bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of classical nonlinear resonances in grazing diatom-surface collisions
Authors: Ruiz Antonia , Palao José P.
Published: August 2012

Energy transfer between vibrational, rotational, and translational degrees of freedom of a molecule during a collision process is enhanced when the classical frequencies associated with the initial state are in the proximity of nonlinear resonance conditions. We present an analysis of the classical resonant effects in the collisions of light diatoms with periodic surfaces, and discuss the initial conditions in which these effects can be observed. In particular, we find that for grazing incidence and resonant initial values of the classical frequencies, corresponding to specific vibro-rotational molecular states and translational energies, an efficient energy transfer between the intramolecular vibro-rotational degrees of freedom and the translational degree of freedom along a symmetry direction on the surface can be found. This efficient energy transfer manifests itself in the emergence of specific peaks in the molecular diffraction patterns. The predictions of the resonance analysis are contrasted with the results of classical trajectory calculations obtained in a diatom-rigid surface collision model.
On the joint distribution of the maximum and its position of the Airy2 process minus a parabola
Authors: Baik Jinho , Liechty Karl , Schehr Grégory
Published: August 2012

The maximal point of the Airy2 process minus a parabola is believed to describe the scaling limit of the end-point of the directed polymer in a random medium. This was proved to be true for a few specific cases. Recently, two different formulas for the joint distribution of the location and the height of this maximal point were obtained, one by Moreno Flores, Quastel, and Remenik, and the other by Schehr. The first formula is given in terms of the Airy function and an associated operator, and the second formula is expressed in terms of the Lax pair equations of the Painlevé II equation. We give a direct proof that these two formulas are the same.
Microscopic models of mode-coupling theory: The $\hbox{\sf{\bfseries{F}}}_{12}$F12 scenario
Authors: Arenzon Jeferson J. , Sellitto Mauro
Published: August 2012

We provide extended evidence that mode-coupling theory (MCT) of supercooled liquids for the ${\mathsf F}_{12}$F12 schematic model admits a microscopic realization based on facilitated spin models with tunable facilitation. Depending on the facilitation strength, one observes two distinct dynamical glass transition lines—continuous and discontinuous—merging at a dynamical tricritical-like point with critical decay exponents consistently related by MCT predictions. The mechanisms of dynamical arrest can be naturally interpreted in geometrical terms: the discontinuous and continuous transitions correspond to bootstrap and standard percolation processes, in which the incipient spanning cluster of frozen spins forms either a compact or a fractal structure, respectively. Our cooperative dynamical facilitation picture of glassy behavior is complementary to the one based on disordered systems and can account for higher-order singularity scenarios in the absence of a finite temperature thermodynamic glass transition. We briefly comment on the relevance of our results to finite spatial dimensions and to the ${\mathsf F}_{13}$F13 schematic model.
The Klein-Gordon equation with ring-shaped potentials: Asymptotic iteration method
Authors: Falaye Babatunde James
Published: August 2012

This study presents the solutions of three dimensional Klein-Gordon equation for the spherically and non-spherically harmonic oscillatory ring-shaped potentials within the framework of asymptotic iteration method. Using the method of variable separation, this study obtains the radial and angular equations. And then the bound states energy eigenvalues and corresponding eigenfunctions are obtained analytically.
Hybrid nanotubes: Single step formation of homogeneous nanotubes of polypyrrole-gold composites and novel switching transition of resistance beyond liquid nitrogen temperature
Authors: Sarma Abhisakh , Sanyal Milan K. , Rahman Atikur , Satpati Biswarup
Published: August 2012

Nanowires of polypyrrole have exhibited switching transition that reduces the resistance of the wires by several orders of magnitude under certain bias around and below 30 K temperature. Here, we have shown that by incorporating gold in these polypyrrole nanotubes using a cost effective template based single-step chemical synthesis technique, this novel resistance switching transition could be extended beyond liquid nitrogen temperature (>90 K) to make this phenomena technologically relevant. The single step synthesis technique, reported here, provides us uniform mixing of gold and polypyrrole during the formation of composite-nanotubes; with appropriate choice of materials, this synthesis technique can be extended to form nanotubes of other metal-polymer composites.
Simultaneous usage of pinhole and penumbral apertures for imaging small scale neutron sources from inertial confinement fusion experiments
Authors: Guler N. , Volegov P. , Danly C. R. , Grim G. P. , Merrill F. E. , Wilde C. H.
Published: August 2012

Inertial confinement fusion experiments at the National Ignition Facility are designed to understand the basic principles of creating self-sustaining fusion reactions by laser driven compression of deuterium-tritium (DT) filled cryogenic plastic capsules. The neutron imaging diagnostic provides information on the distribution of the central fusion reaction region and the surrounding DT fuel by observing neutron images in two different energy bands for primary (13–17 MeV) and down-scattered (6–12 MeV) neutrons. From this, the final shape and size of the compressed capsule can be estimated and the symmetry of the compression can be inferred. These experiments provide small sources with high yield neutron flux. An aperture design that includes an array of pinholes and penumbral apertures has provided the opportunity to image the same source with two different techniques. This allows for an evaluation of these different aperture designs and reconstruction algorithms.
Diffusion enhancement in core-softened fluid confined in nanotubes
Authors: Bordin J. R. , de Oliveira A. B. , Diehl A. , Barbosa Marcia C.
Published: August 2012

