bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical study of detonation transmission in mixtures containing chemical inhibitors
Authors: Papalexandris M. V.
Published: June 2012

In this article, we report on numerical simulations of the evolution of gaseous detonation waves in mixtures that contain chemical inhibitors. In general, these are compounds that consume the radicals that are produced during combustion, thereby inhibiting the exothermic chain-terminating reaction. Also, some of them participate in endothermic reactions, such as dissociation. These properties make them very efficient flame suppressants. In this study, we employ a chemical kinetics model that consists of a three-step chain-branching mechanism for the fuel combustion and a one-step mechanism for the reaction between inhibitor and radicals. Results from both one- and two-dimensional simulations are presented and discussed. It is shown that radical consumption and heat absorption due to the inhibitor's reaction result in longer induction zones. This, in turn, leads to a detachment of the reaction zone from the precursor shock. For small and medium inhibitor concentrations, this detachment is temporary. Eventually, the radical concentration behind the induction zone becomes sufficient to initiate rapid fuel consumption, thus producing pressure waves which reach the precursor shock and re-ignite the detonation. This is followed by large over-pressures and highly irregular oscillations of the shock. Nonetheless, sufficiently high inhibitor concentrations can yield permanent detonation quenching.
Enhancement of hybrid solar cell performance by polythieno [3,4-b]thiophenebenzodithiophene and microplasma-induced surface engineering of silicon nanocrystals
Authors: Švrček V. , Yamanari T. , Mariotti D. , Matsubara K. , Kondo M.
Published: June 2012

We have developed a room temperature fabrication technique for hybrid bulk heterojunction solar cells based on silicon nanocrystals (Si-ncs) embedded in polythieno[3,4-b]thiophenebenzodithiophene (PTB7) and that exhibit a high open-circuit voltage exceeding 1 V. This type of device outperforms the open-circuit voltage of analogous devices based on Si-ncs within poly(hexylthiophene) (P3HT). We also demonstrate that three dimensional surface engineering of Si-ncs by microplasma processing in ethanol can be used to enhance the electronic interactions with PTB7, without using any surfactant, and increasing the power conversion efficiency.
Polymer translocation under time-dependent driving forces: Resonant activation induced by attractive polymer-pore interactions
Authors: Ikonen Timo , Shin Jaeoh , Sung Wokyung , Ala-Nissila Tapio
Published: June 2012

We study the driven translocation of polymers under time-dependent driving forces using N-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.
A density functional study of C1–C4 alkyl adsorption on Cu(111)
Authors: Montemore Matthew M. , Medlin J. Will
Published: June 2012

To better understand the nature of alkyl intermediates often invoked in reactions involving hydrocarbon reactants and products, the adsorption of linear and branched C1–C4 alkyls on Cu(111) at 1/4 ML and 1/9 ML coverages was studied using density functional theory. The adsorption energy and site preference are found to be coverage-dependent, and both direct alkyl–alkyl interactions and changes in the Cu electronic structure play a role in these trends. It was found that methyl strongly prefers the hollow sites, the branched alkyls strongly prefer the top site, and the linear C2–C4 alkyls have weak site preferences that change with coverage. To explain these differences, rationalize alkyl adsorption trends, and predict the binding energy of other alkyls, a simple model was developed in which the binding energy is fit as a linear function of the number of C–Cu and C–H–Cu interactions as well as the C–H bond energy in the corresponding alkane. Site preference can be understood as a compromise between C–Cu interactions and C–H–Cu interactions. Density of states analysis was used to gain a molecular-orbital understanding of the bonding of alkyls to Cu(111).
Synthesis of the superlattice complex oxide Sr5Bi4Ti8O27 and its band gap behavior
Authors: Zurbuchen M. A. , Podraza N. J. , Schubert J. , Jia Y. , Schlom D. G.
Published: June 2012

The n = 8 member of the Aurivillius complex oxide superlattice series of phases, Sr5Bi4Ti8O27, was synthesized by pulsed-laser deposition on (001) SrTiO3 single-crystal substrates. This phase, with a c-axis lattice parameter of 7.25 ± 0.036 nm, and its purity were confirmed by x-ray diffraction and transmission electron microscopy. The film is observed to be single phase and free of intergrowths of other-n members of the series. Using spectroscopic ellipsometry, Sr5Bi4Ti8O27 was determined to exhibit an indirect band gap of 3.53 eV at room temperature.
Magnetic measurements at pressures above 10 GPa in a miniature ceramic anvil cell for a superconducting quantum interference device magnetometer
Authors: Tateiwa Naoyuki , Haga Yoshinori , Matsuda Tatsuma D. , Fisk Zachary
Published: June 2012

