bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy landscapes and global thermodynamics for alanine peptides
Authors: Somani Sandeep , Wales David J.
Published: July 2013

We compare different approaches for computing the thermodynamics of biomolecular systems. Techniques based on parallel replicas evolving via molecular dynamics or Monte Carlo simulations produce overlapping histograms for the densities of states. In contrast, energy landscape methods employ a superposition partition function constructed from local minima of the potential energy surface. The latter approach is particularly powerful for systems exhibiting broken ergodicity, and it is usually implemented using a harmonic normal mode approximation, which has not been extensively tested for biomolecules. The present contribution compares these alternative approaches for small alanine peptides modelled using the CHARMM and AMBER force fields. Densities of states produced from canonical sampling using multiple temperature replicas provide accurate reference data to evaluate the effect of the harmonic normal mode approximation in the superposition calculations. This benchmarking lays foundations for the application of energy landscape methods to larger biomolecules. It will also provide well characterised model systems for developing enhanced sampling methods, and for the treatment of anharmonicity corresponding to individual local minima.
Enhanced modulation of scattered light from phase-change nanoparticles by tailored plasmonic mirror image
Authors: Iida Takuya , Nakamura Atsushi , Hidaka Shimpei , Tamura Mamoru , Shiono Teruhiro , Furumiya Shigeru
Published: July 2013

We theoretically clarified a principle for the highly sensitive detection of a crystalline-amorphous transition in phase-change (PC) nanoparticles by tailoring the mirror image of localized surface plasmons in the crystalline phase. The difference of back scattering (DBS) can be greatly enhanced via the strong coupling of a PC nanostructure with the Ag nanoantenna by designing the dielectric structures around the PC nanoparticle. Remarkably, a DBS of 0.5% can be realized for 12 nm PC nanoparticles using conventional far-field measurements. The results shown here have potential applications in the nanoscale detection of temperature and pressure and for terabyte-class optical storage devices.
Low absorption state of phycocyanin from Acaryochloris marina antenna system: On the interplay between ionic strength and excitonic coupling
Authors: Nganou Collins
Published: July 2013

This paper studies the excitonic factor in the excited state energy transfer of phycobilisome (PBS) by using a polarized time-resolved pump-probe and by changing the ionic strength of the cofactors’ medium in the PBS of Acaryochloris marina (A. marina). As a result, the interplay between the surrounding medium and the closely excited adjacent cofactors is shown to be a negligible factor of the excitonic decay kinetics at 618 nm of the phycocyanin (PC), while it appears as a driving factor of an increase in excitonic delocalization at 630 nm. The obtained anisotropy values are consistent with the contribution of ionic strength in the excitonic mechanism in PBS. These values were 0.38 in high ionic strength and 0.4 in low ionic strength at 618 nm, and 0.52 in high ionic strength and 0.4 in low ionic strength at 630–635 nm. The anisotropy value of 0.52 in high phosphate is similar at 630 nm and 635 nm, which is consistent with an excitonic delocalization band at 635 nm. The 635 nm band is suggested to show the true low energy level of PC in A. marina PBS. The anisotropy decay kinetic at 630 nm suggests that the excited state population of PC is not all equilibrated in 3 ps because of the existence of the 10 ps decay kinetic component. The presence of the slow kinetic decay component in high, and low ionic strength, is consistent with a 10 and 14 ps energy transfer pathway, while the 450 fs kinetic decay component is consistent with the presence of an additional excitation energy transfer pathway between adjacent α84 and β84. Furthermore, the 450 fs decay kinetic is suggested to be trapped in the trimer, while the 400 fs decay kinetic rules out an excitonic flow from low energy level PC to allophycoyanin. This excitonic flow may occur between β84 in adjacent trimers, towards the low energy state of the PBS rod.
Role of zinc coating at liquid-vapor interface during laser material processing of zinc coated steel
Authors: Hwan Lee Seung , Mazumder Jyoti
Published: July 2013

In laser material processing, one of the major interests is characterizing interfacial phenomena induced by thermal phase changes of materials. The interfacial characteristics in the laser processing of multi-coated materials show different behaviors compared to those of single material processing. The difference in thermo-physical properties of the coated and primary materials induces the contrasting characteristics of multiple interfacial phenomena including temperature, recoil pressure, capillary force, and thermo capillary force. The influence of coating layer to the interfacial physics evolutions is difficult to be modeled mathematically when the laser beam penetrates the multi-coated material layer by layer. This paper addresses the role of the zinc coating at the liquid-vapor interface during the laser processing of zinc coated steel, as a representative case of multi-coated materials. Computational modules incorporating the zinc layers were established and selectively applied at the locations where the zinc coatings exist to investigate the interfacial phenomena. The level set method was integrated with the modules to track the evolution of the liquid-vapor interface in a self-consistent manner. The interfacial phenomena characteristics were estimated by a 3D mathematical simulation study. A reflective topography method was employed to validate the mathematical model and to supplement our understandings of the interfacial evolution.
Charge-induced distortion and stabilization of surface transfer doped porphyrin films
Authors: Smets Y. , Stark C. B. , Lach S. , Schmitt F. , Wright C. A. , Wanke M. , Ley L. , Ziegler C. , Pakes C. I.
Published: July 2013

