bluuebunny/crossref_metadata_2025 huggingface dataset:
Lattice dynamics of stishovite from powder inelastic X‐ray scattering
Authors: Bosak A. , Fischer I. , Krisch M. , Brazhkin V. , Dyuzheva T. , Winkler B. , Wilson D. , Weidner D. , Refson K. , Milman V.
Published: October 2009

We have retrieved the full lattice dynamics of stishovite, SiO2, by a combination of powder inelastic x‐ray scattering (IXS) and ab initio calculations. The extracted dispersion curves are confirmed by experiments on a single crystal. Thereby we have shown that IXS powder measurements over a large range of momentum transfers allow an unambiguous validation of lattice dynamics models, which then in turn can be used to derive elastic and thermodynamic properties. The proposed method can be extended to high pressure measurements on in situ synthesized samples and promises to be a valuable tool in studies of materials for which no single crystals can be obtained.
Using DInSAR, airborne LiDAR, and archival air photos to quantify landsliding and sediment transport
Authors: Roering Joshua J. , Stimely Laura L. , Mackey Benjamin H. , Schmidt David A.
Published: October 2009

We demonstrate the ability of coupled remote sensing tools to characterize large, slow‐moving landslides in the Eel River catchment, northern California. From a stack of ALOS interferograms, we identified 5 large (>1 km long) landslides that exhibited significant activity from February 2007 to February 2008. For the Boulder Creek earthflow, we used orthorectified air photos taken in 1964 and unfiltered airborne LiDAR flown in 2006 to map the displacement of trees growing on the landslide surface. Combining those displacement orientations with stacked DInSAR data, we observed average downslope velocities of 0.65 m yr−1 through the central transport zone of the landslide. Given landslide depth estimates, minimum sediment transport and denudation rates are estimated to be 4100 m3 yr−1 and 1.6 mm yr−1, respectively. Our results demonstrate the highly erosive role of large, slow‐moving landslides in landscape evolution and suggest that the superposition of dense, ephemeral gully networks and rapidly moving zones within the landslide may facilitate delivery of slide‐mobilized sediment into adjacent fluvial channels.
Local time dependence of the prompt ionospheric response for the 7, 9, and 10 November 2004 superstorms
Authors: Mannucci Anthony J. , Tsurutani Bruce T. , Kelley Michael C. , Iijima Byron A. , Komjathy Attila
Published: October 2009

In this paper, we study the local time response of the low‐latitude ionosphere during the sequence of geomagnetic storms occurring on 7, 9, and 10 November 2004. Three distinct storm main phases leading to peak negative Dst index of at least −250 nT occur during this period. We analyze total electron content (TEC) measurements from the global network of GPS receivers available from the International Global Navigation Satellite Systems (GNSS) Service. Average TEC within the geomagnetic latitude band ±25° is computed as a function of local time for several hours following storm commencement. We find that significant TEC increases are observed on 7 November (increase of 100%) and 9 November (50%). During 7 November, the increases tend to occur during solar local times 1200–1600 LT. During 9 November, the largest TEC increases tend to occur at earlier local times (∼1000–1200 LT). No daytime TEC increase is observed on 10 November, although the Kp index suggests that this storm is comparable in intensity to the 7 November storm. Vertical drift measurements from the Jicamarca radar (Peruvian sector) for the 7 and 9 November storm periods suggest large (2–3 mV/m) low‐latitude “prompt penetration” eastward electric fields (PPEF), consistent with observed increases in TEC. For the 10 November storm, published estimates of electric fields using the dual‐magnetometer technique near the Japanese sector, which is near ∼1400 LT at storm onset, suggest the absence of eastward directed electric fields during daytime. A time series analysis of TEC in the Japanese sector throughout the 7–11 November period reveals significant daytime TEC reduction of 33% relative to quiet conditions. Reduced TEC occurs coincident with the onset of the 10 November storm period, persisting into the 11th. Global Ultraviolet Imager (GUVI) retrievals of thermospheric atomic oxygen to nitrogen ratio suggest depleted oxygen in the southern hemisphere that may contribute to the TEC reduction on 10 November. Solar rotation reduces solar X‐ray and EUV fluxes from 10 through 12 November, which may be a contributing factor to reduced TEC on 10 and 11 November. In conclusion, we postulate that an additional source of electric field is present on 10 November during daytime that counteracts the PPEF of magnetospheric origin.
An analytical model probing the internal state of coronal mass ejections based on observations of their expansions and propagations
Authors: Wang Yuming , Zhang Jie , Shen Chenglong
Published: October 2009

In this paper, a generic self‐similar flux rope model is proposed to probe the internal state of CMEs in order to understand the thermodynamic process and expansion of CMEs in interplanetary space. Using this model, three physical parameters and their variations with heliocentric distance can be inferred based on coronagraph observations of CMEs' propagation and expansion. One is the polytropic index Γ of the CME plasma, and the other two are the average Lorentz force and the thermal pressure force inside CMEs. By applying the model to the 8 October 2007 CME observed by STEREO/SECCHI, we find that (1) the polytropic index of the CME plasma increased from initially 1.24 to more than 1.35 quickly and then slowly decreased to about 1.34; it suggests that there be continuously heat injected/converted into the CME plasma and the value of Γ tends to be , a critical value inferred from the model for a force‐free flux rope; (2) the Lorentz force directed inward while the thermal pressure force outward, and both of them decreased rapidly as the CME moved out; the direction of the two forces reveals that the thermal pressure force is the internal driver of the CME expansion, whereas the Lorentz force prevented the CME from expanding. Some limitations of the model and approximations are discussed meanwhile.
A new approach for monitoring the 27‐day solar rotation using VLF radio signals on the Earth's surface
Authors: Reuveni Yuval , Price Colin
Published: October 2009