A miniature ceramic anvil high pressure cell (mCAC) was earlier designed by us for magnetic measurements at pressures up to 7.6 GPa in a commercial superconducting quantum interference magnetometer [N. Tateiwa et al., Rev. Sci. Instrum. 82, 053906 (2011)]10.1063/1.3590745. Here, we describe methods to generate pressures above 10 GPa in the mCAC. The efficiency of the pressure generation is sharply improved when the Cu-Be gasket is sufficiently preindented. The maximum pressure for the 0.6 mm culet anvils is 12.6 GPa when the Cu-Be gasket is preindented from the initial thickness of 300–60 μm. The 0.5 mm culet anvils were also tested with a rhenium gasket. The maximum pressure attainable in the mCAC is about 13 GPa. The present cell was used to study YbCu2Si2 which shows a pressure induced transition from the non-magnetic to magnetic phases at 8 GPa. We confirm a ferromagnetic transition from the dc magnetization measurement at high pressure. The mCAC can detect the ferromagnetic ordered state whose spontaneous magnetic moment is smaller than 1 μB per unit cell. The high sensitivity for magnetic measurements in the mCAC may result from the simplicity of cell structure. The present study shows the availability of the mCAC for precise magnetic measurements at pressures above 10 GPa.
Atomic behavior of carbon atoms on a Si removed 3C-SiC (111) surface during the early stage of epitaxial graphene growth
Authors: Hwang Yubin , Lee Eung-Kwan , Choi Heechae , Yun Kyung-Han , Lee Minho , Chung Yong-Chae
Published: June 2012

The understanding of the formation of graphene at the atomic scale on Si-terminated 3C-SiC for obtaining high-quality graphene sheets remains elusive, although epitaxial graphene growth has been shown to be a well-known method for economical mass production of graphene/SiC heterojunctions. In this paper, the atomic behavior of carbon atoms on a Si removed 3C-SiC (111) surface for the formation of graphene buffer layer during the early stage of epitaxial graphene growth was investigated using a molecular dynamics simulation. Observation of the behavior of the remaining carbon atoms on the Si-terminated 3C-SiC (111) surface after removal of the silicon atoms revealed that graphene clusters, which were formed by sp2-bonded carbon atoms, start to appear at annealing temperatures higher than 1300 K. Our simulations indicated that the structural stability of the whole system increased as the number of sp2-bonded carbon atoms on the Si-terminated 3C-SiC (111) surface increased. It was also found that the diffusion energy barrier for the migration of carbon atoms from the on-top site to the bridge site on the Si-terminated 3C-SiC (111) surface mainly determines the critical temperature of graphene cluster formation.
Optical transitions due to native defects in nonlinear optical crystals LiGaS2
Authors: Yelisseyev A. , Lin Z. S. , Starikova M. , Isaenko L. , Lobanov S.
Published: June 2012

LiGaS2 (LGS) is a recently developed nonlinear optical crystal widely used for nonlinear conversion in the mid-infrared spectral region, but its applications are significantly influenced by the native defects present in the lattice. In this work, absorption and photoluminescence (PL) spectra are studied after annealing the as-grown LGS crystal in different chemical environments in order to reveal features related to anion vacancy (VS) and cation antisite defect (GaLi). In addition, irradiation with fast electrons produces VS centers and their complexes in LGS. The VS migration and mutual transformations in these defects take place at room temperature whereas their complete annealing occurs at 670 K. Meanwhile, the first-principles calculations are adopted to identify the relevant optical transitions. A good agreement with the experimental results was obtained. It is established that the dominant defects VS result in the optical absorption at 3.43 eV and violet PL emission, while GaLi is responsible for absorption at 2.95 eV. The intense PL peak at 1.92 eV is associated with the self-trapped excitons in LGS. The other weak PL bands are also related to the recombination of electrons or holes with the VS and GaLi defect states.
Persistent luminescence and its mechanism of Ba5(PO4)3Cl:Ce3+,Eu2+
Authors: Ju Guifang , Hu Yihua , Chen Li , Wang Xiaojuan
Published: June 2012

We investigated the persistent luminescence in europium-doped barium chloroapatite upon codoping with cerium. Luminescence properties of the phosphors, including photoluminescence, luminescence decay, and thermoluminescence are systematically studied. This material holds the key to the unsettled questions in the field of persistent luminescence. We formulated a model of persistent luminescence on the basis of the experimental results. In our model, some Eu2+ ions are oxidized to Eu3+ under short UV excitation, and the released electrons are trapped at positive substitutional defect introduced by Ce3+. The persistent luminescence arises from the recombination of these trapped electrons with the photo-ionized Eu3+ ions. The effects of Coulomb attraction between the substitutional defect and trapped electron, along with electron–electron repulsion, construct a metastable exciton-like trap. To a first approximation, the third ionization energy and ionic radius of lanthanide codopant can be used to rationalize their influence on persistent luminescence of Eu2+. Our model can also explain other systems, such as SrAl2O4:Eu2+,R3+ (R = rare earth elements).
Electron paramagnetic resonance studies of manganese centers in SrTiO3: Non-Kramers Mn3+ ions and spin-spin coupled Mn4+ dimers
Authors: Azamat D. V. , Dejneka A. , Lancok J. , Trepakov V. A. , Jastrabik L. , Badalyan A. G.
Published: June 2012