We study the effect of confinement in the dynamical behavior of a core-softened fluid. The fluid is modeled as a two length scales potential. This potential in the bulk reproduces the anomalous behavior observed in the density and in the diffusion of liquid water. A series of NpT molecular dynamics simulations for this two length scales fluid confined in a nanotube were performed. We obtain that the diffusion coefficient increases with the increase of the nanotube radius for wide channels as expected for normal fluids. However, for narrow channels, the confinement shows an enhancement in the diffusion coefficient when the nanotube radius decreases. This behavior, observed for water, is explained in the framework of the two length scales potential.
Particle-swarm structure prediction on clusters
Authors: Lv Jian , Wang Yanchao , Zhu Li , Ma Yanming
Published: August 2012

We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Lin (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.
Tuning the dynamic properties of electrons between a quantum well and quantum dots
Authors: Cerulo G. , Nevou L. , Liverini V. , Castellano F. , Faist J.
Published: August 2012

We present a study of the dynamic properties of electrons tunneling from an InGaAs quantum well to self assembled InAs quantum dots. The experiments were conducted on three highly asymmetric quantum dot infrared photodetectors, where the quantum well and quantum dots were separated by a composite GaAs/AlGaAs/GaAs barrier, which varied from 3.5 nm to 7.0 nm. We performed interband (photoluminescence) and intraband (photocurrent) measurements to characterize the spectral properties of the well and the dots. The photoluminescence measurements revealed that the two nanostructures are decoupled when the device is at zero bias. By intraband pump-probe experiments and photocurrent saturation experiments, we were able to extrapolate a refilling time τ from the well to the dots, which varied from a few μs for the thinnest barrier and hundreds of μs for the thickest one. The extracted values are in good agreement with characteristic tunneling times computed by using a model based on the theoretically predicted transmission coefficient of the electrons through the composite barrier.
Two-dimensional magnetic Schrödinger equations, Darboux transformations and solutions of associated auxiliary equations
Authors: Schulze-Halberg Axel
Published: August 2012

We extend the formalism of Darboux transformations to magnetic Schrödinger equations in two dimensions. The partner potentials associated with the Darboux transformation are obtained in explicit form through an integral formula. We apply our construction to a particular spectral problem of Dirichlet type, obtaining the Darboux partner, its spectrum and the corresponding solutions in explicit form.
A collinear self-emission and laser-backlighting imaging diagnostic
Authors: Bott S. C. , Collins G. , Gunasekera K. , Mariscal D. , Beg F. N. , Haas D. M. , Veloso F. , Blesener I. C. , Cahill A. D. , Hoyt C. L. , Kusse B. R. , Hammer D. A.
Published: August 2012

In this work we demonstrate a design for obtaining laser backlighting (e.g., interferometry) and time-resolved extreme ultraviolet self-emission images along the same line-of-sight. This is achieved by modifying a single optical component in the laser collection optics with apertures and pinhole arrangements suitable for single or multiple frame imaging onto a gated detector, such as a microchannel plate. Test results for exploding wire experiments show that machining of the optic does not affect the overall quality of the recovered laser images, and that, even with a multiple frame system, the area sacrificed to achieve collinear imaging is relatively small. The diagnostics can therefore allow direct correlation of laser and self-emission images and their derived quantities, such as electron density in the case of interferometry. Simple methods of image correlation are also demonstrated.
Bohm’s criterion in a collisional magnetized plasma with thermal ions
Authors: Hatami M. M. , Shokri B.
Published: August 2012

Using the hydrodynamic model and considering a planar geometry, the modified Bohm’s sheath criterion is investigated in a magnetized, collisional plasma consisting of electron and positive ions with finite temperature. It is assumed that the singly charged positive ions enter into the sheath region obliquely, i.e., their velocity at the sheath edge is not normal to the wall, and the electron densities obey Boltzmann relations. It is shown that there are both upper and lower limit for the Bohm entrance velocity of ions in this case and both of these limits depend on the magnitude and direction of the applied magnetic field. To determine the accuracy of our derived generalized Bohm’s criterion, it reduced to some familiar physical condition. Also, using this generalized Bohm’s criterion, the behavior of the electron and positive ion density distributions are studied in the sheath region.
Design and numerical simulations of a high power 0.15 THz oscillator
Authors: Li Xiaoze , Wang Jianguo , Song Zhiming , Chen Changhua , Sun Jun , Zhang Xiaowei , Zhang Yuchuan
Published: August 2012

An overmoded rectangularly corrugated relativistic surface wave oscillator is designed and theoretically analyzed to produce the high power terahertz radiation with a TM01 mode. The design is fully verified and optimized by 2.5D particle-in-cell simulations. A high power terahertz wave is obtained with the output power of 285 MW at the frequency of 0.148 THz with conversion efficiency 20% when beam voltage is about 400 kV, current 3.8  kA, and the magnetic field 6 T.
Vapor-liquid phase coexistence and transport properties of two-dimensional oligomers
Authors: Patra Tarak K. , Hens Abhiram , Singh Jayant K.
Published: August 2012

