bluuebunny/crossref_metadata_2025 huggingface dataset:
On the influence of outer large-scale structures on near-wall turbulence in channel flow
Authors: Agostini L. , Leschziner M. A.
Published: July 2014

Direct Numerical Simulation (DNS) data for channel flow at 1025 are used to analyse the interaction between large outer scales in the log-law region – referred to as super-streaks – and the small-scale, streaky, streamwise-velocity fluctuations in the viscosity-affected near-wall layer. The study is inspired by extensive experimental investigations by Mathis, Marusic, and Hutchins, culminating in a predictive model that describes, in a supposedly universal manner, the “footprinting” and “modulating” effects of the outer structures on the small-scale near-wall motions. The approach used herein is based on the examination of joint PDFs for the small-scale fluctuations, conditioned on regions of large-scale footprints. The large and small scales are separated by means of the Huang-Hilbert empirical-mode decomposition, the validity of which is demonstrated by way of pre-multiplied energy spectra, correlation maps, and energy profiles for both scales. Observations derived from the PDFs then form the basis of assessing the validity of the assumptions underlying the model. Although the present observations support some elements of the model, the results imply that modulation by negative and positive large-scale fluctuations differ greatly – an asymmetric response that is not compatible with the model. The study is thus extended to examining the validity of an alternative proposal, which is based on the assumption that a universal description of the small-scale response to the large-scale motions has to rely on the velocity fluctuations being scaled with the large-scales-modified local friction velocity, rather than with the mean value. This proposal is partially supported by the present analysis. Finally, an alternative, new phenomenological model is proposed and examined.
Structure and dynamics of polymer melt confined between two solid surfaces: A molecular dynamics study
Authors: Sarabadani Jalal , Milchev Andrey , Vilgis Thomas A.
Published: July 2014

Using large scale molecular dynamics simulations we investigate the static and dynamic properties of a linear polymer melt confined between two solid surfaces. One of the walls is repulsive and the other is attractive wall. The bottom attractive wall is characterized by different degrees of roughness which is tuned by an array of short perpendicular rigid pillars with variable grafting density. We demonstrate that the conformations of polymers at the interfaces do not depend on substrate-polymer interactions, rather they show similar conformations of a single end-grafted chain under critical adsorption condition, consistent with the Silberberg's hypothesis. This observation is found to be in a good agreement with the analysis of the size distributions of trains, loops, and tails of melt chains at the walls known from the theoretical prediction of the end-grafted single chains at critical adsorption. Furthermore, we find that the pressure of the melt \documentclass[12pt]{minimal}\begin{document}$P_{\textrm {N}}$\end{document}PN decreases as \documentclass[12pt]{minimal}\begin{document}$P_{\textrm {N}} - P_\infty \propto N^{-1}$\end{document}PN−P∞∝N−1 with growing length of the chains N (where P∞ is the extrapolated pressure for N → ∞). Moreover, the surface tension γ near both walls is found to follow γN∝N−2/3. Eventually, the lateral dynamics near rough surface drops suddenly when the separation between the neighboring pillars becomes smaller than 2Rg, where Rg is the bulk radius of gyration.
Unraveling halide hydration: A high dilution approach
Authors: Migliorati Valentina , Sessa Francesco , Aquilanti Giuliana , D’Angelo Paola
Published: July 2014

The hydration properties of halide aqua ions have been investigated combining classical Molecular Dynamics (MD) with Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. Three halide-water interaction potentials recently developed [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)], along with three plausible choices for the value of the absolute hydration free energy of the proton (\documentclass[12pt]{minimal}\begin{document}$\Delta G^{\ominus }_{hyd}[H^+]$\end{document}ΔGhyd⊖[H+]), have been checked for their capability to properly describe the structural properties of halide aqueous solutions, by comparing the MD structural results with EXAFS experimental data. A very good agreement between theory and experiment has been obtained with one parameter set, namely LE, thus strengthening preliminary evidences for a \documentclass[12pt]{minimal}\begin{document}$\Delta G^{\ominus }_{hyd}[H^+]$\end{document}ΔGhyd⊖[H+] value of −1100 kJ mol−1 [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)]. The Cl−, Br−, and I− ions have been found to form an unstructured and disordered first hydration shell in aqueous solution, with a broad distribution of instantaneous coordination numbers. Conversely, the F− ion shows more ordered and defined first solvation shell, with only two statistically relevant coordination geometries (six and sevenfold complexes). Our thorough investigation on the effect of halide ions on the microscopic structure of water highlights that the perturbation induced by the Cl−, Br−, and I− ions does not extend beyond the ion first hydration shell, and the structure of water in the F− second shell is also substantially unaffected by the ion.
Sulfur dimers adsorbed on Au(111) as building blocks for sulfur octomers formation: A density functional study
Authors: Hernandez-Tamargo Carlos E. , Montero-Alejo Ana Lilian , Pujals Daniel Codorniu , Mikosch Hans , Hernández Mayra P.
Published: July 2014

