bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of a tropospheric ozone anomaly using a newly developed ozone retrieval algorithm for an up‐looking infrared interferometer
Authors: Lightner K. J. , McMillan W. W. , McCann K. J. , Hoff R. M. , Newchurch M. J. , Hintsa E. J. , Barnet C. D.
Published: March 2009

On 2 June 2003, the Baltimore Bomem Atmospheric Emitted Radiance Interferometer (BBAERI) recorded an infrared spectral time series indicating the presence of a tropospheric ozone anomaly. The measurements were collected during an Atmospheric Infrared Sounder (AIRS) validation campaign called the 2003 AIRS BBAERI Ocean Validation Experiment (ABOVE03) conducted at the United States Coast Guard Chesapeake Light station located 14 miles due east of Virginia Beach, Virginia (36.91°N, 75.71°W). Ozone retrievals were performed with the Kurt Lightner Ozone BBAERI Retrieval (KLOBBER) algorithm, which retrieves tropospheric column ozone, surface to 300 mbar, from zenith‐viewing atmospheric thermal emission spectra. KLOBBER is modeled after the AIRS retrieval algorithm consisting of a synthetic statistical regression followed by a physical retrieval. The physical retrieval is implemented using the k‐Compressed Atmospheric Radiative Transfer Algorithm (kCARTA) to compute spectra. The time series of retrieved integrated ozone column on 2 June 2003 displays spikes of about 10 Dobson units, well above the error of the KLOBBER algorithm. Using instrumentation at Chesapeake Light, satellite imaging, trace gas retrievals from satellites, and Potential Vorticity (PV) computations, it was determined that these sudden increases in column ozone likely were caused by a combination of midtropospheric biomass burning products from forest fires in Siberia, Russia, and stratospheric intrusion by a tropopause fold occurring over central Canada and the midwestern United States.
Implementation of the Community Radiative Transfer Model in Advanced Clear‐Sky Processor for Oceans and validation against nighttime AVHRR radiances
Authors: Liang Xing‐Ming , Ignatov Alexander , Kihai Yury
Published: March 2009

The fast Community Radiative Transfer Model (CRTM) has been integrated into National Environmental Satellite Data and Information Service's newly developed Advanced Clear‐Sky Processor for Oceans (ACSPO). CRTM is used in conjunction with the National Centers for Environmental Prediction (NCEP) Global Forecast System atmospheric profiles and Reynolds weekly version 2 sea surface temperatures (SST) to simulate clear‐sky brightness temperatures (BT). Model BTs are used to improve the ACSPO clear‐sky mask, monitor quality of advanced very high resolution radiometer (AVHRR) BTs, and explore physical SST retrievals. This paper documents CRTM implementation in ACSPO version 1 and evaluates nighttime “model minus observation” (M‐O) BT biases in three bands (3.7, 11, and 12 μm) of four AVHRR/3 instruments onboard NOAA‐16, NOAA‐17, NOAA‐18, and MetOp‐A. With careful treatment of input atmospheric and SST data, the agreement is generally good, showing only weak dependencies of M‐O biases on view zenith angle, column water vapor, and wind speed. The agreement improves if Reynolds weekly SST is used instead of NCEP SST. Including surface reflection also reduces the M‐O bias. After all optimizations, the M‐O biases are within several tenths of a Kelvin. Consistency between different platforms is ∼0.1K, except for NOAA‐16 channel 3B, which is biased low compared to other platforms by ∼0.4K. Our future plans include extending the analyses to daytime data and exploring physical SST retrievals. A web‐based tool is being established to continuously monitor the M‐O biases and physical SSTs. The validation methodology employed in this paper will be used to quantitatively measure the effect of each improvement on the M‐O bias and physical SST.
Dendrochemistry of White Mountain bristlecone pines: An investigation via Synchrotron Radiation Scanning X‐Ray Fluorescence Microscopy
Authors: Pearson C. L. , Dale D. S. , Brewer P. W. , Salzer M. W. , Lipton J. , Manning S. W.
Published: March 2009

Synchrotron Radiation Scanning X‐Ray Fluorescence Microscopy (SXFM) was used for the first spatially/temporally resolved investigation of the multielemental chemistry of bristlecone pine (Pinus longaeva D.K. Bailey). A new protocol was designed to apply this nondestructive method of analysis to this unique palaeoclimatological resource, extracting previously inaccessible dendrochemical information at subannual resolution from tree rings ranging from 1400 to 40 μm. The potential of Pinus longaeva was assessed for the reconstruction of multicentennial annual resolution sequences of elemental change, with specific focus on the identification of multielemental markers for major, climatically effective volcanic eruptions. Increases in calcium (Ca), strontium (Sr), manganese (Mn), and zinc (Zn) were identified in association with frost rings around AD1601, following the eruption of Huaynaputina, Peru, but these could not be directly attributed to volcanogenic changes in environmental chemistry. Elemental patterns for 500 years from five trees demonstrated little agreement indicating that, for the elements detected, this species may be unsuitable for temporal reconstructions of external chemistry. Further development of SXFM dendrochemical technique, however, offers much potential for future work.
Export of inorganic carbon from two Southeast Asian mangrove forests to adjacent estuaries as estimated by the stable isotope composition of dissolved inorganic carbon
Authors: Miyajima Toshihiro , Tsuboi Yoshie , Tanaka Yoshiyuki , Koike Isao
Published: March 2009