Typical solar parameters such as sunspot number, Lyman alpha radiation, and 10.7 cm radio flux exhibit 27‐day variations associated with the rotation of the Sun. We have discovered a robust indicator of this 27‐day rotation from measurements of VLF radio signals produced by lightning around the globe. The solar rotation signal is found only at VLF frequencies close to the Earth‐ionosphere waveguide cutoff frequency (∼2 kHz). Furthermore, the 27‐day solar rotation is detected only during daylight hours, implying a 27‐day periodicity in the daytime collision frequency between free electrons and neutral air molecules in the lower ionosphere (∼80 km). We propose that continuous monitoring of VLF radio noise at frequencies close to the waveguide cutoff could provide a new method of continuously monitoring changes in the solar rotation rate.
Subtidal water level variation controlled by river flow and tides
Authors: Buschman F. A. , Hoitink A. J. F. , van der Vegt M. , Hoekstra P.
Published: October 2009

Subtidal water level dynamics in the Berau river, East Kalimantan, Indonesia, feature a pronounced fortnightly variation. The daily mean water levels at a station about 60 km from the sea are 0.2–0.6 m higher during spring tide than during neap tide. To explain the underlying mechanisms, a local subtidal momentum balance is set up from field data, using continuous discharge estimates inferred from measurements taken with a horizontal acoustic Doppler current profiler. It is demonstrated that terms accounting for friction and variation in the water surface gradient are dominant in the subtidal momentum balance. To further investigate the sources of subtidal water level variation, a generic method of analysis is proposed to decompose the subtidal friction term into contributions caused by river flow, by interaction between tidal motions and river flow, and by the tidal motions alone. At the station under study, mainly the river‐tide interaction term is responsible for generating fortnightly variation of the subtidal water level. The contribution from interaction between diurnal, semidiurnal, and quarterdiurnal tides to subtidal friction is significantly smaller. Provided that the reduction of tidal velocity amplitudes with increasing discharges can be predicted from a regression model, the results presented herein can be used to predict changes in subtidal water levels as a result of increased river discharges.
Increased Brain Microvascular MMP-9 and Incidence of Haemorrhagic Transformation in Obese Mice after Experimental Stroke
Authors: McColl Barry W , Rose Nicola , Robson Fiona H , Rothwell Nancy J , Lawrence Catherine B
Published: October 2009

Obesity is an independent risk factor for stroke and is associated with poorer outcome after stroke. We investigated whether this poorer outcome is related to brain microvascular disruption. Focal cerebral ischaemia was induced in lean or obese ( ob/ob) mice by transient middle cerebral artery occlusion. The incidence of haemorrhagic transformation and the volume of ischaemic brain damage were significantly greater in obese mice. Blood–brain barrier permeability and brain microvascular MMP-9 expression were also markedly increased in obese mice. These effects were independent of leptin or glycaemic status, suggesting that obesity potentiates brain microvascular disruption after experimental stroke.
Characterization of Gadolinium-Based Dynamic Susceptibility Contrast Perfusion Measurements in Permanent and Transient MCAO Models with Volumetric Based Validation by CASL
Authors: Bråtane Bernt T , Walvick Ronn P , Corot Claire , Lancelot Eric , Fisher Marc
Published: October 2009

Perfusion imaging is crucial in imaging of ischemic stroke to determine ‘tissue at risk’ for infarction. In this study we compared the volumetric quantification of the perfusion deficit in two rat middle-cerebral-artery occlusion (MCAO) models using two gadolinium-based contrast agents (P1152 (Guerbet) and Magnevist (Bayer-Schering, Pittsburgh, PA, USA)) as compared with our well established continuous arterial spin labeling (CASL) perfusion imaging technique. Animals underwent either permanent MCAO or transient MCAO with 80-min reperfusion. Imaging was performed at four different time points after MCAO. A region-of-interest (ROI) analysis of the subregions of the ischemic zone (core, penumbra, transient reversal (TR), and sustained reversal (SR)) using P1152 showed significant reduction in blood flow in the core and TR subregions relative to the penumbral and SR subregions while occluded. After reperfusion, a significant increase in blood flow was recorded at all time points after reperfusion in all regions except TR. From the ROI analysis the threshold for the penumbra was determined to be −62±11% and this value was subsequently used for quantification of the volumetric deficit. The ischemic volume as defined by dynamic susceptibility contrast (DSC), was only statistically different from the CASL-derived ischemic volume when using Magnevist at post-reperfusion time points.
Optical description of solid-state dye-sensitized solar cells. II. Device optical modeling with implications for improving efficiency
Authors: Huang David M. , Snaith Henry J. , Grätzel Michael , Meerholz Klaus , Moulé Adam J.
Published: October 2009

