bluuebunny/crossref_metadata_2025 huggingface dataset:
Projectile channeling in chain bundle dusty plasma liquids: Wave excitation and projectile-wave interaction
Authors: Chang Mei-Chu , Tseng Yu-Ping , I Lin
Published: March 2011

The microscopic channeling dynamics of projectiles in subexcitable chain bundle dusty plasma liquids consisting of long chains of negatively charged dusts suspended in low pressure glow discharges is investigated experimentally using fast video-microscopy. The long distance channeling of the projectile in the channel formed by the surrounding dust chain bundles and the excitation of a narrow wake associated with the elliptical motions of the background dusts are demonstrated. In the high projectile speed regime, the drag force due to wake wave excitation increases with the decreasing projectile speed. The excited wave then leads the slowed down projectile after the projectile speed is decreased below the resonant speed of wave excitation. The wave-projectile interaction causes the increasing projectile drag below the resonant speed and the subsequent oscillation around a descending average level, until the projectile settles down to the equilibrium point. Long distance projectile surfing through the resonant crest trapping by the externally excited large amplitude solitary wave is also demonstrated.
A nonlocal wave-wave interaction among Alfvén waves in an intermediate-β plasma
Authors: Zhao J. S. , Wu D. J. , Lu J. Y.
Published: March 2011

A nonlocal coupling mechanism to directly transfer the energy from large-scale magnetohydrodynamic (MHD) Alfvén waves to small-scale kinetic Alfvén waves is presented. It is shown that the interaction between a MHD Alfvén wave and a reversely propagating kinetic Alfvén wave can generate another kinetic Alfvén wave, and this interaction exists in the plasmas where the thermal to magnetic pressure ratio is larger than the electron to ion mass ratio. The proposed nonlocal interaction may have a potential application to account for the observed electron scale kinetic Alfvén waves in the solar wind and solar corona plasmas.
Linearity condition for orbital energies in density functional theory: Construction of orbital-specific hybrid functional
Authors: Imamura Yutaka , Kobayashi Rie , Nakai Hiromi
Published: March 2011

This study proposes a novel approach to construct the orbital-specific (OS) hybrid exchange-correlation functional by imposing the linearity condition: ${{{\partial ^2 E}/{\partial f_i^2 }}} |_{0 \le f_i \le 1} = {{{\partial \varepsilon _i }/{\partial f_i }}} |_{0 \le f_i \le 1} = 0$∂2E/∂fi2|0≤fi≤1=∂ɛi/∂fi|0≤fi≤1=0, where E, εi, and fi represent the total energy, orbital energy, and occupation number of the ith orbital. The OS hybrid exchange-correlation functional, of which the OS Hartree–Fock exchange (HFx) portion is determined by the linearity condition, reasonably reproduces the ionization potentials not only from valence orbitals but also from core ones in a sense of Koopmans’ theorem. The obtained short-range HFx portions are consistent with the parameters empirically determined in core–valence–Rydberg–Becke-3–parameter–Lee–Yang–Parr hybrid functional [Nakata et al., J. Chem. Phys., 124, 094105 (2006); ibid, 125, 064109 (2006)10.1063/1.2227379].
On the impossibility of defining adhesive hard spheres as sticky limit of a hard-sphere-Yukawa potential
Authors: Gazzillo Domenico
Published: March 2011

For fluids of molecules with short-ranged hard-sphere-Yukawa (HSY) interactions, it is proven that the Noro–Frenkel “extended law of corresponding states” cannot be applied down to the vanishing attraction range, since the exact HSY second virial coefficient diverges in such a limit. It is also shown that, besides Baxter's original approach, a fully correct alternative definition of “adhesive hard spheres” can be obtained by taking the vanishing-range-limit (sticky limit) not of a Yukawa tail, as is commonly done, but of a slightly different potential with a logarithmic-Yukawa attraction.
Shell model of assemblies of equicharged particles subject to radial confining potentials
Authors: Cioslowski Jerzy , Grzebielucha Ewa
Published: March 2011