Grand-canonical transition-matrix Monte Carlo and histogram reweighting techniques are used herein to study the vapor-liquid coexistence properties of two-dimensional (2D) flexible oligomers with varying chain lengths (m = 1–8). The phase diagrams of the various 2D oligomers follow the correspondence state (CS) principle, akin to the behavior observed for bulk oligomers. The 2D critical density is not influenced by the oligomer chain length, which contrasts with the observation for the bulk oligomers. Line tension, calculated using Binder's formalism, in the reduced plot is found to be independent of chain length in contrast to the 3D behavior. The dynamical properties of 2D fluids are evaluated using molecular dynamics simulations, and the velocity and pressure autocorrelation functions are investigated using Green-Kubo (GK) relations to yield the diffusion and viscosity. The viscosity determined from 2D non-equilibrium molecular dynamics simulation is compared with the viscosity estimated from the GK relations. The GK relations prove to be reliable and efficient for the calculation of 2D transport properties. Normal diffusive regions are identified in dense oligomeric fluid systems. The influence of molecular size on the diffusivity and viscosity is found to be diminished at specific CS points for the 2D oligomers considered herein. In contrast, the viscosity and diffusion of the 3D bulk fluid, at a reduced temperature and density, are strongly dependent on the molecular size at the same CS points. Furthermore, the viscosity increases and the diffusion decreases multifold in the 2D system relative to those in the 3D system, at the CS points.
High-resolution thermal expansion measurements under helium-gas pressure
Authors: Manna Rudra Sekhar , Wolf Bernd , de Souza Mariano , Lang Michael
Published: August 2012

We report on the realization of a capacitive dilatometer, designed for high-resolution measurements of length changes of a material for temperatures 1.4 K ⩽ T ⩽ 300 K and hydrostatic pressure P ⩽ 250 MPa. Helium (4He) is used as a pressure-transmitting medium, ensuring hydrostatic-pressure conditions. Special emphasis has been given to guarantee, to a good approximation, constant-pressure conditions during temperature sweeps. The performance of the dilatometer is demonstrated by measurements of the coefficient of thermal expansion at pressures P ≃ 0.1 MPa (ambient pressure) and 104 MPa on a single crystal of azurite, Cu3(CO3)2(OH)2, a quasi-one-dimensional spin S = 1/2 Heisenberg antiferromagnet. The results indicate a strong effect of pressure on the magnetic interactions in this system.
Numerical calculation of neoclassical distribution functions and current profiles in low collisionality, axisymmetric plasmas
Authors: Lyons B. C. , Jardin S. C. , Ramos J. J.
Published: August 2012

A new code, the Neoclassical Ion-Electron Solver (NIES), has been written to solve for stationary, axisymmetric distribution functions (f) in the conventional banana regime for both ions and electrons using a set of drift-kinetic equations (DKEs) with linearized Fokker-Planck-Landau collision operators. Solvability conditions on the DKEs determine the relevant non-adiabatic pieces of f (called h). We work in a 4D phase space in which ψ defines a flux surface, θ is the poloidal angle, v is the magnitude of the velocity referenced to the mean flow velocity, and λ is the dimensionless magnetic moment parameter. We expand h in finite elements in both v and λ. The Rosenbluth potentials, Φ and Ψ, which define the integral part of the collision operator, are expanded in Legendre series in cosχ, where χ is the pitch angle, Fourier series in cosθ, and finite elements in v. At each ψ, we solve a block tridiagonal system for hi (independent of fe), then solve another block tridiagonal system for he (dependent on fi). We demonstrate that such a formulation can be accurately and efficiently solved. NIES is coupled to the MHD equilibrium code JSOLVER [J. DeLucia et al., J. Comput. Phys. 37, 183–204 (1980)] allowing us to work with realistic magnetic geometries. The bootstrap current is calculated as a simple moment of the distribution function. Results are benchmarked against the Sauter analytic formulas and can be used as a kinetic closure for an MHD code (e.g., M3D−C1 [S. C. Jardin et al., Comput. Sci. Discovery 5, 014002 (2012)]).
Numerical studies of a plasma diode with external forcing
Authors: Rekaa V. L. , Pécseli H. L. , Trulsen J. K.
Published: August 2012

With reference to laboratory Q-machine studies we analyze the dynamics of a plasma diode under external forcing. Assuming a strong axial magnetic field, the problem is analyzed in one spatial dimension by a particle-in-cell code. The cathode is assumed to be operated in electron rich conditions, supplying an abundance of electrons. We compare different forcing schemes with the results obtained by solving the van der Pol equation. In one method of forcing we apply an oscillation in addition to the DC end plate bias and consider both amplitude and frequency variations. An alternative method of perturbation consists of modelling an absorbing grid at some internal position. Also in this case we can have a constant frequency with varying amplitude or alternatively an oscillation with chirped frequency but constant amplitude. We find that the overall features of the forced van der Pol equation are recovered, but the details in the plasma response need more attention to the harmonic responses, requiring extensions of the model equation. The analysis is extended by introducing collisional effects, where we emphasize charge exchange collisions of ions, since these processes usually have the largest cross sections and give significant modifications of the diode performance. In particular we find a reduction in oscillator frequency, although a linear scaling of the oscillation time with the system length remains also in this case.
Synchronization-based approach for detecting functional activation of brain
Authors: Hong Lei , Cai Shi-Min , Zhang Jie , Zhuo Zhao , Fu Zhong-Qian , Zhou Pei-Ling
Published: August 2012