An X- and Q-band electron paramagnetic resonance (EPR) study is reported on SrTiO3 single crystals doped with 0.5 at. % MnO. The EPR spectra originating from the S = 2 ground state of the Mn3+ ions are shown to belong to three distinct types of Jahn-Teller centers. The ordering of the oxygen vacancies due to the reduction treatment of the samples and the consequent formation of an oxygen vacancy associated with the Mn3+ centers is explained in terms of the localized charge compensation. The EPR spectra of the SrTiO3:Mn crystals show the presence of next-nearest-neighbor exchange coupled Mn4+ pairs in the 〈110〉 directions.
Drift velocity in non-isothermal inhomogeneous systems
Authors: Yang Mingcheng , Ripoll Marisol
Published: June 2012

Drift velocity and driving force are not directly proportional in the case of inhomogeneous suspensions, where a space dependent mobility induces an additional contribution to the drift velocity. Similarly, particle flux and drift velocity are related not only by the gradient of density but also by an additional contribution given by the gradient of the self-diffusion coefficient. We provide quantitative support to this scenario in a non-equilibrium system by means of computer simulations with a temperature gradient. Moreover, our simulation results demonstrate that the temperature gradient-induced mass transport coefficient, namely thermal diffusion coefficient, is not directly proportional to the drift velocity so that the well-accepted relation of proportionality is just an approximation.
Using induced signals to sense position from a microchannel plate detector
Authors: deSouza R. T. , Gosser Z. Q. , Hudan S.
Published: June 2012

We demonstrate a novel concept for a position sensitive microchannel plate detector. This detector provides sub-millimeter spatial resolution by examining the signal induced on a wire harp by the electron cloud from a microchannel plate detector. Wires in the harp are efficiently read out by coupling them to a delay line.
Realizing almost perfect bending waveguides with anisotropic epsilon-near-zero metamaterials
Authors: Luo Jie , Xu Ping , Chen Huanyang , Hou Bo , Gao Lei , Lai Yun
Published: June 2012

We study metamaterials with an anisotropic permittivity tensor in which one component is near zero. We find that such an anisotropic metamaterial can be used to control wave propagation and construct almost perfect bending waveguides with a high transmission rate (>95%). This interesting effect originates in the power flow redistribution by the surface waves on the input and output interfaces, which smoothly matches with the propagating modes inside the metamaterial waveguide. We also find that waves in such anisotropic epsilon-near-zero materials can be reflected by small-sized perfect magnetic conductor defects. Numerical calculations have been performed to confirm the above effects.
Mechanism of electron acceleration by chirped laser pulse
Authors: Wu X. Y. , Wang P. X. , Kawata S.
Published: June 2012

We studied the mechanism of electron acceleration by a chirped laser pulse. We found that, because of the chirp effect, a region exists where the laser wave phase experienced by the electron varies slowly, so that the electron can be accelerated for a long time. The mechanism of chirped laser acceleration is different to that of the capture and acceleration scenario, although both of them have a main acceleration stage in which the electrons are trapped for long periods.
Detection of filament formation in forming-free resistive switching SrTiO3 devices with Ti top electrodes
Authors: Stille S. , Lenser Ch. , Dittmann R. , Koehl A. , Krug I. , Muenstermann R. , Perlich J. , Schneider C. M. , Klemradt U. , Waser R.
Published: June 2012

We investigated the influence of Ti top electrodes on the resistive switching properties of SrTiO3 thin film devices. Above a Ti layer thickness of 5 nm, the initial resistance is strongly reduced, giving rise to forming-free devices. Hard x-ray photoemission experiments reveal the Ti layer to be composed of several oxide phases, induced by the redox-reaction at the Ti/SrTiO3 interface. Grazing incidence small angle x-ray scattering measurements indicate that the reduction of the SrTiO3 thin film occurs in a filamentary way. We attribute this behavior to the preferential reduction of SrTiO3 thin films along highly defective areas.
How to generate high twin densities in nano-ferroics: Thermal quench and low temperature shear
Authors: Salje E. K. H. , Ding X. , Zhao Z. , Lookman T.
Published: June 2012

High domain boundary densities in ferroic nano materials are generated in computer simulation studies by (1) fast quench from a para-elastic into a ferroelastic phase and (2) by shear of small samples at low temperatures inside the stability field of the ferroelastic phase. Quenched samples evolve from tweed to junctions to stripe pattern. In driven systems, no tweed exists and the mesoscopic structure ‘nucleates’ rapidly when a yield stress is surpassed. The nucleated domain patterns are long-lived and change towards the single domain state only when the external strain is further increased.
Self-organization and self-limitation in high power impulse magnetron sputtering
Authors: Anders André
Published: June 2012