Experimental scanning tunneling microscopy (STM) studies have shown for more than two decades rectangular formations when sulfur atoms are deposited on Au(111) surfaces. The precursors have ranged from simple molecules or ions, such as SO2 gas or sulfide anions, to more complex organosulfur compounds. We investigated, within the framework of the Density Functional Theory, the structure of these rectangular patterns assuming them entirely composed of sulfur atoms as the experimental evidence suggests. The sulfur coverage at which the simulations were carried out (0.67 ML or higher) provoked that the sulfur-sulfur association had to be taken into account for achieving a good agreement between the sets of simulated and experimental STM images. A combination of four sulfur dimers per rectangular formation properly explained the trends obtained by the experimental STM analysis which were related with the rectangles' size and shape fluctuations together with sulfur-sulfur distances within these rectangles. Finally, a projected density of states analysis showed that the dimers were capable of altering the Au(5d) electronic states at the same level as atomic sulfur adsorbed at low coverage. Besides, sulfur dimers states were perfectly distinguished, whose presence near and above the Fermi level can explain both: sulfur-sulfur bond elongation and dimers stability when they stayed adsorbed on the surface at high coverage.
Dual array 3D electron cyclotron emission imaging at ASDEX Upgrade
Authors: Classen I. G. J. , Domier C. W. , Luhmann N. C. , Bogomolov A. V. , Suttrop W. , Boom J. E. , Tobias B. J. , Donné A. J. H. ,   ASDEX Upgrade Team
Published: July 2014

In a major upgrade, the (2D) electron cyclotron emission imaging diagnostic (ECEI) at ASDEX Upgrade has been equipped with a second detector array, observing a different toroidal position in the plasma, to enable quasi-3D measurements of the electron temperature. The new system will measure a total of 288 channels, in two 2D arrays, toroidally separated by 40 cm. The two detector arrays observe the plasma through the same vacuum window, both under a slight toroidal angle. The majority of the field lines are observed by both arrays simultaneously, thereby enabling a direct measurement of the 3D properties of plasma instabilities like edge localized mode filaments.
Crystal-liquid interfacial free energy via thermodynamic integration
Authors: Benjamin Ronald , Horbach Jürgen
Published: July 2014

A novel thermodynamic integration (TI) scheme is presented to compute the crystal-liquid interfacial free energy (γcl) from molecular dynamics simulation. The scheme is applied to a Lennard-Jones system. By using extremely short-ranged and impenetrable Gaussian flat walls to confine the liquid and crystal phases, we overcome hysteresis problems of previous TI schemes that stem from the translational movement of the crystal-liquid interface. Our technique is applied to compute γcl for the (100), (110), and (111) orientation of the crystalline phase at three temperatures under coexistence conditions. For one case, namely, the (100) interface at the temperature T = 1.0 (in reduced units), we demonstrate that finite-size scaling in the framework of capillary wave theory can be used to estimate γcl in the thermodynamic limit. Thereby, we show that our TI scheme is not associated with the suppression of capillary wave fluctuations.
Anisotropic magnetoresistance of individual CoFeB and Ni nanotubes with values of up to 1.4% at room temperature
Authors: Rüffer Daniel , Slot Marlou , Huber Rupert , Schwarze Thomas , Heimbach Florian , Tütüncüoglu Gözde , Matteini Federico , Russo-Averchi Eleonora , Kovács András , Dunin-Borkowski Rafal , Zamani Reza R. , Morante Joan R. , Arbiol Jordi , Fontcuberta i Morral Anna , Grundler Dirk
Published: July 2014

Magnetic nanotubes (NTs) are interesting for magnetic memory and magnonic applications. We report magnetotransport experiments on individual 10 to 20 μm long Ni and CoFeB NTs with outer diameters ranging from 160 to 390 nm and film thicknesses of 20 to 40 nm. The anisotropic magnetoresistance (AMR) effect studied from 2 K to room temperature (RT) amounted to 1.4% and 0.1% for Ni and CoFeB NTs, respectively, at RT. We evaluated magnetometric demagnetization factors of about 0.7 for Ni and CoFeB NTs having considerably different saturation magnetization. The relatively large AMR value of the Ni nanotubes is promising for RT spintronic applications. The large saturation magnetization of CoFeB is useful in different fields such as magnonics and scanning probe microscopy using nanotubes as magnetic tips.
Structure and dynamics of water in crowded environments slows down peptide conformational changes
Authors: Lu Cheng , Prada-Gracia Diego , Rao Francesco
Published: July 2014

The concentration of macromolecules inside the cell is high with respect to conventional in vitro experiments or simulations. In an effort to characterize the effects of crowding on the thermodynamics and kinetics of disordered peptides, molecular dynamics simulations were run at different concentrations by varying the number of identical weakly interacting peptides inside the simulation box. We found that the presence of crowding does not influence very much the overall thermodynamics. On the other hand, peptide conformational dynamics was found to be strongly affected, resulting in a dramatic slowing down at larger concentrations. The observation of long lived water bridges between peptides at higher concentrations points to a nontrivial role of the solvent in the altered peptide kinetics. Our results reinforce the idea for an active role of water in molecular crowding, an effect that is expected to be relevant for problems influenced by large solvent exposure areas like in intrinsically disordered proteins.
Broadband patterned magnetic microwave absorber
Authors: Li Wei , Wu Tianlong , Wang Wei , Zhai Pengcheng , Guan Jianguo
Published: July 2014

