bluuebunny/crossref_metadata_2025 huggingface dataset:
Observations of oxygen ions in the dayside magnetosheath associated with southward IMF
Authors: Slapak R. , Nilsson H. , Westerberg L. G. , Eriksson A.
Published: June 2012

We present a case study of high energy oxygen ions (O+) observed in the dayside terrestrial magnetosheath, in the southern hemisphere. It is shown that the presence of O+ is strongly correlated to the IMF direction: O+ is observed only for Bz < 0. Three satellites observe O+ immediately at both sides of the magnetopause and about 2 RE outside the magnetopause. These conditions indicate escape along open magnetic field lines. We show that if outflowing O+ is heated and accelerated sufficiently in the cusp, it takes 15–20 minutes for it to reach the magnetopause, allowing the ions to escape along newly opened field lines on the dayside. Earlier studies show evidence of strong heating and high velocities of O+ in the cusp and mantle at high altitudes, strengthening our interpretation. The observed magnetosheath O+ fluxes are of the same order as measured in the ionospheric upflow, which indicates that this loss mechanism is significant when it takes place.
The relationship between surface rainrate and water paths and its implications to satellite rainrate retrieval
Authors: You Yalei , Liu Guosheng
Published: June 2012

Since brightness temperature measured by a passive microwave radiometer reflects the integrated effects of water paths, not surface rainrate, the accuracy of surface rainrate retrieval based on brightness temperatures relies heavily on the natural correlation between surface rainrate and water paths. In this study, we investigate how the water paths are related to surface rainrates using satellite data. It is found that corresponding to a similar surface rainrate ice water path is larger over land than over ocean. In addition, on average, the correlation (R2) between surface rainrate and ice water path over land (0.36) is also larger than over ocean (0.25). Over ocean, the correlation between surface rainrate and ice water path is greatly reduced where shallow convections exist. The results also show that given a similar surface rainrate, greater values of total water path occur over arid regions than over other land areas while the correlation between surface rainrate and total water path over such regions is smaller. Furthermore, given a similar surface rainrate, over ocean, larger values of liquid water path are observed over the intertropical convergence zone and maritime regions while smaller values appear over regions dominated by shallow convections. The explanation of the above differences in correlations is attempted using the seasonal variability of water paths and the rainfall systems' vertical structures. It is expected that the low correlation between surface rainrate and water paths will be a major obstacle for surface rainrate retrieval using microwave observations. In addition, surface rainrate always possesses a better relationship to liquid water path over ocean (or total water path over land) than to ice water path. Therefore, for surface rainrate retrievals, channels or channel combinations that can capture liquid water signal over ocean (or total water signal over land) are preferable to those solely containing ice water information.
Spirituality and Religion in Psychotherapy: Views of Brazilian Psychotherapists
Authors: Vandenberghe Luc , Prado Fabricia Costa , de Camargo Edivânia Aparecida
Published: June 2012

Twenty-seven Brazilian psychotherapists were interviewed about how religion and spirituality interface with psychotherapy. Transcripts of unstructured interviews were subjected to open analytical coding and categorization according to grounded theory. Two categories emerged. The first category, the more complex one, saw religion as a therapeutic challenge in that therapists must respect client religion, tackle clients' religious issues, and understand how therapists' own religion influences their behavior. The second category depicted religion as providing cultural resources, including healthy activities, teachings and social support, and spirituality as providing a broader sense of meaning. Therapists used clients' religion and spirituality as therapeutic aids. Therapists' own spirituality also served as an asset in improving their interventions and coping with the emotional strains of doing therapy. Applied to practice, the findings can help clinicians deal successfully with religious cultural competence issues and mobilize spirituality and religion according to their own and the client's needs and resources.
Ferromagnetism in Tb doped ZnO nanocrystalline films
Authors: Zou W. Q. , Ge C. N. , Venkataiah G. , Su H. L. , Hsu H. S. , Huang J. C. A. , Liu X. C. , Zhang F. M. , Du Y. W.
Published: June 2012

Nanocrystalline Tb-doped ZnO films have been prepared by ion-beam sputtering technique. Magnetic characterization showed that the films are ferromagnetic with Curie temperature (TC) higher than room temperature. By further treated with a rapid thermal annealing process, both the grain size and the carrier concentration of the films increase, while the saturation magnetization of the films decreases. This magnetic behavior can be hardly explained by either bound magnetic polaron model or free carrier mediation model, thus suggests that the grain boundaries play a key role for the origin of ferromagnetism in these films.
Adsorption-driven translocation of polymer chain into nanopores
Authors: Yang Shuang , Neimark Alexander V.
Published: June 2012

The polymer translocation into nanopores is generally facilitated by external driving forces, such as electric or hydrodynamic fields, to compensate for entropic restrictions imposed by the confinement. We investigate the dynamics of translocation driven by polymer adsorption to the confining walls that is relevant to chromatographic separation of macromolecules. By using the self-consistent field theory, we study the passage of a chain trough a small opening from cis to trans compartments of spherical shape with adsorption potential applied in the trans compartment. The chain transfer is modeled as the Fokker-Plank diffusion along the free energy landscape of the translocation pass represented as a sum of the free energies of cis and trans parts of the chain tethered to the pore opening. We investigate how the chain length, the size of trans compartment, the magnitude of adsorption potential, and the extent of excluded volume interactions affect the translocation time and its distribution. Interplay of these factors brings about a variety of different translocation regimes. We show that excluded volume interactions within a certain range of adsorption potentials can cause a local minimum on the free energy landscape, which is absent for ideal chains. The adsorption potential always leads to the decrease of the free energy barrier, increasing the probability of successful translocation. However, the translocation time depends non-monotonically of the magnitude of adsorption potential. Our calculations predict the existence of the critical magnitude of adsorption potential, which separates favorable and unfavorable regimes of translocation.
A discrete interaction model/quantum mechanical method for simulating surface-enhanced Raman spectroscopy
Authors: Payton John L. , Morton Seth M. , Moore Justin E. , Jensen Lasse
Published: June 2012