The plasma over the racetrack in high power impulse magnetron sputtering develops in traveling ionization zones. Power densities can locally reach 109 W/m2, which is much higher than usually reported. Ionization zones move because ions are “evacuated” by the electric field, exposing neutrals to magnetically confined, drifting electrons. Drifting secondary electrons amplify ionization of the same ionization zone where the primary ions came from, while sputtered and outgassing atoms are supplied to the following zone(s). Strong density gradients parallel to the target disrupt electron confinement: a negative feedback mechanism that stabilizes ionization runaway.
Thickness dependence of magneto-optical effects in (Ga,Mn)As epitaxial layers
Authors: Al-Qadi B. , Nishizawa N. , Nishibayashi K. , Kaneko M. , Munekata H.
Published: June 2012

Rotation angle (θMO) of a linearly polarized light reflected from in-plane, ferromagnetic (Ga,Mn)As layers was measured precisely using a magneto-optical microscope. The θMO value varies non-linearly as a function of (Ga,Mn)As layer thickness d, showing a maximum at d = 50–60 nm. The thickness dependent θMO was analyzed quantitatively with a model based on an interference effect incorporating birefringence and dichroism, and it has been concluded that the contribution of magnetization-vector dependent refractive index, a magnetic birefringence, is responsible for the observed magneto-optical effect. The magnitude of magnetic birefringence appears to be comparable to those of uniaxial birefringence crystals.
First-principles prediction of half-metallic ferromagnetism in five transition-metal chalcogenides: The case of rocksalt structure
Authors: Gao G. Y. , Yao Kai-Lun
Published: June 2012

Motivated by the experimental synthesis of bulk rocksalt MnS, MnSe, and MnTe, we show with first-principles calculations that among all transition-metal pnictides and chalcogenides with rocksalt structure CrTe, VPo, and CrPo are truly half-metallic ferromagnets, and both VTe and CrSe exhibit nearly half-metallicity. Importantly, for these five half-metallic compounds, the rocksalt phase is energetically more stable than the zinc-blende and wurtzite ones, and the total energy differences between the rocksalt and ground-state NiAs phases are very small (0.06-0.43 eV/f.u.) and comparable with that of experimental MnTe (0.24 eV/f.u.), thus like rocksalt manganese chalcogenides, these five rocksalt half-metals would be realized in the form of bulk or at list thin films for spintronic applications. In addition, we study the (111) surface properties of rocksalt CrPo and find both Cr- and Po-terminated (111) surfaces retain the bulk half-metallicity. We also reveal that the spin-orbit coupling has very weak effect on the half-metallicity of rocksalt CrSe, VTe, and CrTe, and the spin polarizations are still high for rocksalt VPo and CrPo although the spin-orbit coupling affects greatly their half-metallicities.
Communication: Phase transitions, criticality, and three-phase coexistence in constrained cell models
Authors: Nayhouse Michael , Kwon Joseph Sang-Il , Orkoulas G.
Published: June 2012

In simulation studies of fluid-solid transitions, the solid phase is usually modeled as a constrained system in which each particle is confined to move in a single Wigner-Seitz cell. The constrained cell model has been used in the determination of fluid-solid coexistence via thermodynamic integration and other techniques. In the present work, the phase diagram of such a constrained system of Lennard-Jones particles is determined from constant-pressure simulations. The pressure-density isotherms exhibit inflection points which are interpreted as the mechanical stability limit of the solid phase. The phase diagram of the constrained system contains a critical and a triple point. The temperature and pressure at the critical and the triple point are both higher than those of the unconstrained system due to the reduction in the entropy caused by the single occupancy constraint.
Classical vortex beams show their discrete side
Authors: Smart Ashley G.
Published: June 2012

Researchers twist sound, testing a fundamental law of the quantization of orbital angular momentum.
Time to reset isotopic clocks?
Authors: Miller Johanna L.
Published: June 2012

Two new studies revise key parameters in radiometric dating.
DNA-based sensors know what the nose knows
Authors: Miller Johanna L.
Published: June 2012

The sensors can “smell” the difference between similar molecules.
Progress in fusion, but not in its US funding
Authors: Feder Toni
Published: June 2012

Although some countries are, like the US, struggling with funding, they are forging ahead with fusion—especially in Asia.
Stove designed by US national lab improves lives in Darfur
Authors: Kramer David
Published: June 2012

In cutting the wood fuel requirement in half, the stove also reduces Darfuri women’s exposure to violence.
Magnetic recording in rocks
Authors: Dunlop David J.
Published: June 2012

Charting the movement of tectonic plates or the evolution of a dynamo ultimately relies on the behavior of often imperfect mineral grains in Earth’s magnetic field.
Physics resources for varied communities
Authors: O’Riordan Catherine
Published: June 2012

Through manifold partnerships, the Physics Resources Center at the American Institute of Physics serves scientific societies,the public, and individuals, including researchers, students, journalists, and administrators.
From black holes to strange metals
Authors: Liu Hong
Published: June 2012

