bluuebunny/crossref_metadata_2025 huggingface dataset:
From neurons to epidemics: How trophic coherence affects spreading processes
Authors: Klaise Janis , Johnson Samuel
Published: June 2016

Trophic coherence, a measure of the extent to which the nodes of a directed network are organised in levels, has recently been shown to be closely related to many structural and dynamical aspects of complex systems, including graph eigenspectra, the prevalence or absence of feedback cycles, and linear stability. Furthermore, non-trivial trophic structures have been observed in networks of neurons, species, genes, metabolites, cellular signalling, concatenated words, P2P users, and world trade. Here, we consider two simple yet apparently quite different dynamical models—one a susceptible-infected-susceptible epidemic model adapted to include complex contagion and the other an Amari-Hopfield neural network—and show that in both cases the related spreading processes are modulated in similar ways by the trophic coherence of the underlying networks. To do this, we propose a network assembly model which can generate structures with tunable trophic coherence, limiting in either perfectly stratified networks or random graphs. We find that trophic coherence can exert a qualitative change in spreading behaviour, determining whether a pulse of activity will percolate through the entire network or remain confined to a subset of nodes, and whether such activity will quickly die out or endure indefinitely. These results could be important for our understanding of phenomena such as epidemics, rumours, shocks to ecosystems, neuronal avalanches, and many other spreading processes.
Intervality and coherence in complex networks
Authors: Domínguez-García Virginia , Johnson Samuel , Muñoz Miguel A.
Published: June 2016

Food webs—networks of predators and prey—have long been known to exhibit “intervality”: species can generally be ordered along a single axis in such a way that the prey of any given predator tend to lie on unbroken compact intervals. Although the meaning of this axis—usually identified with a “niche” dimension—has remained a mystery, it is assumed to lie at the basis of the highly non-trivial structure of food webs. With this in mind, most trophic network modelling has for decades been based on assigning species a niche value by hand. However, we argue here that intervality should not be considered the cause but rather a consequence of food-web structure. First, analysing a set of 46 empirical food webs, we find that they also exhibit predator intervality: the predators of any given species are as likely to be contiguous as the prey are, but in a different ordering. Furthermore, this property is not exclusive of trophic networks: several networks of genes, neurons, metabolites, cellular machines, airports, and words are found to be approximately as interval as food webs. We go on to show that a simple model of food-web assembly which does not make use of a niche axis can nevertheless generate significant intervality. Therefore, the niche dimension (in the sense used for food-web modelling) could in fact be the consequence of other, more fundamental structural traits. We conclude that a new approach to food-web modelling is required for a deeper understanding of ecosystem assembly, structure, and function, and propose that certain topological features thought to be specific of food webs are in fact common to many complex networks.
Optical properties of graphene nanoflakes: Shape matters
Authors: Mansilla Wettstein Candela , Bonafé Franco P. , Oviedo M. Belén , Sánchez Cristián G.
Published: June 2016

In recent years there has been significant debate on whether the edge type of graphene nanoflakes (GNFs) or graphene quantum dots (GQDs) are relevant for their electronic structure, thermal stability, and optical properties. Using computer simulations, we have proven that there is a fundamental difference in the absorption spectra between samples of the same shape, similar size but different edge type, namely, armchair or zigzag edges. These can be explained by the presence of electronic structures near the Fermi level which are localized on the edges. These features are also evident from the dependence of band gap on the GNF size, which shows three very distinct trends for different shapes and edge geometries.
An alternative realization of the exact non-Markovian stochastic Schrödinger equation
Authors: Song Kai , Song Linze , Shi Qiang
Published: June 2016

Based on the path integral approach, we derive a new realization of the exact non-Markovian stochastic Schrödinger equation (SSE). The main difference from the previous non-Markovian quantum state diffusion (NMQSD) method is that the complex Gaussian stochastic process used for the forward propagation of the wave function is correlated, which may be used to reduce the amplitude of the non-Markovian memory term at high temperatures. The new SSE is then written into the recently developed hierarchy of pure states scheme, in a form that is more closely related to the hierarchical equation of motion approach. Numerical simulations are then performed to demonstrate the efficiency of the new method.
Correlation dimension Wonderland theorems
Authors: Carvalho Silas L. , de Oliveira César R.
Published: June 2016

Existence of generic sets of self-adjoint operators, related to correlation dimensions of spectral measures, is investigated in separable Hilbert spaces. Typical results say that, given an orthonormal basis, the set of operators whose corresponding spectral measures are both 0-lower and 1-upper correlation dimensional is generic. The proofs rely on details of the relations among Fourier transform of spectral measures and Hausdorff and packing measures on the real line. Then such results are naturally combined with the Wonderland theorem. Applications are to classes of discrete one-dimensional Schrödinger operators and general (bounded) self-adjoint operators as well. Physical consequences include a proof of exotic dynamical behavior of singular continuous spectrum in some settings.
Optomechanical design and construction of a vacuum-compatible optical parametric oscillator for generation of squeezed light
Authors: Wade A. R. , Mansell G. L. , McRae T. G. , Chua S. S. Y. , Yap M. J. , Ward R. L. , Slagmolen B. J. J. , Shaddock D. A. , McClelland D. E.
Published: June 2016