The interaction between zinc-tetraphenylporphyrin (ZnTPP) and fullerenes (C60 and C60F48) are studied using ultraviolet photoelectron spectroscopy (UPS) and scanning tunneling microscopy (STM). Low temperature STM reveals highly ordered ZnTPP monolayers on Au(111). In contrast to C60, a submonolayer coverage of C60F48 results in long-range disorder of the underlying single ZnTPP layer and distortion of individual ZnTPP molecules. This is induced by substantial charge transfer at the organic-organic interface, revealed by the interface energetics from UPS. However, a second layer of ZnTPP prevents C60F48 guests from breaking the self-assembled porphyrin template. This finding is important for understanding the growth behaviour of “bottom-up” functional nanostructures involving strong donor-acceptor heterojunctions in molecular electronics.
Modified scaling principle for rotational relaxation in a model for suspensions of rigid rods
Authors: Tse Ying-Lung Steve , Andersen Hans C.
Published: July 2013

We have performed simulations of the model of infinitely thin rigid rods undergoing rotational and translational diffusion, subject to the restriction that no two rods can cross one another, for various concentrations well into the semidilute regime. We used a modification of the algorithm of Doi et al. [J. Phys. Soc. Jpn. 53, 3000 (1984)]10.1143/JPSJ.53.3000 that simulates diffusive dynamics using a Monte Carlo method and a nonzero time step. In the limit of zero time step, this algorithm is an exact description of diffusive dynamics subject to the noncrossing restriction. For a wide range of concentrations in the semidilute regime, we report values of the long time rotational diffusion constant of the rods, extrapolated to the limit of zero time step, for various sets of values of the infinite dilution (bare) diffusion constants. These results are compared with the results of a previous simulation of the model by Doi et al. and of previous simulations of rods with finite aspect ratio by Fixman and by Cobb and Butler that had been extrapolated to the limit of infinitely thin rods. The predictions of the Doi-Edwards (DE) scaling law do not hold for this model for the concentrations studied. The simulation data for the model display two deviations from the predictions of the DE theory that have been observed in experimental systems in the semidilute regime, namely, the very slow approach toward DE scaling behavior as the concentration is increased and the large value of the prefactor in the DE scaling law. We present a modified scaling principle for this model that is consistent with the simulation results for a broad range of concentrations in the semidilute regime. The modified scaling principle takes into account two physical effects, which we call “leakage” and “drift,” that were found to be important for the transport properties of a simpler model of nonrotating rods on a lattice [Y.-L. S. Tse and H. C. Andersen, J. Chem. Phys. 136, 024904 (2012)]10.1063/1.3673791.
On the Green-Kubo relationship for the liquid-solid friction coefficient
Authors: Bocquet Lydéric , Barrat Jean-Louis
Published: July 2013

In this paper, we propose a new derivation for the Green-Kubo relationship for the liquid-solid friction coefficient characterizing hydrodynamic slippage at a wall. It is based on a general Langevin approach for the fluctuating wall velocity involving a non-Markovian memory kernel with vanishing time integral. The calculation highlights some subtleties of the wall-liquid dynamics leading to superdiffusive motion of the fluctuating wall position.
Focused electron beam in pyroelectric electron probe microanalyzer
Authors: Imashuku Susumu , Imanishi Akira , Kawai Jun
Published: July 2013

We report a method to focus the electron beam generated using a pyroelectric crystal. An electron beam with a spot size of 100 μm was achieved by applying an electrical field to an electroconductive needle tip set on a pyroelectric crystal. When the focused electron beam bombarded a sample, characteristic X-rays of the sample were only detected due to the production of an electric field between the needle tip and the sample.
Electron temperature dependence of the electron-phonon coupling strength in double-wall carbon nanotubes
Authors: Chatzakis Ioannis
Published: July 2013

We applied Time-Resolved Two-Photon Photoemission spectroscopy to probe the electron-phonon (e-ph) coupling strength in double-wall carbon nanotubes. The e-ph energy transfer rate G(Te, Tl) from the electronic system to the lattice depends linearly on the electron (Te) and lattice (Tl) temperatures for Te>ΘDebye. Moreover, we numerically solved the Two-Temperature Model. We found: (i) a Te decay with a 3.5 ps time constant and no significant change in Tl; (ii) an e-ph coupling factor of 2 × 1016 W/m3; (iii) a mass-enhancement parameter, λ, of (5.4 ± 0.9) × 10−4; and (iv) a decay time of the electron energy density to the lattice of 1.34 ± 0.85 ps.
Comparison of microwave absorption properties of SrFe12O19, SrFe12O19/NiFe2O4, and NiFe2O4 particles
Authors: Mehdipour M. , Shokrollahi H.
Published: July 2013

In this study, ferrimagnetic (SrFe12O19, SrFe12O19/NiFe2O4, and NiFe2O4) nanostructure particles were synthesized by the co-precipitation of chloride salts using the sodium hydroxide solution. The resulting precursors were heat-treated at 1100 °C for 4 h. After cooling in the furnace, the ferrite powders were pressed at 10 bars and then sintered at 1200 °C for 4 h. The saturation magnetization was increased and the coercivity was decreased by sintering (because of morphology changing) and alternating of the ferrite kind. For example, at SrFe12O19, the saturation magnetization was increased from 291 G to 300 G and the coercivity was decreased from 2.8 kOe to 1.8 kOe by sintering. The microwave absorption properties of the nanostructure particles were studied by ferromagnetic resonance and transmit-line theories, as well as Reflection Loss plots. Before sintering, the RL spectra of SrFe12O19 and the composite were below −3 dB, but they reached −6 dB at 11.1 GHz for NiFe2O4. The RL spectra of the samples were increased by sintering due to reduction of porosity and damping factor. The maximum microwave absorption reached −35 dB (at resonance frequency) for the NiFe2O4 state.
Measurement of conductivity and permittivity on samples sealed in nuclear magnetic resonance tubes
Authors: Huang W. , Angell C. A. , Yarger J. L. , Richert R.
Published: July 2013