String theory relates gravity to the physics of a novel phase of matter observed above the superconducting transition temperature.
A Comparison of Two Theories of Perceived Distance on the Ground Plane: The Angular Expansion Hypothesis and the Intrinsic Bias Hypothesis
Authors: Li Zhi , Durgin Frank H
Published: June 2012

Two theories of distance perception—ie, the angular expansion hypothesis (Durgin and Li, 2011 Attention, Perception, & Psychophysics 73 1856–1870) and the intrinsic bias hypothesis (Ooi et al, 2006 Perception 35 605–624)—are compared. Both theories attribute exocentric distance foreshortening to an exaggeration in perceived slant, but their fundamental geometrical assumptions are very different. The intrinsic bias hypothesis assumes a constant bias in perceived geographical slant of the ground plane and predicts both perceived egocentric and exocentric distances are increasingly compressed. In contrast, the angular expansion hypothesis assumes exaggerations in perceived gaze angle and perceived optical slant. Because the bias functions of the two angular variables are different, it allows the angular expansion hypothesis to distinguish two types of distance foreshortening—the linear compression in perceived egocentric distance and the nonlinear compression in perceived exocentric distance. While the intrinsic bias is proposed only for explaining distance biases, the angular expansion hypothesis provides accounts for a broader range of spatial biases.
Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry
Authors: Calabrese Antonio N. , Speechley Lauren A. , Pukala Tara L.
Published: May 2012

This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.
A Solid State Study of Keto-enol Tautomerismin Three Naphthaledene Schiff Bases
Authors: Pierens Gregory K. , Venkatachalam T. K. , Bernhardt Paul V. , Riley Mark J. , Reutens David C.
Published: May 2012

Three naphthaledene Schiff bases were synthesized and a detailed analysis by variable temperature X-ray crystallography and solid state electronic spectra was undertaken to assess the tautomeric composition. The crystal structures showed no significant changes despite the compounds changing colour with temperature. Solid state UV spectra were acquired at low temperature and showed that the major absorption band broadened as the temperature was increased. In one compound absorptions were observed that increased in intensity as the temperature increased. For these compounds, the major contribution to the colour change is the broadening of the absorption band as a function of temperature and not the change in enol-keto tautomeric composition.
Seasonal effects on the relationship between photosynthesis and leaf carbohydrates in orange trees
Authors: Ribeiro Rafael V. , Machado Eduardo C. , Habermann Gustavo , Santos Mauro G. , Oliveira Ricardo F.
Published: June 2012

To understand the effect of summer and winter on the relationships between leaf carbohydrate and photosynthesis in citrus trees growing in subtropical conditions, ‘Valencia’ orange trees were subjected to external manipulation of their carbohydrate concentration by exposing them to darkness and evaluating the maximal photosynthetic capacity. In addition, the relationships between carbohydrate and photosynthesis in the citrus leaves were studied under natural conditions. Exposing the leaves to dark conditions decreased the carbohydrate concentration and increased photosynthesis in both seasons, which is in accordance with the current model of carbohydrate regulation. Significant negative correlations were found between total non-structural carbohydrates and photosynthesis in both seasons. However, non-reducing sugars were the most important carbohydrate that apparently regulated photosynthesis on a typical summer day, whereas starch was important on a typical winter day. As a novelty, photosynthesis stimulation by carbohydrate consumption was approximately three times higher during the summer, i.e. the growing season. Under subtropical conditions, citrus leaves exhibited relatively high photosynthesis and high carbohydrate levels on the summer day, as well as a high nocturnal consumption of starch and soluble sugars. A positive association was determined between photosynthesis and photoassimilate consumption/exportation, even in leaves showing a high carbohydrate concentration. This paper provides evidence that photosynthesis in citrus leaves is regulated by an increase in sink demand rather than by the absolute carbohydrate concentration in leaves.
Amino acids are a nitrogen source for sugarcane
Authors: Vinall Kerry , Schmidt Susanne , Brackin Richard , Lakshmanan Prakash , Robinson Nicole
Published: June 2012

Organic forms of nitrogen (ON) represent potential N sources for crops and an alternative to inorganic N (IN, ammonium nitrate). Sugarcane soils receive organic harvest residues (~40–100 kg ON ha–1), but it is unknown whether ON is a direct N source for crops. We investigated whether sugarcane can use organic monomers in the form of amino acids and whether the use of amino acids as a N source results in distinct metabolic or morphological change when compared with use of inorganic N (IN). Plantlets cultivated in sterile culture and young plants grown in non-sterile soil culture were supplied with IN, ON (five amino acids present in sugarcane soils), or combined IN and ON. All treatments resulted in similar biomass and N content indicating that sugarcane has a well developed capacity to use ON and confirms findings in other species. ON-supplied plants in axenic culture had increased total branch root length per unit primary root axis which has not been reported previously. In both experimental systems, ON supplied plants had increased asparagine concentrations suggesting altered N metabolism. Root of ON-supplied soil-grown plants had significantly reduced nitrate concentrations. We interpret the shift from nitrate to asparagine as indicative of N form use other than or in addition to nitrate by sugarcane. N metabolite profiling could advance knowledge of crop N sources and this will aid in development of N efficient cropping systems with a reduced N pollution footprint.
Imatinib resistance and microcytic erythrocytosis in a Kit
V558Δ;T669I/+
gatekeeper-mutant mouse model of gastrointestinal stromal tumor
Authors: Bosbach Benedikt , Deshpande Shayu , Rossi Ferdinand , Shieh Jae-Hung , Sommer Gunhild , de Stanchina Elisa , Veach Darren R. , Scandura Joseph M. , Manova-Todorova Katia , Moore Malcolm A. S. , Antonescu Cristina R. , Besmer Peter
Published: June 2012