It is a tough task to greatly improve the working bandwidth for the traditional flat microwave absorbers because of the restriction of available material parameters. In this work, a simple patterning method is proposed to drastically broaden the absorption bandwidth of a conventional magnetic absorber. As a demonstration, an ultra-broadband microwave absorber with more than 90% absorption in the frequency range of 4–40 GHz is designed and experimentally realized, which has a thin thickness of 3.7 mm and a light weight equivalent to a 2-mm-thick flat absorber. In such a patterned absorber, the broadband strong absorption is mainly originated from the simultaneous incorporation of multiple λ/4 resonances and edge diffraction effects. This work provides a facile route to greatly extend the microwave absorption bandwidth for the currently available absorbing materials.
Extensions of inhomogeneous polynomial representations for $\mathfrak {sl}(m+1|n)$sl(m+1|n)
Authors: Cao Bintao , Luo Li , Ou Ke
Published: July 2014

We extend an inhomogeneous polynomial representation of special linear Lie superalgebras $\mathfrak {sl}(m+1|n)$sl(m+1|n) to an inhomogeneous representation on the tensor space of any irreducible tensor representation of the general linear Lie superalgebras $\mathfrak {gl}(m|n)$gl(m|n) with this polynomial space via Shen's mixed product. We find a sufficient and necessary condition for irreducibility of these inhomogeneous representations, and get the Jordan-H$\ddot{\mbox{o}}$ölder series of those which are not irreducible. Furthermore, we point out that all these irreducible modules are lowest weight modules. Their lowest weights and character formulas are obtained.
Experimental investigation of compact metamaterial for high efficiency mid-range wireless power transfer applications
Authors: Ranaweera A. L. A. K. , Duong Thuc Phi , Lee Jong-Wook
Published: July 2014

We investigate a compact metamaterial for enhanced magnetic coupling in a resonator coupled wireless power transfer system operating at around 6.5 MHz. The metamaterial is constructed by realizing an array of three-turn spiral resonators on a thin slab. Although the metamaterial has its own loss, the experimental results show that the proposed metamaterial slab enhances the power transmission capability. The number of unit cells in the array is an important parameter, because exceeding a certain number of unit cells does not enhance the efficiency due to the loss of the slab. Furthermore, strong surface mode resonance is observed when two slabs are assembled with proper gap spacing between them. By using the optimization approach, we achieve a significant efficiency improvement at a mid-range distance. The measured efficiencies are 71.1% and 54.3% at a 0.6 and 1.0 m distance, respectively. At a 1.0 m distance, this efficiency performance corresponds to a 270% improvement compared to a case with no metamaterial slab. In addition, we experimentally confirm the threshold distances above which the metamaterial shows enhanced performance.
Intrinsic and extrinsic effects on the electrostatic field at the surface of Bi2Se3
Authors: Xu Chao , Hewitt Andy , Wang Jingying , Guan Tianshuai , Boltersdorf Jonathan , Maggard Paul A. , Dougherty Daniel B. , Gundogdu Kenan
Published: July 2014

The time evolution of electrostatic fields near a Bi2Se3 surface after a mechanical cleave was observed using Second Harmonic Generation. By comparing samples with different bulk doping levels and samples cleaved in different gas environments, these observations indicate multiple contributions to electric field evolution. These include the intrinsic process of Se vacancy diffusion as well as extrinsic processes due to both reactive and nonreactive surface adsorbates.
Ferroelectrics based absorbing layers
Authors: Hao Jianping , Sadaune Véronique , Burgnies Ludovic , Lippens Didier
Published: July 2014

We show that ferroelectrics-based periodic structure made of BaSrTiO3 (BST) cubes, arrayed onto a metal plate with a thin dielectric spacer film exhibit a dramatic enhancement of absorbance with value close to unity. The enhancement is found around the Mie magnetic resonance of the Ferroelectrics cubes with the backside metal layer stopping any transmitted waves. It also involves quasi-perfect impedance matching resulting in reflection suppression via simultaneous magnetic and electrical activities. In addition, it was shown numerically the existence of a periodicity optimum, which is explained from surface waves analysis along with trade-off between the resonance damping and the intrinsic loss of ferroelectrics cubes. An experimental verification in a hollow waveguide configuration with a good comparison with full-wave numerical modelling is at last reported by measuring the scattering parameters of single and dual BST cubes schemes pointing out coupling effects for densely packed structures.
Investigations on the thermal and piezoelectric properties of fresnoite Ba2TiSi2O8 single crystals
Authors: Shen Chuanying , Zhang Huaijin , Cong Hengjiang , Yu Haohai , Wang Jiyang , Zhang Shujun
Published: July 2014