We present a broadband impedance spectroscopy instrument designed to measure conductivity and/or permittivity for samples that are sealed in glass tubes, such as the standard 5 mm tubes used for nuclear magnetic resonance experiments. The calibrations and corrections required to extract the dielectric properties of the sample itself are outlined. It is demonstrated that good estimates of the value of dc-conductivity can be obtained even without correcting for the effects of glass or air on the overall impedance. The approach is validated by comparing data obtained from samples sealed in nuclear magnetic resonance tubes with those from standard dielectric cells, using glycerol and butylmethylimidazolium-hexafluorophosphate as respective examples of a molecular and an ionic liquid. This instrument and approach may prove useful for other studies of permittivity and conductivity where contact to the metal electrodes or to the ambient atmosphere needs to be avoided.
Formation of magnetic nanocolumns during vapor phase deposition of a metal-polymer nanocomposite: Experiments and kinetic Monte Carlo simulations
Authors: Rosenthal L. , Greve H. , Zaporojtchenko V. , Strunskus T. , Faupel F. , Bonitz M.
Published: July 2013

Metal-polymer nanocomposites have been investigated extensively during the last years due to their interesting functional applications. They are often produced by vapor phase deposition which generally leads to the self-organized formation of spherical metallic nanoparticles in an organic matrix, while nanocolumns are only obtained under very specific conditions. Experiments [Greve et al. Appl. Phys. Lett. 88, 123103 (2006)] have shown that co-evaporation of the metallic and organic components in a simple single-step process can give rise to the formation of ultrahigh-density Fe-Ni-Co nanocolumnar structures embedded in a fluoropolymer matrix. Here we present a kinetic Monte Carlo approach which is based on a new model involving the depression of the melting point on the nanoscale and a critical nanoparticle size required for solidification. In addition we present new experimental results on the formation of Fe-Ni-Co nanocolumns in a Teflon AF matrix via co-evaporation down to a deposition temperature of −70 °C and also report the magnetic properties of the nanocolumns. The simulations provide a detailed understanding of the transition from spherical cluster growth to formation of elongated structures and are in good agreement with the experiments.
Size-effects in photoemission and optical second harmonic generation spectroscopy of Ge nano-dots on Si(111)
Authors: Rafaelsen Jens , Pedersen Kjeld , Li Zheshen
Published: July 2013

Ge nano-dots have been grown on Si(111) covered by a thin oxide layer using a wedge shaped deposition profile, resulting in varying nano-dot size along the sample profile. Samples were investigated by optical second harmonic generation (SHG) and photoemission spectroscopy (PES). The growth of the nano-dots was characterized by core level PES and scanning electron microscopy, and size effects were found in valence band PES. SHG spectra reveal two clearly resolvable resonances related to the E1 transitions in Si and Ge, respectively. Deposition of Ge leads to a field at the surface that modifies the SHG response from the Si substrate. The Ge SHG signal grows up during deposition and shifts towards lower energy with increasing particle size, demonstrating that size effects are also present in the optical transitions.
A model of coupled thermal, mechanical, and electrostatic field effects in III-N thin film heterostructures
Authors: Shenoy Bhamy Maithry , Mahapatra D. Roy , Hegde Gopalkrishna
Published: July 2013

A one-dimensional coupled multi-physics based model has been developed to accurately compute the effects of electrostatic, mechanical, and thermal field interactions on the electronic energy band structure in group III-nitrides thin film heterostructures. Earlier models reported in published literature assumes electro-mechanical field with uniform temperature thus neglecting self-heating. Also, the effects of diffused interface on the energy band structure were not studied. We include these effects in a self-consistent manner wherein the transport equation is introduced along with the electro-mechanical models, and the lattice structural variation as observed in experiments are introduced at the interface. Due to these effects, the electrostatic potential distribution in the heterostructure is altered. The electron and hole ground state energies decrease by 5% and 9%, respectively, at a relative temperature of 700 K, when compared with the results obtained from the previously reported electro-mechanical model assuming constant and uniform temperature distribution. A diffused interface decreases the ground state energy of electrons and holes by about 11% and 9%, respectively, at a relative temperature of 700 K when compared with the predictions based on uniform temperature based electro-mechanical model.
Complete bandgaps in two-dimensional phononic crystal slabs with resonators
Authors: Wang Yan-Feng , Wang Yue-Sheng
Published: July 2013

The bandgap properties of an open or covered phononic crystal slab with resonators are studied by using the finite element method. The results show that complete bandgap comes up for the proposed slabs with resonators due to the local resonance. The effects of the topological geometry of the resonators on the bandgaps are discussed, and optimal geometry is suggested. The mechanism of the bandgap generation is analyzed by studying the eigen modes at the bandgap edges. Equivalent spring-mass/pendulum models are developed to predict the eigen frequencies at the lower bandgap edges. The evaluated results obtained by the equivalent models are in general agreement with the numerical ones. The work in this paper is indispensable to the optimal design of the bandgaps of phononic crystal slabs.
Domain wall and bifurcation analysis of the Klein-Gordon Zakharov equation in (1 + 2)-dimensions with power law nonlinearity
Authors: Song Ming , Ahmed Bouthina S. , Zerrad Essaid , Biswas Anjan
Published: July 2013