The influence of mangrove forests on the dynamics of dissolved inorganic carbon (DIC) in tropical estuaries was estimated quantitatively using newly developed isotope (δ13C) mass balance models that take into account both the input of DIC and the air‐water exchange of CO2. To this aim, the concentration and δ13C of DIC were determined across the salinity gradient of two river estuaries facing the Andaman Sea. The longitudinal distribution of DIC could be explained by conservative mixing of the river water and seawater DIC in the low‐discharge period (March 2006), while a net accumulation of DIC up to 190 μmol L−1 was observed in the high‐discharge period (December 2006). δ13CDIC values were generally lower than expected for the mixing of the river water and seawater DIC, due to the 13C‐depleted DIC inputs from the riverside mangroves. The concentration of mangrove‐derived DIC in the estuarine waters was estimated by the proposed models to be as much as 856 μmol L−1, and was higher during the low‐discharge period. This suggested that the mangroves exported much higher levels of DIC to the estuaries than indicated by the net accumulation of DIC. Our results confirm that mangroves function as an effective CO2 pump that takes CO2 from the atmosphere and releases it into estuarine waters. This study illustrates that δ13CDIC is a sensitive and quantitative indicator for DIC emission to the sea from coastal wetlands including mangroves.
Evidence of Tropospheric Effects on the Ionosphere
Authors: Immel Thomas J. , Mende Stephen B. , Hagan Maure E. , Kintner Paul M. , England Scott L.
Published: March 2009

A new paradigm in upper atmospheric and ionospheric physics has begun to emerge, starting with discoveries from observations taken with the Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE) satellite in 2002. These discoveries [Immel et al., 2006] show that the entire ionosphere, sometimes referred to as “the inner edge of space,” regularly responds to the tropospheric weather systems below. The likely mechanism for effectively carrying tropospheric energy upward to the edge of space to modify the ionosphere is the generation and upward propagation of large‐scale waves, known as atmospheric tides. The coupling of these tides to the ionosphere is inferred from the strong similarity in longitudinal structure of the tidal winds and the ionospheric densities at low latitudes. However, the appearance of this behavior in the upper ionosphere is surprising because the tides that are forced by tropospheric weather are believed to dissipate at the base of the ionosphere and are expected to have little effect at higher altitudes.
Enzyme Mechanisms: Fast Reaction and Computational Approaches
Authors: Munro Andrew W. , Scrutton Nigel S.
Published: March 2009

Now, more than ever, enzymology and its development can be considered of vital importance to the progression of the biological sciences. With an increase in the numbers of enzymes being identified from genomic studies, enzymology is key to defining the structural and functional properties of these enzymes in order to establish their mechanisms of action and how they fit into metabolic networks. Along with the efforts of the bioinformaticians and systems biologists, such studies will ultimately lead to detailed descriptions of intricate biochemical pathways and allow identification of the most appropriate target enzymes for intervention in disease therapy. Thus the timing for the recent Biochemical Society Focused Meeting entitled ‘Enzyme Mechanisms: Fast Reaction and Computational Approaches’ was highly appropriate. The present paper represents an overview of this meeting, which was held at the Manchester Interdisciplinary Biocentre on 9–10 October 2008.
The petite purple photosynthetic powerpack
Authors: Jones Michael R.
Published: March 2009

Photoreaction centres are Nature's solar batteries. These nanometre-scale power producers are responsible for transducing the energy of sunlight into a form that can be used by biological systems, thereby powering most of the biological activity on the planet. Although to the layman the word ‘photosynthesis’ is usually associated with green plants, much of our understanding of the molecular basis of biological transduction of light energy has come from studies of purple photosynthetic bacteria. Their RCs (reaction centres) and attendant light-harvesting complexes have been subjected to an intensive spectroscopic scrutiny, coupled with genetic manipulation and structural studies, that has revealed many of the molecular and mechanistic details of biological energy transfer, electron transfer and coupled proton translocation. This review provides a short overview of the structure and mechanism of the purple bacterial RC, focusing in the main on the most heavily studied complex from Rhodobacter sphaeroides.
The single-nucleotide primer extension (SNuPE) method for the multiplex detection of various DNA sequences: from detection of point mutations to microbial ecology
Authors: Nikolausz Marcell , Chatzinotas Antonis , Táncsics András , Imfeld Gwenaël , Kästner Matthias
Published: March 2009

Methods based on SNuPE (single-nucleotide primer extension) have become invaluable tools for the rapid and highly specific detection of point mutations and single-nucleotide polymorphisms in the field of human genetics. In the primer extension reaction, a DNA polymerase is used to label a specific primer hybridized to the target sequence by incorporating a single labelled ddNTP (dideoxynucleotide). This labelling provides not only information about the complementary nucleotide of interest in the opposite strand but also a semiquantitative analysis of the sequence targeted by the primer. Since several subdisciplines of microbiology increasingly require cultivation-independent molecular screening tools for elucidating differences between either strains or community structures based on sequence variations of marker genes, SNuPE offers a promising alternative to the existing tool box. The present review describes the method in detail and reports the state-of-the-art applications of this technique both in the field of nucleic acid detections in human genetics and in microbiology.
Dissolved oxygen alteration of the spectrophotometric analysis and quantification of nucleic acid solutions
Authors: Doshi Rupak , Day Philip J.R. , Tirelli Nicola
Published: March 2009