A shell model of an assembly of N equicharged particles subject to an arbitrary radial confining potential N W(r), where W(r) is parameterized in terms of an auxiliary function Λ(t), is presented. The validity of the model requires that Λ(t) is strictly increasing and concave for any t ∈ (0, 1), Λ′(0) is infinite, and \documentclass[12pt]{minimal}\begin{document}$\tilde{\Lambda }(t)=-t^{-1}\:\Lambda ^{\prime }(t)/\Lambda ^{\prime \prime }(t)$\end{document}Λ̃(t)=−t−1Λ′(t)/Λ′′(t) is finite at t = 0. At the bulk limit of N → ∞, the model is found to correctly reproduce the energy per particle pair and the mean crystal radius R(N), which are given by simple functionals of Λ(t) and Λ′(t), respectively. Explicit expressions for an upper bound to the cohesive energy and the large-N asymptotics of R(N) are obtained for the first time. In addition, variational formulation of the cohesive energy functional leads to a closed-form asymptotic expression for the shell occupancies. All these formulae involve the constant ξ that enters the expression −(ξ/2) n3/2 for the leading angular-correlation correction to the minimum energy of n electrons on the surface of a sphere with a unit radius (the solution of the Thomson problem). The approximate energies, which constitute rigorous upper bounds to their exact counterparts for any value of N, include the cohesive term that is not accounted for by the mean-field (fluidlike) theory and its simple extensions but completely neglect the surface-energy correction proportional to N.
Inhibition of DNA ejection from bacteriophage by Mg+2 counterions
Authors: Lee Sell , Tran C. V. , Nguyen T. T.
Published: March 2011

The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg+2 counterions, is studied. Experimentally, it is known that MgSO4 salt has a strong and nonmonotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg+2 multivalent counterions. As Mg+2 concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg+2 concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA−DNA short range attraction energies, mediated by Mg+2, is found to be −0.004 kBT per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in agreement qualitatively with values for tri- and tetravalent counterions.
Compact wave functions for the beryllium isoelectronic series, Li− to Ne6+: A standard Hylleraas approach
Authors: King Frederick W. , Quicker David , Langer John
Published: March 2011

Variational calculations have been carried out for the ground states of several members of the beryllium isoelectronic series using a standard Hylleraas approach involving Slater-type basis functions. The species examined are Li−, Be, B+, C2+, N3+, O4+, F5+, and Ne6+. For each species, the nonrelativistic energy, the electronic density at the nucleus, the expectation value 〈∇i·∇j〉, the moments $\langle r_i^n \rangle$⟨rin⟩ for n = −1, 1, 2, and 3, and $\langle r_{ij}^n \rangle$⟨rijn⟩ for n = −1, 1, and 2, are reported. With relatively compact basis sets, the ground state energies are obtained with uncertainties ranging from 50 parts per million to just under 4 parts per million.
Generation of very low energy-spread electron beams using low-intensity laser pulses in a low-density plasma
Authors: Upadhyay Ajay K. , Samant Sushil Arun , Sarkar Deepangkar , Jha Pallavi , Krishnagopal Srinivas
Published: March 2011

The possibility of obtaining high-energy electron beams of high quality by using a low-density homogeneous plasma and a low-intensity laser (just above the self-injection threshold in the bubble regime) has been explored. Three-dimensional simulations are used to demonstrate, for the first time, an energy-spread of less than 1%, from self-trapping. More specifically, for a plasma density of 2×1018 cm−3 and a laser intensity of a0=2, a high-energy (0.55 GeV), ultrashort (1.4 fs) electron beam with very low energy-spread (0.55%) and high current (3 kA) is obtained. These parameters satisfy the requirements for drivers of short-wavelength free-electron lasers. It is also found that the quality of the electron beam depends strongly on the plasma length, which therefore needs to be optimized carefully to get the best performance in the experiments.
Plasma wave undulator for laser-accelerated electrons
Authors: Corde S. , Ta Phuoc K.
Published: March 2011

Laser-plasma accelerators have become compact sources of ultrashort electron bunches at energies up to the gigaelectronvolt range thanks to the remarkable progress made over the past decade. A direct application of these electron bunches is the production of short pulse x-ray radiation sources. In this letter, we study a fully optically driven x-ray source based on the combination of a laser-plasma accelerator and a plasma wave undulator. The longitudinal electric field of a laser-generated plasma wave is used to wiggle electrons transversally. The period of this plasma undulator being equal to the plasma wavelength, tunable photon energies in the 10 keV range can be achieved with electron energies in the 100–200 MeV range. Considering a 10s TW class femtosecond laser system, undulators with a strength parameter K∼0.5 and with about ten periods can be combined with a laser-plasma accelerator, resulting in several 10−2 emitted x-ray photons per electron.
Cost reduction of high-order coupled-cluster methods via active-space and orbital transformation techniques
Authors: Rolik Zoltán , Kállay Mihály
Published: March 2011

We discuss several techniques which have the potential to decrease the computational expenses of high-order coupled-cluster (CC) methods with a reasonable loss in accuracy. In particular, the CC singles, doubles, and triples (CCSDT) as well as the CC singles, doubles, triples, and perturbative quadruples [CCSDT(Q)] methods are considered, which are frequently used in high-precision model chemistries for the calculation of iterative triples and quadruples corrections. First, we study the possibilities for using active spaces to decrease the computational costs. In this case, an active space is defined and some indices of cluster amplitudes are restricted to be in the space. Second, the application of transformed virtual orbitals is investigated. In this framework, to reduce the computation time the dimension of the properly transformed virtual one-particle space is truncated. We have found that the orbital transformation techniques outperform the active-space approaches. Using the transformation techniques, the computational time can be reduced in average by an order of magnitude without significant loss in accuracy. It is demonstrated that high-order CC calculations are possible for considerably larger systems than before using the implemented techniques.
Magnetic field-induced reactions on the surface of chloroaluminum phthalocyanine thin films
Authors: Basova Tamara , Plyashkevich Vladimir , Petraki Fotini , Peisert Heiko , Chassé Thomas
Published: March 2011