This paper studies the Klein-Gordon Zakharov equation with power law nonlinearity in (1 + 2)-dimensions. The ansatz method will be applied to obtain the 1-soliton solution, also known as domain wall solution, along with several constraint conditions that naturally fall out. Subsequently, the bifurcation analysis is carried out where the phase portrait is given. Additionally, this analysis leads to several solutions to the equation with the traveling wave scheme. This gives soliton solution as well as singular periodic solutions. Finally, the numerical simulations for the domain wall solution were obtained where the finite difference scheme is applied.
Modeling large nonuniform optical antenna arrays for metasurface application
Authors: Dong Tianyu , Ma Xikui , Mittra Raj
Published: July 2013

We analyze large non-uniform optical antenna arrays of nanorods, which form optical vortices, axicons and lenses, by using a numerically efficient technique, called the Characteristics Basis Function Method (CBFM). The efficiency is realized by deriving an accurate, efficient simplified representation of nanorod, and by using the CBFM, which not only reduces the number of unknowns significantly without sacrificing the computational accuracy, but also enables us to handle large, truncated and non-uniform arrays. The method is numerically rigorous and includes all of the mutual coupling effects to obtain accurate results. Furthermore, it is readily parallelizable and can be generalized to handle more complex shapes of nanoantennas, without any difficulty.
Mn1-xFexCoGe: A strongly correlated metal in the proximity of a noncollinear ferromagnetic state
Authors: Samanta Tapas , Dubenko Igor , Quetz Abdiel , Prestigiacomo Joseph , Adams Philip W. , Stadler Shane , Ali Naushad
Published: July 2013

An unusually large Kadowaki–Woods ratio of A/γ2 ∼ 43 μΩ·cm·mol2·K2·J−2 has been observed for intermetallic Mn1-xFexCoGe compounds in the proximity of x = 0.2 where the magnetic state of itinerant electrons system changes. The ratio is approximately four times larger than observed for heavy fermion systems. The manifestation of the strong electron correlations can be realized from the anisotropic origin of the effect through the substantial reduction of interlayer transport of heavy quasiparticles with comparable mean-free path and interlayer spacing in the proximity of a noncollinear ferromagnetic state associated with a large density of states at the Fermi level.
The unsaturated bistable stochastic resonance system
Authors: Zhao Wenli , Wang Juan , Wang Linze
Published: July 2013

We investigated the characteristics of the output saturation of the classical continuous bistable system (saturation bistable system) and its impact on stochastic resonance (SR). We further proposed a piecewise bistable SR system (unsaturated bistable system) and developed the expression of signal-to-noise ratio (SNR) using the adiabatic approximation theory. Compared with the saturation bistable system, the SNR is significantly improved in our unsaturated bistable SR system. The numerical simulation showed that the unsaturated bistable system performed better in extracting weak signals from strong background noise than the saturation bistable system.
Direct and converse magnetoelectric effects in Metglas/LiNbO3/Metglas trilayers
Authors: Timopheev A. A. , Vidal J. V. , Kholkin A. L. , Sobolev N. A.
Published: July 2013

Electromechanical and magnetoelectric properties of Metglas/LiNbO3/Metglas trilayers have been studied in the frequency range from 20 Hz to 0.4 MHz. A trilayer of Metglas/PMN-PT/Metglas prepared in the same way was used as a reference. Though PMN-PT has much larger charge piezocoefficients than LiNbO3 (LNO), the direct magnetoelectric voltage coefficient is found to be comparable in both trilayers due to the much lower dielectric permittivity of LNO. The magnitude of the direct magnetoelectric effect in the LNO trilayers is about 0.4 V/cm Oe in the quasistatic regime and about 90 V/cm Oe at the electromechanical resonance. Calculations show that the magnetoelectric properties can be significantly improved (up to 500 V/cm Oe) via controlling the cut angle of LNO, choosing the appropriate thickness ratio of the ferroelectric/ferromagnetic layers and a better bonding between Metglas and LNO. Advantages of using LiNbO3-type ferroelectrics in magnetoelectric composites are discussed.
Quasiparticle band-edge energy and band offsets of monolayer of molybdenum and tungsten chalcogenides
Authors: Liang Yufeng , Huang Shouting , Soklaski Ryan , Yang Li
Published: July 2013

We report the quasiparticle band-edge energy of monolayer of molybdenum and tungsten dichalcogenides, MX2 (M = Mo, W; X = S, Se, Te). Beyond calculating bandgaps, we have achieved converged absolute band-edge energies relative to the vacuum level. Compared with the results from other approaches, the GW calculation reveals substantially larger bandgaps and different absolute quasiparticle energies because of enhanced many-electron effects. Interestingly, our GW calculations ratify the band-gap-center approximation, making it a convenient way to estimate band-edge energy. The absolute band-edge energies and band offsets obtained in this work are important for designing heterojunction devices and chemical catalysts based on monolayer dichalcogenides.
Phonon heat conduction in corrugated silicon nanowires below the Casimir limit
Authors: Blanc Christophe , Rajabpour Ali , Volz Sebastian , Fournier Thierry , Bourgeois Olivier
Published: July 2013