In this paper, we investigate a synchronization-based, data-driven clustering approach for the analysis of functional magnetic resonance imaging (fMRI) data, and specifically for detecting functional activation from fMRI data. We first define a new measure of similarity between all pairs of data points (i.e., time series of voxels) integrating both complete phase synchronization and amplitude correlation. These pairwise similarities are taken as the coupling between a set of Kuramoto oscillators, which in turn evolve according to a nearest-neighbor rule. As the network evolves, similar data points naturally synchronize with each other, and distinct clusters will emerge. The clustering behavior of the interaction network of the coupled oscillators, therefore, mirrors the clustering property of the original multiple time series. The clustered regions whose cross-correlation coefficients are much greater than other regions are considered as the functionally activated brain regions. The analysis of fMRI data in auditory and visual areas shows that the recognized brain functional activations are in complete correspondence with those from the general linear model of statistical parametric mapping, but with a significantly lower time complexity. We further compare our results with those from traditional K-means approach, and find that our new clustering approach can distinguish between different response patterns more accurately and efficiently than the K-means approach, and therefore more suitable in detecting functional activation from event-related experimental fMRI data.
Comment on “Generalized projective synchronization in time-delayed systems: Nonlinear observer approach” [Chaos 19, 013102 (2009); 20, 029902 (2010)]
Authors: Jeeva Sathya Theesar S. , Balasubramaniam P. , Banerjee Santo
Published: August 2012

In Chaos 19, 013102 (2009), the author proposed generalized projective synchronization for time delay systems using nonlinear observer and obtained sufficient condition to ensure projective synchronization for modulated time varying delay. There are concerns with the obtained conditions as the result was applicable only to trivial case of time varying delay τ̇1(t)=dτ1(t)/dt<1. In this paper, we note the drawbacks of the proposed sufficient condition. The new improved sufficient condition for ensuring the projective synchronization of time varying delayed systems is presented. The proposed new criteria have been verified by adopting the Ikeda system.
Note: Rotaphone, a new self-calibrated six-degree-of-freedom seismic sensor
Authors: Brokešová Johana , Málek Jiří , Evans John R.
Published: August 2012

We have developed and tested (calibration, linearity, and cross-axis errors) a new six-degree-of-freedom mechanical seismic sensor for collocated measurements of three translational and three rotational ground motion velocity components. The device consists of standard geophones arranged in parallel pairs to detect spatial gradients. The instrument operates in a high-frequency range (above the natural frequency of the geophones, 4.5 Hz). Its theoretical sensitivity limit in this range is 10−9 m/s in ground velocity and 10−9 rad/s in rotation rate. Small size and weight, and easy installation and maintenance make the instrument useful for local-earthquake recording and seismic prospecting.
The nonlinear dispersion relation of geodesic acoustic modes
Authors: Hager Robert , Hallatschek Klaus
Published: August 2012

The energy input and frequency shift of geodesic acoustic modes (GAMs) due to turbulence in tokamak edge plasmas are investigated in numerical two-fluid turbulence studies. Surprisingly, the turbulent GAM dispersion relation is qualitatively equivalent to the linear GAM dispersion but can have drastically enhanced group velocities. As a consequence radially broad (∼cm) GAM eigenmodes may form. Those may lead to experimentally observable deviations from the expected scaling of the GAM frequency with the square root of the plasma temperature. In up-down asymmetric geometry, the energy input due to turbulent transport may favor the excitation of GAMs with one particular sign of the radial phase velocity relative to the magnetic drifts. Including the radial gradient of the GAM frequency may lead to periodic bursts of the GAM and the turbulence intensity.
Thermodynamic evaluation of dry reforming of vegetable oils for production of synthesis gas
Authors: Reddy Yenumala Sudhakara , Maity Sunil K.
Published: August 2012