Nucleic acids are routinely and readily analysed using the A260/A280 ratio, although this method is known to be prone to erroneous results owing to contaminants in solution that absorb at similar wavelengths. The aim of the present review, while highlighting the problems and alternatives of using UV spectrophotometry for nucleic acid measurements, is to bring forth an observational result from our recent studies, namely that DO (dissolved oxygen) and nitrogen can alter the A260 of aqueous DNA solutions. Our finding is of importance because DO is highly variable between protocols and storage conditions of DNA preparations. The physicochemical nature of the oxygen–DNA interactions is briefly discussed.
Real-time DNA microarrays: reality check
Authors: Chagovetz Alexander , Blair Steve
Published: March 2009

DNA microarrays are plagued with inconsistent quantifications and false-positive results. Using established mechanisms of surface reactions, we argue that these problems are inherent to the current technology. In particular, the problem of multiplex non-equilibrium reactions cannot be resolved within the framework of the existing paradigm. We discuss the advantages and limitations of changing the paradigm to real-time data acquisition similar to real-time PCR methodology. Our analysis suggests that the fundamental problem of multiplex reactions is not resolved by the real-time approach itself. However, by introducing new detection chemistries and analysis approaches, it is possible to extract target-specific quantitative information from real-time microarray data. The possible scope of applications for real-time microarrays is discussed.
Perpendicular anisotropy and oscillatory interlayer coupling in Fe0.5Co0.5/Rh/Fe0.5Co0.5 bilayers on Rh(001)
Authors: Yildiz F. , Przybylski M. , Kirschner J.
Published: March 2009

Tetragonal distortion in Fe0.5Co0.5 alloy films grown epitaxially on Rh(001) substrates results in an easy magnetization axis perpendicular to the film plane up to the thickness of 17 ML. The distortion is supported by a Rh-overlayer; thus the strong perpendicular anisotropy can be kept when another Fe0.5Co0.5 film is grown on top of the Rh/Fe0.5Co0.5/Rh(001) structure. Depending on the thickness of the Rh spacer, the top and bottom Fe0.5Co0.5 films are either ferro- or antiferromagnetically coupled. The net magnetization of the antiferromagnetically coupled Fe0.5Co0.5/Rh/Fe0.5Co0.5 bilayer switches at the field which depends on the difference between magnetizations of both the Fe0.5Co0.5 layers. The final covering of the Fe0.5Co0.5/Rh/Fe0.5Co0.5/Rh(001) structure with Rh increases the switching field. The effect is explained by a locally enhanced magnetization in the Rh/Fe1−xCox interfaces.
Spatially resolved spectroscopy of MgO–Fe(100)–MgO(100) structure
Authors: Lee Jookyung , Krafft Charles , Gomez R. D.
Published: March 2009

Using scanning tunneling spectroscopy and microscopy, the local density of electronic states was correlated with the topography of Fe on MgO and MgO on Fe. The growth mode of Fe on MgO is by island formation that leads to an electronically inhomogeneous surface. Fe (100) surface states were observed on flat terraces that diminish at the step edges, while bandgaps were observed in some deep trenches that separate the islands. MgO on Fe (100), on the other hand, grows by the simpler layer-by-layer mode. The electronic states evolved as a function of thickness from less than one to several monolayers. The bulklike MgO behavior with more than 6 V bandgap was found for the thickest films (∼1 nm). However, the spectra for very thin MgO depended upon whether it was measured on top of Fe atoms or on the MgO grains. At one monolayer, the measured density of states was different from either very thick or very thin MgO, which suggests the possibility of an interfacial layer that is distinct from the Fe (100) and MgO (100) surfaces. The observed local inhomogeneity may account for the reduced tunneling magnetoresistance of these systems.
Functionalization-induced improvement in magnetic properties of Fe3O4 nanoparticles for biomedical applications
Authors: Nagesha Dattatri K. , Plouffe Brian D. , Phan Minh , Lewis Laura H. , Sridhar Srinivas , Murthy Shashi K.
Published: March 2009

Fe 3 O 4 were synthesized nanoparticles by thermal decomposition method with oleic acid as the surfactant, and to make them suitable for aqueous environments, dopamine ligand exchange was carried out on the particles. The nanoparticle size and phase was quantified by transmission electron microscopy (TEM) and x-ray diffraction (XRD), respectively. Superconducting quantum interference device magnetometry confirmed superparamagnetic behavior in both nanoparticles. A surprising and significant increase in the remanence MR, saturation magnetization MS, and blocking temperature TB of the particles was found after dopamine functionalization, even though TEM and XRD studies revealed no change in the particles’ size and/or structure. The results are consistent with an increase in the magnetic size of the nanoparticle core induced by the dopamine ligand exchange process. These effects are tentatively attributed to surface bonding effects that alter the canted magnetic state of the Fe3O4 nanoparticles.
Measurement of thin film permeability by direct contact and optimization
Authors: Yabukami S.
Published: March 2009