The thermal conductance of straight and corrugated monocrystalline silicon nanowires has been measured between 0.3 K and 5 K. It is demonstrated that the corrugation strongly reduces the thermal transport by reducing the mean free path of the phonons. The experimental averaged mean free path is remarkably smaller than the smaller diameter of the nanowire, evidencing a phonon thermal transport reduced below the Casimir limit. Monte Carlo simulations highlight that this effect can be attributed to significant multiple scattering of ballistic phonons occurring on the corrugated surfaces. This result suggests an original approach to transforming a monocrystalline material into a phonon glass.
Photovoltaic response in a resonant tunneling wire-dot-wire junction
Authors: Berbezier Aude , Autran Jean-Luc , Michelini Fabienne
Published: July 2013

Using the Green's function technique, we investigated the nonequilibrium photovoltaic response in a double barrier wire-dot-wire junction for tunneling coupling stronger than optical coupling. In the narrow window of photon-gap energy resonance, the photocurrent increases when the voltage increases from zero, which means a negative shunt conductance in the generator equivalent circuit, and forces a fill factor above one. We then show a counterintuitive behavior of such resonant tunneling photovoltaic systems: the photocurrent increases when the tunneling rate through contact decreases. The negative shunt conductance we observed hence rises in the density of states of semi-infinite wires that vanishes at band edges.
High efficient GaN-based laser diodes with tunnel junction
Authors: Feng M. X. , Liu J. P. , Zhang S. M. , Jiang D. S. , Li Z. C. , Zhou K. , Li D. Y. , Zhang L. Q. , Wang F. , Wang H. , Chen P. , Liu Z. S. , Zhao D. G. , Sun Q. , Yang H.
Published: July 2013

High-efficient GaN-based laser diodes (LDs) with tunnel junction are designed by replacing conventional p-type AlGaN cladding layers and p-type GaN contact with lower-resistant n-type AlGaN cladding layers and n-type GaN contact. In addition, the characteristics of the LDs with tunnel junction are numerically investigated by using the commercial software lastip. It is found that the performance of these LDs is greatly improved. As a comparison, the absorption loss and non-radiative recombination are greatly reduced. The threshold current and series resistance are decreased by 12% and 59%, respectively, and the slope efficiency is raised up by 22.3%. At an injection current of 120 mA, the output power and wall-plug-efficiency are increased by 34% and 79%, respectively.
Formation of quasi-icosahedral structures with multi-conjoint fivefold deformation twins in fivefold twinned metallic nanowires
Authors: Jiang Shan , Shen Yonggang , Zheng Yonggang , Chen Zhen
Published: July 2013

We show by molecular dynamics simulations that symmetrical quasi-icosahedral structures can be formed in fivefold twinned metallic nanowires (Cu, Au, and Ag) under dynamic tensile loading. The quasi-icosahedral structure, different from the icosahedral nanoclusters found in the past, consists of a twisted original fivefold twinned axis and ten secondary fivefold deformation twins, with five preexisting prismatic and fifteen tetrahedral subunits joined adjacently. Formation of these structures is observed in the necking region during the plastic deformation with successive twinning processes and is found to be independent on the cross-sectional shape as well as the tensile strain rate of the nanowires.
Effects of higher-order Kerr nonlinearity and plasma diffraction on multiple filamentation of ultrashort laser pulses in air
Authors: Huang T. W. , Zhou C. T. , Zhang H. , He X. T.
Published: July 2013

The effect of higher-order Kerr nonlinearity on channel formation by, and filamentation of, ultrashort laser pulses propagating in air is considered. Filament patterns originating from multiphoton ionization of the air molecules with and without the higher-order Kerr and molecular-rotation effects are investigated. It is found that diverging multiple filaments are formed if only the plasma-induced defocusing effect is included. In the presence of the higher-order Kerr effects, the light channel can exist for a long distance. The effect of noise on the filament patterns is also discussed.
Model for charged dust expansion across a magnetic field
Authors: Fu H. , Scales W. A.
Published: July 2013

Plasma fluctuations arise in the boundary region between charged dust clouds and background plasmas. A self-consistent computational model is developed to study expansion of a charged dust cloud across a magnetic field, creation of the inhomogeneous boundary layer and associated processes. The charging of the dust particulates produces a boundary layer and associated ambipolar electric field. This ambipolar field provides a source for low frequency dust acoustic waves in unmagnetized plasmas. A background magnetic field if sufficiently strong, may impact the dust acoustic wave evolution and dust density structures due to E×B and diamagnetic current generation. The dust acoustic density fluctuation generation across a strong magnetic field (ωpe/Ωce≪1) may be suppressed as compared to an unmagnetized dusty plasma, which will be discussed. Fluctuations generated at longer timescales propagating along the dust boundary layer will also be investigated in the lower hybrid and dust lower hybrid frequency range. Applications to space and laboratory plasmas are discussed.
Differential all-optical tuning of eigenmodes in coupled microdisks
Authors: Schmidt C. , Chipouline A. , Käsebier T. , Kley E.-B. , Tünnermann A. , Pertsch T.
Published: July 2013

A differential all-optical resonance tuning of whispering-gallery-modes (WGMs) in a system of three coupled microdisks in a line arrangement is investigated. Utilizing the temperature induced nonlinear effects observable in coupled WGM microresonators, a tunable, narrow bandwidth, three-wavelength filter is demonstrated. Variable tuning scenarios for the signal resonances are achieved at the same sample, depending on the coupling conditions of the control signal at low control powers of up to 4 mW only.
Electronic structures of silicene/GaS heterosheets
Authors: Ding Yi , Wang Yanli
Published: July 2013