With the recent detection of gravitational waves, non-classical light sources are likely to become an essential element of future detectors engaged in gravitational wave astronomy and cosmology. Operating a squeezed light source under high vacuum has the advantages of reducing optical losses and phase noise compared to techniques where the squeezed light is introduced from outside the vacuum. This will ultimately provide enhanced sensitivity for modern interferometric gravitational wave detectors that will soon become limited by quantum noise across much of the detection bandwidth. Here we describe the optomechanical design choices and construction techniques of a near monolithic glass optical parametric oscillator that has been operated under a vacuum of 10−6 mbar. The optical parametric oscillator described here has been shown to produce 8.6 dB of quadrature squeezed light in the audio frequency band down to 10 Hz. This performance has been maintained for periods of around an hour and the system has been under vacuum continuously for several months without a degradation of this performance.
Measuring shape and size of micrometric particles from the analysis of the forward scattered field
Authors: Villa S. , Sanvito T. , Paroli B. , Pullia A. , Delmonte B. , Potenza M. A. C.
Published: June 2016

Characterizing nano- and micro-particles in fluids still proves to be a significant challenge for both science and industry. Here, we show how to determine shape and size distributions of polydisperse water suspensions of micron-sized particles by the analysis of the field scattered in the forward direction by single particles illuminated by a laser beam. We exploit the novel Single Particle Extinction and Scattering method in connection with shear conditions which give preferred orientations to the particles passing through the scattering volume. Water suspensions of calibrated non-spherical particles, polydisperse standard monophasic mineral samples of quartz and kaolinite, and a mixture of quartz and illite are studied in detail. Application and limitation of the method are discussed.
Characterization for Cassie-Wenzel wetting transition based on the force response in the process of squeezing liquid drops by two parallel superhydrophobic surfaces
Authors: Li Jian
Published: June 2016

Application of superhydrophobic surfaces is partly limited by the escaping of the entrapped air beneath the liquid sitting on the superhydrophobic surfaces, i.e., the so-called Cassie-Wenzel wetting transition. Here, to characterize this wetting transition, a linear force response relation with certain abnormal systematic deflection showing the wetting transition information is constructed for the process of squeezing the test liquid drop by two parallel structured (superhydrophobic) surfaces. The linear force response relation is validated by replotting the experimental data from the former work. And then the wetting transition information is investigated on a numerically generated force response curve with certain errors by taking into account the liquid pressure variation during the wetting transition. Results show that the wetting transition can cause an obvious bulge on the linear force response curve. We believe that this method has a potential application in characterizing the robustness of superhydrophobic surfaces.
Fast phase stabilization of a low frequency beat note for atom interferometry
Authors: Oh E. , Horne R. A. , Sackett C. A.
Published: June 2016

Atom interferometry experiments rely on the ability to obtain a stable signal that corresponds to an atomic phase. For interferometers that use laser beams to manipulate the atoms, noise in the lasers can lead to errors in the atomic measurement. In particular, it is often necessary to actively stabilize the optical phase between two frequency components of the beams. Typically this is achieved using a time-domain measurement of a beat note between the two frequencies. This becomes challenging when the frequency difference is small and the phase measurement must be made quickly. The method presented here instead uses a spatial interference detection to rapidly measure the optical phase for arbitrary frequency differences. A feedback system operating at a bandwidth of about 10 MHz could then correct the phase in about 3 μs. This time is short enough that the phase correction could be applied at the start of a laser pulse without appreciably degrading the fidelity of the atom interferometer operation. The phase stabilization system was demonstrated in a simple atom interferometer measurement of the 87Rb recoil frequency.
Design and construction of a point-contact spectroscopy rig with lateral scanning capability
Authors: Tortello M. , Park W. K. , Ascencio C. O. , Saraf P. , Greene L. H.
Published: June 2016

The design and realization of a cryogenic rig for point-contact spectroscopy measurements in the needle-anvil configuration is presented. Thanks to the use of two piezoelectric nano-positioners, the tip can move along the vertical (z) and horizontal (x) direction and thus the rig is suitable to probe different regions of a sample in situ. Moreover, it can also form double point-contacts on different facets of a single crystal for achieving, e.g., an interferometer configuration for phase-sensitive measurements. For the later purpose, the sample holder can also host a Helmholtz coil for applying a small transverse magnetic field to the junction. A semi-rigid coaxial cable can be easily added for studying the behavior of Josephson junctions under microwave irradiation. The rig can be detached from the probe and thus used with different cryostats. The performance of this new probe has been tested in a Quantum Design PPMS system by conducting point-contact Andreev reflection measurements on Nb thin films over large areas as a function of temperature and magnetic field.
Thermal conductivity and mechanical properties of AlN-based thin films
Authors: Moraes V. , Riedl H. , Rachbauer R. , Kolozsvári S. , Ikeda M. , Prochaska L. , Paschen S. , Mayrhofer P. H.
Published: June 2016