A highly sensitive method for obtaining the permeability of magnetic film without a limitation of sample size was developed based on the electrical impedance of magnetic film in contact with a copper conductor. The permeability of a CoNbZr thin film (25×25 mm2, 4 μm thick) was evaluated in the frequency range of 10 MHz–4 GHz, the measured values roughly corresponding to those obtained by the Landau–Lifshitz–Gilbert equation. The proposed method shows promise for permeability measurement of wafer-sized samples because the method is free of size limitation.
Exchange-coupled suppression of vortex formation in permalloy nanodot chain arrays
Authors: Hernandez Sarah C. , Dou Jian , Yu Chengtao , Pechan Michael J. , Folks Liesl , Katine Jordan A. , Carey Matthew J.
Published: March 2009

The effect of interdot exchange coupling on the magnetization reversal processes in nanodots has been investigated in a study on permalloy dot arrays with dot diameters of 300 nm and thicknesses of 40 nm. The dots, fabricated using e-beam lithography and ion beam deposition, are exchange coupled via 50 nm long permalloy bridges of widths ranging from 0 to 60 nm. Chains of five collinear coupled dots form the unit cell of the array structure. Magneto-optical Kerr effect hysteresis loops are reported with comparison to simulations. With field applied along the coupling direction, vortex nucleation occurs sequentially from the outer to the inner dots of the chain. Compared with uncoupled dots, nucleation is suppressed by the interdot exchange coupling resulting in highly correlated magnetization patterns. Buildup of exchange energy in the inner dots ultimately drives the bridge magnetization to switch, followed by abrupt, simultaneous vortex nucleation in these dots. Along the perpendicular-to-the-coupling direction, the exchange interaction has little effect and magnetic reversal is almost identical to arrays of isolated dots of the same geometry.
Landau–Lifshitz–Gilbert study of the effect of pulse width on spin-transfer torque magnetization switching
Authors: Sugano R. , Ichimura M. , Takahashi S. , Maekawa S.
Published: March 2009

We studied the effect of a current pulse width on current-induced magnetization switching in magnetic tunnel junctions based on a macrospin model of the free layer. We performed finite temperature Langevin simulations of the Landau–Lifshitz–Gilbert–Slonczewski equation with an additional spin-torque term. By evaluating the switching current density, we obtained the diagram in the plane of the critical current density and the pulse width at 300 K. As the pulse width increased, we observed an adiabatic regime in the shorter pulse widths, an intermediate crossover regime, and a thermally activated regime in long pulse widths. We found that the easy-plane anisotropy field shifts the crossover pulse width to the lower pulse width, suggesting that the reversed region is enhanced by controlling the device shape. Our results are consistent with those of recent experiments over the pulse widths ranging from 10−1 to 105 ns.
Magnetic characterization of ultrathin EuO films with XMCD
Authors: Negusse Ezana , Dvorak J. , Holroyd J. S. , Liberati M. , Santos T. S. , Moodera J. S. , Arenholz E. , Idzerda Y. U.
Published: March 2009

We present work done on EuO films with thicknesses varying from 10 to 60 Å grown as a stepped wedge on Si/SiO2/Cr(20 Å)/Cu(90 Å) and capped with Y(20 Å)/Al(80 Å). The films were characterized by x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD) at the europium M5 and copper L3 edges. The films' high quality and consistent magnetic properties were confirmed by superconducting quantum interference device magnetometry, which revealed a constant saturation moment independent of film thickness. XAS at the Cu L3 edge showed that the bottom Cu electrode is metallic (oxidation free). We report an XMCD intensity of 52% (±4.3), in excellent agreement with theoretical calculations.
Spin Hall effect in Molybdenum wires
Authors: Morota M. , Ohnishi K. , Kimura T. , Otani Y.
Published: March 2009

The spin Hall effect in molybdenum wires has been experimentally investigated by means of spin absorption method using lateral spin valve structure. The spin Hall conductivity of Mo wire is negative and decreases with increasing the resistivity. These tendencies are surprisingly consistent with the recent theoretical calculation based on the intrinsic spin Hall effect.
Poly(styrene-co-vinylbenzylchloride-co-divinylbenzene) coated iron oxide: Synthesis and effects on size and morphology
Authors: Shultz M. D. , Marin J. R. , Naik S. H. , Wilkins J. , Laza J. M. , Vilas J. L. , Rodriguez M. , Perez N. , Carpenter E. E.
Published: March 2009

Iron oxide nanoparticles were coated with a polymer synthesized from the monomers of styrene, divinylbenzene, and vinylbenzylchloride. The resultant polymer microspheres from synthesis without nanoparticle loading are primarily monodispersed with a diameter of 3.45 μm as measured by scanning electron microscopy. The addition of 1% nanoparticles by mass appears to decrease the size of the microspheres down to 2.04 μm as well as increase the polydispersity. This trend is also seen to continue as you add more nanoparticles to the system going from 3.45 μm with 0% nanoparticles down to below 1 μm for 5% nanoparticles. This indicates that the particles are not just incorporated into the polymer matrix but act as nucleation sites to begin the polymerization process. The polymerization process was found to have no effect on the nanoparticles themselves as the magnetic characterization showed only a mass dilution in saturation when corrected by thermal gravimetric analysis.
Optical properties of a-plane InGaN/GaN multiple quantum wells on r-plane sapphire substrates with different indium compositions
Authors: Chiu C. H. , Kuo S. Y. , Lo M. H. , Ke C. C. , Wang T. C. , Lee Y. T. , Kuo H. C. , Lu T. C. , Wang S. C.
Published: March 2009