The dry reforming (DR) is a promising technology for utilization of greenhouse gas, carbon dioxide, to produce synthesis gas for downstream synthesis of valuable chemicals and fuels. In this study, equilibrium of DR and autothermal dry reforming (ATDR) of vegetable oils was investigated by Gibbs free energy minimization method. The effects of various process variables of DR and ATDR of vegetable oils such as temperature (673–1273 K), carbon dioxide-to-carbon mole ratio (CCMR) (0.5–3.0), and oxygen-to-carbon mole ratio (OCMR) (0–1.0) were studied to obtain equilibrium products composition, thermodynamically promising operating conditions, and thermoneutral conditions of the process. The study revealed that insignificant amount of coke and compounds containing two or more carbon atoms were formed for both DR and ATDR of vegetable oils. The hydrogen yield was found to increase with increase in temperatures for DR of vegetable oil. At temperature 983 K and above, the hydrogen yield was found to increase with CCMR, reach maxima, and then decrease with further increase in CCMR. The carbon dioxide conversion and yield of CO and water were increased and yield of methane was decreased with increase in temperature. The yield of CO and water were increased and the conversion of carbon dioxide and yield of methane were decreased with increase of CCMR. For ATDR of vegetable oils, the reduced yield of CO and methane and enhanced yield of water and hydrogen (up to temperature of maximum hydrogen yield) were observed compared to that of DR. From critical analysis of the results of DR and ATDR of vegetable oil, the optimum conditions for maximum yield of hydrogen with very low yield of methane were determined as 1000–1050 K, CCMR of about 1, and oxygen-to-carbon mole ratio of 0.6–0.7. It was observed that about 80% hydrogen yield with 78–83 moles of CO and 0.2–0.6 moles of methane per mole of vegetable oil could be obtained under the optimum conditions.
Heat transfer and friction characteristics of impinging jet solar air heater
Authors: Chauhan Ranchan , Thakur N. S.
Published: August 2012

This paper presents an experimental investigation on heat transfer and friction characteristics to study the effect of streamwise and spanwise jet to jet spacing due to inline arrangement of circular jets in a duct flow of solar air heater. The effect of geometrical parameters, especially the streamwise and spanwise pitch has been investigated. The rectangular duct has an aspect ratio of 11.6. The streamwise and spanwise spacing of jets has been varied from 0.435 to 1.739 and 0.435 to 0.869, respectively, and Reynolds number range covered is 3800–16000. The heat transfer and friction factor data obtained is compared with that of smooth duct under similar geometrical and flow conditions. Results show that increase in streamwise pitch and spanwise pitch increases the heat transfer coefficient from the absorber surface to the flowing fluid, as the distance between the jets increases the interference between the jets prior to impingement decreases which leads to development of very thin impingement boundary layer in the vicinity of the heat transferring surface thus enhances heat transfer. As compared to smooth duct, maximum enhancement in heat transfer and friction factor is 2.67 and 3.5 times, respectively.
Summary of Savonius wind turbine development and future applications for small-scale power generation
Authors: Abraham J. P. , Plourde B. D. , Mowry G. S. , Minkowycz W. J. , Sparrow E. M.
Published: August 2012

Wind turbine use is expanding throughout the world as a means to provide electricity without contributing to the increase in global-warming gases. Most commonly, very large, horizontal-axis turbines are constructed in fleets that are connected to national-level electrical grid systems. More recently, there has been a desire for more local, small-scale power production that can be used to power very specific pieces of equipment or buildings. Some of the small-scale turbines are designed differently from their larger counterparts—they are driven by drag forces rather than by lift. Drag-driven turbines are typically called Savonius turbines. This paper, which presents a historical perspective on Savonius turbines, will illustrate their potential for providing local power. Finally, we will discuss recent developments in analysis methods which intend to optimize Savonius turbines for powering cellular communication towers in developing parts of the world.
Heat transfer enhancement of a thermal storage unit consisting of a phase change material and nano-particles
Authors: Abolghasemi Mehran , Keshavarz Ali , Ali Mehrabian Mozaffar
Published: August 2012

A thermal energy storage unit consisting of two concentric cylinders is studied in this article. The thermal storage unit is filled with a phase change material (PCM). In order to improve the performance of the unit two different methods were used and the methods were analyzed from irreversibility point of view. In the first method the unit is charged periodically, meaning that the temperature gradient inside the PCM drops between two consecutive charging periods and builds up during the next charging period. In the second method nano-particles are added to the PCM, where their high thermal conductivity improves the performance of the unit. The governing equations describing the heat exchange between the working fluid and the PCM were solved numerically. In order to validate the numerical predictions, sample results were compared with the reliable experimental results available in the literature. The agreement between the two sets of results proves the accuracy of numerical predictions. The numerical results indicate that the techniques explained in this paper significantly reduce the entropy generation of the system.
Electronegativity and doping in semiconductors
Authors: Schwingenschlögl U. , Chroneos A. , Schuster C. , Grimes R. W.
Published: August 2012

Charge transfer predicted by standard models is at odds with Pauling’s electronegativities but can be reconciled by the introduction of a cluster formation model [Schwingenschlögl et al., Appl. Phys. Lett. 96, 242107 (2010)]. Using electronic structure calculations, we investigate p- and n-type doping in silicon and diamond in order to facilitate comparison as C has a higher electronegativity compared to Si. All doping conditions considered can be explained in the framework of the cluster formation model. The implications for codoping strategies and dopant-defect interactions are discussed.
Adiabatic magnetocaloric temperature change in polycrystalline gadolinium – A new approach highlighting reversibility
Authors: Ghahremani Mohammadreza , Seyoum Hailemichael M. , ElBidweihy Hatem , Torre Edward Della , Bennett Lawrence H.
Published: August 2012