While many research activities concentrate on mechanical properties and thermal stabilities of protective thin films, only little is known about their thermal properties being essential for the thermal management in various industrial applications. Based on the 3ω-method, we show the influence of Al and Cr on the temperature dependent thermal conductivity of single-phase cubic structured TiN and single-phase wurtzite structured AlN thin films, respectively, and compare them with the results obtained for CrN thin films. The dc sputtered AlN thin films revealed a highly c-axis oriented growth for deposition temperatures of 250 to 700 °C. Their thermal conductivity was found to increase strongly with the film thickness, indicating progressing crystallization of the interface near amorphous regions during the sputtering process. For the 940 nm AlN film, we found a lower boundary for the thermal conductivity of 55.3 W m-1 K-1. By the substitution of only 10 at. % Al with Cr, κ significantly reduces to ∼5.0 W m-1 K-1, although the single-phase wurtzite structure is maintained. The single-phase face centered cubic TiN and Ti0.36Al0.64N thin films exhibit κ values of 3.1 W m-1 K-1 and 2.5 W m-1 K-1, respectively, at room temperature. Hence, also here, the substitutional alloying reduces the thermal conductivity, although at a significantly lower level. Single-phase face centered cubic CrN thin films show κ values of 3.6 W m-1 K-1. For all nitride based thin films investigated, the thermal conductivity slightly increases with increasing temperature between 200 and 330 K. This rather unusual behavior is based on the high defect density (especially point defects) within the thin films prepared by physical vapor deposition.
LoFEx — A local framework for calculating excitation energies: Illustrations using RI-CC2 linear response theory
Authors: Baudin Pablo , Kristensen Kasper
Published: June 2016

We present a local framework for the calculation of coupled cluster excitation energies of large molecules (LoFEx). The method utilizes time-dependent Hartree-Fock information about the transitions of interest through the concept of natural transition orbitals (NTOs). The NTOs are used in combination with localized occupied and virtual Hartree-Fock orbitals to generate a reduced excitation orbital space (XOS) specific to each transition where a standard coupled cluster calculation is carried out. Each XOS is optimized to ensure that the excitation energies are determined to a predefined precision. We apply LoFEx in combination with the RI-CC2 model to calculate the lowest excitation energies of a set of medium-sized organic molecules. The results demonstrate the black-box nature of the LoFEx approach and show that significant computational savings can be gained without affecting the accuracy of CC2 excitation energies.
Symmetries of stochastic differential equations: A geometric approach
Authors: De Vecchi Francesco C. , Morando Paola , Ugolini Stefania
Published: June 2016

A new notion of stochastic transformation is proposed and applied to the study of both weak and strong symmetries of stochastic differential equations (SDEs). The correspondence between an algebra of weak symmetries for a given SDE and an algebra of strong symmetries for a modified SDE is proved under suitable regularity assumptions. This general approach is applied to a stochastic version of a two dimensional symmetric ordinary differential equation and to the case of two dimensional Brownian motion.
A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water
Authors: Kitabata Masahiro , Fujimoto Kazushi , Yoshii Noriyuki , Okazaki Susumu
Published: June 2016

To obtain the radial (normal) and lateral (transverse) components of the local pressure tensor, PN(R) and PT(R), respectively, and the interfacial tension of micelles, molecular dynamics (MD) calculations were performed for spherical sodium dodecyl sulfate (SDS) micelles. The local pressure tensor was calculated as a function of radial distance R using the Irving-Kirkwood formula. Similar MD calculations were also carried out for an n-dodecane droplet in water to compare the differences in the local pressure and interfacial tension values with those of the micelles. The calculated interfacial tensions were 20 ± 5 and 44 ± 10 mN/m for the SDS micelles and dodecane droplets, respectively. The excess free energies due to the interfacial tension were 340 and 1331 kJ/mol for the SDS micelle and dodecane droplet, respectively. The micelles are stabilized by 991 kJ/mol by covering their hydrophobic cores with hydrophilic groups. The dodecane droplet has a large interfacial tension caused by the zero or positive values of PN(R) − PT(R) at all values of R. In contrast, the small interfacial tension in the SDS micelles comes from the negative PN(R) − PT(R) values over a wide range of R. The pressure difference between the inside and outside of the oil droplet and its interfacial tension well satisfies the Laplace equation. However, the hydrophobic core of the SDS micelle is quite different from the liquid alkane, and the SDS micelles do not follow Laplace’s picture. Decomposing the interfacial tension into contributions from various interactions, it is found that those between charged and polar groups dominate the interfacial tension of the SDS micelles. The positive electrostatic potential (1.3 V) on the micelle surface and the negative potential (−0.15 V) on the oil droplet contribute to the interfacial tensions by 19 and 0.5 mN/m, respectively. Thus, the interfacial tension of the SDS micelles is produced by electrostatic interactions, in contrast to the dodecane droplet.
Mean flows and blob velocities in scrape-off layer (SOLT) simulations of an L-mode discharge on Alcator C-Mod
Authors: Russell D. A. , Myra J. R. , D'Ippolito D. A. , LaBombard B. , Hughes J. W. , Terry J. L. , Zweben S. J.
Published: June 2016

