaolo , Cingolani Roberto , Boffi Patrizia , Pisignano Dario
Published: March 2009

Rapid prototyping of packaging elements realized by stereolithography for the encapsulation of plastic optoelectronic devices is demonstrated. We measure the operational lifetime behavior of a polymeric laser before and after the device packaging. The operational lifetime of a polymer vertical-cavity surface-emitting laser is increased by a factor of three upon continuous pumping at an excitation fluence (250 μJ/cm2) three times larger than the lasing threshold, corresponding to an overall laser duration of more than 3×103 h at a repetition rate of 10 Hz. These findings suggest rapid prototyping stereolithography as promising highly scalable technology for the encapsulation of organic light-emitting devices.
The structure of the Au(111)/methylthiolate interface: New insights from near-edge x-ray absorption spectroscopy and x-ray standing waves
Authors: Chaudhuri A. , Odelius M. , Jones R. G. , Lee T.-L. , Detlefs B. , Woodruff D. P.
Published: March 2009

The local structure of the Au(111)(√3×√3)R30°-methylthiolate surface phase has been investigated by S K-edge near-edge s-ray absorption fine structure (NEXAFS) both experimentally and theoretically and by experimental normal-incidence x-ray standing waves (NIXSW) at both the C and S atomic sites. NEXAFS shows not only excitation into the intramolecular σ∗ S–C resonance but also into a σ∗ S–Au orbital perpendicular to the surface, clearly identifying the local S headgroup site as atop a Au atom. Simulations show that it is not possible, however, to distinguish between the two possible adatom reconstruction models; a single thiolate species atop a hollow-site Au adatom or a dithiolate moiety comprising two thiolate species bonded to a bridge-bonded Au adatom. Within this dithiolate moiety a second σ∗ S–Au orbital that lies near parallel to the surface has a higher energy that overlaps that of the σ∗ S–C resonance. The new NIXSW data show the S–C bond to be tilted by 61° relative to the surface normal, with a preferred azimuthal orientation in ⟨211⟩, corresponding to the intermolecular nearest-neighbor directions. This azimuthal orientation is consistent with the thiolate being atop a hollow-site Au adatom, but not consistent with the originally proposed Au-adatom-dithiolate moiety. However, internal conformational changes within this species could, perhaps, render this model also consistent with the experimental data.
Periodic alignment of Si quantum dots on hafnium oxide coated single wall carbon nanotubes
Authors: Olmedo Mario , Martinez-Morales Alfredo A. , Liu Gang , Yengel Emre , Ozkan Cengiz S. , Lau Chun Ning , Ozkan Mihrimah , Liu Jianlin
Published: March 2009

We demonstrate a bottom up approach for the aligned epitaxial growth of Si quantum dots (QDs) on one-dimensional (1D) hafnium oxide (HfO2) ridges created by the growth of HfO2 thin film on single wall carbon nanotubes. This growth process creates a high strain 1D ridge on the HfO2 film, which favors the formation of Si seeds over the surrounding flat HfO2 area. Periodic alignment of Si QDs on the 1D HfO2 ridge was observed, which can be controlled by varying different growth conditions, such as growth temperature, growth time, and disilane flow rate.
Electrical characterization of a tuning fork crystal oscillator using dual-phase lock-in technique
Authors: Song Sang-Hun
Published: March 2009

We performed an electrical characterization of a tuning fork crystal oscillator using a dual-phase lock-in amplifier. Direct measurements of the complex admittance allowed us to extract all four values of the equivalent circuit model components of the tuning fork crystal oscillator.
Three-dimensional two-component velocity measurement of the flow field induced by the Vorticella picta microorganism using a confocal microparticle image velocimetry technique
Authors: Nagai Moeto , Oishi Masamichi , Oshima Marie , Asai Hiroshi , Fujita Hiroyuki
Published: March 2009