We have derived and implemented analytical gradients for the discrete interaction model/quantum mechanics (DIM/QM) method. DIM/QM combines an atomistic electrodynamics model with time-dependent density functional theory and thus enables modeling of the optical properties for a molecule while taking into account the local environment of a nanoparticle's surface. The DIM/QM analytical gradients allow for geometry optimizations, vibrational frequencies, and Raman spectra to be simulated for molecules interacting with metal nanoparticles. We have simulated the surface-enhanced Raman scattering (SERS) spectra for pyridine adsorbed on different sites of icosahedral nanoparticles with diameters between 1 and 8 nm. To describe the adsorption of the pyridine molecule onto the metal surface, we have implemented a coordination-dependent force field to differentiate the various local surface environments. We find that the DIM/QM method predicts geometries and frequencies that are in good agreement with full QM simulations and experiments. For the simulated SERS spectra of pyridine, we find a significant dependence on the adsorption site and the size of the metal nanoparticle. This illustrates the importance of accounting for the local environment around the molecule. The Raman enhancement factors are shown to roughly mirror the magnitude of the nanoparticle's local field about the molecule. Because the simulated nanoparticles are small, the plasmon peaks are quite broad which results in weak local electric fields and thus modest Raman enhancement factors.
Theory of collisional electron spectroscopy for gas analysis
Authors: Panasyuk George Y. , Tsyganov Alexander B.
Published: June 2012

We develop an analytical model for a proposed method of gas analysis. The method is based on collisional electron spectroscopy, where a limited number of electron scatterings on gas molecules inside the analyzer is permitted. The proposed method can be used to identify impurity species in a main gas from the resulted energy spectra of photoelectrons collected by the cathode. The photoelectrons are produced by vacuum ultraviolet-ionization of impurity species. Physical processes are explored in the case of detecting impurities in atmospheric air. The electron velocity distribution function inside the detector is derived. It is shown that the voltage dependence of the second derivative of the cathode current with respect to the applied cathode voltage can provide electron energy spectrum and subsequent identification of the impurity species.
Phase difference mapping of two-dimensional metallic nanohole arrays
Authors: Wong S. L. , Ong H. C.
Published: June 2012

By using angle-resolved reflectivity and common-path phase quadrature interferometry, we have measured the dispersion relations and the p-s polarization phase difference mappings of Au nanohole arrays. The distinctive phase difference profile is strongly correlated with the surface plasmon polariton resonance and exhibits strong dependence on decay rate. We have developed an analytical model based on Fano resonance to describe the dependence. As decay rate is controlled by geometry, we can tune the phase difference profile by changing geometry, which is of importance in phase-based surface plasmon resonance sensing.
Electronic excitation spectrum of the photosensitizer [Ir(ppy)2(bpy)]+
Authors: Bokarev Sergey I. , Bokareva Olga S. , Kühn Oliver
Published: June 2012

The vertical singlet-singlet and singlet-triplet electronic excitation energies of bis(2-phenylpyridinato-)(2,2′-bipyridine)iridium(III) ([Ir(ppy)2(bpy)]+) are calculated on the basis of a comparative quantum chemical study using wave function methods such as CASSCF/CASPT2 and density functional theory (TDDFT) with local and range-separated functionals. The TDDFT results show a strong dependence of the charge-transfer transition energies on the amount of the exact exchange in the functional. In general, TDDFT with range-separated functionals provides a good agreement with the experimental spectra. As a result a new assignment of the absorption spectrum of the title compound is proposed.
Microfluidic-driven viral infection on cell cultures: Theoretical and experimental study
Authors: Cimetta Elisa , Franzoso Mauro , Trevisan Marta , Serena Elena , Zambon Alessandro , Giulitti Stefano , Barzon Luisa , Elvassore Nicola
Published: June 2012

Advanced cell culture systems creating a controlled and predictable microenvironment together with computational modeling may be useful tools to optimize the efficiency of cell infections. In this paper, we will present a phenomenological study of a virus-host infection system, and the development of a multilayered microfluidic platform used to accurately tune the virus delivery from a diffusive-limited regime to a convective-dominated regime. Mathematical models predicted the convective-diffusive regimes developed within the system itself and determined the dominating mass transport phenomena. Adenoviral vectors carrying the enhanced green fluorescent protein (EGFP) transgene were used at different multiplicities of infection (MOI) to infect multiple cell types, both in standard static and in perfused conditions. Our results validate the mathematical models and demonstrate how the infection processes through perfusion via microfluidic platform led to an enhancement of adenoviral infection efficiency even at low MOIs. This was particularly evident at the longer time points, since the establishment of steady-state condition guaranteed a constant viral concentration close to cells, thus strengthening the efficiency of infection. Finally, we introduced the concept of effective MOI, a more appropriate variable for microfluidic infections that considers the number of adenoviruses in solution per cell at a certain time.
[N]pT Monte Carlo simulations of the cluster-crystal-forming penetrable sphere model
Authors: Zhang Kai , Charbonneau Patrick
Published: June 2012