Two-dimensional scrape-off layer turbulence (SOLT) code simulations are compared with an L-mode discharge on the Alcator C-Mod tokamak [Greenwald et al., Phys. Plasmas 21, 110501 (2014)]. Density and temperature profiles for the simulations were obtained by smoothly fitting Thomson scattering and mirror Langmuir probe (MLP) data from the shot. Simulations differing in turbulence intensity were obtained by varying a dissipation parameter. Mean flow profiles and density fluctuation amplitudes are consistent with those measured by MLP in the experiment and with a Fourier space diagnostic designed to measure poloidal phase velocity. Blob velocities in the simulations were determined from the correlation function for density fluctuations, as in the analysis of gas-puff-imaging (GPI) blobs in the experiment. In the simulations, it was found that larger blobs moved poloidally with the E × B flow velocity, vE, in the near-SOL, while smaller fluctuations moved with the group velocity of the dominant linear (interchange) mode, vE + 1/2 vdi, where vdi is the ion diamagnetic drift velocity. Comparisons are made with the measured GPI correlation velocity for the discharge. The saturation mechanisms operative in the simulation of the discharge are also discussed. It is found that neither sheared flow nor pressure gradient modification can be excluded as saturation mechanisms.
Instability of surface electron cyclotron TM-modes influenced by non-monochromatic alternating electric field
Authors: Girka I. O. , Girka V. O. , Sydora R. D. , Thumm M.
Published: June 2016

The influence of non-monochromaticity of an external alternating electric field on excitation of TM eigenmodes at harmonics of the electron cyclotron frequency is considered here. These TM-modes propagate along the plasma interface in a metal waveguide. An external static constant magnetic field is oriented perpendicularly to the plasma interface. The problem is solved theoretically using the kinetic Vlasov-Boltzmann equation for description of plasma particles motion and the Maxwell equations for description of the electromagnetic mode fields. The external alternating electric field is supposed to be a superposition of two waves, whose amplitudes are different and their frequencies correlate as 2:1. An infinite set of equations for electric field harmonics of these modes is derived with the aid of nonlinear boundary conditions. This set is solved using the wave packet approach consisting of the main harmonic frequency and two nearest satellite temporal harmonics. Analytical studies of the obtained set of equations allow one to find two different regimes of parametric instability, namely, enhancement and suppression of the instability. Numerical analysis of the instability is carried out for the three first electron cyclotron harmonics.
Tearing mode dynamics and locking in the presence of external magnetic perturbations
Authors: Fridström R. , Munaretto S. , Frassinetti L. , Chapman B. E. , Brunsell P. R. , Sarff J. S.
Published: June 2016

In normal operation, Madison Symmetric Torus (MST) [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)] reversed-field pinch plasmas exhibit several rotating tearing modes (TMs). Application of a resonant magnetic perturbation (RMP) results in braking of mode rotation and, if the perturbation amplitude is sufficiently high, in a wall-locked state. The coils that produce the magnetic perturbation in MST give rise to RMPs with several toroidal harmonics. As a result, simultaneous deceleration of all modes is observed. The measured TM dynamics is shown to be in qualitative agreement with a magnetohydrodynamical model of the RMP interaction with the TM [R. Fitzpatrick, Nucl. Fusion 33, 1049 (1993)] adapted to MST. To correctly model the TM dynamics, the electromagnetic torque acting on several TMs is included. Quantitative agreement of the TM slowing-down time was obtained for a kinematic viscosity in the order of νkin≈10–20 m2/s. Analysis of discharges with different plasma densities shows an increase of the locking threshold with increasing density. Modeling results show good agreement with the experimental trend, assuming a density-independent kinematic viscosity. Comparison of the viscosity estimates in this paper to those made previously with other techniques in MST plasmas suggests the possibility that the RMP technique may allow for estimates of the viscosity over a broad range of plasmas in MST and other devices.
Phase response curves for models of earthquake fault dynamics
Authors: Franović Igor , Kostić Srdjan , Perc Matjaž , Klinshov Vladimir , Nekorkin Vladimir , Kurths Jürgen
Published: June 2016