The adiabatic temperature change (ΔT) during the magnetization and demagnetization processes of bulk gadolinium is directly measured for several applied magnetic fields in the temperature range 285 K to 305 K. During the magnetization process, ΔT measurements display the same maximum for each applied field when plotted against the initial temperature (Ti). However, during the demagnetization process, the maximum ΔT varies for each applied field. This discrepancy between the magnetization and demagnetization measurements appears inconsistent with the reversibility of the magnetocaloric effect. A new approach is undertaken to highlight the reversibility of the magnetocaloric effect by plotting ΔT against the average temperature change (Tavg) instead of Ti. The value of Tavg which corresponds to the maximum ΔT is found to increase linearly with the applied magnetic field, consistently for both the magnetization and demagnetization measurements. Solving the linear-fitting equations of these measurements gives a new, and more precise, Curie temperature measurement. This new approach confirmed that the relationship between the maximum adiabatic temperature change (ΔTpeak) and the applied magnetic field is perfectly linear.
Tunneling anisotropic magnetoresistance in single-molecule magnet junctions
Authors: Xie Haiqing , Wang Qiang , Jiao Hujun , Liang J.-Q.
Published: August 2012

We theoretically investigate quantum transport through single-molecule magnet (SMM) junctions with ferromagnetic and normal-metal leads in the sequential regime. The current obtained by means of the rate-equation gives rise to the tunneling anisotropic magnetoresistance (TAMR), which varies with the angle between the magnetization direction of ferromagnetic lead and the easy axis of SMM. The angular dependence of TAMR can serve as a probe to determine experimentally the easy axis of SMM. Moreover, it is demonstrated that both the magnitude and the sign of TAMR are tunable by the bias voltage, suggesting a new spin-valve device with only one magnetic electrode in molecular spintronics.
Simultaneous stimulated Raman, Brillouin, and electron-acoustic scattering reveals a potential saturation mechanism in Raman plasma amplifiers
Authors: Turnbull D. , Li S. , Morozov A. , Suckewer S.
Published: August 2012

In a Raman plasma amplifier, the aim is to create plasma conditions in which Raman backscattering is the fastest growing instability, outrunning all competing effects so that it is possible to amplify and compress a laser beam to unprecedented unfocused intensities by utilizing that instability. However, achieving high efficiencies via this scheme has proven very difficult experimentally. Recent data show the simultaneous occurrence of stimulated Raman scattering (SRS), stimulated Brillouin scattering (SBS), and stimulated electron-acoustic scattering (SEAS). The appearance of SEAS is indicative of strong particle trapping, the existence of which is hard to justify without highlighting the interplay between SRS and SBS.
Large enhanced perpendicular magnetic anisotropy in CoFeB/MgO system with the typical Ta buffer replaced by an Hf layer
Authors: Liu T. , Cai J. W. , Sun Li
Published: August 2012

By systematically comparing the magnetic properties of the Ta/CoFeB/Ta and MgO/CoFeB/MgO structures with and without a submonolayer of MgO, Ta, V, Nb, Hf and W inserted in the middle of the CoFeB layer, we have proved that the observed perpendicular magnetic anisotropy (PMA) in Ta/CoFeB/MgO sandwiches is solely originated from the CoFeB/MgO interface with the Ta buffer acting to enhance the CoFeB/MgO interface anisotropy significantly. Moreover, replacing Ta with Hf causes the CoFeB/MgO interfacial PMA further enhanced by 35%, and the CoFeB layer with perpendicular magnetization has a much larger critical thickness accordingly, leaving a wider thickness margin for the CoFeB/MgO-based perpendicular magnetic tunnel junction optimization. Also the sputter deposited thin Hf films are amorphous with low surface roughness. These results will ensure the Hf/CoFeB/MgO more promising material system for PMA device development.
Compliant Si nanostructures on SOI for Ge nanoheteroepitaxy—A case study for lattice mismatched semiconductor integration on Si(001)
Authors: Zaumseil P. , Kozlowski G. , Yamamoto Y. , Bauer J. , Schubert M. A. , Schülli T. U. , Tillack B. , Schroeder T.
Published: August 2012

The integration of lattice mismatched semiconductors on Si(001) is of fundamental importance to further increase the performance and/or functionality of today’s Si integrated circuits. The theory of compliant substrate effects offers the vision to integrate defect-free alternative semiconductor structures on Si. This concept is based on balancing the mismatch strain between the overgrowing epitaxial semiconductor and the Si substrate by a strain partitioning phenomenon. Using the Ge/Si heterosystem as a case study, we report by advanced 3rd generation synchrotron as well as laboratory techniques for materials characterization on the nanoscale clear experimental evidence for the compliance of Si nanoislands on SOI for selective Ge nanoheteroepitaxy. This integration concept is not limited to Ge but extendable to semiconductors like III-V and II-VI materials.
The 3D-tomography of the nano-clusters formed by Fe-coating and annealing of diamond films for enhancing their surface electron field emitters
Authors: Chen Huang-Chin , Lo Shen-Chuan , Lin Li-Jiaun , Huang Pin-Chang , Shih Wen-Ching , Lin I-Nan , Lee Chi-Young
Published: August 2012