Certain models with purely repulsive pair interactions can form cluster crystals with multiply-occupied lattice sites. Simulating these models’ equilibrium properties is, however, quite challenging. Here, we develop an expanded isothermal-isobaric [N]pT ensemble that surmounts this problem by allowing both particle number and lattice spacing to fluctuate. It is particularly efficient at high T, where particle insertion is facile. Using this expanded ensemble and thermodynamic integration, we solve the phase diagram of a prototypical cluster-crystal former, the penetrable sphere model, and compare the results with earlier theoretical predictions. At high temperatures and densities, the equilibrium occupancy \documentclass[12pt]{minimal}\begin{document}$n_{\mathrm{c}}^{\mathrm{eq}}$\end{document}nc eq of face-centered cubic crystal increases linearly. At low temperatures, although \documentclass[12pt]{minimal}\begin{document}$n_{\mathrm{c}}^{\mathrm{eq}}$\end{document}nc eq plateaus at integer values, the crystal behavior changes continuously with density. The previously ambiguous crossover around T ∼ 0.1 is resolved.
Preparation of Fe2Ni2N and investigation of its magnetic and electromagnetic properties
Authors: Zhang Jingwei , Yan Chao , Liu Shijiang , Pan Haoshuai , Gong Chunhong , Yu Laigui , Zhang Zhijun
Published: June 2012

In this work, Fe2Ni2N powders were prepared by calcinating a nanofiber-like precursor in flowing ammonia. It was found that the nitridation temperature is critical to controlling the phase composition of the target products, and the single-phased Fe2Ni2N with high saturation magnetization is obtained after calcinations of the precursor at 800 °C in flowing ammonia. Dielectric permittivity and magnetic permeability of paraffin composites having 50 and 70 wt. % filler amount were measured within a frequency range of 2.0–18.0 GHz, respectively. Reflection loss maxima of −25.5 dB at 8.0 GHz were achieved for 50 wt. % Fe2Ni2N composite of 3 mm thickness, suggesting that as-prepared Fe2Ni2N could be a promising candidate as microwave absorbing filler, which is to help to practicably broaden the scope of microwave absorbing materials.
Two-dimensional magnetic field dependence of Josephson current and resonant current steps at finite voltage of square shape superconducting tunnel junctions
Authors: Nakayama Akiyoshi , Abe Susumu , Watanabe Norimichi
Published: June 2012

In this article, modulation characteristics of Josephson current through square shape niobium/aluminum-oxide/niobium superconducting junction by two-dimensional scanning of external magnetic field have been studied. Two pairs of Helmholtz coils are controlled by two current sources with general purpose interface bus system to obtain the magnetic field dependence automatically. The distribution of Josephson current density inside the square junction area is obtained. The 2-D magnetic field dependences of the resonant current steps of the current-voltage characteristics of the Nb/Al-oxide/Nb tunnel junction have also been measured using the junction voltage as the parameter.
High-frequency electromagnetic properties of compositionally graded FeCoB-SiO2 granular films deposited on flexible substrates
Authors: Yang F. F. , Yan S. S. , Yu M. X. , Dai Y. Y. , Kang S. S. , Chen Y. X. , Pan S. B. , Zhang J. L. , Bai H. L. , Xu T. S. , Zhu D. P. , Qiao S. Z. , Liu G. L. , Mei L. M.
Published: June 2012

In order to break through the conductive percolation threshold limitation of the conventional granular films to increase resistivity (ρ), while keeping large complex permeability (μ̃), a series of compositionally graded FeCoB-SiO2 granular films with different multilayer structures were deposited on flexible substrates. The high-frequency electromagnetic properties were investigated. The experimental results showed that the compositionally graded granular films had obvious in-plane uniaxial magnetic anisotropy and the coercivity in the easy axis (Hce) was as low as 3.97 Oe. Both the ρ (∼15.4 mΩ·cm) and μ̃ (μi'=276.3 and μ″max=441.4) of the compositionally graded FeCoB-SiO2 granular films were simultaneously higher than those of the conventional FeCoB-SiO2 granular films. Two resonance peaks of complex permeability spectrum were also observed.
Searching for THz Gunn oscillations in GaN planar nanodiodes
Authors: Íñiguez-de-la-Torre A. , Íñiguez-de-la-Torre I. , Mateos J. , González T. , Sangaré P. , Faucher M. , Grimbert B. , Brandli V. , Ducournau G. , Gaquière C.
Published: June 2012

A detailed study of GaN-based planar asymmetric nanodiodes, promising devices for the fabrication of room temperature THz Gunn oscillators, is reported. By using Monte Carlo simulations, an analysis of the static I-V curves and the time-domain evolution of the current obtained when varying some simulation parameters in the diodes has been made. Oscillation frequencies of hundreds of GHz are predicted by the simulations in diodes with micrometric channel lengths. Following simulation guidelines, a first batch of diodes was fabricated. It was found that surface charge depletion effects are stronger than expected and inhibit the onset of the oscillations. Indeed, a simple standard constant surface charge model is not able to reproduce experimental measurements and a self-consistent model must be included in the simulations. Using a self-consistent model, it was found that to achieve oscillations, wider channels and improved geometries are necessary.
Evolution of ferromagnetic clustering in Pr0.5Ca0.5MnO3 and its effect on the critical temperature of YBa2Cu3O7 thin film
Authors: Kumar Baisnab Dipak , Geetha Kumary T. , Satya A. T. , Mani Awadhesh , Nithya R. , Vaidhyanathan L. S. , Janawadkar M. P. , Bharathi A.
Published: June 2012