We use the optical transfer-matrix method to quantify the spatial distribution of light in solid-state dye-sensitized solar cells (DSCs), employing material optical properties measured experimentally in the accompanying article (Part I) as input into the optical model. By comparing the optical modeling results with experimental photovoltaic action spectra for solid-state DSCs containing either a ruthenium-based dye or an organic indoline-based dye, we show that the internal quantum efficiency (IQE) of the devices for both dyes is around 60% for almost all wavelengths, substantially lower than the almost 100% IQE measured for liquid DSCs, indicating substantial electrical losses in solid-state DSCs that can account for much of the current factor-of-two difference between the efficiencies of liquid and solid-state DSCs. The model calculations also demonstrate significant optical losses due to absorption by 2,2′,7,7′-tetrakis-(N,N-di-p-methoxyphenyl-amine)-9,9′-spirobifluorene (spiro-OMeTAD) and TiO2 in the blue and to a lesser extent throughout the visible. As a consequence, the more absorptive organic dye, D149, should outperform the standard ruthenium complex sensitizer, Z907, for all device thicknesses, underlining the potential benefits of high extinction coefficient dyes optimized for solid-state DSC operation.
Formation and coarsening of Ga droplets on focused-ion-beam irradiated GaAs surfaces
Authors: Wu J. H. , Ye W. , Cardozo B. L. , Saltzman D. , Sun K. , Sun H. , Mansfield J. F. , Goldman R. S.
Published: October 2009

We have investigated the formation and coarsening of Ga droplets on focused-ion-beam (FIB) irradiated GaAs surfaces. To separately examine formation and coarsening, Ga droplets were fabricated by Ga+ FIB irradiation of GaAs substrates with and without pre-patterned holes. We determined the droplet growth rate and size distribution as a function of FIB energy following irradiation. The data suggest a droplet formation mechanism that involves Ga precipitation from a Ga-rich layer, followed by droplet coarsening via a combination of diffusion and Ostwald ripening or coalescence via droplet migration (dynamic coalescence).
Calculations of synchrotron radiation emission in the transverse coherent limit
Authors: Hulbert S. L. , Williams G. P.
Published: October 2009

We present approximations for the synchrotron radiation emission for low emittance light sources, which provide a connection between user needs and the electron beam parameters. The results and calculations are a consequence of the phase coherence in the emission from the electrons. We derive the remarkable result that if the electron beam is energetic enough, the emitted flux is independent of the photon energy, electron beam energy, or bending radius in the transverse coherent limit. Similarly the brightness is identical for all machines at a given current.
Methane combustion on Pd-based model catalysts: Structure sensitive or insensitive?
Authors: Lv Cun-Qin , Ling Kai-Cheng , Wang Gui-Chang
Published: October 2009

The C–H breaking of methane on the clean and the oxygen precovered palladium single crystal surfaces with the simplest orientations, namely, the dense (111), (100), the more open (110), and the stepped (111) surfaces, the corresponding O/Pd surfaces with different coverage of oxygen, as well as the palladium oxide PdO(100) and PdO(110) surfaces, has been studied with the density functional theory-generalized gradient approximation method using the repeated slab models. The adsorption energies under the most stable configuration of the possible species and the activation energy barriers of the reaction are obtained in the present work. Through systematic calculations for the C–H breaking of methane CH4→CH3+H on these surfaces, it is found that such a reaction is structure sensitive on clean palladium and oxygen precovered palladium surfaces with lower oxygen coverage, but it is insensitive on oxygen precovered palladium surfaces with higher oxygen coverage and on palladium oxides. These results are in general agreement with the experimental observations.
Highly p-doped regions in silicon solar cells quantitatively analyzed by small angle beveling and micro-Raman spectroscopy
Authors: Becker M. , Gösele U. , Hofmann A. , Christiansen S.
Published: October 2009

Highly p-doped regions in multicrystalline silicon solar cells, such as the back surface field region, are analyzed by means of small angle beveling and micro-Raman spectroscopy. Small angle beveling and subsequent Secco etching are used to enhance the lateral resolution of the micro-Raman spectroscopic measurements and to investigate the microstructure of the back surface field region in detail. The position-dependent analysis of the free carrier concentrations within the back surface field region is based on the Raman specific Fano resonances. The Raman spectroscopic measurement results are compared to results obtained from electrochemical capacitance-voltage measurements, which allows a subsequent calibration of the Raman data for the quantitative analysis of the free carrier concentrations within the highly p-doped regions of silicon solar cells and other devices. Our investigations show that the free carrier as well as the dopant concentration profiles within the back surface field region exhibit a nearly step-functional shape instead of the extended gradient shape which the electrochemical capacitance-voltage measurements suggest. Moreover, we show that the shape of the back surface field is often influenced by grain boundaries and other defects that occur in multicrystalline silicon wafers.
Temperature-dependent Hall and photoluminescence evidence for conduction-band edge shift induced by alloying ZnO with magnesium
Authors: Pan X. H. , Guo W. , Ye Z. Z. , Liu B. , Che Y. , Tian W. , Schlom D. G. , Pan X. Q.
Published: October 2009

This work discusses the effect of conduction-band edge shift induced by alloying ZnO with magnesium. Temperature-dependent Hall and temperature-dependent photoluminescence measurements are used to characterize the epitaxial Zn1−xMgxO thin films grown on (111) Si using intervening epitaxial Lu2O3 buffer layers, which prove that the addition of Mg in ZnO shifts the conduction-band edge to higher energy, thus increasing the activation energy of the defect donor states and reducing the n-type background carrier concentration.
Magnetic force microscopy investigation of the static magnetic domain structure and domain rotation in Fe-x at. %Ga alloys
Authors: Bai Feiming , Zhang Huaiwu , Li Jiefang , Viehland D.
Published: October 2009