Fresnoite crystals with the nominal composition Ba2TiSi2O8 (BTS) were grown using the Czochralski technique. The full matrix material constants were determined based on the IEEE standards, with d31, d33, and d15 coefficients being on the order of 2.7, 4.0, and 17.5 pC/N, respectively. A positive sign of d31 was confirmed using strain measurements and rotated crystal cuts, where a maximum d33* value of 9.1 pC/N was achieved for ZXl50° crystal cut. The dielectric, piezoelectric, and related thermal properties were investigated as a function of temperature, showing strong anisotropic behavior, inherently associated with its layered crystal structure. The temperature dependence of d15 and d33* revealed a variations of <6% over the temperature range of 20–700 °C. The good thermal stability, together with the high piezoelectric properties and electrical resistivity (>107 Ω·cm at 600 °C), makes fresnoite BTS crystals promising candidates for high temperature sensing applications.
Effect of oxygen plasma and thermal oxidation on shallow nitrogen-vacancy centers in diamond
Authors: Kim M. , Mamin H. J. , Sherwood M. H. , Rettner C. T. , Frommer J. , Rugar D.
Published: July 2014

We investigate the effect of two different surface treatments on shallow nitrogen-vacancy (NV) centers in diamond. Short duration oxygen plasma exposure is found to damage near-surface NV centers, resulting in their disappearance in fluorescence images. Subsequent annealing creates large numbers of new NV centers, attributed to plasma-induced vacancy creation. By tracking individual NV centers during thermal oxidation, we show that oxidation at 550 °C results in modest improvement of spin coherence. Higher temperature oxidations correlate with gradual decline in spin coherence and eventual instability of NV centers before ultimate disappearance. This is indicative of a reduction of the NV-to-surface distance due to oxidative etching. Thermal oxidation can offer controlled access to near-surface NV spins at the nanometer scale, an important requirement for many applications of NV-based nanomagnetometry.
Observation of atomic ordering of triple-period-A and -B type in GaAsBi
Authors: Wu Mingjian , Luna Esperanza , Puustinen Janne , Guina Mircea , Trampert Achim
Published: July 2014

We report the observation of atomic ordering of triple-period (TP)-A and -B type in low temperature (LT) grown GaAsBi alloy using transmission electron microscopy (TEM). In addition to previous reports, where only TP-A ordering was identified in III-V alloys, here, we confirm by electron diffraction, high-resolution (HR) TEM, and HR Z-contrast scanning TEM that two ordering variants coexists for LT-GaAsBi. We find that the TP-A ordering variant dominates over the TP-B variant. TP-A domains extend over 50–100 nm (projected lateral width) and are of higher perfection compared to TP-B domains. HR Z-contrast scanning TEM on different domains reveals a variation in the Bi occupancy in the {111} planes with triple period sequence. Since the formation of ordered phases has been directly linked to the occurrence of specific surface reconstructions, our results suggest a correlation between the TP-A and B type domains and the multiple stability of n × 3 and 3 × n reconstructions on the (001) surface of GaAsBi under low temperature growth.
Polymer thin film instability from a patterned edge
Authors: Guo Yunlong , Zhang Chuan , Priestley Rodney D.
Published: July 2014

Patterning of polymer thin films with nanoscale features is a critical step in nanoscale technologies. Here, we investigate the dewetting process from both a mechanically patterned edge (ME) and a hole edge of a thin polymer film, as a means to assess the influence of residual stresses induced during patterning on stability. At low temperature in which hole nucleation is not observed dewetting can still proceed from the ME. Under conditions in which dewetting proceeded from both edges that from the ME exhibited a crossover to a dramatically reduced dewetting velocity. These results suggest mechanical stress concentrated along the ME remarkably depresses the dewetting process by decreasing the rim growth rate.
Origin of the responsivity characteristics of Au/ZnO/MgZnO and Au/MgZnO/ZnO structured ultraviolet photodetectors
Authors: Liu Rusheng , Jiang Dayong , Duan Qian , Sun Long , Tian Chunguang , Liang Qingcheng , Gao Shang , Qin Jieming
Published: July 2014

We report on the ultraviolet photodetectors based on the MgZnO/ZnO and ZnO/MgZnO double-layer films prepared by magnetron sputtering method. The spectral response shows only one responsivity peak in the 1.0 and 1.5 h photodetectors (denoted by the deposition time of one layer of the films) and two peaks in the 0.5 h photodetectors. To our surprise, the Au/MgZnO/ZnO photodetectors have larger responsivity than that of the Au/ZnO/MgZnO ones. A physical mechanism focused on depletion width is given to explain the above results.
Circular grating interferometer for mapping transverse coherence area of X-ray beams
Authors: Shi Xianbo , Marathe Shashidhara , Wojcik Michael J. , Kujala Naresh G. , Macrander Albert T. , Assoufid Lahsen
Published: July 2014

A circular grating interferometer was used to map the transverse coherence area of an X-ray beam. Due to the radial symmetry of the circular grating, coherence lengths along all transverse directions were obtained simultaneously by measuring the visibility decay of interferograms recorded at different distances behind a single circular π/2 phase grating. The technique is model-free and provides direct measurement of the complex coherence factor of the beam. The use of a circular grating also enables the unique capability of measuring the source shape profile. Sensitivity of this technique was demonstrated by detecting the small source tilt of a few degrees.
Coupling of Er light emissions to plasmon modes on In2O3: Sn nanoparticle sheets in the near-infrared range
Authors: Matsui Hiroaki , Badalawa Wasanthamala , Hasebe Takayuki , Furuta Shinya , Nomura Wataru , Yatsui Takashi , Ohtsu Motoichi , Tabata Hitoshi
Published: July 2014