Although Dirac-like electronic properties are predicted for silicene, recent experiments find substrate-induced complex bucklings would destruct such feature [C.-L. Lin et al., Phys. Rev. Lett. 110, 076801 (2013)]. Here, using first-principles calculations, we propose that the recently synthesized gallium sulfide (GaS) nanosheet could be an appropriate substrate for silicene, which can form commensurate Si/GaS heterosheets akin to graphene/BN systems. More importantly, in these heterosheets, the characteristic Dirac-like band feature of linear dispersions is retained, and due to the intrinsic electric field, a sizable band gap is opened at the Dirac point, which could be further tuned by bias voltage or strains.
Acidity control in Latosols under long-term pastures in the Cerrado region, Brazil
Authors: Vendrame P. R. S. , Brito O. R. , Martins E. S. , Quantin C. , Guimarães M. F. , Becquer T.
Published: July 2013

High acidity and aluminium saturation are among the main limiting factors for crop production in tropical soils. The aim of this work was to measure the acidity of Latosols under pastures in the Brazilian Cerrado and to assess the influence of clay mineralogy as a controlling parameter of soil acidity. Topsoils (n = 73, 0–0.2 m depth) of Latosols developed on different parent materials were sampled in two sub-regions of the Cerrado region. The main chemical characteristics were determined by standard procedures, and kaolinite and gibbsite contents were determined by dissolution with sulfuric acid and thermogravimetric analyses. The exchangeable concentrations of calcium (Ca), magnesium (Mg), and potassium (K) varied considerably among soil samples, with ranges of 0–13.9 cmolc kg–1 (mean ± standard deviation 1.77 ± 1.91 cmolc kg–1) for Ca; 0.2–3.2 cmolc kg–1 (1.13 ± 0.68 cmolc kg–1) for Mg; and 0–1.0 cmolc kg–1 (0.24 ± 0.24 cmolc kg–1) for K. The mean concentration of exchangeable aluminium (Al) was 0.55 ± 0.61 cmolc kg–1 (range 0–2.3 cmolc kg–1). The content of kaolinite (282 ± 96 g kg–1) was higher than of gibbsite (106 ± 77 g kg–1). The amount of exchangeable Al and Al saturation rate varied according to the mineralogy of the clay fraction of the soils. The content of exchangeable Al3+ remained low when gibbsite was the predominant mineral, whereas it increased with kaolinite content. The ratio kaolinite/(kaolinite + gibbsite) could be used as a useful indicator of the sensitivity of soils affected by acidity and Al toxicity.
Macrophage migration inhibitory factor (MIF) is a critical mediator of the innate immune response to
Mycobacterium tuberculosis
Authors: Das Rituparna , Koo Mi-Sun , Kim Bae Hoon , Jacob Shevin T. , Subbian Selvakumar , Yao Jie , Leng Lin , Levy Rebecca , Murchison Charles , Burman William J. , Moore Christopher C. , Scheld W. Michael , David John R. , Kaplan Gilla , MacMicking John D. , Bucala Richard
Published: July 2013

Significance

Failure of the host immune system to control infection with
Mycobacterium tuberculosis
is a major determinant of tuberculosis (TB) disease. In this work, we examined the role of macrophage migration inhibitory factor (MIF), a cytokine that is encoded in a functionally polymorphic locus in humans, in TB. We found genetic low expressers of MIF to be enriched in a population of patients with HIV and disseminated TB. From our work in cellular and mouse models, we propose a key mechanism by which MIF regulates bacterial recognition as the first step in triggering inflammatory pathways to enable mycobacterial control.
Brief Educational Intervention to Improve Medical Student Competence in Managing Patients Exposed to Secondhand Smoke
Authors: Merlo Lisa J. , Sutton Jill A. , Gold Mark S.
Published: July 2013

Background

Secondhand smoke (SHS) exposure may lead to the development of various diseases and conditions. One way to reduce SHS exposure is to screen for it within each primary care examination so that appropriate counseling can be directed to affected individuals. There has been little attention to improving medical education about SHS exposure and screening. The goal of this study was to develop an SHS-related educational intervention for medical students, with the purpose of improving knowledge regarding consequences of SHS exposure, and increasing intent to screen patients for exposure.

Methods

Medical students ( N = 405) were given a measure assessing their knowledge of SHS exposure and intent to screen. Two groups of students served as controls (i.e., a posttest-only group and a pre/posttest group), and one group participated in the SHS education intervention. A factorial analysis with repeated measures and chi-square analyses were used to assess the differences between the groups to determine the impact of the SHS education intervention (ie, online lectures and a standardized patient interaction) on knowledge and intent to screen.

Results

Results of pretesting demonstrated that medical students had little knowledge of SHS exposure, averaging scores between 63% and 69% on the examination. One control group was reassessed a year later with no educational intervention. They did not demonstrate a significant change in their pre- to posttest scores, although the vast majority (∼95%) reported intending to screen future patients. Students who participated in the SHS educational intervention significantly improved their scores from pre- to posttest ( P <.001), and 100% also reported intending to screen future patients.