Magnetic domain structures and domain rotation process in Fe-x at. %Ga (x=12, 19, and 25) alloys have been studied by magnetic force microscopy. Our results show that the missing connection between magnetic domains and the underlying microstructure [Xing and Lograsso, Appl. Phys. Lett. 93, 182501 (2008)] is (i) a perpendicular magnetic anisotropy; and (ii) domain irregularities/fluctuations induced by a quenched random-field condition: both of which may have direct relations with dispersed low-symmetry nanoprecipitates [Cao, et al., Phys. Rev. Lett. 102, 127201 (2009)].
Growth and ellipsometric studies on C60 thin films for solar cell applications
Authors: Datta Debjit , Kumar Satyendra
Published: October 2009

C 60 have been used as an important active layer in organic solar cells and require elaborate understanding of its thin film properties. In this work, we present detailed morphological and ellipsometric studies on C60 thin films for understanding its growth and optical characteristics. At the initial stages of growth, C60 was found to form nanocrystalline granular domains in three-dimensional growth mode that coalesce to form large islandlike structures. As the film grows, comparatively smooth surfaces are obtained by uniform distribution of the nanocrystalline domains. Ellipsometric studies required the use of a bilayer structural model. The applicability of crucial model dielectric functions including Classical-Oscillator model, Forouhi–Bloomer model, and Tauc–Lorentz model for extraction of optical constants [Ñ(E)=n(E)+ik(E)] was investigated. The optical constants extracted from the three models are reported. Tauc–Lorentz model was found to be suitable model dielectric function as compared to the other models. Parameters including transition energy, amplitude, and broadening corresponding to five optical transitions, as well as the optical band gap of C60, are extracted. The optical constants are further used to model growth of the C60 film by studying evolution of the film and the roughness layers in the ellipsometric bilayer model.
Magnetization processes and spin reorientation in epitaxial NdCo5±x thin films
Authors: Seifert M. , Schultz L. , Neu V.
Published: October 2009

Nd–Co thin films with a nominal composition of 17% Nd have been prepared by pulsed laser deposition on MgO(1 1 0) substrates. Texture measurements prove a single epitaxial in-plane texture and suggest that the films consist of a NdCo5+x and a Nd2Co7 phase. The very good texture is a precondition for precise angle dependent measurements of the anisotropic magnetic behavior and thus enables the investigation of spin reorientation transitions in these thin films. Hysteresis measurements at various temperatures find the change in the easy magnetization direction from easy axis along c to easy cone and further to easy axis along a at transition temperatures of 310 and 255 K. Both in the easy c-axis (400 K) and the easy a-axis (200 K) states, the hysteresis is square shaped for applied fields parallel to the easy magnetization direction and the switching field increases with increasing deviation of the field angle φ according to Kondorsky’s 1/cos φ dependence [J. Phys. (USSR) 2, 161 (1940)]. This is interpreted as an indication for a pinning dominated coercivity mechanism.
Thermal stability of deep levels between room temperature and 1500 °C in as-grown 3C-SiC
Authors: Alfieri G. , Nagasawa H. , Kimoto T.
Published: October 2009

We report on the thermal stability of deep levels detected in as-grown bulk 3C-SiC. The investigation was performed by Fourier-transform deep level transient spectroscopy and an isochronal annealing series was carried out in the 100–1500 °C temperature range. We found three traps located between 0.14–0.50 eV below the conduction band edge minimum (EC). The shallower trap anneals out at temperatures below 1200 °C while the others display a high thermal stability up to at least 1500 °C. The nature of the former trap is discussed in detail on the basis of its annealing behavior and previous theoretical data found in the literature.
Complete set of material constants of Pb(In1/2Nb1/2)O3–Pb(Mg1/3Nb2/3)O3–PbTiO3 single crystal with morphotropic phase boundary composition
Authors: Liu Xiaozhou , Zhang Shujun , Luo Jun , Shrout Thomas R. , Cao Wenwu
Published: October 2009

Using combined resonance and ultrasonic methods, a full set of material constants has been measured for morphotropic phase boundary (MPB) composition xPb(In1/2Nb1/2)O3–(1−x−y)Pb(Mg1/3Nb2/3)O3–yPbTiO3 (PIN-PMN-PT) single crystals poled along [001]c. Compared with the MPB composition (1−x)Pb(Mg1/3Nb2/3)O3–xPbTiO3 (PMN-PT) single crystals, the PIN-PMN-PT single crystals have smaller anisotropy, higher Curie temperature (Tc≈197 °C), and higher rhombohedral to tetragonal phase transition temperature (TR-T≈96 °C). The electromechanical properties obtained here are the best found so far for this ternary system with d33≈2742 pC/N, d31≈−1337 pC/N, k33≈95%, and k31≈65%.
Digital metamorphic alloys
Authors: Lee Kenneth E. , Fitzgerald Eugene A.
Published: October 2009