The Fe-coating and H2-annealed processes markedly increased the conductivity and enhanced the surface electron field emission (s-EFE) properties for the diamond films. The enhancement on the s-EFE properties for the diamond films is presumably owing to the formation of nano-graphite clusters on the surface of the films via the Fe-to-diamond interaction. However, the extent of enhancement varied with the granular structure of the diamond films. For the microcrystalline (MCD) films, the s-EFE process can be turned on at (E0)MCD = 1.9 V/μm, achieving a large s-EFE current density of (Je)MCD = 315 μA/cm2 at an applied field of 8.8 V/μm. These s-EFE properties are markedly better than those for Fe-coated/annealed ultrananocrystalline diamond (UNCD) films with (E0)UNCD = 2.0 V/μm and (Je)UNCD = 120 μA/cm2. The transmission electron microscopy showed that the nano-graphite clusters formed an interconnected network for MCD films that facilitated the electron transport more markedly, as compared with the isolated nano-graphitic clusters formed at the surface of the UNCD films. Therefore, the Fe-coating/annealing processes improved the s-EFE properties for the MCD films more markedly than that for the UNCD films. The understanding on the distribution of the nano-clusters is of critical importance in elucidating the authentic factor that influences the s-EFE properties of the diamond films. Such an understanding is possible only through the 3D-tomographic investigations.
Birth of cloned calves from vitrified–warmed zona-free buffalo (Bubalus bubalis) embryos produced by hand-made cloning
Authors: Saha Ambikaprasanna , Panda Sudeepta K. , Chauhan Manmohan S. , Manik Radhey S. , Palta Prabhat , Singla Suresh K.
Published: August 2012

The availability of techniques for the vitrification of cloned blastocysts can improve their effective use. The present study compared the developmental competence of buffalo cloned embryos derived from adult (BAF), newborn (BNF) and fetal fibroblast (BFF) before and after vitrification. Despite similar cleavage rates among the three groups, the blastocyst rate was lower for BAF- than BNF- and BFF-derived embryos (30.2 ± 2.2% vs 41.7 ± 1.7% and 39.1 ± 2.1%, respectively; P < 0.01). The total cell number of BNF-derived blastocysts was significantly higher (P < 0.01) than that of BFF-derived blastocysts, which, in turn, was higher (P < 0.01) than that of BAF-derived blastocysts. Following transfer of vitrified–warmed blastocysts to recipients, no pregnancy was obtained with fresh (n = 8) or vitrified–warmed (n = 18) BAF-derived blastocysts, whereas transfer of fresh BNF- (n = 53) and BFF-derived (n = 32) blastocysts resulted in four and three pregnancies, respectively, which aborted within 90 days of gestation. The transfer of vitrified–warmed BNF-derived blastocysts (n = 39) resulted in the live birth of a calf weighing 41 kg, which is now 23 months old and has no apparent abnormality, whereas the transfer of vitrified–warmed BFF-derived blastocysts (n = 18) resulted in one live birth of a calf that died within 6 h. These results demonstrate that cloned buffalo embryos cryopreserved by vitrification can be used to obtain live offspring.
Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in
Populus trichocarpa
Authors: Li Quanzi , Lin Ying-Chung , Sun Ying-Hsuan , Song Jian , Chen Hao , Zhang Xing-Hai , Sederoff Ronald R. , Chiang Vincent L.
Published: August 2012

Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of
TF
and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in
Arabidopsis
and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of
SND1
. Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative
SND1
splice variant,
PtrSND1
-
A2

IR

, that acts as a dominant negative of SND1 transcriptional network genes in
Populus trichocarpa
.
PtrSND1
-
A2

IR

derives from
PtrSND1-A2
, one of the four fully spliced
PtrSND1
gene family members (
PtrSND1
-
A1
, -
A2
, -
B1
, and -
B2
). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common
MYB
gene (
PtrMYB021
). PtrSND1-A2
IR
represses the expression of its
PtrSND1
member genes and
PtrMYB021
. Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2
IR
lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2
IR
is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2
IR
is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2
IR
lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2
IR
may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.
A simple proof of 𝐿^{𝑞}-estimates for the steady-state Oseen and Stokes equations in a rotating frame. Part II: Weak solutions
Authors: Galdi Giovanni , Kyed Mads
Published: August 2012

This is the second of two papers in which simple proofs of

L

q

L^{q}

-estimates of solutions to the steady-state three-dimensional Oseen and Stokes equations in a rotating frame of reference are given. In this part, estimates are established in terms of data in homogeneous Sobolev spaces of negative order.
Diacylglycerol kinase ζ regulates RhoA activation via a kinase-independent scaffolding mechanism
Authors: Ard Ryan , Mulatz Kirk , Abramovici Hanan , Maillet Jean-Christian , Fottinger Alexandra , Foley Tanya , Byham Michèle-Renée , Iqbal Tasfia Ahmed , Yoneda Atsuko , Couchman John R. , Parks Robin J. , Gee Stephen H.
Published: August 2012