Near-infrared Er photoluminescence (PL) is markedly modified using a plasmonic In2O3: Sn nanoparticle (NP) sheet. Modeling and optical measurements reveal the presence of different electric fields (E-field) in the NP sheet. The local E-field excited at the interface between the NP sheet and Er-emitting layer of ZnO contributes significantly towards the spectral modifications of Er PL due to matching with the photon energy of Er PL. We also determine the critical temperature for Er PL modifications, which is related to the energy transfer efficiency between Er transition dipoles in ZnO and the plasmon modes on the NP sheet.
Nonlinear effects in a metamaterial with double negativity
Authors: Fan Li , Chen Zhe , Deng Yuan-chen , Ding Jin , Ge Huan , Zhang Shu-yi , Yang Yue-tao , Zhang Hui
Published: July 2014

Physical phenomena induced by nonlinear effects in an acoustic metamaterial with double-negativity based on two types of scatterers, side holes and membrane, located along a pipe are theoretically and experimentally studied. We find that the pass and forbidden bands related to double-negativity and single-negativity effects in the metamaterial vary with the input acoustic intensities because of the nonlinearities of both types of scatterers. The nonlinearities can disrupt the unique features associated with these characteristic frequency bands of the metamaterial; however, the nonlinear effects may also lead to applications as automatically triggered acoustic isolators, tunable acoustic metamaterials, and so on.
Femtosecond laser induced damage characterization of transmission volume phase gratings
Authors: Martínez-Matos Ó. , Hernández-Garay M. P. , Izquierdo J. G. , Vaveliuk P. , Bañares L. , Calvo M. L.
Published: July 2014

A procedure to characterize the induced damage and the incubation effects in volume transmission gratings under femtosecond laser pulse train illumination is presented. It was also developed a formalism that explains the damage processes. Our proposal was employed on glass gratings to show the effectiveness of the method and its potential to design transmission gratings with enhanced laser induced damage threshold. This procedure is able to be extended to any transmission grating composed by chemically non-uniform material, opening up new perspectives to femtosecond laser pulse shaping.
Simplified prototyping of perfusable polystyrene microfluidics
Authors: Tran Reginald , Ahn Byungwook , R. Myers David , Qiu Yongzhi , Sakurai Yumiko , Moot Robert , Mihevc Emma , Trent Spencer H. , Doering Christopher , A. Lam Wilbur
Published: July 2014

Cell culture in microfluidic systems has primarily been conducted in devices comprised of polydimethylsiloxane (PDMS) or other elastomers. As polystyrene (PS) is the most characterized and commonly used substrate material for cell culture, microfluidic cell culture would ideally be conducted in PS-based microsystems that also enable tight control of perfusion and hydrodynamic conditions, which are especially important for culture of vascular cell types. Here, we report a simple method to prototype perfusable PS microfluidics for endothelial cell culture under flow that can be fabricated using standard lithography and wet laboratory equipment to enable stable perfusion at shear stresses up to 300 dyn/cm2 and pumping pressures up to 26 kPa for at least 100 h. This technique can also be extended to fabricate perfusable hybrid PS-PDMS microfluidics of which one application is for increased efficiency of viral transduction in non-adherent suspension cells by leveraging the high surface area to volume ratio of microfluidics and adhesion molecules that are optimized for PS substrates. These biologically compatible microfluidic devices can be made more accessible to biological-based laboratories through the outsourcing of lithography to various available microfluidic foundries.
Theobromine enhances absorption of cacao polyphenol in rats
Authors: Yamamoto Takayuki , Takahashi Haruya , Suzuki Koichiro , Hirano Akira , Kamei Masanori , Goto Tsuyoshi , Takahashi Nobuyuki , Kawada Teruo
Published: July 2014

Several concentrations of theobromine (TB) and (−)-epicatechin (EC) were coadministered to rats, and plasma EC and its metabolites were determined using ultra-high-performance liquid chromatography–tandem mass spectrometry. It has been demonstrated that TB increases the absorption of EC in a dose-dependent manner. Cocoa powder had a similar effect, and the mechanism involved is not thought to depend on tight junctions.
Quantitative method for the assignment of hinge and shear mechanism in protein domain movements
Authors: Taylor Daniel , Cawley Gavin , Hayward Steven
Published: July 2014

Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains.

Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms.

Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ .

Contact:  sjh@cmp.uea.ac.uk .

Supplementary information:  Supplementary data are available at Bioinformatics online.
The effect of novel mutations on the structure and enzymatic activity of unconventional myosins associated with autosomal dominant non-syndromic hearing loss
Authors: Kwon Tae-Jun , Oh Se-Kyung , Park Hong-Joon , Sato Osamu , Venselaar Hanka , Choi Soo Young , Kim SungHee , Lee Kyu-Yup , Bok Jinwoong , Lee Sang-Heun , Vriend Gert , Ikebe Mitsuo , Kim Un-Kyung , Choi Jae Young
Published: July 2014