A thin film bilayer of Pr0.5Ca0.5MnO3 and YBa2Cu3O7 has been deposited on LaAlO3 substrate by pulsed laser deposition. XRD pattern confirms the formation of the bilayer. Current and magnetic field dependent resistance measurements have been carried out to study the proximity effect. These measurements have shown that the superconducting transition temperature (Tc) of YBa2Cu3O7 is suppressed to lower temperatures with a progressive increase in current. In addition, a hump like feature appears in resistivity near Tc with increase in applied current. The results are explained on the basis of the formation and growth of ferromagnetic clusters on account of charge order melting in Pr0.5Ca0.5MnO3 upon application of high current and magnetic field.
Numerical investigation on the implosion dynamics of wire-array Z-pinches in (r, θ) geometry
Authors: Huang Jun , Ding Ning , Ning Cheng , Sun Shun-Kai , Zhang Yang , Xiao De-Long , Xue Chuang
Published: June 2012

The implosion dynamics of wire-array Z-pinches are investigated numerically in 2D (r, θ) geometry by using a resistive MHD code. It is assumed that the wires have expanded to plasmas with diameter d0, which is used as the initial condition for the consequent implosion process. In fact, the explosion process of individual wires is not included. By changing d0, the effects of the wire expansion degree on the implosion dynamics are analyzed. When d0 is larger, the current density is more concentrated at the outer side of the wires and the fraction of current flow around the wire plasmas is nearly in proportion to d0. As a result, the ablation rate of wires is increased and the implosion phase starts earlier. This conclusion agrees with the simulation works of other authors [Chittenden et al., Phys. Plasmas 11(3), 1118 (2004)]. When the array radius and initial wire plasma diameter are fixed, the increase of wire number leads to the azimuthal merge of wires during implosion. When the wires number exceed a critical value, which is related to d0, wire plasmas can merge to a continuous shell with an azimuthal perturbation in density, which depends on the initial wires number.
Electrically pumped wavelength-tunable blue random lasing from CdZnO films on silicon
Authors: Tian Ye , Ma Xiangyang , Jin Lu , Li Dongsheng , Yang Deren
Published: June 2012

Electrically pumped lasing actions from the metastable CdZnO films have hardly been achieved as yet. Herein, we have demonstrated electrically pumped wavelength-tunable blue random lasing from the hexagonal CdZnO films with different Cd contents, with central wavelength changing from ∼490 to 425 nm. The devices based on the metal-insulator-semiconductor structures of Au/SiO2/CdZnO on silicon substrates are constructed for electrical pumping of the CdZnO films. The insulator layers of SiO2 onto the CdZnO films in the devices should be annealed at sufficiently low temperature such as 400 °C so that the CdZnO films can be kept their integrity in terms of near-band-edge emissions.
Controlled addressing of quantum dots by nanowire plasmons
Authors: Gruber Christian , Kusar Primoz , Hohenau Andreas , Krenn Joachim R.
Published: June 2012

We demonstrate optical near field coupling of small quantum dot (QD) ensembles and surface plasmons propagating along a silver nanowire. The nanowire fabrication and the aligned QD deposition close to one nanowire end rely on a two-step electron beam lithography procedure. We observe both the addressing of QDs by plasmons and the excitation of plasmonic nanowire modes by QDs. We use the fluorescence signals to quantify the QD/plasmon coupling and show that part of the plasmon-induced QD fluorescence couples back to plasmonic modes.
Spectacular switching from ferrimagnetism to antiferromagnetism by zinc doping in “114” orthorhombic CaBaCo4O7
Authors: Sarkar Tapati , Motin Seikh Md. , Pralong V. , Caignaert V. , Raveau B.
Published: June 2012

We report a spectacular switching from ferrimagnetism to antiferromagnetism in orthorhombic “114” CaBaCo4O7 by doping with a diamagnetic cation, Zn2+. Magnetic hysteresis loops, together with M(T) and χ′(T) curves at various frequencies, show that ferrimagnetism is abruptly converted to antiferromagnetism below T ∼ 80 K for less than 3% Zn doping, with the simultaneous appearance of local magnetic frustration. A model is proposed based on the ordered doping of Zn2+ at Co2+ sites in the ferromagnetic zig-zag chains of CaBaCo4O7, leading, by domino effect, to ferrimagnetic domains distributed at random and ordered at 180°. The boundaries of the junction of these domains contain Zn2+ and are magnetically frustrated. The crucial role of such ferromagnetic zig-zag chains for designing and tuning magnetic properties in oxides with a triangular metallic lattice is emphasized.
High-speed Lissajous-scan atomic force microscopy: Scan pattern planning and control design issues
Authors: Bazaei A. , Yong Yuen K. , Moheimani S. O. Reza
Published: June 2012