A -plane InxGa1−xN/GaN (x=0.09, 0.14, 0.24, and 0.3) multiple-quantum-wells (MQWs) samples, with a well width of about 4.5 nm, were achieved by utilizing r-plane sapphire substrates. Optical quality was investigated by means of photoluminescence (PL), cathodoluminescence, and time resolved PL measurements (TRPL). Two distinguishable emission peaks were examined from the low temperature PL spectra, where the high- and low-energy peaks were ascribed to quantum wells and localized states, respectively. Due to an increase in the localized energy states and absence of quantum confined Stark effect, the quantum efficiency was increased with increasing indium composition up to 24%. As the indium composition reached 30%, however, pronounced deterioration in luminescence efficiency was observed. The phenomenon could be attributed to the high defect densities in the MQWs resulted from the increased accumulation of strain between the InGaN well and GaN barrier. This argument was verified from the much shorter carrier lifetime at 15 K and smaller activation energy for In0.3Ga0.7N/GaN MQWs. In addition, the polarization-dependent PL revealed that the degree of polarization decreased with increasing indium compositions because of the enhancement of zero-dimensional nature of the localizing centers. Our detailed investigations indicate that the indium content in a-plane InGaN/GaN MQWs not only has an influence on optical performance, but is also important for further application of nitride semiconductors.
Structure of the dissipation region in fluid simulations of asymmetric magnetic reconnection
Authors: Cassak P. A. , Shay M. A.
Published: March 2009

The structure of the dissipation region during asymmetric magnetic reconnection is studied assuming antiparallel magnetic fields in two dimensions. A physics-based prediction for the scaling of the thickness of the dissipation region in (collisionless) Hall reconnection is presented and confirmed with two-fluid simulations. However, the substructure of the dissipation region in these and additional single-fluid (magnetohydrodynamics) simulations disagrees with a recent model [Cassak and Shay, Phys. Plasmas 14, 102114 (2007)]. We attribute the disagreement to the lack of plasma mixing along newly reconnected field lines in fluid models, rendering the use of a fluid description of questionable validity for determining the dissipation region substructure. Applications to the dayside magnetopause are discussed.
Henry’s law, surface tension, and surface adsorption in dilute binary mixtures
Authors: Onuki Akira
Published: March 2009

Equilibrium properties of dilute binary fluid mixtures are studied in two-phase states on the basis of a Helmholtz free energy including the gradient free energy. The solute partitioning between gas and liquid (Henry’s law) and the surface tension change Δγ are discussed. A derivation of the Gibbs law Δγ=−TΓ is given with Γ being the surface adsorption. Calculated quantities include the derivatives dTc/dX and dpc/dX of the critical temperature and pressure with respect to the solute molar fraction X and the temperature-derivative (∂γ/∂T)cx,p of the surface tension at fixed pressure p on the coexistence surface. Here (∂γ/∂T)cx,p can be both positive and negative, depending on the solute molecular size and the solute-solvent interaction, and diverges on the azeptropic line. Explicit expressions are given for all these quantities in the van der Waals model.
Probing the proton location in a water bilayer on Pd (111) by inelastic spectroscopy simulations
Authors: Bocquet Marie-Laure , Lorente Nicolás
Published: March 2009

First-principles inelastic electron tunneling spectroscopy simulations give distinct signals for different phases of a water bilayer on a Pd (111) surface. Based on our recent electrochemical modeling of the water-Pd interface, we report on elastic and inelastic scanning tunneling microscopy simulations on two ice phases. Both phases exhibit only two tunneling-active optical phonons: the one corresponding to a stretching mode at higher frequency and the rocking/wagging one at lower frequency. However, the inelastic efficiencies at the phonon thresholds are very different between phases, enabling the discrimination of ice phases on metal surfaces.
Two-dimensional envelope electron-acoustic waves under transverse perturbations
Authors: Gill Tarsem Singh , Bedi Chanchal , Bains Amandeep Singh
Published: March 2009

As is well known, the envelope electron-acoustic (EA) nonlinear waves in one dimension are governed by the nonlinear Schrödinger equation. If transverse perturbations are considered, then this type of nonlinear wave can be described by the general form of the Davey–Stewartson equation. In this work, modulational properties of EA wave and its stability regions in two-dimensional plasma have been studied.
Harmonically forced enclosed swirling flow
Authors: Cui Y. D. , Lopez J. M. , Lim T. T. , Marques F.
Published: March 2009

The response of steady state vortex flows in an enclosed circular cylinder driven by the harmonic modulation of the rotating end wall is investigated experimentally and numerically. Three dynamic regimes have been identified, with a continuous variation in forcing frequency between them. For very low forcing frequency, the synchronous flow approaches quasistatic adjustment, and for very large forcing frequencies the oscillations in the synchronous flow are localized in the boundary layers on the various cylinder walls. These localized wall oscillations drive the synchronous flow in the cylinder interior to the underlying axisymmetric steady basic state. The third regime occurs for forcing frequencies in the range of the most dangerous axisymmetric Hopf eigenfrequencies, with the 1:1 resonances leading to greatly enhanced oscillation amplitudes localized in the axis region where the flow manifests vortex breakdown recirculation zones.
Nonlinear evolution of the Weibel instability of relativistic electron beams
Authors: Shvets Gennady , Polomarov Oleg , Khudik Vladimir , Siemon Carl , Kaganovich Igor
Published: March 2009