Mutations in five unconventional
myosin
genes have been associated with genetic hearing loss (HL). These genes encode the motor proteins myosin IA, IIIA, VI, VIIA and XVA. To date, most mutations in
myosin
genes have been found in the Caucasian population. In addition, only a few functional studies have been performed on the previously reported myosin mutations. We performed screening and functional studies for mutations in the
MYO1A
and
MYO6
genes in Korean cases of autosomal dominant non-syndromic HL. We identified four novel heterozygous mutations in
MYO6
. Three mutations (p.R825X, p.R991X and Q918fsX941) produce a premature truncation of the myosin VI protein. Another mutation, p.R205Q, was associated with diminished actin-activated ATPase activity and actin gliding velocity of myosin VI in an
in vitro
analysis. This finding is consistent with the results of protein modelling studies and corroborates the pathogenicity of this mutation in the
MYO6
gene. One missense variant, p.R544W, was found in the
MYO1A
gene, and
in silico
analysis suggested that this variant has deleterious effects on protein function. This finding is consistent with the results of protein modelling studies and corroborates the pathogenic effect of this mutation in the MYO6 gene.
A depth-averaged debris-flow model that includes the effects of evolving dilatancy. II. Numerical predictions and experimental tests
Authors: George David L. , Iverson Richard M.
Published: July 2014

We evaluate a new depth-averaged mathematical model that is designed to simulate all stages of debris-flow motion, from initiation to deposition. A companion paper shows how the model's five governing equations describe simultaneous evolution of flow thickness, solid volume fraction, basal pore-fluid pressure and two components of flow momentum. Each equation contains a source term that represents the influence of state-dependent granular dilatancy. Here, we recapitulate the equations and analyse their eigenstructure to show that they form a hyperbolic system with desirable stability properties. To solve the equations, we use a shock-capturing numerical scheme with adaptive mesh refinement, implemented in an open-source software package we call D-Claw. As tests of D-Claw, we compare model output with results from two sets of large-scale debris-flow experiments. One set focuses on flow initiation from landslides triggered by rising pore-water pressures, and the other focuses on downstream flow dynamics, runout and deposition. D-Claw performs well in predicting evolution of flow speeds, thicknesses and basal pore-fluid pressures measured in each type of experiment. Computational results illustrate the critical role of dilatancy in linking coevolution of the solid volume fraction and pore-fluid pressure, which mediates basal Coulomb friction and thereby regulates debris-flow dynamics.
Texture analysis with a time-of-flight neutron strain scanner
Authors: Malamud Florencia , Santisteban Javier R. , Vicente Alvarez Miguel Angel , Bolmaro Raúl , Kelleher Joe , Kabra Saurabh , Kockelmann Winfried
Published: July 2014

A time-of-flight (TOF) neutron strain scanner is a white-beam instrument optimized to measure diffractograms at precise locations within bulky specimens, typically along two perpendicular sample orientations. Here, a method is proposed that exploits the spatial resolution (∼1 mm) provided by such an instrument to determine in a nondestructive manner the crystallographic texture at selected locations within a macroscopic object. The method is based on defining the orientation distribution function (ODF) of the crystallites from several incomplete pole figures, and it has been implemented on ENGIN-X, a neutron strain scanner at the ISIS facility in the UK. This method has been applied to determine the texture at different locations of Al alloy plates welded along the rolling direction and to study a Zr2.5%Nb pressure tube produced for a CANDU nuclear power plant. For benchmarking, the results obtained with this instrument for samples of ferritic steel, copper, Al alloys and Zr alloys have been compared with measurements performed using conventional X-ray diffractometers and more established neutron techniques. For cases where pole figure coverage is incomplete, the use of TOF neutron transmission measurements simultaneously performed on the specimens is proposed as a simple and powerful test to validate the resulting ODF.
All-diamond optical assemblies for a beam-multiplexing X-ray monochromator at the Linac Coherent Light Source
Authors: Stoupin S. , Terentyev S. A. , Blank V. D. , Shvyd'ko Yu. V. , Goetze K. , Assoufid L. , Polyakov S. N. , Kuznetsov M. S. , Kornilov N. V. , Katsoudas J. , Alonso-Mori R. , Chollet M. , Feng Y. , Glownia J. M. , Lemke H. , Robert A. , Sikorski M. , Song S. , Zhu D.
Published: July 2014

A double-crystal diamond (111) monochromator recently implemented at the Linac Coherent Light Source (LCLS) enables splitting of the primary X-ray beam into a pink (transmitted) and a monochromatic (reflected) branch. The first monochromator crystal, with a thickness of ∼100 µm, provides sufficient X-ray transmittance to enable simultaneous operation of two beamlines. This article reports the design, fabrication and X-ray characterization of the first and second (300 µm-thick) crystals utilized in the monochromator and the optical assemblies holding these crystals. Each crystal plate has a region of about 5 × 2 mm with low defect concentration, sufficient for use in X-ray optics at the LCLS. The optical assemblies holding the crystals were designed to provide mounting on a rigid substrate and to minimize mounting-induced crystal strain. The induced strain was evaluated using double-crystal X-ray topography and was found to be small over the 5 × 2 mm working regions of the crystals.
Site-specific electronic structures of ferrimagnetic Fe3O4 measured by resonant X-ray magnetic scattering
Authors: Okube Maki , Sasaki Satoshi
Published: July 2014