Tracking of triangular or sawtooth waveforms is a major difficulty for achieving high-speed operation in many scanning applications such as scanning probe microscopy. Such non-smooth waveforms contain high order harmonics of the scan frequency that can excite mechanical resonant modes of the positioning system, limiting the scan range and bandwidth. Hence, fast raster scanning often leads to image distortion. This paper proposes analysis and design methodologies for a nonlinear and smooth closed curve, known as Lissajous pattern, which allows much faster operations compared to the ordinary scan patterns. A simple closed-form measure is formulated for the image resolution of the Lissajous pattern. This enables us to systematically determine the scan parameters. Using internal model controllers (IMC), this non-raster scan method is implemented on a commercial atomic force microscope driven by a low resonance frequency positioning stage. To reduce the tracking errors due to actuator nonlinearities, higher order harmonic oscillators are included in the IMC controllers. This results in significant improvement compared to the traditional IMC method. It is shown that the proposed IMC controller achieves much better tracking performances compared to integral controllers when the noise rejection performances is a concern.
Communication: Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles
Authors: Berezhkovskii Alexander M. , Dagdug Leonardo , Lizunov Vladimir A. , Zimmerberg Joshua , Bezrukov Sergey M.
Published: June 2012

Trapping of diffusing particles by a cluster of absorbing disks on the otherwise reflecting wall is a manifestly many-body problem because of the disk competition for the particles. By replacing the cluster with an effective uniformly absorbing spot, we derive a simple formula for the rate constant that characterizes the trapping. The formula shows how the rate constant depends on the size and shape of the cluster.
InGaP microdisk optical resonators embedded in indium tin oxide
Authors: Su Shu-Yu , Yoshie Tomoyuki
Published: June 2012

InGaP microdisk optical resonators are embedded in indium tin oxide (ITO) to investigate how the optical absorption in electrodes impacts the resonance properties. The quality factor is slightly reduced in comparison with air-embedding microdisks, and the measured quality factor is 960 for a 1.2 μm diameter, 170 nm thick disk embedded in ITO media. The experiments show that the absorption loss in ITO media has smaller contribution to the reduction of total quality factor than the scattering and radiation losses. The analysis indicates that the suppression of non-absorption loss would improve the quality factor to 104.
Frequency conversion of radio-frequency edge magnetoplasmons using a quantum point contact
Authors: Hashisaka M. , Murata R. , Muraki K. , Fujisawa T.
Published: June 2012

We report a frequency-conversion technique for edge magnetoplasmons in a quantum Hall device. The nonlinear conductance of a quantum point contact (QPC) results in the generation of high harmonics of an input microwave and the mixing of two input frequencies. We controlled the conversion efficiency by tuning the nonlinear conductance via a gate voltage. The amplitudes of the frequency-converted waves agree well with those expected from the measured dc nonlinear conductance. We demonstrate the technique up to our instrumental limit of 12 GHz and show that formation of charge-density waves does not change the nonlinear characteristics of the QPC.
Analysis of micromachined Fabry-Pérot cavities using phase-sensitive optical low coherence interferometry: Insight on dimensional measurements of dielectric layers
Authors: Malak M. , Obaton A.-F. , Marty F. , Pavy N. , Didelon S. , Basset P. , Bourouina T.
Published: June 2012

Herein, we highlight a behavior underlying the physics of Fabry-Pérot micro-cavities with distributed reflectors as there is a need to discriminate between effective and physical cavity lengths. Hence, Phase-Sensitive Optical Low Coherence Interferometry has been implemented to characterize micro-cavities with planar or curved reflectors. Beside the retrieved physical length, we obtain valuable information about the reflector thickness and number of layers. The accuracy of the technique has been estimated. Results suggest that this technique might be suitable to retrieve dimensional characteristics of any device constructed from multiple dielectric layers, whose thickness ranges from 2 micrometers up to hundreds of micrometers.
The effect of electromagnetic fields on a charged catenary
Authors: Morawetz K.
Published: June 2012

A new solution of a charged catenary is presented which allows to determine the static stability conditions where charged liquid bridges or charged hanging chains are possible.
Perspective: Quantum or classical coherence?
Authors: Miller William H.
Published: June 2012

Some coherence effects in chemical dynamics are described correctly by classical mechanics, while others only appear in a quantum treatment—and when these are observed experimentally it is not always immediately obvious whether their origin is classical or quantum. Semiclassical theory provides a systematic way of adding quantum coherence to classical molecular dynamics and thus provides a useful way to distinguish between classical and quantum coherence. Several examples are discussed which illustrate both cases. Particularly interesting is the situation with electronically non-adiabatic processes, where sometimes whether the coherence effects are classical or quantum depends on what specific aspects of the process are observed.
An investigation of optimal interfacial film condition for Cu-Mn alloy based source/drain electrodes in hydrogenated amorphous silicon thin film transistors
Authors: Asanuma Haruhiko , Suzuki Takaaki , Kusunoki Toshiaki
Published: June 2012

To aid in developing next generation Cu-Mn alloy based source/drain interconnects for thin film transistor liquid crystal displays (TFT-LCDs), we have investigated the optimal structure of a pre-formed oxide layer on phosphorus doped hydrogenated amorphous silicon (n+a-Si:H) that does not degrade TFT electrical properties. We use transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) to examine composition depth profiles of and structural information for the Cu-Mn alloy/n+a-Si:H interface region. In aiming to achieve the same electrical properties as those of TFTs having conventional Mo source/drain electrodes, we have obtained three important findings: (1) in typical TFT-LCD manufacturing processes, no Mn complex oxide layer is formed because Mn cannot diffuse substantially into an n+a-Si:H surface during low temperature (below 300°C) processes and the growth of Mn complex oxide layer would also be limited by the absence of excess oxygen species; (2) a pre-formed silicon oxide layer much thicker than 1 nm severely degrades TFT electrical properties and therefore an ultrathin (≈1 nm) silicon oxide layer is required to prevent the degradation; (3) Cu diffuses into an n+a-Si:H layer at oxygen-deficient spots and thus uniform surface oxidation is required to prevent the diffusion.
Growth and characterization of Bi2Se3 crystals by chemical vapor transport
Authors: Jiao W. H. , Jiang S. , Feng C. M. , Xu Z. A. , Cao G. H. , Xu M. , Feng D. L. , Yamada A. , Matsubayashi K. , Uwatoko Y.
Published: June 2012