Physics of the long-term evolution of the Weibel instability (WI) of an electron beam propagating through the plasma is described. Several phenomena occurring during the WI are identified: (i) the exponential growth stage resulting in beam breakup into small current filaments; (ii) merger of the small filaments and beam particles’ trapping inside them; (iii) filaments’ compression and expulsion of the ambient plasma from the filaments; (iv) formation of high-current filaments and their merger. It is shown that during the final stage these beam filaments can carry super-Alfvenic currents and form hollow current density profiles similar to the Hammer–Rostoker equilibrium. This explains why the initially increasing magnetic field energy eventually decreases during the late stage of the instability. Different computational approaches to modeling both collisionless and collisional WI are also described.
Hopf bifurcations in the wake of a square cylinder
Authors: Sau Amalendu
Published: March 2009

In the present numerical study we report growths of four different unsteady modes of Hopf bifurcations in the wake of a square cylinder. Extensive three-dimensional simulations of the flow are conducted with six different Reynolds numbers (60, 100, 115, 125, 200, and 300) and three different (nondimensional) cylinder lengths (7.5, 10, and 12). At a near-critical Reynolds number (Re), 60, the initiation of near-wake spanwise pressure oscillation along the coreline of the shedded vortices, and formation of a local pressure maximum over its midsection led to the growth of a single mode Hopf bifurcation. At Re=100, the enhanced spanwise oscillation of pressure, and the resultant occurrence of two distinct local pressure maxima along the vortex corelines facilitated the growth of a second mode. For 100≤Re≤125 the spanwise wake was noted evolve predominantly through this nearly symmetrically distributed second mode. As the Reynolds number gradually increased, the spanwise asymmetric pressure and velocity oscillations along the vortex corelines gained momentum, and owing to enhanced flow instability, higher order bifurcation modes started to grow. For supercritical transitional flows with Re≥200 there occurred frequent switching between the transient bifurcation modes, and the instantaneous wake thereby evolved through single/multiple modes of Hopf bifurcations with variable length scales. The growth of a number of local pressure maxima over the spanwise extended vortex corelines and gradual decrease in pressure along their two sides are found to be responsible for initiating these bifurcations. Our study further reveals that the formation of a Karman vortex street in the supercritical transitional regime is essentially governed by the spontaneous generations of sequences of Hopf bifurcations in the near wake.
Replica exchange statistical temperature Monte Carlo
Authors: Kim Jaegil , Keyes Thomas , Straub John E.
Published: March 2009

The replica exchange statistical temperature Monte Carlo algorithm (RESTMC) is presented, extending the single-replica STMC algorithm [J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601 (2006)] to alleviate the slow convergence of the conventional temperature replica exchange method (t-REM) with increasing system size. In contrast to the Gibbs–Boltzmann sampling at a specific temperature characteristic of the standard t-REM, RESTMC samples a range of temperatures in each replica and achieves a flat energy sampling employing the generalized sampling weight, which is automatically determined via the dynamic modification of the replica-dependent statistical temperature. Faster weight determination, through the dynamic update of the statistical temperature, and the flat energy sampling, maximizing energy overlaps between neighboring replicas, lead to a considerable acceleration in the convergence of simulations even while employing significantly fewer replicas. The performance of RESTMC is demonstrated and quantitatively compared with that of the conventional t-REM under varying simulation conditions for Lennard-Jones 19, 31, and 55 atomic clusters, exhibiting single- and double-funneled energy landscapes.
Proton radiography of dynamic electric and magnetic fields in laser-produced high-energy-density plasmas
Authors: Li C. K. , Séguin F. H. , Frenje J. A. , Manuel M. , Casey D. , Sinenian N. , Petrasso R. D. , Amendt P. A. , Landen O. L. , Rygg J. R. , Town R. P. J. , Betti R. , Delettrez J. , Knauer J. P. , Marshall F. , Meyerhofer D. D. , Sangster T. C. , Shvarts D. , Smalyuk V. A. , Soures J. M. , Back C. A. , Kilkenny J. D. , Nikroo A.
Published: March 2009

Time-gated, monoenergetic-proton radiography provides unique measurements of the electric (E) and magnetic (B) fields produced in laser-foil interactions and during the implosion of inertial-confinement-fusion capsules. These experiments resulted in the first observations of several new and important features: (1) observations of the generation, decay dynamics, and instabilities of megagauss B fields in laser-driven planar plastic foils, (2) the observation of radial E fields inside an imploding capsule, which are initially directed inward, reverse direction during deceleration, and are likely related to the evolution of the electron pressure gradient, and (3) the observation of many radial filaments with complex electromagnetic field striations in the expanding coronal plasmas surrounding the capsule. The physics behind and implications of such observed fields are discussed.
Comparison between integrated and parallel tempering methods in enhanced sampling simulations
Authors: Yang Lijiang , Shao Qiang , Gao Yi Qin
Published: March 2009