Most gastrointestinal stromal tumors (GISTs) harbor a gain-of-function mutation in the Kit receptor. GIST patients treated with the tyrosine kinase inhibitor imatinib frequently develop imatinib resistance as a result of second-site Kit mutations. To investigate the consequences of second-site Kit mutations on GIST development and imatinib sensitivity, we engineered a mouse model carrying in the endogenous
Kit
locus both the
Kit
V558Δ
mutation found in a familial case of GIST and the
Kit
T669I
(human
KIT
T670I
) “gatekeeper” mutation found in imatinib-resistant GIST patients. Similar to
Kit
V558∆/+
mice,
Kit
V558∆;T669I/+
mice developed gastric and colonic interstitial cell of Cajal hyperplasia as well as cecal GIST. In contrast to the single-mutant
Kit
V558∆/+
control mice, treatment of the
Kit
V558∆;T669I/+
mice with either imatinib or dasatinib failed to inhibit oncogenic Kit signaling and GIST growth. However, this resistance could be overcome by treatment of
Kit
V558∆;T669I/+
mice with sunitinib or sorafenib. Although tumor lesions were smaller in
Kit
V558∆;T669I/+
mice than in single-mutant mice, both interstitial cell of Cajal hyperplasia and mast cell hyperplasia were exacerbated in
Kit
V558∆;T669I/+
mice. Strikingly, the
Kit
V558∆;T669I/+
mice developed a pronounced polycythemia vera-like erythrocytosis in conjunction with microcytosis. This mouse model should be useful for preclinical studies of drug candidates designed to overcome imatinib resistance in GIST and to investigate the consequences of oncogenic KIT signaling in hematopoietic as well as other cell lineages.
Radar observations of individual rain drops in the free atmosphere
Authors: Schmidt Jerome M. , Flatau Piotr J. , Harasti Paul R. , Yates Robert D. , Littleton Ricky , Pritchard Michael S. , Fischer Jody M. , Fischer Erin J. , Kohri William J. , Vetter Jerome R. , Richman Scott , Baranowski Dariusz B. , Anderson Mark J. , Fletcher Ed , Lando David W.
Published: June 2012

Atmospheric remote sensing has played a pivotal role in the increasingly sophisticated representation of clouds in the numerical models used to assess global and regional climate change. This has been accomplished because the underlying bulk cloud properties can be derived from a statistical analysis of the returned microwave signals scattered by a diverse ensemble comprised of numerous cloud hydrometeors. A new Doppler radar, previously used to track small debris particles shed from the NASA space shuttle during launch, is shown to also have the capacity to detect individual cloud hydrometeors in the free atmosphere. Similar to the traces left behind on film by subatomic particles, larger cloud particles were observed to leave a well-defined radar signature (or streak), which could be analyzed to infer the underlying particle properties. We examine the unique radar and environmental conditions leading to the formation of the radar streaks and develop a theoretical framework which reveals the regulating role of the background radar reflectivity on their observed characteristics. This main expectation from theory is examined through an analysis of the drop properties inferred from radar and in situ aircraft measurements obtained in two contrasting regions of an observed multicellular storm system. The observations are placed in context of the parent storm circulation through the use of the radar’s unique high-resolution waveforms, which allow the bulk and individual hydrometeor properties to be inferred at the same time.
Folding pathways of proteins with increasing degree of sequence identities but different structure and function
Authors: Giri Rajanish , Morrone Angela , Travaglini-Allocatelli Carlo , Jemth Per , Brunori Maurizio , Gianni Stefano
Published: June 2012

Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by Φ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called
G

A

(a 3-
α
helix fold) and
G

B

(an
α
/
β
fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the
G

A

domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the
G

B

s, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed.
Homologation and functionalization of carbon monoxide by a recyclable uranium complex
Authors: Gardner Benedict M. , Stewart John C. , Davis Adrienne L. , McMaster Jonathan , Lewis William , Blake Alexander J. , Liddle Stephen T.
Published: June 2012