Regularly-shaped high-quality Bi2Se3 crystals were grown by a chemical vapor transport using iodine as the transport agent. In addition to exhibiting a characteristic Dirac cone for a topological insulator, the Bi2Se3 crystals show some outstanding properties including additional crystallographic surfaces, large residual resistance ratio (∼10), and high mobility (∼8000 cm2·V−1·s−1). The low-temperature resistivity abnormally increases with applying pressures up to 1.7 GPa, and no superconductivity was observed down to 0.4 K.
Microbial interspecies electron transfer via electric currents through conductive minerals
Authors: Kato Souichiro , Hashimoto Kazuhito , Watanabe Kazuya
Published: June 2012

In anaerobic biota, reducing equivalents (electrons) are transferred between different species of microbes [interspecies electron transfer (IET)], establishing the basis of cooperative behaviors and community functions. IET mechanisms described so far are based on diffusion of redox chemical species and/or direct contact in cell aggregates. Here, we show another possibility that IET also occurs via electric currents through natural conductive minerals. Our investigation revealed that electrically conductive magnetite nanoparticles facilitated IET from
Geobacter sulfurreducens
to
Thiobacillus denitrificans
, accomplishing acetate oxidation coupled to nitrate reduction. This two-species cooperative catabolism also occurred, albeit one order of magnitude slower, in the presence of Fe ions that worked as diffusive redox species. Semiconductive and insulating iron-oxide nanoparticles did not accelerate the cooperative catabolism. Our results suggest that microbes use conductive mineral particles as conduits of electrons, resulting in efficient IET and cooperative catabolism. Furthermore, such natural mineral conduits are considered to provide ecological advantages for users, because their investments in IET can be reduced. Given that conductive minerals are ubiquitously and abundantly present in nature, electric interactions between microbes and conductive minerals may contribute greatly to the coupling of biogeochemical reactions.
Pathogenesis of emerging severe fever with thrombocytopenia syndrome virus in C57/BL6 mouse model
Authors: Jin Cong , Liang Mifang , Ning Junyu , Gu Wen , Jiang Hong , Wu Wei , Zhang Fushun , Li Chuan , Zhang Quanfu , Zhu Hua , Chen Ting , Han Ying , Zhang Weilun , Zhang Shuo , Wang Qin , Sun Lina , Liu Qinzhi , Li Jiandong , Wang Tao , Wei Qiang , Wang Shiwen , Deng Ying , Qin Chuan , Li Dexin
Published: June 2012

The discovery of an emerging viral disease, severe fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV), has prompted the need to understand pathogenesis of SFTSV. We are unique in establishing an infectious model of SFTS in C57/BL6 mice, resulting in hallmark symptoms of thrombocytopenia and leukocytopenia. Viral RNA and histopathological changes were identified in the spleen, liver, and kidney. However, viral replication was only found in the spleen, which suggested the spleen to be the principle target organ of SFTSV. Moreover, the number of macrophages and platelets were largely increased in the spleen, and SFTSV colocalized with platelets in cytoplasm of macrophages in the red pulp of the spleen. In vitro cellular assays further revealed that SFTSV adhered to mouse platelets and facilitated the phagocytosis of platelets by mouse primary macrophages, which in combination with in vivo findings, suggests that SFTSV-induced thrombocytopenia is caused by clearance of circulating virus-bound platelets by splenic macrophages. Thus, this study has elucidated the pathogenic mechanisms of thrombocytopenia in a mouse model resembling human SFTS disease.
Implanted adipose progenitor cells as physicochemical regulators of breast cancer
Authors: Chandler Emily M. , Seo Bo Ri , Califano Joseph P. , Andresen Eguiluz Roberto C. , Lee Jason S. , Yoon Christine J. , Tims David T. , Wang James X. , Cheng Le , Mohanan Sunish , Buckley Mark R. , Cohen Itai , Nikitin Alexander Yu , Williams Rebecca M. , Gourdon Delphine , Reinhart-King Cynthia A. , Fischbach Claudia
Published: June 2012

Multipotent adipose-derived stem cells (ASCs) are increasingly used for regenerative purposes such as soft tissue reconstruction following mastectomy; however, the ability of tumors to commandeer ASC functions to advance tumor progression is not well understood. Through the integration of physical sciences and oncology approaches we investigated the capability of tumor-derived chemical and mechanical cues to enhance ASC-mediated contributions to tumor stroma formation. Our results indicate that soluble factors from breast cancer cells inhibit adipogenic differentiation while increasing proliferation, proangiogenic factor secretion, and myofibroblastic differentiation of ASCs. This altered ASC phenotype led to varied extracellular matrix (ECM) deposition and contraction thereby enhancing tissue stiffness, a characteristic feature of breast tumors. Increased stiffness, in turn, facilitated changes in ASC behavior similar to those observed with tumor-derived chemical cues. Orthotopic mouse studies further confirmed the pathological relevance of ASCs in tumor progression and stiffness in vivo. In summary, altered ASC behavior can promote tumorigenesis and, thus, their implementation for regenerative therapy should be carefully considered in patients previously treated for cancer.
Plant tropane alkaloid biosynthesis evolved independently in the Solanaceae and Erythroxylaceae
Authors: Jirschitzka Jan , Schmidt Gregor W. , Reichelt Michael , Schneider Bernd , Gershenzon Jonathan , D’Auria John Charles
Published: June 2012