We have combined thin layers of constituent materials such that they act in a mechanically similar fashion as a random alloy. We term this combination of many thin layers of constituent materials as digital metamorphic alloy (DMA). The constituent materials can be elemental (e.g., Si, Ge) or binary (e.g., GaP, GaAs, InP, InAs, etc.) semiconductors. The DMAs are used to replace alloys in a metamorphic buffer layer. Such a DMA buffer potentially has superior thermal conductivities to, and avoids material growth-related problems associated with, conventional compositionally graded random-alloy metamorphic buffers. The method of fabricating DMAs with binary III–V materials is described. Lattice-constant grading from GaAs to InP has been carried out using both the DMA concept, and a hybrid analog-buffer/DMA approach.
Misfit dislocation density and strain relaxation in graded semiconductor heterostructures with arbitrary composition profiles
Authors: Bertoli B. , Suarez E. N. , Ayers J. E. , Jain F. C.
Published: October 2009

We present a computational approach for the determination of the equilibrium misfit dislocation density and strain in a semiconductor heterostructure with an arbitrary compositional profile. We demonstrate that there is good agreement between our computed results and known analytical solutions for heterostructures containing a single linearly graded layer or a single uniform composition layer. We have calculated the dislocation density and strain profiles in Si1−xGex/Si(001), InxGa1−xAs/GaAs(001), and ZnSySe1−y/GaAs(001) heterostructures, each containing a uniform composition layer (uniform layer) on a linearly graded buffer layer (graded layer). The density of misfit dislocations in the graded layer is inversely proportional to its grading coefficient and is unchanged by the presence of the uniform layer, but the dislocated thickness increases with the uniform layer thickness. If the uniform layer is sufficiently thick, misfit dislocations will exist throughout the graded layer, but additional misfit dislocations are not produced in the uniform layer. The biaxial strain in the uniform layer is inversely proportional to its thickness and is unchanged by the graded layer. We have also calculated the equilibrium configuration in a convex, exponentially graded Si1−xGex/Si(001) layer, for which the misfit dislocation density is tapered with distance from the interface. Other nonlinear grading profiles offer opportunities to tailor the misfit dislocation density and strain profile.
Spectral shape and broadening of emission from AlGaInP light-emitting diodes
Authors: Chen N. C. , Lien W. C. , Yang Y. K. , Shen C. , Wang Y. S. , Chen J. F.
Published: October 2009

This work presents a model for describing the shape of the spontaneous emission spectrum from a quantum-well structure. A function is introduced to specify the probability distribution for the effective band gap. Based on this model, the coexisting carrier thermal broadening and effective band gap broadening in the spontaneous emission spectrum can be separated from each other. Applying this model to the spectra of AlGaInP light-emitting diodes reveals that the probability distribution functions are almost Gaussian. Therefore, the emission spectra can be described by an analytical expression with fitted parameters. Possible reasons for this band gap broadening are discussed. The determination of the junction temperatures from the emission spectra and possible deviations of the results thus determined are also elaborated.
An improved long-range corrected hybrid functional with vanishing Hartree–Fock exchange at zero interelectronic distance (LC2gau-BOP)
Authors: Song Jong-Won , Watson Mark A. , Hirao Kimihiko
Published: October 2009

We present a new long-range corrected (LC) density functional theory (DFT) scheme, named “LC2gau,” which combines the best features of our two recently developed hybrid functionals, “LCgau” [J.-W. Song et al., J. Chem. Phys. 127, 154109 (2007)] and “LCgau-core” [J.-W. Song et al., J. Chem. Phys. 129, 184113 (2008)]. By introducing a flexible mixing of Hartree–Fock and DFT exchange in the LCgau scheme, we showed that a DFT functional could simultaneously achieve high accuracy in the reproduction of thermochemical properties, molecular geometries, as well as charge transfer and valence-Rydberg excitation energies. With an alternative mixing of short-range exchange, LCgau-core can reproduce core excitations with high accuracy, especially in the C, N, and O atoms, but at the expense of slightly higher atomization energy errors. We now show that LC2gau can simultaneously perform well for all types of excitations, as well as thermochemistry. In contrast to the previously proposed LC functionals, a notable feature is the inclusion of 100% DFT exchange as the interelectronic distance vanishes, showing that pure DFT approximations can be successfully used at short range, and the importance of including an appropriate correction in the midrange. This is achieved using two Gaussian functions in combination with the error function to describe the exchange partitioning. We rationalize the success of LC2gau by demonstrating a near-linear behavior of the total energies of the C atom as a function of the fractional number of electrons, both in the valence and core regions, which indicates an alleviation of significant self-interaction errors observed with other functionals.
Transport properties of a spin-split two-dimensional electron gas in an In0.53Ga0.47As∕InP quantum well structure
Authors: Zhou Y. M. , Shang L. Y. , Yu G. , Gao K. H. , Zhou W. Z. , Lin T. , Guo S. L. , Chu J. H. , Dai N. , Austing D. G.
Published: October 2009

We study the magnetotransport properties of a gated In0.53Ga0.47As∕InP quantum well structure in the presence of spin splitting when only one electronic subband is occupied. We develop an analytical method to extract the quantum mobilities for the two spin subbands. Ionized impurity scattering and alloy disorder scattering are determined to be important in this system. Larger quantum mobility is found for the higher-energy spin subband. We also demonstrate that the difference between the quantum mobilities for the two spin subbands can be altered with the gate.
Atomic structure and diffusion in Cu60Zr40 metallic liquid and glass: molecular dynamics simulations
Authors: Sun Yong Li , Shen Jun , Valladares Ariel A.
Published: October 2009