The μ-(oxo)bis[phthalocyaninato] aluminum(III) (AlPc)2O films, with the crystallites oriented preferably in one direction, were obtained via chemical transformation of chloroaluminum(III) phthalocyanine AlClPc film upon its annealing in magnetic field. A comparative analysis of the influence of postdeposition annealing without and under applied magnetic field of 1 T on composition and morphology of AlClPc films has been carried out. The chemical transformation of AlClPc to (AlPc)2O on the substrate surface is studied by the methods of UV-vis and infrared spectroscopies, Raman, x-ray photoelectron spectroscopy as well as atomic force microscopy. Two interesting effects were observed upon heating the AlClPc films in magnetic field of 1 T. First, the temperature of the chemical transformation of AlClPc to (AlPc)2O decreased from 300 °C to 200 °C when magnetic field was applied during postdeposition annealing. Second, the formation of (AlPc)2O films with elongated crystallites with a preferential orientation was observed. The heating of (AlPc)2O films in a magnetic field at the same conditions did not demonstrate any effect on the structure and morphology of these films.
Understanding quantum interference in general nonlocality
Authors: Wang Hai-Jun
Published: March 2011

In this paper we attempt to give a new understanding of quantum double-slit interference of fermions in the framework of general nonlocality (GN) [J. Math. Phys. 49, 033513 (2008)] by studying the self-(inter)action of matter wave. From the metric of the GN, we derive a special formalism to interpret the interference contrast when the self-action is perturbative. According to the formalism, the characteristic of interference pattern is in agreement with experiment qualitatively. As examples, we apply the formalism to the cases governed by Schrödinger current and Dirac current, respectively, both of which are relevant to topology. The gap between these two cases corresponds to the fermion magnetic moment, which is possible to test in the near future. In addition, a general interference formalism for both perturbative and nonperturbative self-actions is presented. By analyzing the general formalism we predict that in the nonperturbative limit there is no interference at all. And by comparison with the special formalism of Schrödinger current, the coupling strength of self-action in the limit is found to be ∞. In the perturbative case, the interference from self-action turns out to be the same as that from the standard approach of quantum theory. Then comparing the corresponding coefficients quantitatively we conclude that the coupling strength of self-action in this case falls in the interval [0, 1].
Ionic bonding in free nanoscale NaCl clusters as seen by photoelectron spectroscopy
Authors: Zhang Chaofan , Andersson Tomas , Svensson Svante , Björneholm Olle , Huttula Marko , Mikkelä Mikko-Heikki , Tchaplyguine Maxim , Öhrwall Gunnar
Published: March 2011

The free neutral nanoscale NaCl clusters have been produced in a beam and studied with x-ray photoelectron spectroscopy. High resolution spectra simultaneously containing cluster and molecular-monomer, featuring in both the valence and core-level Na 2p and Cl 2p regions, have been obtained. Cluster-level energy shifts of around 3 eV toward lower binding energy for Na 2p and ≈1 eV toward higher binding energy for Cl 2p relative to the monomer levels have been unambiguously established. To rationalize the core-level energy shifts of the nanoscale NaCl clusters, the ionic model taking into account all charge–charge and polarization interactions has been developed and implemented. A satisfactory agreement between the experimental and model results has been obtained. The model calculations have also shed additional light on the size- and site-specific cluster responses.
Stimulated backward Brillouin scattering in two ion-species plasmas
Authors: Liu Z. J. , Zheng C. Y. , He X. T. , Wang Yugang
Published: March 2011

Stimulated Brillouin back-scattering in mixed carbon and hydrogen plasmas is studied using one-dimensional Vlasov–Maxwell simulation. It is found that both the fast and slow ion acoustic waves can scatter the incident light. Carbon ions can be trapped in the slow ion acoustic wave, and the hydrogen ions can be trapped in both the fast and slow waves. The trapped ions tend to reduce the Landau damping of the ion acoustic waves, and both the fast and slow ion acoustic waves can be excited. From the time-integrated scattering spectra, the scattering peaks of the fast and slow ion acoustic waves can be clearly distinguished.
The impact of edge gradients in the pressure, density, ion temperature, and electron temperature on edge-localized modes
Authors: Kleva Robert G. , Guzdar Parvez N.
Published: March 2011