Understanding the biological feeding strategy and characteristics of a microorganism as an actuator requires the detailed and quantitative measurement of flow velocity and flow rate induced by the microorganism. Although some velocimetry methods have been applied to examine the flow, the measured dimensions were limited to at most two-dimensional two-component measurements. Here we have developed a method to measure three-dimensional two-component flow velocity fields generated by the microorganism Vorticella picta using a piezoscanner and a confocal microscope. We obtained the two-component velocities of the flow field in a two-dimensional plane denoted as the XY plane, with an observation area of 455×341 μm2 and the resolution of 9.09 μm per each velocity vector by a confocal microparticle image velocimetry technique. The measurement of the flow field at each height took 37.5 ms, and it was repeated in 16 planes with a 2.50 μm separation in the Z direction. We reconstructed the three-dimensional two-component flow velocity field. From the reconstructed data, the flow velocity field [u(x,y,z),v(x,y,z)] in an arbitrary plane can be visualized. The flow rates through YZ and ZX planes were also calculated. During feeding, we examined a suction flow to the mouth of the Vorticella picta and measured it to be to 300 pl/s.
Size and composition dependent electronic and optical properties of GaxAl1−xAs and AlxGa1−xAs alloyed nanocrystals
Authors: Ghosh Chanchal , Pal Sougata , Sarkar Pranab , Frauenheim Thomas
Published: March 2009

By using density-functional tight-binding method, we have shown the size and composition dependent variation of band gap and excitation spectra of both GaxAl1−xAs and AlxGa1−xAs alloyed semiconductor nanocrystals. The two systems differ with respect to the surface atoms, while in one case the surface atoms are Ga, while in another case it is Al, and hence the effect of structural relaxations in GaxAl1−xAs and AlxGa1−xAs are different leading to different final structures and properties. We observed a bowing effect in the band gap values as it is experimentally found in many semiconductor alloys.
Origin of Structural and Kinematic Properties of the Small Magellanic Cloud
Authors: Bekki Kenji , Chiba Masashi
Published: April 2009

We investigate structural, kinematic and chemical properties of stars and gas in the Small Magellanic Cloud (SMC) interacting with the Large Magellanic Cloud (LMC) and the Galaxy based on a series of self-consistent chemodynamical simulations. We adopt a new ‘dwarf spheroidal model’ in which the SMC initially has both old stars with a spherical spatial distribution and an extended Hi gas disk. We mainly investigate the evolution of the SMC for the last ∼3 Gyr, during which the Magellanic Stream (MS) and the Magellanic Bridge (MB) could have formed as a result of the LMC–SMC–Galaxy interaction. Our principal results, which can be tested against observations, are as follows: The final spatial distribution of the old stars projected onto the sky is spherical, even after strong LMC–SMC–Galaxy interaction, whereas that of the new ones is significantly flattened and appears to form a bar structure. Old stars have a line-of-sight velocity dispersion σ ≃ 30 km s−1 and slow rotation, with a maximum rotational velocity, V < 20 km s−1 and show asymmetry in the radial profiles. New stars have a smaller Σ than old ones and a significant amount of rotation (V/σ > 1). Hi gas shows velocity dispersions of σ = 10–40 km s−1, a high maximum rotational velocity (V ∼ 50 km s−1) and a spatial distribution similar to that of new stars. New stars with ages younger than 3 Gyr show a negative metallicity gradient in the sense that more metal-rich stars are located in the inner regions of the SMC. The MB inevitably contains old stars with surface mass densities of 6−300 × 104 M⊙ deg−2 depending on initial stellar distributions of the modeled SMC. We find that the dwarf spheroidal model can explain more self-consistently the observed kinematic properties of stars and gas, compared with another type of the model (‘the disk model’) in which the SMC initially consists of stellar and gas disks. We suggest that, to better understand its evolution, the SMC needs to be modeled as having a spheroidal component, rather than being a pure disk.
A mobile kinesin-head intermediate during the ATP-waiting state
Authors: Asenjo Ana B. , Sosa Hernando
Published: March 2009

Kinesin1 is a motor protein that uses the energy from ATP hydrolysis to move intracellular cargoes along microtubules. It contains 2 identical motor domains, or heads, that coordinate their mechano-chemical cycles to move processively along microtubules. The molecular mechanism of coordination between head domains remains unclear, partly because of the lack of structural information on critical intermediates of the kinesin1 mechano-chemical cycle. A point of controversy has been whether before ATP binding, in the so called ATP-waiting state, 1 or 2 motor domains are bound to the microtubule. To address this issue, here we use ensemble and single molecule fluorescence polarization microscopy (FPM) to determine the mobility and orientation of the kinesin1 heads at different ATP concentrations and in heterodimeric constructs with microtubule binding impaired in 1 head. We found evidence for a mobile head during the ATP-waiting state. We incorporate our results into a model for kinesin translocation that accounts well for many reported experimental results.
Branner-Hubbard-Lavaurs deformations for real cubic polynomials with a parabolic fixed point
Authors: Nakane Shizuo
Published: March 2009