We systematically study effects of external perturbations on models describing earthquake fault dynamics. The latter are based on the framework of the Burridge-Knopoff spring-block system, including the cases of a simple mono-block fault, as well as the paradigmatic complex faults made up of two identical or distinct blocks. The blocks exhibit relaxation oscillations, which are representative for the stick-slip behavior typical for earthquake dynamics. Our analysis is carried out by determining the phase response curves of first and second order. For a mono-block fault, we consider the impact of a single and two successive pulse perturbations, further demonstrating how the profile of phase response curves depends on the fault parameters. For a homogeneous two-block fault, our focus is on the scenario where each of the blocks is influenced by a single pulse, whereas for heterogeneous faults, we analyze how the response of the system depends on whether the stimulus is applied to the block having a shorter or a longer oscillation period.
Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks
Authors: Kolb Brian , Zhao Bin , Li Jun , Jiang Bin , Guo Hua
Published: June 2016

The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H2 → H2 + H, H + H2O → H2 + OH, and H + CH4 → H2 + CH3. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.
Comparison of the telegraph and hyperdiffusion approximations in cosmic-ray transport
Authors: Litvinenko Yuri E. , Noble P. L.
Published: June 2016

The telegraph equation and its generalizations have been repeatedly considered in the models of diffusive cosmic-ray transport. Yet the telegraph model has well-known limitations, and analytical arguments suggest that a hyperdiffusion model should serve as a more accurate alternative to the telegraph model, especially on the timescale of a few scattering times. We present a detailed side-by-side comparison of an evolving particle density profile, predicted by the telegraph and hyperdiffusion models in the context of a simple but physically meaningful initial-value problem, compare the predictions with the solution based on the Fokker–Planck equation, and discuss the applicability of the telegraph and hyperdiffusion approximations to the description of strongly anisotropic particle distributions.
Ultralow lattice thermal conductivity in topological insulator TlBiSe2
Authors: Ding Guangqian , Carrete Jesús , Li Wu , Gao G. Y. , Yao Kailun
Published: June 2016

We present ab-initio calculations of the phonon thermal transport properties of topological insulator TlBiSe2. Our results point to a very low lattice thermal conductivity, comparable or lower than those of some popular good thermoelectric materials. Furthermore, we find a slight thermal anisotropy between the in-plane and cross-plane directions in TlBiSe2, markedly smaller than those of van-der-Waals topological insulators explored so far. These conclusions are confirmed and explained by comprehensive analysis of the phonon spectrum of TlBiSe2. The combination of ultralow lattice thermal conductivity and small anisotropy makes TlBiSe2 a promising candidate for thermoelectric applications.
Temperature-sensitive photoluminescent CdSe-ZnS polymer composite film for lock-in photothermal characterization
Authors: Liu Liwang , Zhong Kuo , Meng Lei , Van Hemelrijck Danny , Wang Ling , Glorieux Christ
Published: June 2016

The temperature dependence of the fluorescence spectrum of CdSe−ZnS core–shell quantum dots embedded in a polystyrene matrix is characterized between 30 °C and 60 °C. The spectrally integrated photoluminescence intensity is found to linearly decrease with −1.3%/ °C. This feature is exploited in a dual coating-substrate-configuration, consisting of a layer of this nanocomposite material, acting as a temperature sensor with optical readout, on top of an optically absorbing and opaque layer, acting as a photothermal excitation source, and covering a substrate material or structure of interest. From the frequency dependence of the optically detected photothermal signal in the frequency range between 5 Hz and 150 Hz, different thermal parameters of the constituent layers are determined. The fitted values of thermal properties of the different layers, determined in different scenarios in terms of the used a priori information about the layers, are found to be internally consistent, and consistent with literature values.
Room temperature d ferromagnetism in ZnS nanocrystals
Authors: Proshchenko Vitaly , Horoz Sabit , Tang Jinke , Dahnovsky Yuri
Published: June 2016

Room temperature ferromagnetic semiconductors have a great deal of advantage because of their easy integration into semiconductor devices. ZnS nanocrystals (NCs), bulk, and surfaces exhibit d0 ferromagnetism at room temperature. The experiments reveal that NC ferromagnetism takes place at low and room temperatures only due to Zn vacancies (S vacancies do not contribute). To understand the mechanism of d0 ferromagnetism, we introduce the surface-bulk model of a nanocrystal, which includes both surface and bulk magnetizations. The calculations demonstrate that the surface has the higher than bulk magnetization. We find the mechanism of the ferromagnetism is due to sulfur s- and p-electrons in a tetrahedral crystal field. The bulk magnetic moment increases with Zn vacancy concentration at small concentrations and then goes down at larger concentrations. A surface magnetic moment behaves differently with the concentration. It is always a monotonically rising function. We find that the total NC magnetic moment increases with the size and concentration of Zn vacancies (only low concentrations). We also study the magnetization per unit cell where we find that it decreases for the surface and increases for bulk magnetism with the NC size.
Realizing stable fully spin polarized transport in SiC nanoribbons with dopant
Authors: Tao Xixi , Hao Hua , Wang Xianlong , Zheng Xiaohong , Zeng Zhi
Published: June 2016