The magnitude of the energy and particle fluxes in simulations of edge-localized modes (ELMs) is determined by the edge gradients in the pressure, density, ion temperature, and electron temperature. The total edge pressure gradient is the dominant influence on ELMs by far. An increase (decrease) of merely 2% in the pressure gradient results in an increase (decrease) of more than a factor of ten in the size of the ELM bursts. At a fixed pressure gradient, the size of the ELM bursts decreases as the density gradient increases, while the size of the bursts increases as the electron temperature gradient or, especially, the ion temperature gradient increases.
A magnetospheric energy principle extended to include neutral atmosphere
Authors: Miura Akira
Published: March 2011

The problem of ideal magnetohydrodynamic stability of plasmas in a magnetosphere-atmosphere system, in which the unperturbed magnetic field is assumed to be perpendicular to the plasma-atmosphere interface (ionospheric surface), is investigated by means of an extended magnetospheric energy principle. The derivation of the principle and conditions under which it applies to a real terrestrial magnetosphere is given. In the principle, the atmosphere is considered to be a very heavy and compressible gas with finite pressure. A thin ionospheric layer is taken into account as boundary conditions, but energetics within it are neglected. The solid-earth surface is assumed to be a perfectly conducting wall for perturbations. For a perturbation that satisfies either rigid or horizontally free boundary conditions at the plasma-atmosphere interface, the self-adjointness of the force operator is satisfied and an extended magnetospheric energy principle can be developed on the basis of the extended energy principle for fusion plasmas. These two boundary conditions are shown to be realized in the magnetosphere when the ionospheric conductivity is either very large or very small. Whereas in fusion plasmas the perturbed magnetic energy in the vacuum makes a stabilizing contribution to the potential energy, in the magnetosphere the perturbed magnetic energy in the atmosphere makes no such stabilizing contribution. This is due to the difference of the assumed field configurations of the magnetospheric and fusion plasmas. The ionospheric surface makes a destabilizing negative contribution to the potential energy owing to a horizontal plasma displacement on the spherical ionospheric surface. The method is applied to magnetospheric ballooning and interchange instabilities. The existence of a new type of magnetospheric interchange instability is shown and its structure in the magnetosphere-atmosphere system is clarified. Possible consequences of the instabilities and their relevance to magnetospheric physics are discussed.
Plasma wave propagation with a plasma density gradient
Authors: Cho Guangsup , Choi Eun-Ha , Uhm Han Sup
Published: March 2011

Plasma waves with the plasma diffusion velocity un due to a plasma density gradient are described in a positive column plasma. The ion wave is generated by the perturbation of the operating frequency 106 s−1 and it propagates with the group velocity ug∼cs2/un∼(105–106) m/s, where cs is the acoustic velocity in a fine tube fluorescent lamp, while the electron wave cannot be generated with a turbulence of low frequency less than the electron oscillation frequency ωpe. The propagation of the lighting signal observed in long tube fluorescent lamps is well understood with the propagation of ion waves occurring along the plasma density gradient.
Rupture kinetics of liquid bridges during a pulling process: A kinetic density functional theory study
Authors: Men Yumei , Zhang Xianren , Wang Wenchuan
Published: March 2011

Capillary bridge is a common phenomenon in nature and can significantly contribute to the adhesion of biological and artificial micro- and nanoscale objects. Especially, it plays a crucial role in the operation of atomic force microscopy (AFM) and influences in the measured force. In the present work, we study the rupture kinetics and transition pathways of liquid bridges connecting an AFM tip and a flat substrate during a process of pulling the tip off. Depending on thermodynamic conditions and the tip velocity, two regimes corresponding to different transition pathways are identified. In the single-bridge regime, the initial equilibrium bridge persists as a single one during the pulling process until the liquid bridge breaks. While, in the multibridge regime the stretched liquid bridge transforms into an intermediate state with a collection of slender liquid bridges, which then break gradually during the pulling process. Moreover, the critical rupture distance at which the bridges break changes with the tip velocity and thermodynamic conditions, and its maximum value occurs near the boundary between the single-bridge regime and the multibridge regime, where the longest range capillary force is produced. In this work, the effects of tip velocity, tip size, tip–fluid interaction, and humidity on rupture kinetics and transition pathways are also systematically studied.
Three-dimensional stability of dust-ion acoustic solitary waves in a magnetized multicomponent dusty plasma with negative ions
Authors: El-Taibany W. F. , El-Bedwehy N. A. , El-Shamy E. F.
Published: March 2011