In this article, we study what we call the Branner-Hubbard- Lavaurs deformation of real cubic polynomials with a parabolic fixed point of multiplier one. It turns out that the existence of non-trivial deformations corresponds to the oscillation of stretching rays and discontinuity of the wring operation.
Plastin 1 Binds to Keratin and Is Required for Terminal Web Assembly in the Intestinal Epithelium
Authors: Grimm-Günter Eva-Maria S. , Revenu Céline , Ramos Sonia , Hurbain Ilse , Smyth Neil , Ferrary Evelyne , Louvard Daniel , Robine Sylvie , Rivero Francisco
Published: March 2009

Plastin 1 (I-plastin, fimbrin) along with villin and espin is a prominent actin-bundling protein of the intestinal brush border microvilli. We demonstrate here that plastin 1 accumulates in the terminal web and interacts with keratin 19, possibly contributing to anchoring the rootlets to the keratin network. This prompted us to investigate the importance of plastin 1 in brush border assembly. Although in vivo neither villin nor espin is required for brush border structure, plastin 1-deficient mice have conspicuous ultrastructural alterations: microvilli are shorter and constricted at their base, and, strikingly, their core actin bundles lack true rootlets. The composition of the microvilli themselves is apparently normal, whereas that of the terminal web is profoundly altered. Although the plastin 1 knockout mice do not show any overt gross phenotype and present a normal intestinal microanatomy, the alterations result in increased fragility of the epithelium. This is seen as an increased sensitivity of the brush border to biochemical manipulations, decreased transepithelial resistance, and increased sensitivity to dextran sodium sulfate-induced colitis. Plastin 1 thus emerges as an important regulator of brush border morphology and stability through a novel role in the organization of the terminal web, possibly by connecting actin filaments to the underlying intermediate filament network.
CNVVdb: a database of copy number variations across vertebrate genomes
Authors: Chen Feng-Chi , Chen Yen-Zho , Chuang Trees-Juen
Published: March 2009

Summary: CNVVdb is a web interface for identification of putative copy number variations (CNVs) among 16 vertebrate species using the-same-species self-alignments and cross-species pairwise alignments. By querying genomic coordinates in the target species, all the potential paralogous/orthologous regions that overlap ≥80–100% (adjustable) of the query sequences with user-specified sequence identity (≥60%∼≥90%) are returned. Additional information is also given for the genes that are included in the returned regions, including gene description, alternatively spliced transcripts, gene ontology descriptions and other biologically important information. CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions. Moreover, multiple sequence alignments of shared CNVs across species are also provided. With the combination of CNV, SNP, pseudogene and functional information, CNVVdb can be very useful for comparative and functional studies in vertebrates.

Availability: CNVVdb is freely accessible at http://CNVVdb.genomics.sinica.edu.tw.

Contact:  trees@gate.sinica.edu.tw
GetBonNie for building, analyzing and sharing rule-based models
Authors: Hu Bin , Matthew Fricke G. , Faeder James R. , Posner Richard G. , Hlavacek William S.
Published: March 2009

Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.

Availability: GetBonNie is free at http://getbonnie.org.

Contact:  getbonnie@cs.unm.edu
Mitochondrial function, morphology and metabolic parameters improve after switching from stavudine to a tenofovir-containing regimen
Authors: Gerschenson Mariana , Kim Courtney , Berzins Baiba , Taiwo Babafemi , Libutti Daniel E. , Choi Julia , Chen Diana , Weinstein Jill , Shore Jessica , da Silva Barbara , Belsey Elizabeth , McComsey Grace A. , Murphy Robert L.
Published: March 2009

Objectives

HIV-associated lipoatrophy has been associated with mitochondrial dysfunction induced by nucleoside reverse transcriptase inhibitor therapy. We hypothesize that lipid profiles and markers of mitochondrial function will improve in HIV-lipoatrophic patients switched to the nucleotide analogue tenofovir.