Temperature effects on the structural evolution and diffusivity of Cu60Zr40 in the liquid and glassy states were studied by molecular dynamics simulations using the Finnis–Sinclair potential. The pair distribution functions and common-neighbor analysis were used to investigate the structural variations. It is found that the amount of pentagonal bipyramids increases sharply in a short temperature range of about 200 K above the glass transition temperature Tg, leading to the increasing of the icosahedral cluster centered by Cu atom and larger Kasper polyhedral cluster centered by Zr atom. The mean square displacement and the self part of the van Hove function were calculated to evaluate the relaxation and transport properties. The cage effect is found to appear at 1100 K. The mode-coupling theory equation is more suitable than the Vogel–Fulcher–Tammann equation to describe the change in diffusivity in the liquid state. The critical temperature Tc, a predicted glass transition temperature in mode-coupling theory, for Cu60Zr40 glass former is 1008.2 K. At temperatures near Tc, there is a dynamic crossover. In supercooled liquid state, the dynamic heterogeneity is detected. The comparison of the activation enthalpies of the two components shows that the small atoms transport faster obeying the size effect.
Regularity criteria of weak solutions to the three-dimensional micropolar flows
Authors: Dong Bo-Qing , Chen Zhi-Min
Published: October 2009

Regularity criteria of weak solutions to the three-dimensional micropolar fluid motion equations are discussed. Sufficient conditions for the regularity of weak solutions are presented by imposing Serrin’s type growth conditions on the velocity field in Lorentz spaces, multiplier spaces, bounded mean oscillation spaces, and Besov spaces, respectively. The findings demonstrate that the velocity field plays a dominant role in the regularity problem of micropolar fluid motion equations.
Stretchable metal-elastomer nanovoids for tunable plasmons
Authors: Cole Robin M. , Mahajan Sumeet , Baumberg Jeremy J.
Published: October 2009

A range of flexible metal-elastomer nanostructures are fabricated using a self-assembly and casting technique. Such nanostructures support plasmons, which have energies and field distributions that are strongly dependent on the structure geometry or position within an array. In particular, truncated spherical metal cavities embedded within a flexible three-dimensional elastomer film can be elastically deformed without tearing, modifying their shape and mechanically tuning their resonant plasmon modes. Such structures make possible the fabrication of low cost elasto-optic films and tunable substrates for surface enhanced Raman spectroscopy.
Magnetoresistance effect in antiferromagnet/nonmagnet/antiferromagnet multilayers
Authors: Wang L. , Wang S. G. , Rizwan Syed , Qin Q. H. , Han X. F.
Published: October 2009

The magnetoresistance (MR) effect between two antiferromagnetic layers separated by a nonmagnetic Cu layer was investigated. The MR ratio of 0.5% was observed in the structure of IrMn(8)/Cu(2.8)/IrMn(0.5)/CoFe(8) (in nanometers), where IrMn stands for Ir22Mn78 and CoFe for Co90Fe10. The study of different structures with and without top IrMn layer indicates that the MR effect originates from the giant magnetoresistance effect between the uncompensated magnetic moments at the IrMn interfaces across nonmagnetic Cu spacer.
Tuning exchange bias in Ni/FeF2 heterostructures using antidot arrays
Authors: Kovylina M. , Erekhinsky M. , Morales R. , Villegas J. E. , Schuller I. K. , Labarta A. , Batlle X.
Published: October 2009

The transition from positive to negative exchange bias can be systematically tuned with antidot arrays artificially introduced into Ni/FeF2 ferromagnetic/antiferromagnetic heterostructures. These results are a consequence of the energy balance and suggest that the nanostructure plays a key role in the formation of pinned uncompensated spin regions in the antiferromagnetic FeF2 layer. These noninterfacial magnetic moments created at the antidot faces favor the onset of positive exchange bias at lower cooling fields.
The significance of core-level electron binding energies on the proper analysis of InGaAs interfacial bonding
Authors: Hinkle C. L. , Milojevic M. , Vogel E. M. , Wallace R. M.
Published: October 2009

The detection and removal of interfacial oxides on InGaAs semiconductors is of critical importance for their implementation as high-mobility channels for improved complementary metal oxide semiconductor device performance. X-ray photoelectron spectroscopy is a powerful tool to determine the chemical bonding at these interfaces. To correctly analyze these spectra, one must consider the binding energies and escape depths of the core-level electrons being detected, as monolayer level interfacial oxides (As–O and Ga–O) are detectable only in certain surface sensitive spectral regions. Also, inherent asymmetries associated with the In spectra must be taken into account for analysis of In-oxide bonding.
Alkaloids in Australian rye ergot (Claviceps purpurea) sclerotia: implications for food and stockfeed regulations
Authors: Blaney Barry J. , Molloy John B. , Brock Ian J.
Published: October 2009