Using the small-k expansion perturbation method, the three-dimensional stability of dust-ion acoustic solitary waves (DIASWs) in a magnetized multicomponent dusty plasma containing negative heavy ions and stationary variable-charge dust particles is analyzed. A nonlinear Zakharov–Kuznetsov equation adequate for describing these solitary structures is derived. Moreover, the basic features of the DIASWs are studied. The determination of the stability region leads to two different cases depending on the oblique propagation angle. In addition, the growth rate of the produced waves is estimated. The increase of either the negative ion number density or their temperatures or even the number density of the dust grains results in reducing the wave growth rate. Finally, the present results should elucidate the properties of DIASWs in a multicomponent plasma with negative ions, particularly in laboratory experiment and plasma process.
Self-focusing of cosh-Gaussian laser beam in a plasma with weakly relativistic and ponderomotive regime
Authors: Gill Tarsem Singh , Mahajan Ranju , Kaur Ravinder
Published: March 2011

This paper presents an investigation of the self-focusing of cosh-Gaussian laser beam in a plasma with linear absorption taking into account the combined effects of relativistic and ponderomotive type nonlinearities. Nonlinear parabolic partial differential equation governing the evolution of complex envelope in slowly varying envelope approximation is solved using variational approach. Self-focusing and self-phase modulation as well as self-trapping of cosh-Gaussian beam are studied at various values of decentered parameter b, with different absorption levels ki′. Numerical analysis shows that these parameters play vital role on propagation characteristics.
Characteristics of probe current harmonics based on various applied voltage waveforms in low temperature plasmas
Authors: Kim Young-Do , Kim Yu-Sin , Lee Hyo-Chang , Bang Jin-Young , Chung Chin-Wook
Published: March 2011

The characteristics of probe currents induced by applying various probe voltage waveforms, such as sinusoidal, sawtooth, square, and triangular, were investigated at a floating potential. It was found that the measured probe currents have many harmonics depending on the voltage waveforms. This was mainly due to the nonlinearity of the sheath in the plasma and was analyzed using the fast Fourier transform and a circuit model. By applying a triangular voltage waveform to a probe, plasma parameters such as electron temperature and plasma density could be obtained and compared to those of a single Langmuir probe and a floating harmonic method.
Effect of polydispersity and soft interactions on the nematic versus smectic phase stability in platelet suspensions
Authors: Martínez-Ratón Y. , Velasco E.
Published: March 2011

We theoretically discuss, using density-functional theory, the phase stability of nematic and smectic ordering in a suspension of platelets of the same thickness but with a high polydispersity in diameter, and study the influence of polydispersity on this stability. The platelets are assumed to interact like hard objects, but additional soft attractive and repulsive interactions, meant to represent the effect of depletion interactions due to the addition of nonabsorbing polymer, or of screened Coulomb interactions between charged platelets in an aqueous solvent, respectively, are also considered. The aspect (diameter-to-thickness) ratio is taken to be very high, in order to model solutions of mineral platelets recently explored experimentally. In this regime a high degree of orientational ordering occurs; therefore, the model platelets can be taken as completely parallel and are amenable to analysis via a fundamental-measure theory. Our focus is on the nematic versus smectic phase interplay, since a high degree of polydispersity in diameter suppresses the formation of the columnar phase. When interactions are purely hard, the theory predicts a continuous nematic-to-smectic transition, regardless of the degree of diameter polydispersity. However, polydispersity enhances the stability of the smectic phase against the nematic phase. Predictions for the case where an additional soft interaction is added are obtained using mean-field perturbation theory. In the case of the one-component fluid, the transition remains continuous for repulsive forces, and the smectic phase becomes more stable as the range of the interaction is decreased. The opposite behavior with respect to the range is observed for attractive forces, and in fact the transition becomes of first order below a tricritical point. Also, for attractive interactions, nematic demixing appears, with an associated critical point. When platelet polydispersity is introduced the tricritical temperature shifts to very high values.
Thermodynamics of water entry in hydrophobic channels of carbon nanotubes
Authors: Kumar Hemant , Mukherjee Biswaroop , Lin Shiang-Tai , Dasgupta Chandan , Sood A. K. , Maiti Prabal K.
Published: March 2011

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius.
Cavitation-induced ignition of cryogenic hydrogen-oxygen fluids
Authors: Osipov V. V. , Muratov C. B. , Ponizovskaya-Devine E. , Foygel M. , Smelyanskiy V. N.
Published: March 2011

The Challenger disaster and purposeful experiments with liquid hydrogen (H2) and oxygen (Ox) tank breaches demonstrated that cryogenic H2/Ox fluids always self-ignite in the process of their sudden mixing. Here, we propose a cavitation-induced self-ignition mechanism that may be realized under these conditions. In one possible scenario, self-ignition is caused by the strong shock waves generated by the collapse of pure Ox vapor bubble near the surface of the Ox liquid that may initiate detonation of the gaseous H2/Ox mixture next to the gas-liquid interface. This effect is further enhanced by H2/Ox combustion inside the collapsing bubble in the presence of admixed H2 gas.
Perpendicular anisotropy L1-FePt based pseudo spin valve with Ag spacer layer
Authors: Ho P. , Han G. C. , Evans R. F. L. , Chantrell R. W. , Chow G. M. , Chen J. S.
Published: March 2011