Methods

Ten patients receiving stavudine, lamivudine and lopinavir/ritonavir (Kaletra®) for over 6 years were switched from stavudine to tenofovir for 48 weeks. Subcutaneous fat tissue biopsies, fasting metabolic tests, HIV RNA, CD4 cell count and whole body dual energy X-ray absorptiometry (DEXA) scans were obtained at study entry and week 48. Mitochondrial DNA (mtDNA) copies/cell and mitochondrial morphology were assessed in adipose tissue biopsies, mtDNA 8-oxo-deoxyguanine in peripheral blood mononuclear cells, and glutathione (GSH) and F2-isoprostane in plasma.

Results

There was no change in limb fat mass by DEXA; however, trunk fat mass increased by 18.9% (P = 0.01). Fasting total cholesterol decreased by 33 mg/dL (P = 0.005) and serum glucose decreased by 4 mg/dL (P = 0.039). mtDNA copies/cell increased from 386 to 1537 (P < 0.001). Transmission electron microscopy showed that mitochondrial cristae were lacking or poorly defined at study entry, whereas mitochondrial inner structures were more well defined and outer membranes were intact at 48 weeks. Oxidative damage decreased in 8/10 patients, GSH increased and F2-isoprostane decreased.

Conclusions

The results from this study demonstrate that systemic and peripheral fat mitochondria improve in patients switched to tenofovir following long-term exposure to stavudine, while continuing protease inhibitor therapy.
Tiger moths and the threat of bats: decision-making based on the activity of a single sensory neuron
Authors: Ratcliffe John M. , Fullard James H. , Arthur Benjamin J. , Hoy Ronald R.
Published: March 2009

Echolocating bats and eared moths are a model system of predator–prey interaction within an almost exclusively auditory world. Through selective pressures from aerial-hawking bats, noctuoid moths have evolved simple ears that contain one to two auditory neurons and function to detect bat echolocation calls and initiate defensive flight behaviours. Among these moths, some chemically defended and mimetic tiger moths also produce ultrasonic clicks in response to bat echolocation calls; these defensive signals are effective warning signals and may interfere with bats' ability to process echoic information. Here, we demonstrate that the activity of a single auditory neuron (the A1 cell) provides sufficient information for the toxic dogbane tiger moth,Cycnia tenera, to decide when to initiate defensive sound production in the face of bats. Thus, despite previous suggestions to the contrary, these moths' only other auditory neuron, the less sensitive A2 cell, is not necessary for initiating sound production. However, we found a positive linear relationship between combined A1 and A2 activity and the number of clicks the dogbane tiger moth produces.
Modelling mitochondrial site polymorphisms to infer the number of segregating units and mutation rate
Authors: Hendy Michael D. , Woodhams Michael D. , Dodd Andrew
Published: March 2009

We present a mathematical model of mitochondrial inheritance evolving under neutral evolution to interpret the heteroplasmies observed at some sites. A comparison of the levels of heteroplasmies transmitted from mother to her offspring allows us to estimate the number
N

x

of inherited mitochondrial genomes (segregating units). The model demonstrates the necessity of accounting for both the multiplicity of an unknown number
N

x

, and the threshold
θ
, below which heteroplasmy cannot be detected reliably, in order to estimate the mitochondrial mutation rate
μ
m
in the maternal line of descent. Our model is applicable to pedigree studies of any eukaryotic species where site heteroplasmies are observed in regions of the mitochondria, provided neutrality can be assumed. The model is illustrated with an analysis of site heteroplasmies in the first hypervariable region of mitochondrial sequence data sampled from Adélie penguin families, providing an estimate
N

x

and
μ
m
. This estimate of
μ
m
was found to be consistent with earlier estimates from ancient DNA analysis.
Mathematics in English printed books, 1473–1800: a bibliometric analysis
Authors: Wardhaugh Benjamin
Published: March 2009

This essay represents a first attempt to make sense of the mass of early modern English publications that deal with or refer to mathematics, using a bibliometric approach made possible by the new electronic databases:
Early English books online
and
Eighteenth-century collections online
. I present statistical information about references to mathematics in this corpus of books, perform some statistical analysis of the trends that the data show, comment on the methodological problems raised, and assess what these results do and do not tell us about early modern English discussion of mathematics.
Time distributed-order diffusion-wave equation. I. Volterra-type equation
Authors: Atanackovic Teodor M. , Pilipovic Stevan , Zorica Dusan
Published: March 2009