Rye ergot (Claviceps purpurea) occasionally causes toxicity (chiefly expressed as hyperthermia) in Australian livestock, either as a result of grazing infected annual (Lolium rigidum) and perennial (L. perenne) rye grasses, or if the ergot sclerotia produced in rye grasses contaminate grain crops used as stockfood. Alkaloids in 30 samples of Australian rye ergot sclerotia taken from rye grasses and grain screenings, and some feed samples contaminated with rye grass ergot sclerotia, were assayed by high performance liquid chromatography. Samples originated from across southern Australia. Ergotamine was the dominant alkaloid in all samples, followed by α-ergocryptine, ergocornine, ergosine and their respective -imine epimers. Ergotamine concentrations in sclerotia ranged up to 2257 mg/kg (as received basis). Ergocristine was a very minor component (<50 mg/kg) in all samples. Total alkaloids in freshly collected sclerotia ranged from 1003 to 3321 mg/kg (0.10 to 0.33%), and up to 3766 mg/kg with epimers included, although lower concentrations were found in samples stored for some time. Alkaloid profiles in sclerotia were all very similar, and concentrations did not appear to be related to size of sclerotia, source region, nor to the rye grass or grain from which they were taken. Previous cases of toxicity in livestock are reviewed and several new cases are reported. The implications of variable alkaloid contents of rye ergot sclerotia are discussed in terms of Australian food and stockfeed regulations.
Physiological mechanism of low purine derivative excretion in urine of buffaloes compared with Bos taurus cattle
Authors: Thanh Vo Thi Kim , Orskov E. R. , Susmel P.
Published: October 2009

Three cattle calves (Bos taurus) and three buffalo calves (Bos bubalus) were weaned after receiving colostrum and then reared on bottle-fed milk. During the first month the animals did not have access to solid food. Urinary purine derivative concentration (PD), basal PD excretion and glomerular filtrate rate (GFR) were determined during fasting and feeding. After 1 month the animals were given access to solid feed (urea-treated rice straw 80% and molasses 20%) to stimulate rumen development. At 3 months of age, while the solid food was given, urinary PD, basal PD excretion and GFR were again determined. Urinary PD excretion both during fasting and milk feeding did not differ significantly between buffaloes and cattle during the milk-feeding period (P > 0.05), but there were highly significant (P < 0.01) differences between cattle and buffaloes after 3 months of age and 2 months of access to solid feed (P < 0.01). The GFR was lower in buffaloes than cattle in both the milk-fed and solid-feed periods (P < 0.05). It is suggested that the differences between buffaloes and cattle are due to differences in GFR as PD will stay longer in the blood and thus provide a greater possibility for recycling to the rumen. This, however, needs further confirmation. Whether permeability of PD from blood to rumen is an additional factor is not known.
A wave of nascent transcription on activated human genes
Authors: Wada Youichiro , Ohta Yoshihiro , Xu Meng , Tsutsumi Shuichi , Minami Takashi , Inoue Kenji , Komura Daisuke , Kitakami Jun'ichi , Oshida Nobuhiko , Papantonis Argyris , Izumi Akashi , Kobayashi Mika , Meguro Hiroko , Kanki Yasuharu , Mimura Imari , Yamamoto Kazuki , Mataki Chikage , Hamakubo Takao , Shirahige Katsuhiko , Aburatani Hiroyuki , Kimura Hiroshi , Kodama Tatsuhiko , Cook Peter R. , Ihara Sigeo
Published: October 2009

Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-α (TNFα) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at ≈3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites.
Tracking lineages of single cells in lines using a microfluidic device
Authors: Rowat Amy C. , Bird James C. , Agresti Jeremy J. , Rando Oliver J. , Weitz David A.
Published: October 2009

Cells within a genetically identical population exhibit phenotypic variation that in some cases can persist across multiple generations. However, information about the temporal variation and familial dependence of protein levels remains hidden when studying the population as an ensemble. To correlate phenotypes with the age and genealogy of single cells over time, we developed a microfluidic device that enables us to track multiple lineages in parallel by trapping single cells and constraining them to grow in lines for as many as 8 divisions. To illustrate the utility of this method, we investigate lineages of cells expressing one of 3 naturally regulated proteins, each with a different representative expression behavior. Within lineages deriving from single cells, we observe genealogically related clusters of cells with similar phenotype; cluster sizes vary markedly among the 3 proteins, suggesting that the time scale of phenotypic persistence is protein-specific. Growing lines of cells also allows us to dynamically track temporal fluctuations in protein levels at the same time as pedigree relationships among the cells as they divide in the chambers. We observe bursts in expression levels of the heat shock protein Hsp12-GFP that occur simultaneously in mother and daughter cells. In contrast, the ribosomal protein Rps8b-GFP shows relatively constant levels of expression over time. This method is an essential step toward understanding the time scales of phenotypic variation and correlations in phenotype among single cells within a population.
Bacillus subtilis
spreads by surfing on waves of surfactant
Authors: Angelini Thomas E. , Roper Marcus , Kolter Roberto , Weitz David A. , Brenner Michael P.
Published: October 2009

The bacterium
Bacillus subtilis
produces the molecule surfactin, which is known to enhance the spreading of multicellular colonies on nutrient substrates by lowering the surface tension of the surrounding fluid, and to aid in the formation of aerial structures. Here we present experiments and a mathematical model that demonstrate how the differential accumulation rates induced by the geometry of the bacterial film give rise to surfactant waves. The spreading flux increases with increasing biofilm viscosity. Community associations are known to protect bacterial populations from environmental challenges such as predation, heat, or chemical stresses, and enable digestion of a broader range of nutritive sources. This study provides evidence of enhanced dispersal through cooperative motility, and points to nonintuitive methods for controlling the spread of biofilms.
A genetic variation of the noradrenergic system is related to differential amygdala activation during encoding of emotional memories
Authors: Rasch B. , Spalek K. , Buholzer S. , Luechinger R. , Boesiger P. , Papassotiropoulos A. , de Quervain D. J.-F.
Published: October 2009