Intrinsic half-metallicity recently reported in zigzag edged SiC nanoribbons is basically undetectable due to negligible energy difference between the antiferromagnetic (AFM) and ferromagnetic (FM) configurations. In this Letter, by density functional theory calculations, we demonstrate a scheme of N doping at the carbon edge to selectively close the edge state channel at this edge and achieve 100% spin filtering, no matter whether it is in an AFM state or FM state. This turns SiC nanoribbon into a promising material for obtaining stable and completely spin polarized transport and may find application in spintronic devices.
Wave-breaking amplitudes of relativistic upper-hybrid oscillations in a cold magnetized plasma
Authors: Karmakar Mithun , Maity Chandan , Chakrabarti Nikhil
Published: June 2016

A travelling wave solution is presented for relativistic upper-hybrid oscillations (RUHOs) in a cold magnetized plasma. An expression for the wave-breaking amplitudes of RUHOs is derived. The wave-breaking amplitudes of RUHOs are found to decrease with the increase of the strength of an ambient magnetic field. These results will be of relevance to the laboratory context of particle acceleration by wake-fields in which magnetic field plays a central role.
Magnetic curvature effects on plasma interchange turbulence
Authors: Li B. , Liao X. , Sun C. K. , Ou W. , Liu D. , Gui G. , Wang X. G.
Published: June 2016

The magnetic curvature effects on plasma interchange turbulence and transport in the Z-pinch and dipole-like systems are explored with two-fluid global simulations. By comparing the transport levels in the systems with a different magnetic curvature, we show that the interchange-mode driven transport strongly depends on the magnetic geometry. For the system with large magnetic curvature, the pressure and density profiles are strongly peaked in a marginally stable state and the nonlinear evolution of interchange modes produces the global convective cells in the azimuthal direction, which lead to the low level of turbulent convective transport.
Simultaneous realization of negative group velocity, fast and slow acoustic waves in a metamaterial
Authors: Li Xiao-juan , Xue Cheng , Fan Li , Zhang Shu-yi , Chen Zhe , Ding Jin , Zhang Hui
Published: June 2016

An acoustic metamaterial is designed based on a simple and compact structure of one string of side pipes arranged along a waveguide, in which diverse group velocities are achieved. Owing to Fabry-Perot resonance of the side pipes, a negative phase time is achieved, and thus, acoustic waves transmitting with negative group velocities are produced near the resonant frequency. In addition, both fast and slow acoustic waves are also observed in the vicinity of the resonance frequency. The extraordinary group velocities can be explained based on spectral rephasing induced by anomalous dispersion on the analogy of Lorentz dispersion in electromagnetic waves.
External modes in quantum dot light emitting diode with filtered optical feedback
Authors: Al Husseini Hussein B. , Al Naimee Kais A. , Al-Khursan Amin H. , Khedir Ali. H.
Published: June 2016

This research reports a theoretical investigation on the role of filtered optical feedback (FOF) in the quantum dot light emitting diode (QD-LED). The underlying dynamics is affected by a sidle node, which returns to an elliptical shape when the wetting layer (WL) is neglected. Both filter width and time delay change the appearance of different dynamics (chaotic and mixed mode oscillations, MMOs). The results agree with the experimental observations. Here, the fixed point analysis for QDs was done for the first time. For QD-LED with FOF, the system transits from the coherence collapse case in conventional optical feedback to a coherent case with a filtered mode in FOF. It was found that the WL washes out the modes which is an unexpected result. This may attributed to the longer capture time of WL compared with that between QD states. Thus, WL reduces the chaotic behavior.
Experimental evaluation of electrical conductivity imaging of anisotropic brain tissues using a combination of diffusion tensor imaging and magnetic resonance electrical impedance tomography
Authors: Sajib Saurav Z. K. , Jeong Woo Chul , Kyung Eun Jung , Kim Hyun Bum , Oh Tong In , Kim Hyung Joong , Kwon Oh In , Woo Eung Je
Published: June 2016

Anisotropy of biological tissues is a low-frequency phenomenon that is associated with the function and structure of cell membranes. Imaging of anisotropic conductivity has potential for the analysis of interactions between electromagnetic fields and biological systems, such as the prediction of current pathways in electrical stimulation therapy. To improve application to the clinical environment, precise approaches are required to understand the exact responses inside the human body subjected to the stimulated currents. In this study, we experimentally evaluate the anisotropic conductivity tensor distribution of canine brain tissues, using a recently developed diffusion tensor-magnetic resonance electrical impedance tomography method. At low frequency, electrical conductivity of the biological tissues can be expressed as a product of the mobility and concentration of ions in the extracellular space. From diffusion tensor images of the brain, we can obtain directional information on diffusive movements of water molecules, which correspond to the mobility of ions. The position dependent scale factor, which provides information on ion concentration, was successfully calculated from the magnetic flux density, to obtain the equivalent conductivity tensor. By combining the information from both techniques, we can finally reconstruct the anisotropic conductivity tensor images of brain tissues. The reconstructed conductivity images better demonstrate the enhanced signal intensity in strongly anisotropic brain regions, compared with those resulting from previous methods using a global scale factor.
Experimental realization of the analogy of quantum dense coding in classical optics
Authors: Yang Zhenwei , Sun Yifan , Li Pengyun , Zhang Xiong , Song Xinbing , Zhang Xiangdong
Published: June 2016