A single-order time-fractional diffusion-wave equation is generalized by introducing a time distributed-order fractional derivative and forcing term, while a Laplacian is replaced by a general linear multi-dimensional spatial differential operator. The obtained equation is (in the case of the Laplacian) called a time distributed-order diffusion-wave equation. We analyse a Cauchy problem for such an equation by means of the theory of an abstract Volterra equation. The weight distribution, occurring in the distributed-order fractional derivative, is specified as the sum of the Dirac distributions and the existence and uniqueness of solutions to the Cauchy problem, and the corresponding Volterra-type equation were proven for a general linear spatial differential operator, as well as in the special case when the operator is Laplacian.
Time distributed-order diffusion-wave equation. II. Applications of Laplace and Fourier transformations
Authors: Atanackovic Teodor M. , Pilipovic Stevan , Zorica Dusan
Published: March 2009

A Cauchy problem for a time distributed-order multi-dimensional diffusion-wave equation containing a forcing term is reinterpreted in the space of tempered distributions, and a distributional diffusion-wave equation is obtained. The distributional equation is solved in the general case of weight function (or distribution). Solutions are given in terms of solution kernels (Green's functions), which are studied separately for two cases. The first case is when the order of the fractional derivative is in the interval [0, 1], while, in the second case, the order of the fractional derivative is in the interval [0, 2]. Solutions of fractional diffusion-wave and fractional telegraph equations are obtained as special cases. Numerical experiments are also performed. An analogue of the maximum principle is also presented.
It takes two to tango: reproductive skew and social correlates of male mating success in a lek-breeding bird
Authors: Ryder Thomas B. , Parker Patricia G. , Blake John G. , Loiselle Bette A.
Published: March 2009

Variance in reproductive success among individuals is a defining characteristic of many social vertebrates. Yet, our understanding of which male attributes contribute to reproductive success is still fragmentary in most cases. Male–male reproductive coalitions, where males jointly display to attract females, are of particular interest to evolutionary biologists because one male appears to forego reproduction to assist the social partner. By examining the relationship between social behaviour and reproductive success, we can elucidate the proximate function of coalitions in the context of mate choice. Here, we use data from a 4-year study of wire-tailed manakins (
Pipra filicauda
) to provide molecular estimates of reproductive skew and to test the hypothesis that male–male social interactions, in the context of coordinated displays, positively influence a male's reproductive success. More specifically, we quantify male–male social interactions using network metrics and predict that greater connectivity will result in higher relative reproductive success. Our data show that four out of six leks studied had significant reproductive skew, with success apportioned to very few individuals in each lek. Metrics of male social affiliations derived from our network analysis, especially male connectivity, measured as the number of males with whom the focal male has extended interactions, were strong predictors of the number of offspring sired. Thus, network connectivity is associated with male fitness in wire-tailed manakins. This pattern may be the result of shared cues used by both sexes to assess male quality, or the result of strict female choice for coordinated display behaviour.
Temperature has a causal effect on avian timing of reproduction
Authors: Visser Marcel E. , Holleman Leonard J.M. , Caro Samuel P.
Published: March 2009

Many bird species reproduce earlier in years with high spring temperatures, but little is known about the causal effect of temperature. Temperature may have a direct effect on timing of reproduction but the correlation may also be indirect, for instance via food phenology. As climate change has led to substantial shifts in timing, it is essential to understand this causal relationship to predict future impacts of climate change. We tested the direct effect of temperature on laying dates in great tits (
Parus major
) using climatized aviaries in a 6-year experiment. We mimicked the temperature patterns from two specific years in which our wild population laid either early (‘warm’ treatment) or late (‘cold’ treatment). Laying dates were affected by temperature directly. As the relevant temperature period started three weeks prior to the mean laying date, with a range of just 4°C between the warm and the cold treatments, and as the birds were fed ad libitum, it is likely that temperature acted as a cue rather than lifting an energetic constraint on the onset of egg production. We furthermore show a high correlation between the laying dates of individuals reproducing both in aviaries and in the wild, validating investigations of reproduction of wild birds in captivity. Our results demonstrate that temperature has a direct effect on timing of breeding, an important step towards assessing the implication of climate change on seasonal timing.