The pharmacologically important tropane alkaloids have a scattered distribution among angiosperm families, like many other groups of secondary metabolites. To determine whether tropane alkaloids have evolved repeatedly in different lineages or arise from an ancestral pathway that has been lost in most lines, we investigated the tropinone-reduction step of their biosynthesis. In species of the Solanaceae, which produce compounds such as atropine and scopolamine, this reaction is known to be catalyzed by enzymes of the short-chain dehydrogenase/reductase family. However, in
Erythroxylum coca
(Erythroxylaceae), which accumulates cocaine and other tropane alkaloids, no proteins of the short-chain dehydrogenase/reductase family were found that could catalyze this reaction. Instead, purification of
E. coca
tropinone-reduction activity and cloning of the corresponding gene revealed that a protein of the aldo-keto reductase family carries out this reaction in
E. coca
. This protein, designated methylecgonone reductase, converts methylecgonone to methylecgonine, the penultimate step in cocaine biosynthesis. The protein has highest sequence similarity to other aldo-keto reductases, such as chalcone reductase, an enzyme of flavonoid biosynthesis, and codeinone reductase, an enzyme of morphine alkaloid biosynthesis. Methylecgonone reductase reduces methylecgonone (2-carbomethoxy-3-tropinone) stereospecifically to 2-carbomethoxy-3β-tropine (methylecgonine), and has its highest activity, protein level, and gene transcript level in young, expanding leaves of
E. coca
. This enzyme is not found at all in root tissues, which are the site of tropane alkaloid biosynthesis in the Solanaceae. This evidence supports the theory that the ability to produce tropane alkaloids has arisen more than once during the evolution of the angiosperms.
Capturing directed molecular motion in the nuclear pore complex of live cells
Authors: Cardarelli Francesco , Lanzano Luca , Gratton Enrico
Published: June 2012

Nuclear pore complexes (NPCs) are gateways for nucleocytoplasmic exchange. Intrinsically disordered nucleoporins (Nups) form a selective filter inside the NPC, taking a central role in the vital nucleocytoplasmic transport mechanism. How such intricate meshwork relates to function and gives rise to a transport mechanism is still unclear. Here we set out to tackle this issue in intact cells by an established combination of fluorescence correlation spectroscopy and real-time tracking of the center of mass of single NPCs. We find the dynamics of nucleoporin Nup153 to be regulated so as to produce rapid, discrete exchange between two separate positions within the NPC. A similar behavior is also observed for both karyopherinβ1 transport-receptor and cargoes destined to nuclear import. Thus, we argue that directed Nup-mediated molecular motion may represent an intrinsic feature of the overall selective gating through intact NPCs.
Late Middle Eocene primate from Myanmar and the initial anthropoid colonization of Africa
Authors: Chaimanee Yaowalak , Chavasseau Olivier , Beard K. Christopher , Kyaw Aung Aung , Soe Aung Naing , Sein Chit , Lazzari Vincent , Marivaux Laurent , Marandat Bernard , Swe Myat , Rugbumrung Mana , Lwin Thit , Valentin Xavier , Zin-Maung-Maung-Thein  , Jaeger Jean-Jacques
Published: June 2012

Reconstructing the origin and early evolutionary history of anthropoid primates (monkeys, apes, and humans) is a current focus of paleoprimatology. Although earlier hypotheses frequently supported an African origin for anthropoids, recent discoveries of older and phylogenetically more basal fossils in China and Myanmar indicate that the group originated in Asia. Given the Oligocene-Recent history of African anthropoids, the colonization of Africa by early anthropoids hailing from Asia was a decisive event in primate evolution. However, the fossil record has so far failed to constrain the nature and timing of this pivotal event. Here we describe a fossil primate from the late middle Eocene Pondaung Formation of Myanmar,Afrasia djijidaegen. et sp. nov., that is remarkably similar to, yet dentally more primitive than, the roughly contemporaneous North African anthropoidAfrotarsius. Phylogenetic analysis suggests thatAfrasiaandAfrotarsiusare sister taxa within a basal anthropoid clade designated as the infraorder Eosimiiformes. Current knowledge of eosimiiform relationships and their distribution through space and time suggests that members of this clade dispersed from Asia to Africa sometime during the middle Eocene, shortly before their first appearance in the African fossil record. Crown anthropoids and their nearest fossil relatives do not appear to be specially related toAfrotarsius, suggesting one or more additional episodes of dispersal from Asia to Africa. Hystricognathous rodents, anthracotheres, and possibly other Asian mammal groups seem to have colonized Africa at roughly the same time or shortly after anthropoids gained their first toehold there.
Gaucher disease geneGBAfunctions in immune regulation
Authors: Liu Jun , Halene Stephanie , Yang Mei , Iqbal Jameel , Yang Ruhua , Mehal Wajahat Z. , Chuang Wei-Lien , Jain Dhanpat , Yuen Tony , Sun Li , Zaidi Mone , Mistry Pramod K.
Published: June 2012