We report on the experimental realization of the analogy of quantum dense coding in classical optical communication using classical optical correlations. Compared to quantum dense coding that uses pairs of photons entangled in polarization, we find that the proposed design exhibits many advantages. Considering that it is convenient to realize in optical communication, the attainable channel capacity in the experiment for dense coding can reach 2 bits, which is higher than that of the usual quantum coding capacity (1.585 bits). This increased channel capacity has been proven experimentally by transmitting ASCII characters in 12 quaternary digitals instead of the usual 24 bits.
SiC/Si3N4 nanotubes from peanut shells
Authors: Qadri S. B. , Rath B. B. , Gorzkowski E. P. , Feng C.R.
Published: June 2016

Nanotubes and nanoparticles of SiC and Si3N4 were produced from the thermal treatment of peanut shells in argon and nitrogen atmospheres respectively, at temperatures in excess of 1350°C. Using x-ray diffraction, Raman spectroscopy and transmission electron microscopy analysis, the processed samples in argon atmosphere were shown to consist of 2H and 3C polytypes of SiC nanoparticles and nanotubes. Whereas the samples prepared in nitrogen atmosphere consisted of α-phase of Si3N4. Nanostructures formed by a single direct reaction provide a sustainable synthesis route for nanostructured SiC and Si3N4, for potential engineering applications due to their exceptional mechanical and electro-optic properties.
Radio-transmitter attachment methods for monitoring the endangered eastern barred bandicoot (Perameles gunnii)
Authors: Coetsee Amy , Harley Dan , Lynch Michael , Coulson Graeme , de Milliano Jasmine , Cooper Michelle , Groenewegen Rebecca
Published: June 2016

Radio-tracking is a key technique for monitoring threatened species during ecological research and reintroduction programs. In the case of the endangered eastern barred bandicoot (Perameles gunnii), it has not been possible to radio-track for extended periods (≥3 months) due to difficulties in reliably and safely attaching radio-transmitters. In this study we compared eight attachment methods. Transmitters weighing 1.2–28 g were either mounted with adhesive, attached to a collar or implanted into the peritoneum. Intraperitoneal transmitters were superior in terms of attachment duration, but were considered inferior overall as they could not be fitted in the field and had a very short detection range once implanted (≤50 m). Retention times for external transmitters differed greatly between methods, ranging from 1 to 102 days. One tail-mount attachment technique caused minimal adverse effects but another caused tail amputation in one animal, and both had short retention times (3–33 days). Neither of the glue-on transmitter methods resulted in substantial periods of attachment (2–30 days) and flank-mounted transmitters also caused severe skin trauma. Radio-collars were generally retained for longer periods (42–102 days) but resulted in limb entanglement when they were fitted too loosely or subconjunctival haemorrhages when they were too tight. Cable tie collars are recommended as the most suitable attachment technique for bandicoots, as when fitted correctly they cause minimal impact to individuals and permit long retention times, but precise fitting is essential.
Patchy distribution and varied habitats of Macrozamia lucida cycads explained by constancy in a key environmental variable
Authors: Kaye L. A. , Walter G. H. , Raghu S.
Published: June 2016

Identifying the influence of environmental variables on the spatio-temporal distribution of organisms remains a central goal of ecology. Although environmental limits to the geographic range of species have been investigated, less information is available regarding the influence of environmental variables limiting species to discrete patches within their geographic range. Identifying environmental variables of importance to the species in question is further complicated where the patches appear to be distributed across a variety of outwardly dissimilar habitats. We assessed the influence of environmental variables on the patchy distribution of Macrozamia lucida L.A.S. Johnson (Zamiaceae) cycads endemic to south-east Queensland, Australia. Here we show that patches of M. lucida are consistently associated with elevated moisture, despite the patches being located in contrasting habitats and topographic positions. Our survey results across five field sites demonstrate that both cycad abundance and adult cycad condition (estimated from measures of adult cycad leaf production and reproductive output) are positively correlated with elevated moisture, as measured by mean minimum relative humidity at the plant–soil interface. The historical biogeography of the genus Macrozamia may be intimately linked with the contraction and fragmentation of Australia’s mesic biomes during the Miocene. It is plausible that current distribution pattern of M. lucida, restricted to discrete patches that meet the species’ environmental requirements, reflects a contraction and fragmentation within its range from a more regular historical distribution under more favourable climatic regimes.
Comparing modal patterns in Chinese-English interpreted and translated discourses in diplomatic setting
Authors: Fu Rongbo
Published: June 2016