The effects of post-annealing temperature of the Ag spacer layer on the structural, magnetic, spin, and magneto-transport properties of perpendicular anisotropy pseudo spin valves L10-Fe50Pt50/Ag/L10-Fe50Pt50 had been investigated. The Ag spacer layer was post-annealed at various temperatures of 300, 400, and 500 °C. A giant magnetoresistance ratio of 1.1% and 2.2% was achieved at room temperature and 77 K, respectively, when Ag was post-annealed at 300 °C. This was a significant improvement from the use of Au, Pt, and Pd spacer materials.
Photogenerated cumulenic structure of adamantyl endcapped linear carbon chains: An experimental and computational investigation based on infrared spectroscopy
Authors: Yildizhan Melike Mercan , Fazzi Daniele , Milani Alberto , Brambilla Luigi , Del Zoppo Mirella , Chalifoux Wesley A. , Tykwinski Rik R. , Zerbi Giuseppe
Published: March 2011

The infrared (IR) spectrum of an adamantyl endcapped α, ω-polyyne (the hexayne, Ad–C12–Ad) is investigated both experimentally and computationally. A new IR band is observed upon UV photoexcitation of the compound (embedded in a poly methyl methacrylate matrix at 78 K), thus, revealing the existence of new photogenerated molecular structure trapped at low temperature. Complete reversibility is found, thus, demonstrating that the photoexcitation is responsible for the generation of metastable excited states of the molecule. Density functional theory and time dependent density functional theory calculations indicate that these metastable states result from the forbidden singlet (S1) or triplet (T1) excited states, and geometry optimizations of the polyyne trapped in either S1 and/or T1 states demonstrate that the carbon chain takes on a cumulenic structure. Comparison of the experimental and the computed IR spectra for the molecule trapped in the forbidden states confirms that the new IR features are clear markers of cumulenic species. The temperature and time dependent behavior of the new IR band is analyzed, while the experimentally determined value of the activation energy highlights the low stability of these molecular structures.
Characterization of microfluidic mixing and reaction in microchannels via analysis of cross-sectional patterns
Authors: Fang Wei-Feng , Hsu Miao-Hsing , Chen Yu-Tzu , Yang Jing-Tang
Published: March 2011

For the diagnosis of biochemical reactions, the investigation of microflow behavior, and the confirmation of simulation results in microfluidics, experimentally quantitative measurements are indispensable. To characterize the mixing and reaction of fluids in microchannel devices, we propose a mixing quality index (Mqi) to quantify the cross-sectional patterns (also called mixing patterns) of fluids, captured with a confocal-fluorescence microscope (CFM). The operating parameters of the CFM for quantification were carefully tested. We analyzed mixing patterns, flow advection, and mass exchange of fluids in the devices with overlapping channels of two kinds. The mixing length of the two devices derived from the analysis of Mqi is demonstrated to be more precise than that estimated with a commonly applied method of blending dye liquors. By means of fluorescence resonance-energy transfer (FRET), we monitored the hybridization of two complementary oligonucleotides (a FRET pair) in the devices. The captured patterns reveal that hybridization is a progressive process along the downstream channel. The FRET reaction and the hybridization period were characterized through quantification of the reaction patterns. This analytical approach is a promising diagnostic tool that is applicable to the real-time analysis of biochemical and chemical reactions such as polymerase chain reaction (PCR), catalytic, or synthetic processes in microfluidic devices.
Real-time monitoring of mitochondrial adenosine 5′-triphosphate synthesis and hydrolysis by surface infrared spectroscopy
Authors: Yamaguchi Ryo-taro , Hirano-Iwata Ayumi , Aonuma Yuki , Yoshimura Yuya , Shinohara Yasuo , Kimura Yasuo , Niwano Michio
Published: March 2011

We have developed a method for in situ real-time monitoring of adenosine 5′-triphosphate (ATP) synthesis in mitochondria using infrared absorption spectroscopy with the multiple internal reflection geometry. Spectral changes corresponding to ATP synthesis and hydrolysis were monitored under oxygenation and constant stirring condition. It was demonstrated that the reversible process of ATP synthesis in mitochondria can be monitored by analyzing stretching modes of α- and β-PO2− in adenine nucleotides. Our method has potential to evaluate mitochondrial toxicity in terms of mitochondrial activities of ATP synthesis and hydrolysis.
Growth of tin oxide nanorods induced by nanocube-oriented coalescence mechanism
Authors: Liu L. Z. , Li X. X. , Wu X. L. , Chen X. T. , Chu Paul K.
Published: March 2011