Resonant magnetic scattering of circularly polarized synchrotron X-rays has revealed the site-specific magnetic moments at two non-equivalent Fe ion sites in Fe3O4. The energy-dependent peaks for the 026 and 266 reflections were attributed ferrimagnetically to the e and t
2 energy levels of Fe 3d at the A site, and to the t
2g and e
g levels at the B site, respectively, having a sequence of t
2g, e, e
g and t
2 in order of energy. This sequence agrees with the local spin-density approximation calculations in the literature [Anisimov, Elfimov, Hamada & Terakura, (1996). Phys. Rev.
54, 4387–4390], in which the spin-down band at the Fermi energy corresponds to t
2g
. Resonant magnetic Fourier synthesis reveals the electron densities of the ferrimagnetic moments.
The strongly defective double perovskite Sr11Mo4O23: crystal structure in relation to ionic conductivity
Authors: López Carlos A. , Pedregosa José C. , Lamas Diego G. , Alonso José A.
Published: July 2014

The crystal structure and ionic conductivity properties of a novel microcrystalline Sr11Mo4O23 ceramic material are presented. This material has been prepared by thermal treatment up to 1473 K, in air, of previously decomposed citrate precursors. The complex crystal structure was refined from combined X-ray powder diffraction and neutron powder diffraction data. The formula of this phase can be rewritten as Sr1.75□0.25SrMoO5.75, highlighting the relationship with double perovskites A
2
B′B′′O6. At room temperature, the crystal structure is tetragonal in space group I41/a, with a = 11.6107 (6) Å, c = 16.422 (1) Å and V = 2213.8 (2) Å3. The crystal network contains O anion and Sr cation vacancies. The structure is complex, with Sr, Mo and O atoms distributed over four, two and six distinct Wyckoff sites, respectively. Only one of the Sr sites (SrO6) corresponds to the octahedral network; one of the two MoO6 types of octahedra is axially distorted. The three other Sr positions occupy the A site with higher coordination. There is an occupational deficit of O atoms of 22 (4)%. This defective framework material presents an interesting ionic mobility, enhanced above 773 K owing to a further reduction in the oxygen content.
A simple approach to determine the polarization coefficient at synchrotron radiation stations
Authors: Sulyanov Sergei , Dorovatovskii Pavel , Boysen Hans
Published: July 2014

A simple procedure for the measurement of the degree of linear polarization at a synchrotron radiation station is described. The diffraction pattern from a glass plate set perpendicular to the incident beam is registered using a two-dimensional area detector. The intensity variation along the azimuth angle ρ at a constant diffraction angle is fitted to the theoretical cos2ρ dependence. The results of measurements performed at a synchrotron radiation station with a CCD detector on the beam from a bending magnet are presented.
Neutron and X-ray diffraction study of ferrite nanocrystals obtained by microwave-assisted growth. A structural comparison with the thermal synthetic route. Corrigendum
Authors: Solano Eduardo , Frontera Carlos , Puente Orench Inés , Puig Teresa , Obradors Xavier , Ricart Susagna , Ros Josep
Published: July 2014

In the paper by Solano et al. [J. Appl. Cryst. (2014), 47, 414–420], Inés Puente Orench is missing from the list of authors. The complete list of authors should be Eduardo Solano, Carlos Frontera, Inés Puente Orench, Teresa Puig, Xavier Obradors, Susagna Ricart and Josep Ros.
Ronchi test for characterization of X-ray nanofocusing optics and beamlines
Authors: Uhlén Fredrik , Rahomäki Jussi , Nilsson Daniel , Seiboth Frank , Sanz Claude , Wagner Ulrich , Rau Christoph , Schroer Christian G. , Vogt Ulrich
Published: July 2014

A Ronchi interferometer for hard X-rays is reported in order to characterize the performance of the nanofocusing optics as well as the beamline stability. Characteristic interference fringes yield qualitative data on present aberrations in the optics. Moreover, the visibility of the fringes on the detector gives information on the degree of spatial coherence in the beamline. This enables the possibility to detect sources of instabilities in the beamline like vibrations of components or temperature drift. Examples are shown for two different nanofocusing hard X-ray optics: a compound refractive lens and a zone plate.
Disentangling customer orientation – executive perspective
Authors: Saarijärvi Hannu , Kuusela Hannu , Neilimo Kari , Närvänen Elina
Published: July 2014

Purpose

– Despite the fact that customer orientation is increasingly used as a strategic guideline to ensure companies’ long-term success, it is too often left at conceptual level without any managerial or executive translation. To address this practical gap, the purpose of the paper is to build an executive perspective on customer orientation through the mechanism of customer value dimensions.

Design/methodology/approach

– An intensive case study from a successful retail service business is used to illustrate how customer orientation is applied in actual strategic decision making at the executive level. The case business is a multi-sector service business that took a strategic turn toward customer orientation in the 2000s. As a result, the company has been able to increase their market share to become the market leader as well as stay ahead of the competition and increase customer loyalty.

Findings

– The study provides a practical tool of disentangling customer orientation into four customer value dimensions and linking them with appropriate executive level strategic decision making.

Practical implications

– The study helps executives uncover the inner meaning of customer orientation, move beyond traditional conceptualization of customer orientation, and adopt customer value orientation. This necessitates not only understanding customer value criteria, but also linking the diverse criteria to executive level strategic decision making.