Carbon monoxide (CO) is in principle an excellent resource from which to produce industrial hydrocarbon feedstocks as alternatives to crude oil; however, CO has proven remarkably resistant to selective homologation, and the few complexes that can effect this transformation cannot be recycled because liberation of the homologated product destroys the complexes or they are substitutionally inert. Here, we show that under mild conditions a simple triamidoamine uranium(III) complex can reductively homologate CO and be recycled for reuse. Following treatment with organosilyl halides, bis(organosiloxy)acetylenes, which readily convert to furanones, are produced, and this was confirmed by the use of isotopically
13
C-labeled CO. The precursor to the triamido uranium(III) complex is formed concomitantly. These findings establish that, under appropriate conditions, uranium(III) can mediate a complete synthetic cycle for the homologation of CO to higher derivatives. This work may prove useful in spurring wider efforts in CO homologation, and the simplicity of this system suggests that catalytic CO functionalization may soon be within reach.
Pfirsch–Schlüter current-driven edge electric fields and their effect on the L–H transition power threshold
Authors: Aydemir A.Y.
Published: June 2012

An important contribution to the magnetohydrodynamic equilibrium at the tokamak edge comes from the Pfirsch–Schlüter current. The parallel electric field that can be associated with these currents is necessarily poloidally asymmetric and makes a similarly nonuniform contribution to the radial electric field on a flux surface. Here the role of the poloidal variation of this radial electric field in the L–H transition power threshold is investigated. Dependence of the resulting electric fields on magnetic topology, geometric factors such as the upper/lower triangularity and elongation, and the relative position of the X-point(s) in the poloidal plane are examined in detail. Starting with the assumption that an initially more negative radial electric field at the edge helps lower the transition power threshold, we find that our results are in agreement with a variety of experimental observations. In particular, for a ‘normal’ configuration of the plasma current and toroidal field we show the following. (i) The net radial electric field contribution by the Pfirsch–Schlüter currents at the plasma edge is negative for a lower single null and positive for a corresponding upper single null geometry. (ii) It becomes more negative as the X-point height is reduced. (iii) It also becomes more negative as the X-point radius is increased. These observations are consistent with the observed changes in the L–H transition power threshold P
LH under similar changes in the experimental conditions. In addition we find that (iv) in USN with an unfavourable ion ∇
B drift direction, the net radial electric field contribution is positive but decreases as the X-point radius decreases. This is consistent with the C-Mod observation that an L–I mode transition can be triggered by increasing the upper triangularity in this configuration. (v) Locally the radial electric field is positive above the outer mid-plane and reverses sign with reversal of the toroidal field, consistent with DIII-D observations in low-power L-mode discharges. Thus, taken as a whole, the Pfirsch–Schlüter current-driven fields can explain a number of observations on the L–H or L–I transition and the required power threshold P
LH levels not captured by simple scaling laws. They may indeed be an important ‘hidden variable’.
Testing gyrokinetic simulations of electron turbulence
Authors: Holland C. , DeBoo J.C. , Rhodes T.L. , Schmitz L. , Hillesheim J.C. , Wang G. , White A.E. , Austin M.E. , Doyle E.J. , Peebles W.A. , Petty C.C. , Zeng L. , Candy J.
Published: June 2012

An extensive set of tests comparing gyrokinetic predictions of temperature-gradient driven electron turbulence to power balance transport analyses and fluctuation measurements are presented. These tests use data from an L-mode validation study on the DIII-D tokamak (Luxon 2002 Nucl. Fusion
42 614) in which the local value of

is varied by modulated electron cyclotron heating; the GYRO code (Candy and Waltz 2003 J. Comput. Phys.
186 545) is used to make the gyrokinetic predictions. Using a variety of novel measures, both local and global nonlinear simulations are shown to predict key characteristics of the electron energy flux Q
e and long-wavelength (low-k) T
e fluctuations, but systematically underpredict (by roughly a factor of two) the ion energy flux Q
i. A new synthetic diagnostic for comparison to intermediate wavelength Doppler backscattering measurements is presented, and used to compare simulation predictions against experiment. In contrast to the agreement observed in the low-k
T
e fluctuation comparisons, little agreement is found between the predicted and measured intermediate-k density fluctuation responses. The results presented in this paper significantly expand upon those previously reported in DeBoo et al (2010 Phys. Plasmas
17 056105), comparing transport and multiple turbulence predictions from numerically converged local and global simulations for all four experimental heating configurations (instead of only fluxes and low-k
T
e fluctuations for one condition) to measurements and power balance analyses.
Detector configuration of KAGRA–the Japanese cryogenic gravitational-wave detector
Authors: Somiya Kentaro ,   for the KAGRA Collaboration
Published: June 2012

The construction of the Japanese second-generation gravitational-wave detector KAGRA (previously called LCGT) has been started. In the next 6–7 years, we will be able to observe the spacetime ripple from faraway galaxies. KAGRA is equipped with the latest advanced technologies. The entire 3 km long detector is located in the underground to be isolated from the seismic motion, the core optics are cooled down to 20 K to reduce thermal fluctuations and quantum non-demolition techniques are used to decrease quantum noise. In this paper, we introduce the detector configuration of KAGRA, its design, strategy and downselection of parameters.
Data quality studies of enhanced interferometric gravitational wave detectors
Authors: McIver Jessica ,   for the LIGO Scientific Collaboration and the Virgo Collaboration
Published: June 2012