Conclusions

This study suggests that brief education regarding the consequences of SHS exposure may improve medical students’ knowledge and increase intent to screen. Future research should assess the long-term impact of educational programs on improved clinical care.
Salmonellae in Fish Feces Analyzed by In Situ Hybridization and Quantitative Polymerase Chain Reaction
Authors: Sha Qiong , Forstner Michael R. J. , Bonner Timothy H. , Hahn Dittmar
Published: July 2013

The potential of fish to transfer salmonellae from heterogeneous aquatic biofilms into feces was assessed in controlled aquarium studies with Suckermouth Catfish Hypostomus plecostomus and with biofilms inoculated with salmonellae. Neither the presence of catfish nor inoculation with salmonellae had detectable effects on the abundance of the microbial community. Densities of the microbial community were about 105 cells/mL in the water during a 1-week period, whereas densities of the microbial community increased 10-fold (106 to 107 cells/mg) in catfish feces during the same period. Salmonellae were detected by both quantitative polymerase chain reaction (qPCR) and situ hybridization in water samples immediately after inoculation, in numbers of about 104 cells/mL, representing up to 20% of the cells of the microbial community. Numbers decreased by three orders of magnitude within the first 3 d of the study, which represented only 0.01% of the community, and became undetectable after day 5. In catfish feces, numbers of Salmonella initially increased to up to 6% of the cells of the community but then declined. These results suggest that Salmonella are not biomagnified during gut passage, and thus, fish only provide a means for the translocation of this pathogen.

Received November 25, 2012; accepted March 25, 2013
First Report of Citrus tristeza virus in Citrus Orchards in Bosnia and Herzegovina
Authors: Delić D. , Afechtal M. , Djelouah K. , Lolić B. , Karačić A.
Published: July 2013

The citrus growing area in Bosnia and Herzegovina (B&H) is limited to the confluence of the river Neretva, which is close to the Adriatic coastal region. Approximately 6 ha are grown in the country. Mandarins (Citrus reticulata Blanco) and lemons (Citrus limon L.) grafted on trifoliate orange (Poncirus trifoliata (L.) Raf.) are the most cultivated species. In June 2012, 25 samples were collected from individual trees from three locations in Herzegovina district of B&H (Mostar, Čapljina, and Ljubuški). Samples of different Citrus spp. (C. reticulata Blanco, C. aurantium L., C. limon L., C. sinensis (L.) Osbeck, P. trifoliata (L.) Raf., and Fortunella margarita Lour) and varieties were collected from infield plants, commercial citrus orchards, and a nursery. Out of 25, 10 citrus trees exhibited leaves chlorosis, whereas as all others were apparently symptomless. Double antibody sandwich (DAS)-ELISA test, using commercial kit from the DSMZ, Germany (product code AS-0988), was carried out to confirm the presence of Citrus tristeza virus (CTV). In addition, further analyses were performed using reverse transcription (RT)-PCR targeting the coat protein gene (2). CTV was detected in 8 out of the 25 tested samples with DAS-ELISA, whereas CTV was detected in 14 samples by RT-PCR. Being grafted on P. trifoliata rootstock, no typical CTV symptoms in the field were observed on the CTV-infected trees; interestingly, the lab analyses evidenced the CTV presence in all inspected locations of the Herzegovina district. To our knowledge, this is the first report of CTV in Bosnia and Herzegovina; nevertheless, the virus presence is also reported from neighboring countries Croatia (1) and Montenegro (3). The PCR products of four samples were additionally analyzed by sequencing. The preliminary results by sequencing of the coat protein gene of four selected CTV isolates (Accessions HF947341, HF947342, HF947343, and HF947347) showed 99% nucleotide identity with the CTV resistance breaking isolates from Montenegro (FR871866) and Croatia (EU579422). Although a very small number of samples were tested in this study, CTV appears to be widely distributed in the citrus orchards of the country. This could be related to the traditional use of tolerant P. trifoliata rootstock that prevents the development of the tristeza decline as well as to the virus isolates present in the region, which appear not to cause another economically devastating CTV disease such as stem pitting. Further research will be dedicated to the biological properties of the genetic variability of these identified CTV isolates and the assessment of potential aphid vectors.

References: (1) S. Černi et al. Plant Dis. 89:342, 2005. (2) M. E. Hilf et al. Options Méditerranéennes B 65:89, 2009. (3) T. Papic et al. Plant Dis. 89:434, 2005.
Phenazine Production by Pseudomonas sp. LBUM223 Contributes to the Biological Control of Potato Common Scab
Authors: Arseneault Tanya , Goyer Claudia , Filion Martin
Published: July 2013

Common scab of potato is mainly caused by Streptomyces scabies. Currently, no method can efficiently control this economically important disease. We have previously determined that Pseudomonas sp. LBUM223 exhibits antagonistic properties toward S. scabies under in vitro conditions. Inhibition was mainly attributed to phenazine-1-carboxylic acid (PCA) production because an isogenic mutant of LBUM223 (phzC–), not producing PCA, was incapable of significantly reducing S. scabies growth. In order to understand the impact of PCA production by LBUM223 in controlling common scab under soil conditions, pot experiments were performed to determine its effect on (i) reducing scab symptoms development, (ii) S. scabies population dynamics, and (iii) txtA expression in S. scabies, a key gene involved in thaxtomin A biosynthesis and required for pathogenesis. Symptoms were significantly reduced following inoculation with LBUM223 but not its mutant. Surprisingly, pathogen populations increased in the geocaulosphere in the presence of both wild-type and mutant strains of LBUM223; however, significant repression of txtA expression in S. scabies was only observed in the presence of PCA-producing LBUM223, not its mutant. These results suggest that, under soil conditions, PCA production by LBUM223 does not control common scab development by antibiosis but, instead, reduces S. scabies thaxtomin A production in the geocaulosphere, leading to reduced virulence.
Development of a Disease Risk Prediction Model for Downy Mildew (Peronospora sparsa) in Boysenberry
Authors: Kim Kwang Soo , Beresford Robert M. , Walter Monika
Published: July 2013