This paper, with an eye to the interpersonal component in translational activities, adopts a systemic functional approach to the examination and comparison of modal patterns in interpreted and translated discourses of Chinese Premier’s press conferences and his reports on the work of the government from 2008 to 2012. Following a comprehensive analysis of modality in terms of type, orientation and value, the study shows that, despite their differences in translational mode (i.e. written and spoken) and temporal constraint (i.e. prepared and impromptu), interpreted and translated diplomatic discourses share some common trends in modal distribution. In particular, the massive use of modulation and the favorite collocation of first person pronouns with volitive modal verbs such aswillare classic in discourses as such. Additionally, only a minimal number of low-valued modality is used in both translation and interpretation. Given the political sensitivity and policy orientation of diplomatic translation and the institutional identity of diplomatic translators, it is argued that an effective manipulation of modality is essential to their fulfillment of the capacity of “policy endorsers” in reproducing interpersonal connotations embedded in the source language. The paper may also shed some light on the research on translator/interpreters’ role.
“Global Warming” versus “Climate Change” and the Influence of Labeling on Public Perceptions
Authors: Schuldt Jonathon P.
Published: June 2016

Communicating about climate change involves more than choices about which content to convey and how to convey it. It also involves a choice about how to label the issue itself, given the various terms used to represent the issue in public discourse—including “global warming,” “climate change,” and “global environmental change,” among others. An emerging literature in climate change communication and survey methodology has begun to examine the influence of labeling on public perceptions, including the cognitive accessibility of climate-related knowledge, affective responses and related judgments (problem seriousness and personal concern), and certainty that the phenomenon exists. The present article reviews this emerging work, drawing on framing theory and related social-cognitive models of information processing to shed light on the possible mechanisms that underlie labeling effects. In doing so, the article highlights the value of distinguishing between labeling and framing effects in communication research and theory, and calls for additional research into the boundary conditions of these and other labeling effects in science communication.
GHap: an R package for genome-wide haplotyping
Authors: Utsunomiya Yuri T. , Milanesi Marco , Utsunomiya Adam T. H. , Ajmone-Marsan Paolo , Garcia José F.
Published: June 2016

The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers.

Availability and implementation:  https://cran.r-project.org/package=GHap

Contact:  ytutsunomiya@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
A knowledge-based approach for predicting gene–disease associations
Authors: Zhou Hongyi , Skolnick Jeffrey
Published: June 2016

Motivation: Recent advances of next-generation sequence technologies have made it possible to rapidly and inexpensively identify gene variations. Knowing the disease association of these gene variations is important for early intervention to treat deadly diseases and provide possible targets to cure these diseases. Genome-wide association studies (GWAS) have identified many individual genes associated with common diseases. To exploit the large amount of data obtained from GWAS studies and leverage our understanding of common as well as rare diseases, we have developed a knowledge-based approach to predict gene–disease associations. We first derive gene–gene mutual information by utilizing the cooccurrence of genes in known gene–disease association data. Subsequently, the mutual information is combined with known protein–protein interaction networks by a boosted tree regression method.

Results: The method called Know-GENE is compared with the method of random walking on the heterogeneous network using the same input data. For a set of 960 diseases, using the same training data in testing in 3-fold cross-validation, the average recall rate within the top ranked 100 genes by Know-GENE is 65.0% compared with 37.9% by the state of the art random walking on heterogeneous network. This significant improvement is mostly due to the inclusion of knowledge-based mutual information.

Availability and Implementation: Predictions for genes associated with the 960 diseases are available at http://cssb2.biology.gatech.edu/knowgene.

Contact: skolnick@gatech.edu
A framework for self-experimentation in personalized health
Authors: Karkar Ravi , Zia Jasmine , Vilardaga Roger , Mishra Sonali R , Fogarty James , Munson Sean A , Kientz Julie A
Published: June 2016

Objective To describe an interdisciplinary and methodological framework for applying single case study designs to self-experimentation in personalized health. The authors examine the framework’s applicability to various health conditions and present an initial case study with irritable bowel syndrome (IBS).

Methods and Materials An in-depth literature review was performed to develop the framework and to identify absolute and desired health condition requirements for the application of this framework. The authors developed mobile application prototypes, storyboards, and process flows of the framework using IBS as the case study. The authors conducted three focus groups and an online survey using a human-centered design approach for assessing the framework’s feasibility.

Results All 6 focus group participants had a positive view about our framework and volunteered to participate in future studies. Most stated they would trust the results because it was their own data being analyzed. They were most concerned about confounds, nonmeaningful measures, and erroneous assumptions on the timing of trigger effects. Survey respondents (N = 60) were more likely to be adherent to an 8- vs 12-day study length even if it meant lower confidence results.

Discussion Implementation of the self-experimentation framework in a mobile application appears to be feasible for people with IBS. This framework can likely be applied to other health conditions. Considerations include the learning curve for teaching self-experimentation to non-experts and the challenges involved in operationalizing and customizing study designs.

Conclusion Using mobile technology to guide people through self-experimentation to investigate health questions is a feasible and promising approach to advancing personalized health.