Rho GTPases share a common inhibitor, Rho guanine nucleotide dissociation inhibitor (RhoGDI), which regulates their expression levels, membrane localization, and activation state. The selective dissociation of individual Rho GTPases from RhoGDI ensures appropriate responses to cellular signals, but the underlying mechanisms are unclear. Diacylglycerol kinase ζ (DGKζ), which phosphorylates diacylglycerol to yield phosphatidic acid, selectively dissociates Rac1 by stimulating PAK1-mediated phosphorylation of RhoGDI on Ser-101/174. Similarly, phosphorylation of RhoGDI on Ser-34 by protein kinase Cα (PKCα) selectively releases RhoA. Here we show DGKζ is required for RhoA activation and Ser-34 phosphorylation, which were decreased in DGKζ-deficient fibroblasts and rescued by wild-type DGKζ or a catalytically inactive mutant. DGKζ bound directly to the C-terminus of RhoA and the regulatory arm of RhoGDI and was required for efficient interaction of PKCα and RhoA. DGKζ-null fibroblasts had condensed F-actin bundles and altered focal adhesion distribution, indicative of aberrant RhoA signaling. Two targets of the RhoA effector ROCK showed reduced phosphorylation in DGKζ-null cells. Collectively our findings suggest DGKζ functions as a scaffold to assemble a signaling complex that functions as a RhoA-selective, GDI dissociation factor. As a regulator of Rac1 and RhoA activity, DGKζ is a critical factor linking changes in lipid signaling to actin reorganization.
Intensity quantile estimation and mapping—a novel algorithm for the correction of image non-uniformity bias in HCS data
Authors: Lo Ernest , Soleilhac Emmanuelle , Martinez Anne , Lafanechère Laurence , Nadon Robert
Published: August 2012

Motivation: Image non-uniformity (NU) refers to systematic, slowly varying spatial gradients in images that result in a bias that can affect all downstream image processing, quantification and statistical analysis steps. Image NU is poorly modeled in the field of high-content screening (HCS), however, such that current conventional correction algorithms may be either inappropriate for HCS or fail to take advantage of the information available in HCS image data.

Results: A novel image NU bias correction algorithm, termed intensity quantile estimation and mapping (IQEM), is described. The algorithm estimates the full non-linear form of the image NU bias by mapping pixel intensities to a reference intensity quantile function. IQEM accounts for the variation in NU bias over broad cell intensity ranges and data acquisition times, both of which are characteristic of HCS image datasets. Validation of the method, using simulated and HCS microtubule polymerization screen images, is presented. Two requirements of IQEM are that the dataset consists of large numbers of images acquired under identical conditions and that cells are distributed with no within-image spatial preference.

Availability and implementation: MATLAB function files are available at http://nadon-mugqic.mcgill.ca/.

Contact:  robert.nadon@mcgill.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
shortran: a pipeline for small RNA-seq data analysis
Authors: Gupta Vikas , Markmann Katharina , Pedersen Christian N. S. , Stougaard Jens , Andersen Stig U.
Published: August 2012

Summary: High-throughput sequencing currently generates a wealth of small RNA (sRNA) data, making data mining a topical issue. Processing of these large data sets is inherently multidimensional as length, abundance, sequence composition, and genomic location all hold clues to sRNA function. Analysis can be challenging because the formulation and testing of complex hypotheses requires combined use of visualization, annotation and abundance profiling. To allow flexible generation and querying of these disparate types of information, we have developed the shortran pipeline for analysis of plant or animal short RNA sequencing data. It comprises nine modules and produces both graphical and MySQL format output.

Availability:  shortran is freely available and can be downloaded from http://users-mb.au.dk/pmgrp/shortran/

Contact:  vgupta@cs.au.dk or sua@mb.au.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Systematic comparison of RNA-Seq normalization methods using measurement error models
Authors: Sun Zhaonan , Zhu Yu
Published: August 2012

Motivation: Further advancement of RNA-Seq technology and its application call for the development of effective normalization methods for RNA-Seq data. Currently, different normalization methods are compared and validated by their correlations with a certain gold standard. Gene expression measurements generated by a different technology or platform such as Real-time reverse transcription polymerase chain reaction (qRT–PCR) or Microarray are usually used as the gold standard. Although the current approach is intuitive and easy to implement, it becomes statistically inadequate when the gold standard is also subject to measurement error (ME). Furthermore, the current approach is not informative, because the correlation of a normalization method with a certain gold standard does not provide much information about the exact quality of the normalized RNA-Seq measurements.

Results: We propose to use the system of ME models based on qRT–PCR, Microarray and RNA-Seq gene expression data to compare and validate RNA-Seq normalization methods. This approach does not assume the existence of a gold standard. The performance of a normalization method can be characterized by a group of parameters of the system, which are referred to as the performance parameters, and these performance parameters can be consistently estimated. Different normalization methods can thus be compared by comparing their corresponding estimated performance parameters. We applied the proposed approach to compare five existing RNA-Seq normalization methods using the gene expression data of two RNA samples from the microArray Quality Control and Sequencing Quality Control projects and gained much insight about the pros and cons of these methods.

Contact:  sunz@purdue.edu; yuzhu@purdue.edu