Originality/value

– The study concretizes and uncovers how customer orientation can be implemented by incorporating both economic, functional, emotional, and symbolic customer value dimensions into executive level strategic decision making.
A cyclical evaluation model of information security maturity
Authors: Alencar Rigon Evandro , Merkle Westphall Carla , Ricardo dos Santos Daniel , Becker Westphall Carlos
Published: July 2014

Purpose

– This paper aims at presenting a cyclical evaluation model of information security (IS) maturity. The lack of a security evaluation method might expose organizations to several risky situations.

Design/methodology/approach

– This model was developed through the definition of a set of steps to be followed to obtain periodical evaluation of maturity and continuous improvement of controls.

Findings

– This model, based on controls present in ISO/IEC 27002, provides a means to measure the current situation of IS management through the use of a maturity model and provides a subsidy to take appropriate and feasible improvement actions, based on risks. A case study is performed, and the results indicate that the method is efficient for evaluating the current state of IS, to support IS management, risks identification and business and internal control processes.

Research limitations/implications

– It is possible that modifications to the process may be needed where there is less understanding of security requirements, such as in a less mature organization.

Originality/value

– This paper presents a generic model applicable to all kinds of organizations. The main contribution of this paper is the use of a maturity scale allied to the cyclical process of evaluation, providing the generation of immediate indicators for the management of IS.
An empirical investigation of the factors that influence Internet user’s ability to correctly identify a phishing website
Authors: Purkait Swapan , Kumar De Sadhan , Suar Damodar
Published: July 2014

Purpose

– The aim of this study is to report on the results of an empirical investigation of the various factors which have significant impacts on the Internet user’s ability to correctly identify a phishing website.

Design/methodology/approach

– The research participants were Internet users who have had at least some experience of financial transactions over the Internet. This study conducted a quantitative research with the help of a structured survey questionnaire along with three experimental tasks. A total of 621 valid samples were collected and the multiple regression analysis technique was used to deduce the answers to the research question.

Findings

– The results show that the model is useful and has explanatory power. And adjustedR2 computed as 0.927, means that 92.7 per cent of the variations in the Internet user’s ability to identify phishing website can be explained by the predictors selected for the model.

Research limitations/implications

– Future research should account for the Internet user’s general security practices and behaviour, attitude towards online financial activity, risk-taking ability or risk behaviour and their potential effects on Internet users' ability to identify a phishing website.

Practical implications

– The implications of this study provide the foundation for future research on the areas that intend to explain the Internet user’s necessity to take protection or avoid risky behaviour while performing financial transaction over the Internet.

Originality/value

– This study provides the body of knowledge with an empirical analysis of impact of various factors on an Internet user’s ability to identify phishing websites. The results of this study can help practitioners create a more successful research model and help researchers better understand user behaviour on the Internet.
Abnormal audit delays, earnings quality and firm value in the USA
Authors: Asthana Sharad
Published: July 2014

Purpose

– This paper aims to address three questions: Does the abnormal delay in the audit process signal poor earnings quality? Is this information about earnings quality incremental to that contained in earnings report delay? Does the market use this information about earnings quality in valuing the firm?

Design/methodology/approach

– Data are obtained from four databases: Compustat, Audit Analytics, Compact-Disclosure and I/B/E/S. Complete data are available for 5,298 firms for 22,492 firm-years. The paper uses a two-stage model. In the first stage, a detailed model using determinants from extant research tries to explain the audit delay. In the second stage, the unexplained delay from the first stage is used in the association tests with earnings quality.

Findings

– The paper presents evidence that abnormal delays in the audit process are inversely associated with earnings quality. When the market values a dollar of reported earnings, it appears to discount the valuation by the extent of abnormal audit delay.

Originality/value

– The current paper contributes to existing research in several ways. First, it establishes a comprehensive model to explain audit delays and provides a tool to measure abnormal audit delays. Second, it provides evidence of inverse association between abnormal audit delay and seven proxies of earnings quality. Finally, the paper shows that abnormal audit delay creates skepticism among investors about earnings quality and they value the disclosed earnings after discounting for such delay.
Preemption of compliance costs and the voluntary adoption of SFAS No. 123(R)
Authors: Ebrahim Ahmed , Bradford Bruce
Published: July 2014

Purpose

– This paper aims to study a preemption proposition for the compliance costs associated with stock option expensing under SFAS 123(R) by examining whether early adopters used their discretion over option pricing model inputs to mitigate the adoption effect.

Design/methodology/approach

– The paper uses a matched sample approach of firms that voluntarily adopted stock option expensing during the 2002-2004 period and similar firms that waited until the mandatory expensing. The paper empirically examines some determinants of voluntary adoption, and the changes in option pricing model inputs during the period leading to mandatory expensing.

Findings

– The paper reports evidence that voluntary adopters of stock option expensing during the 2002-2004 period have used the period leading to mandatory expensing to preempt its compliance cost effect. The authors exercised their discretion by decreasing estimates for stock price volatility and time-to-maturity to preempt or minimize the reduction in earnings before mandatory adoption date.

Originality/value

– Results of this paper are useful to accounting regulators in understanding the reaction of financial statement preparers to deliberations, effective dates and voluntary early adoption terms of the accounting standards setting process.