SnO 2 nanocrystals (NCs) with spherical, cubic, and cuboid nanorod morphologies are obtained at different stages in hydrothermal synthesis using a SnCl4⋅5H2O to CO(NH2)2 ratio of 1 to 10. Microstructural examination and theoretical derivation reveal that small spherical NCs are formed initially and some of them morph into cylindrical NCs because of the low surface free energy. These NCs transform into bigger cubic NCs with time finally evolving into cuboid nanorods due to Brownian motion. The cuboid nanorods have a lower surface free energy than the cubic NCs and constitute a stable nanostructure.
Lasing in a metal-clad microring resonator
Authors: Kim Min W. , Ku P.-C.
Published: March 2011

Metal cladding was experimentally demonstrated to be a feasible method to further scale down the size of a microring laser. Shrinking the physical dimensions of semiconductor microring resonators has been difficult due to a large waveguide bending loss. We experimentally show that light can be better confined into a much tighter space by using the plasmonic metal structure, thereby enabling miniaturization of a microring laser.
Phylogenetic relationships in Pterostylidinae (Cranichideae: Orchidaceae): combined evidence from nuclear ribomsomal and plastid DNA sequences
Authors: Clements Mark A. , Tupac Otero J. , Miller Joseph T.
Published: March 2011

A study to evaluate the relationships in subtribe Pterostylidinae (Cranichideae: Orchidaceae) was undertaken using DNA sequences from the nuclear ribosomal ITS region (256 taxa) and plastid matK (subset of 37 taxa). Parsimony analysis of nuclear, plastid and combined datasets revealed that there is strong support for the monophyly of Pterostylidinae, and three major groups therein. Clades A–C contain nine, possibly 10, identifiable groups supported by morphological synapomorphies. Clade A comprises the following two major, strongly supported groups that correlate with morphological synapomorphies: (1) Speculantha (including Petrorchis) and (2) Linguella and Eremorchis, sister to an unresolved polytomy containing Taurantha, a paraphyletic Crangonorchis and polyphyletic Diplodium. There is no support for continued recognition of Taurantha, Crangonorchis, Linguella and Eremorchis, all of which are embedded within the broader, strongly supported, monophyletic Diplodium. Clade B represents true Pterostylis. Clade C contains the morphologically disparate Bunochilus, Hymenochilus, Oligochaetochilus, Pharochilum, Plumatichilos, Stamnorchis and Urochilus (including Ranorchis) in a partially resolved tree. There is strong molecular and morphological synapomorphic internal support for the recognition of these taxa as genera. Our results revealed that none of the presently proposed classification systems for Pterostylidinae truly accounts for the underlying phylogenetic signal. A streamlined classification system, therefore, seems warranted, although further research based on a larger plastid DNA dataset is required to elucidate relationships in Clade C.
First karyotype, DNA C-value and AT/GC base composition of macaw palm (Acrocomia aculeata, Arecaceae) - a promising plant for biodiesel production
Authors: Abreu Isabella Santiago , Carvalho Carlos Roberto , Carvalho Guilherme Mendes Almeida , Motoike Sérgio Yoshimitsu
Published: March 2011

The oleaginous species Acrocomia aculeata produces high-quality oil and is considered a potential plant for sustainable production of food and biodiesel. In spite of its economical, social and environmental importance, few data concerning the genome size and chromosomal characterisation of this crop have been reported. In order to contribute to basic genetic knowledge on A. aculeata, this work aimed to assemble the first karyogram and to determine genome size and base composition of this species. Concerning the cytogenetic approach, we developed a protocol based on root tips treatment with an anti-mitotic agent, followed by enzymatic maceration and slide preparation by the air-drying technique. This method provided well resolved metaphasic chromosomes, which are important for an accurate and informative cytogenetical characterisation. A chromosome number of 2n = 30 was observed. Content of 2C DNA and base composition were estimated by flow cytometry of G0/G1 nuclei stained with propidium iodide and 4′,6-diamidino-2-phenylindole, respectively. The mean 2C-value and base composition corresponded to 2C = 5.81 pg and AT = 58.3%. These new data support basic genetic knowledge on A. aculeata, relevant for its conservation, diversity studies and consequent development of breeding programs, which may foment the biofuel production in the world.
Frequency of visits and efficiency of pollination by diurnal and nocturnal lepidopterans for the dioecious tree Randia itatiaiae (Rubiaceae)
Authors: Samuel de Avila Rubem , Freitas Leandro
Published: March 2011