Downy mildew caused by Peronospora sparsa has resulted in serious production losses in boysenberry (Rubus hybrid), blackberry (Rubus fruticosus), and rose (Rosa sp.) in New Zealand, Mexico, and the United States and the United Kingdom, respectively. Development of a model to predict downy mildew risk would facilitate development and implementation of a disease warning system for efficient fungicide spray application in the crops affected by this disease. Because detailed disease observation data were not available, a two-step approach was applied to develop an empirical risk prediction model for P. sparsa. To identify the weather patterns associated with a high incidence of downy mildew berry infections (dryberry disease) and derive parameters for the empirical model, classification and regression tree (CART) analysis was performed. Then, fuzzy sets were applied to develop a simple model to predict the disease risk based on the parameters derived from the CART analysis. High-risk seasons with a boysenberry downy mildew incidence >10% coincided with months when the number of hours per day with temperature of 15 to 20°C averaged >9.8 over the month and the number of days with rainfall in the month was >38.7%. The Fuzzy Peronospora Sparsa (FPS) model, developed using fuzzy sets, defined relationships among high-risk events, temperature, and rainfall conditions. In a validation study, the FPS model provided correct identification of both seasons with high downy mildew risk for boysenberry, blackberry, and rose and low risk in seasons when no disease was observed. As a result, the FPS model had a significant degree of agreement between predicted and observed risks of downy mildew for those crops (P = 0.002).
Sexual Reproduction in Aspergillus flavus Sclerotia Naturally Produced in Corn
Authors: Horn Bruce W. , Sorensen Ronald B. , Lamb Marshall C. , Sobolev Victor S. , Olarte Rodrigo A. , Worthington Carolyn J. , Carbone Ignazio
Published: July 2013

Aspergillus flavus is the major producer of carcinogenic aflatoxins worldwide in crops. Populations of A. flavus are characterized by high genetic variation and the source of this variation is likely sexual reproduction. The fungus is heterothallic and laboratory crosses produce ascospore-bearing ascocarps embedded within sclerotia. However, the capacity for sexual reproduction in sclerotia naturally formed in crops has not been examined. Corn was grown for 3 years under different levels of drought stress at Shellman, GA, and sclerotia were recovered from 146 ears (0.6% of ears). Sclerotia of A. flavus L strain were dominant in 2010 and 2011 and sclerotia of A. flavus S strain were dominant in 2012. The incidence of S strain sclerotia in corn ears increased with decreasing water availability. Ascocarps were not detected in sclerotia at harvest but incubation of sclerotia on the surface of nonsterile soil in the laboratory resulted in the formation of viable ascospores in A. flavus L and S strains and in homothallic A. alliaceus. Ascospores were produced by section Flavi species in 6.1% of the 6,022 sclerotia (18 of 84 ears) in 2010, 0.1% of the 2,846 sclerotia (3 of 36 ears) in 2011, and 0.5% of the 3,106 sclerotia (5 of 26 ears) in 2012. For sexual reproduction to occur under field conditions, sclerotia may require an additional incubation period on soil following dispersal at crop harvest.
Distinct molecular targets including SLO‐1 and gap junctions are engaged across a continuum of ethanol concentrations in Caenorhabditis elegans
Authors: Dillon James , Andrianakis Ioannis , Mould Richard , Ient Ben , Liu Wei , James Christopher , O'Connor Vincent , Holden‐Dye Lindy
Published: July 2013

Ethanol (alcohol) interacts with diverse molecular effectors across a range of concentrations in the brain, eliciting intoxication through to sedation. Invertebrate models including the nematode worm Caenorhabditis elegans have been deployed for molecular genetic studies to inform on key components of these alcohol signaling pathways. C. elegans studies have typically employed external dosing with high (>250 mM) ethanol concentrations: A careful analysis of responses to low concentrations is lacking. Using the C. elegans pharyngeal system as a paradigm, we report a previously uncharacterized continuum of cellular and behavioral responses to ethanol from low (10 mM) to high (300 mM) concentrations. The complexity of these responses indicates that the pleiotropic action of ethanol observed in mammalian brain is conserved in this invertebrate model. We investigated two candidate ethanol effectors, the calcium‐activated K+ channel SLO‐1 and gap junctions, and show that they contribute to, but are not sole determinants of, the low‐ and high‐concentration effects, respectively. Notably, this study shows cellular and whole organismal behavioral responses to ethanol in C. elegans that directly equate to intoxicating through to supralethal blood alcohol concentrations in humans and provides an important benchmark for interpretation of paradigms that seek to inform on human alcohol use disorders.—Dillon, J., Andrianakis, I., Mould, R., Ient, B., Liu, W., James, C, O'Connor, V., Holden‐Dye, L., Distinct molecular targets including SLO‐1 and gap junctions are engaged across a continuum of ethanol concentrations in Caenorhabditis elegans. FASEB J. 27, 4266–4278 (2013). www.fasebj.org