Data quality assessment plays an essential role in the quest to detect gravitational wave signals in data from the LIGO and Virgo interferometric gravitational wave detectors. Interferometer data contain a high rate of noise transients from the environment, the detector hardware and the detector control systems. These transients severely limit the statistical significance of gravitational wave candidates of short duration and/or poorly modeled waveforms. This paper describes the data quality studies that have been performed in recent LIGO and Virgo observing runs to mitigate the impact of transient detector artifacts on the gravitational wave searches.
Recent results for the search of continuous waves with the LIGO and Virgo detectors
Authors: Astone P ,   for the LIGO Scientific Collaboration and for the Virgo Collaboration
Published: June 2012

The ‘First Generation Era’ of gravitational wave detectors is now over, but the data analysis effort for the search of continuous gravitational waves is still ongoing and active. Many results have been produced but still many searches are underway. I present and discuss here the most recent results for this search, together with short discussions on analysis which are now underway and plans for the near future. The discussion on long-term plans and perspectives for the so-called Advanced Detector Era are beyond the scope of this paper.
Closed planar curves without inflections
Authors: Ohno Shuntaro , Ozawa Tetsuya , Umehara Masaaki
Published: June 2012

We define a computable topological invariant

μ
(
γ
)

\mu (\gamma )

for generic closed planar regular curves

γ
\gamma

, which gives an effective lower bound for the number of inflection points on a given generic closed planar curve. Using it, we classify the topological types of locally convex curves (i.e. closed planar regular curves without inflections) whose numbers of crossings are less than or equal to five. Moreover, we discuss the relationship between the number of double tangents and the invariant

μ
(
γ
)

\mu (\gamma )

of a given

γ
\gamma

.
SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY FINDINGS IN TAMOXIFEN RETINOPATHY—A CASE REPORT
Authors: Nair Sandhya Narayanan , Anantharaman Giridhar , Gopalakrishnan Mahesh , Vyas Jyothiprakash
Published: June 2012

Purpose:

To report spectral domain optical coherence tomography findings in a case of typical tamoxifen retinopathy.

Methods:

In this observational case report, a patient with tamoxifen retinopathy was imaged with spectral domain optical coherence tomography and fundus auto fluorescence.

Results:

Spectral domain optical coherence tomography showed numerous hyperreflective spots within the retina, mainly in the inner retinal layers in both the eyes. The external limiting membrane, the Inner Segment-Outer Segment junction, and the photoreceptors were not discernable at the fovea in the right eye. In the left eye, there was foveal atrophy with total loss of photoreceptors. The autofluorescent images showed macular hypofluorescence with foveal hyperfluorescence.

Conclusion:

Spectral domain optical coherence tomography demonstrated abnormalities in the outer retinal layers in tamoxifen retinopathy. There were also characteristic alterations in the autofluorescence pattern at the macula in tamoxifen retinopathy.
Halobellus limi sp. nov. and Halobellus salinus sp. nov., isolated from two marine solar salterns
Authors: Cui Heng-Lin , Yang Xin , Zhou Yu-Guang , Liu Hong-Can , Zhou Pei-Jin , Dyall-Smith Mike L.
Published: June 2012

Two halophilic archaea, strains TBN53T and CSW2.24.4T, were characterized to elucidate their taxonomic status. Strain TBN53T was isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China, whereas strain CSW2.24.4T was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53T was able to grow at 25–55 °C (optimum 45 °C), with 1.4–5.1 M NaCl (optimum 2.6–3.9 M NaCl), with 0–1.0 M MgCl2 (optimum 0–0.1 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0), whereas strain CSW2.24.4T was able to grow at 25–45 °C (optimum 37 °C), with 2.6–5.1 M NaCl (optimum 3.4 M NaCl), with 0.01–0.7 M MgCl2 (optimum 0.05 M MgCl2) and at pH 5.5–9.5 (optimum pH 7.0–7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53T and 12 % (w/v) for strain CSW2.24.4T. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53T and CSW2.24.4T showed 94.1 % similarity to each other and were closely related to

Halobellus clavatus

TNN18T (95.0 and 94.7 % similarity, respectively). Levels of rpoB′ gene sequence similarity between strains TBN53T and CSW2.24.4T, and between these strains and

Halobellus clavatus

TNN18T were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53T and CSW2.24.4T were 69.2 and 67.0 mol%, respectively. The level of DNA–DNA relatedness between strain TBN53T and strain CSW2.24.4T was 25 %, and these two strains showed low levels of DNA–DNA relatedness with

Halobellus clavatus

TNN18T (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus

Halobellus

are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53T = CGMCC 1.10331T = JCM 16811T) and Halobellus salinus sp. nov. (type strain CSW2.24.4T = DSM 18730T = CGMCC 1.10710T = JCM 14359T).