Recently, we introduced an integrated tempering approach to enhance sampling in the energy and configuration space for large systems. In this paper, we show that this new method has a higher efficiency than bias potential and generalized ensemble methods, such as accelerated molecular dynamics and replica-exchange molecular dynamics (parallel tempering) methods, in yielding thermodynamic averages. Particularly, the sampling efficiencies in both energy and configuration spaces are compared in details between integrated and parallel tempering methods. Related issues regarding the efficiency involved in the usage of the parallel tempering method are also discussed.
Nonadiabatic coupling vectors within linear response time-dependent density functional theory
Authors: Tavernelli Ivano , Tapavicza Enrico , Rothlisberger Ursula
Published: March 2009

A method is developed to compute the nonadiabatic coupling vectors (NACVs) between electronic ground and excited states as well as between any possible pair of excited states within the framework of linear response time-dependent density functional theory (TDDFT) in the adiabatic approximation. The development is an extension to our previous work on surface hopping dynamics [E. Tapavicza et al., Phys. Rev. Lett. 98, 023001 (2007)] for which we improve the description of the TDDFT approximation of the excited state wavefunctions by means of linear response orbitals. The method is first validated on the H+H2 system that has a region of strong coupling near the conical intersection at the equilateral geometry. These results confirm the quality and the numerical efficiency of the approach, which has an accuracy comparable to the one achieved with wavefunction-based methods. Finally, we apply the method to the calculation of the NACVs of protonated formaldimine (NH2CH2+) along a surface hopping trajectory initiated in the second excited state.
Magnetic semiconducting diode of p-Ge1−xMnx/n-Ge layers on silicon substrate
Authors: Majumdar S. , Das A. K. , Ray S. K.
Published: March 2009

We have synthesized Ge-based magnetic diode composed of a Mn-doped Ge film grown on lightly As-doped Ge on silicon substrate. p-Ge1−xMnx/n-Ge heterostructure behaves like a conventional diode under forward and reverse biases and works like a spin valve below Curie temperature (∼50 K) under zero (B=0) and nonzero (B=300 mT) magnetic fields at forward bias (+2 V). A hysteretic behavior of p-n junction current with small coercive magnetic field implies the nonvolatility of the diode. Thus, a single element of p-Ge1−xMnx/n-Ge on silicon substrate deserves nonvolatility, rectification, and spin-valve-like functionality.
From Cu2(OH)3Cl to nanostructured sisal-like Cu(OH)2 and CuO: Synthesis and characterization
Authors: Jia Wenzhao , Reitz Eliot , Sun Hui , Li Baikun , Zhang Heng , Lei Yu
Published: March 2009

Cu 2 ( OH ) 3 Cl with an average size of 5–10 μm have been synthesized by a simple hydrothermal reaction with a yield of ∼100%. After the as-prepared Cu2(OH)3Cl was treated with NaOH solution, the green crystals were converted to blue sisal-like Cu(OH)2 with needle-like nanorods pointing out radially from the core. These nanorods were about 100–200 nm in diameter and 10 μm in length. Using the sisal-like Cu(OH)2 as sacrificial precursor, CuO with a well-preserved morphological feature of the precursor was formed through thermal treatment. The samples were characterized by scanning electron microscopy, energy dispersive X-ray, X-ray diffraction, X-ray photoelectron spectroscopy, BET nitrogen adsorption, and UV-visible absorption spectroscopy. The conversion of the synthesized Cu2(OH)3Cl to sisal-like Cu(OH)2 was optically visualized and confirmed by corresponding SEM images, and an “etching-and-growing” mechanism was proposed. The results also show that the as-prepared CuO possesses a band gap of 2.27 eV and high specific surface area (75.8 m2/g), and its surface is highly rich in O.
Influence of A-site size and disorder on metamagnetic transformation in A-site substituted Pr0.5Ca0.5MnO3
Authors: Zhu Deliang , Tan Xiaoan , Cao Peijiang , Jia Fang , Ma Xiaocui , Lu Youming
Published: March 2009

The influence of A-site size and disorder on metamagnetic transformation in polycrystalline Pr0.5−xLaxCa0.5MnO3 and Pr0.5Ca0.5−xBaxMnO3 at low temperature has been systematically investigated. The introduction of larger A-site cations such as La3+ or Ba2+ will locally suppress the lattice distortion. This “counterdistortion” effect becomes more pronounced with the increase in the A-site average ionic radius ⟨rA⟩, which is favorable to ferromagnetism. Thus the critical field HC1 corresponding to the first sharp metamagnetic step will decrease, and the field-induced magnetization M5 T will increase. However, the A-site ionic radii variance σ2 will dramatically increase when more barium is introduced and a spin glasslike state is induced, which is unfavorable to the stability of ferromagnetism state. Therefore, HC1 will increase and M5 T will decrease. Moreover, the evolution of resistivity at low temperature with σ2 exhibits strong correlation with that of magnetic properties.
Correlation between sputtering parameters and composition of SmCo-based films for microelectromechanical system applications
Authors: Peng Long , Zhang Huaiwu , Yang Qinghui , Li Yuanxun , Song Yuanqiang , Shen Jian
Published: March 2009