Emotionally arousing events are typically well remembered, but there is a large interindividual variability for this phenomenon. We have recently shown that a functional deletion variant of
ADRA2B
, the gene encoding the α2b-adrenergic receptor, is related to enhanced emotional memory in healthy humans and enhanced traumatic memory in war victims. Here, we investigated the neural mechanisms of this effect in healthy participants by using fMRI. Carriers of the
ADRA2B
deletion variant exhibited increased activation of the amygdala during encoding of photographs with negative emotional valence compared with noncarriers of the deletion. Additionally, functional connectivity between amygdala and insula was significantly stronger in deletion carriers. The present findings indicate that the
ADRA2B
deletion variant is related to increased responsivity and connectivity of brain regions implicated in emotional memory.
Fractional modelling applied to heat conductivity and diffusivity estimation
Authors: Gabano J D , Poinot T
Published: October 2009

Heat transfer in a homogeneous medium obeys diffusion phenomena, which can be modelled with the help of fractional systems. In this paper, we use fractional models based on an original fractional integrator whose order 1/2 acts only over a limited spectral band. These models, not linear in thermal parameters but linear in structural parameters, allow us to provide accurate simulations for transients with which it is possible to apply an output error technique to estimate the thermophysical parameters. Simulations of front face thermal characterization consisting of measuring the temperature at the surface of a material where a random heat flux is applied are carried out. These simulations allow us to validate the ability of the proposed estimation algorithms not only to rebuild the surface temperature but also to identify with a good accuracy the heat conductivity and diffusivity. Monte Carlo simulations are also performed in order to provide statistical properties of the thermal parameter estimates.
Constructing Weyl group multiple Dirichlet series
Authors: Chinta Gautam , Gunnells Paul
Published: October 2009

Let

Φ
\Phi

be a reduced root system of rank

r
r

. A Weyl group multiple Dirichlet series for

Φ
\Phi

is a Dirichlet series in

r
r

complex variables

s
1

,
…
,

s
r

s_1,\dots ,s_r

, initially converging for

R
e

(

s
i

)

\mathrm {Re}(s_i)

sufficiently large, that has meromorphic continuation to

C

r

{\mathbb C}^r

and satisfies functional equations under the transformations of

C

r

{\mathbb C}^r

corresponding to the Weyl group of

Φ
\Phi

. A heuristic definition of such a series was given by Brubaker, Bump, Chinta, Friedberg, and Hoffstein, and they have been investigated in certain special cases by others. In this paper we generalize results by Chinta and Gunnells to construct Weyl group multiple Dirichlet series by a uniform method and show in all cases that they have the expected properties.
Stable pairs and BPS invariants
Authors: Pandharipande R. , Thomas R.
Published: October 2009

We define the BPS invariants of Gopakumar-Vafa in the case of irreducible curve classes on Calabi-Yau 3-folds. The main tools are the theory of stable pairs in the derived category and Behrend’s constructible function approach to the virtual class. For irreducible curve classes, we prove that the stable pairs’ generating function satisfies the strong BPS rationality conjectures.

We define the contribution of each curve

C
C

to the BPS invariants and show that the contributions lie between the geometric genus and arithmetic genus of

C
C

. Complete formulae are derived for nonsingular and nodal curves.

A discussion of primitive classes on

K
3

K3

surfaces from the point of view of stable pairs is given in the Appendix via calculations of Kawai-Yoshioka. A proof of the Yau-Zaslow formula for rational curve counts is obtained. A connection is made to the Katz-Klemm-Vafa formula for BPS counts in all genera.
Detailing regulatory networks through large scale data integration
Authors: Huttenhower Curtis , Mutungu K. Tsheko , Indik Natasha , Yang Woongcheol , Schroeder Mark , Forman Joshua J. , Troyanskaya Olga G. , Coller Hilary A.
Published: October 2009

Motivation: Much of a cell's regulatory response to changing environments occurs at the transcriptional level. Particularly in higher organisms, transcription factors (TFs), microRNAs and epigenetic modifications can combine to form a complex regulatory network. Part of this system can be modeled as a collection of regulatory modules: co-regulated genes, the conditions under which they are co-regulated and sequence-level regulatory motifs.

Results: We present the Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction (COALESCE) system for regulatory module prediction. The algorithm is efficient enough to discover expression biclusters and putative regulatory motifs in metazoan genomes (>20 000 genes) and very large microarray compendia (>10 000 conditions). Using Bayesian data integration, it can also include diverse supporting data types such as evolutionary conservation or nucleosome placement. We validate its performance using a functional evaluation of co-clustered genes, known yeast and Escherichea coli TF targets, synthetic data and various metazoan data compendia. In all cases, COALESCE performs as well or better than current biclustering and motif prediction tools, with high accuracy in functional and TF/target assignments and zero false positives on synthetic data. COALESCE provides an efficient and flexible platform within which large, diverse data collections can be integrated to predict metazoan regulatory networks.

Availability: Source code (C++) is available at http://function.princeton.edu/sleipnir, and supporting data and a web interface are provided at http://function.princeton.edu/coalesce.

Contact:  ogt@cs.princeton.edu; hcoller@princeton.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.