Inherited deficiency of acid β-glucosidase (GCase) due to biallelic mutations in theGBA(glucosidase, β, acid) gene causes the classic manifestations of Gaucher disease (GD) involving the viscera, the skeleton, and the lungs. Clinical observations point to immune defects in GD beyond the accumulation of activated macrophages engorged with lysosomal glucosylceramide. Here, we show a plethora of immune cell aberrations in mice in which theGBAgene is deleted conditionally in hematopoietic stem cells (HSCs). The thymus exhibited the earliest and most striking alterations reminiscent of impaired T-cell maturation, aberrant B-cell recruitment, enhanced antigen presentation, and impaired egress of mature thymocytes. These changes correlated strongly with disease severity. In contrast to the profound defects in the thymus, there were only limited cellular defects in peripheral lymphoid organs, mainly restricted to mice with severe disease. The cellular changes in GCase deficiency were accompanied by elevated T-helper (Th)1 and Th2 cytokines that also tracked with disease severity. Finally, the proliferation of GCase-deficient HSCs was inhibited significantly by both GL1 and Lyso-GL1, suggesting that the “supply” of early thymic progenitors from bone marrow may, in fact, be reduced inGBAdeficiency. The results not only point to a fundamental role forGBAin immune regulation but also suggest thatGBAmutations in GD may cause widespread immune dysregulation through the accumulation of substrates.
Aldosterone-independent regulation of the epithelial Na
+
channel (ENaC) by vasopressin in adrenalectomized mice
Authors: Mironova Elena , Bugaj Vladislav , Roos Karl P. , Kohan Donald E. , Stockand James D.
Published: June 2012

The epithelial Na
+
channel (ENaC) in the aldosterone-sensitive distal nephron (ASDN) is under negative-feedback regulation by the renin–angiotensin–aldosterone system in protection of sodium balance and blood pressure. We test here whether aldosterone is necessary and sufficient for ENaC expression and activity in the ASDN. Surprisingly, ENaC expression and activity are robust in adrenalectomized (Adx) mice. Exogenous mineralocorticoid increases ENaC activity equally well in control and Adx mice. Plasma [AVP] is significantly elevated in Adx vs. control mice. Vasopressin (AVP) stimulates ENaC. Inhibition of the V
2
AVP receptor represses ENaC activity in Adx mice. The absence of aldosterone combined with elevated AVP release compromises normal feedback regulation of ENaC in Adx mice in response to changes in sodium intake. These results demonstrate that aldosterone is sufficient but not necessary for ENaC activity in the ASDN. Aldosterone-independent stimulation by AVP shifts the role of ENaC in the ASDN from protecting Na
+
balance to promoting water reabsorption. This stimulation of ENaC likely contributes to the hyponatremia of adrenal insufficiency.
Intersystem crossing and dynamics in O(
3
P) + C
2
H
4
multichannel reaction: Experiment validates theory
Authors: Fu Bina , Han Yong-Chang , Bowman Joel M. , Angelucci Luca , Balucani Nadia , Leonori Francesca , Casavecchia Piergiorgio
Published: June 2012

The O(
3
P) + C
2
H
4
reaction, of importance in combustion and atmospheric chemistry, stands out as a paradigm reaction involving triplet- and singlet-state potential energy surfaces (PESs) interconnected by intersystem crossing (ISC). This reaction poses challenges for theory and experiments owing to the ruggedness and high dimensionality of these potentials, as well as the long lifetimes of the collision complexes. Primary products from five competing channels (H + CH
2
CHO, H + CH
3
CO, H
2
 + CH
2
CO, CH
3
 + HCO, CH
2
 + CH
2
O) and branching ratios (BRs) are determined in crossed molecular beam experiments with soft electron-ionization mass-spectrometric detection at a collision energy of 8.4 kcal/mol. As some of the observed products can only be formed via ISC from triplet to singlet PESs, from the product BRs the extent of ISC is inferred. A new full-dimensional PES for the triplet state as well as spin-orbit coupling to the singlet PES are reported, and roughly half a million surface hopping trajectories are run on the coupled singlet-triplet PESs to compare with the experimental BRs and differential cross-sections. Both theory and experiment find almost equal contributions from the two PESs to the reaction, posing the question of how important is it to consider the ISC as one of the nonadiabatic effects for this and similar systems involved in combustion chemistry. Detailed comparisons at the level of angular and translational energy distributions between theory and experiment are presented for the two primary channel products, CH
3
 + HCO and H + CH
2
CHO. The agreement between experimental and theoretical functions is excellent, implying that theory has reached the capability of describing complex multichannel nonadiabatic reactions.
Regulation of innate CD8+T-cell activation mediated by cytokines
Authors: Freeman Bailey E. , Hammarlund Erika , Raué Hans-Peter , Slifka Mark K.
Published: June 2012

Virus-specific CD8+T cells develop the ability to function in an “innate” capacity by responding to a remarkable array of cytokines in a TCR-independent manner. Although several cytokines such as IL-12 and IL-18 have been identified as key regulators of CD8+T-cell activation, the role of other cytokines and the ways in which they interact with each other remain unclear. Here, we have used an unbiased, systematic approach to examine the effects of 1,849 cytokine combinations on virus-specific CD8+T-cell activation. This study identifies several unexpected cytokine combinations that synergize to induce antigen-independent IFNγ production and CD69 up-regulation by CD8+T cells in addition to cytokines that exhibit differential regulatory functions, with the ability to either enhance or inhibit T-cell IFNγ production, depending on which cytokine partner is present. These findings underscore the complexity of cytokine interactions while also providing insight into the multifaceted regulatory network controlling virus-specific CD8+T-cell functions.