About 3.0 μm thick SmCo-based films with additives of Fe, Cu, and Zr were deposited on Si substrates. Based on a developed semiempirical theoretical model, the dependence of the film composition on the sputtering parameters was discussed. The experimental results show that the Sm concentration increases with decreasing sputtering power or increasing Ar gas pressure, which are in good agreement with the calculated results when the preferential sputtering effect is disregarded. The effect of the sputtering parameters on the film composition provides an opportunity for the same composite target to fabricate films with Sm concentration varying from 13.8 to 17.3 at. %, which is reasonable for the permanent magnetic phase transformation (Sm2Co17→SmCo7→SmCo5). Furthermore, the observed TbCu7-type film shows a better crystal texture with a low remanence ratio for the hysteresis loops measured out plane to in plane of 0.08.
Carbon-deuterium vibrational probes of peptide conformation: Alanine dipeptide and glycine dipeptide
Authors: Miller C. S. , Ploetz E. A. , Cremeens M. E. , Corcelli S. A.
Published: March 2009

The utility of α-carbon deuterium-labeled bonds (Cα–D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: Cα–D labeled alanine dipeptide (Adp-d1) and Cα–D2 labeled glycine dipeptide (Gdp-d2). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d1 and Gdp-d2, we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of φ and ψ, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5° spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic Cα–D and Cα–D2 stretch transition frequencies for each structure. For Adp-d1 the Cα–D stretch frequency exhibited a maximum variability of 39.4 cm−1 between the six stable structures identified in the gas phase. The Cα–D2 frequencies of Gdp-d2 show an even more substantial difference between its three stable conformations: there is a 40.7 cm−1 maximum difference in the symmetric Cα–D2 stretch frequencies and an 81.3 cm−1 maximum difference in the asymmetric Cα–D2 stretch frequencies. Moreover, the splitting between the symmetric and asymmetric Cα–D2 stretch frequencies of Gdp-d2 is remarkably sensitive to its conformation.
High-performance, fully transparent, and flexible zinc-doped indium oxide nanowire transistors
Authors: Zhang W. F. , He Z. B. , Yuan G. D. , Jie J. S. , Luo L. B. , Zhang X. J. , Chen Z. H. , Lee C. S. , Zhang W. J. , Lee S. T.
Published: March 2009

We report the fabrication of fully transparent and flexible nanowire transistors by combining a high-quality In2O3:Zn nanowire channel, a SiNx high-κ dielectric, and conducting Sn-doped In2O3 electrodes on a polyethylene terephthalate substrate. The devices show excellent operating characteristics with high carrier mobilities up to 631 cm2 V−1 s−1, a drain-source current on/off modulation ratio ∼1×106, a high on-state current ∼1×10−5 A, a small subthreshold gate voltage swing of 120 mV decade−1, and a near zero threshold voltage. The devices further show high reproducibility and stable performance under bending condition. The high-performance nanowire transistors would enable application opportunities in flexible and transparent electronics.
Growth of deformation twins in room-temperature rolled nanocrystalline nickel
Authors: Zhang X. Y. , Wu X. L. , Zhu A. W.
Published: March 2009

Deformation twinning has been observed in room-temperature rolled nanocrystalline Ni. The growth of the deformation twins via the emission of partial dislocations from a grain boundary has been examined in detail. Partial dislocations on neighboring slip planes may migrate for different distances and then remain in the grain interior, leading to the formation of a steplike twin boundary (TB). With continued twin growth, the TBs become gradually distorted and lose their coherent character due to accumulated high stresses. Moreover, we propose that microtwins may form near such TBs due to the emission of partial dislocations from the TB.
Half-metallicity and Gilbert damping constant in Co2FexMn1−xSi Heusler alloys depending on the film composition
Authors: Kubota Takahide , Tsunegi Sumito , Oogane Mikihiko , Mizukami Shigemi , Miyazaki Terunobu , Naganuma Hiroshi , Ando Yasuo
Published: March 2009

Transport properties in magnetic tunnel junctions (MTJs) with Co2FexMn1−xSi (CFMS, x=0–1.0)/Al–O/Co75Fe25 structure and Gilbert damping constant in the epitaxial CFMS films were investigated. The tunnel magnetoresistance ratio is as high as 75% in MTJs with x=0.6 at room temperature. The Gilbert damping constant is minimal at x=0.4. Relations between half-metallicity and the Gilbert damping constant in CFMS films were examined, revealing that the damping constant is small in half-metallic CFMS films.
Epitaxial Mn2.5Ga thin films with giant perpendicular magnetic anisotropy for spintronic devices
Authors: Wu Feng , Mizukami Shigemi , Watanabe Daisuke , Naganuma Hiroshi , Oogane Mikihiko , Ando Yasuo , Miyazaki Terunobu
Published: March 2009

We report on epitaxial growth and magnetic properties of Mn2.5Ga thin films, which were deposited on Cr/MgO single crystal substrates by magnetron sputtering. X-ray diffraction results revealed the epitaxial relationships as Mn2.5Ga(001)[100]∥Cr(001)[110]∥MgO(001)[100]. The presence of (002) and (011) superlattice peaks indicates that the films were crystallized into DO22 ordered structures. The perpendicular magnetic anisotropy (PMA) properties were found to be related to the extent of DO22 chemical ordering. A giant PMA (Kueff=1.2×107 erg/cm3) and low saturation magnetization (Ms=250 emu/cm3) can be obtained for the film with highest chemical ordering parameter (S=0.8).