In plants pollinated by different groups of animals, the most frequent visitors may not be the most effective for fitness because of their differential efficiency in pollen transfer. We addressed this question by studying a rare dioecious species of Rubiaceae in Brazil. The flowers of Randia itatiaiae are gender-heteromorphic and hypocrateriform with greenish corolla tubes ~2 cm long, and exhale a strong sweet scent during the entire period of anthesis, which starts at sunset for female flowers. Sucrose was the dominant or co-dominant nectar sugar for both genders. In spite of these typical sphingophilous-phalaenophilous traits, the flowers last for 6 days, and nectar was available in both diurnal and nocturnal assessments. Moreover, the flowering of R. itatiaiae did not overlap the phenodynamics of the Sphingidae community. Accordingly, two functional groups of Lepidoptera – Hesperiidae during the day and Sphingidae and Noctuidae at night – visited the flowers. Visits by either group resulted in equivalent fruit set and seed number per fruit, although the frequency of visits to flowers was higher during the day than at night. Diurnal and nocturnal lepidopterans may exert similar pressures on floral morphology, in addition to divergent pressures on other characters, such as the temporal dynamics of anthesis and nectar production. The pollination system of R. itatiaiae is specialised at the coarse scale, because its floral morphology precludes pollination by animals other than lepidopterans; however, its floral phenotype also represents a generalist compromise between the conflicting pressures exerted by diurnal and nocturnal groups of lepidopterans.
Quantifying physiological determinants of genetic variation for yield potential in sunflower. SUNFLO: a model-based analysis
Authors: Lecoeur Jérémie , Poiré-Lassus Richard , Christophe Angélique , Pallas Benoît , Casadebaig Pierre , Debaeke Philippe , Vear Felicity , Guilioni Lydie
Published: March 2011

Present work focussed on improving the description of organogenesis, morphogenesis and metabolism in a biophysical plant model (SUNFLO) applied to sunflower (Helianthus annuus L.). This first version of the model is designed for potential growth conditions without any abiotic or biotic stresses. A greenhouse experiment was conducted to identify and estimate the phenotypic traits involved in plant productivity variability of 26 sunflower genotypes. The ability of SUNFLO to discriminate the genotypes was tested on previous results of a field survey aimed at evaluating the genetic progress since 1960. Plants were phenotyped in four directions; phenology, architecture, photosynthesis and biomass allocation. Twelve genotypic parameters were chosen to account for the phenotypic variability. SUNFLO was built to evaluate their respective contribution to the variability of yield potential. A large phenotypic variability was found for all genotypic parameters. SUNFLO was able to account for 80% of observed variability in yield potential and to analyse the phenotypic variability of complex plant traits such as light interception efficiency or seed yield. It suggested that several ways are possible to reach high yields in sunflower. Unlike classical statistical analysis, this modelling approach highlights some efficient parameter combinations used by the most productive genotypes. The next steps will be to evaluate the genetic determinisms of the genotypic parameters.
Spatial characterization of the meltwater field from icebergs in the Weddell Sea
Authors: Helly John J. , Kaufmann Ronald S. , Vernet Maria , Stephenson Gordon R.
Published: March 2011

We describe the results from a spatial cyberinfrastructure developed to characterize the meltwater field around individual icebergs and integrate the results with regional- and global-scale data. During the course of the cyberinfrastructure development, it became clear that we were also building an integrated sampling planning capability across multidisciplinary teams that provided greater agility in allocating expedition resources resulting in new scientific insights. The cyberinfrastructure-enabled method is a complement to the conventional methods of hydrographic sampling in which the ship provides a static platform on a station-by-station basis. We adapted a sea-floor mapping method to more rapidly characterize the sea surface geophysically and biologically. By jointly analyzing the multisource, continuously sampled biological, chemical, and physical parameters, using Global Positioning System time as the data fusion key, thissurface-mappingmethod enables us to examine the relationship between the meltwater field of the iceberg to the larger-scale marine ecosystem of the Southern Ocean. Through geospatial data fusion, we are able to combine very fine-scale maps of dynamic processes with more synoptic but lower-resolution data from satellite systems. Our results illustrate the importance of spatial cyberinfrastructure in the overall scientific enterprise and identify key interfaces and sources of error that require improved controls for the development of future Earth observing systems as we move into an era of peta- and exascale, data-intensive computing.
Calcium-dependent copper redistributions in neuronal cells revealed by a fluorescent copper sensor and X-ray fluorescence microscopy
Authors: Dodani Sheel C. , Domaille Dylan W. , Nam Christine I. , Miller Evan W. , Finney Lydia A. , Vogt Stefan , Chang Christopher J.
Published: March 2011

Dynamic fluxes of s-block metals like potassium, sodium, and calcium are of broad importance in cell signaling. In contrast, the concept of mobile transition metals triggered by cell activation remains insufficiently explored, in large part because metals like copper and iron are typically studied as static cellular nutrients and there are a lack of direct, selective methods for monitoring their distributions in living cells. To help meet this need, we now report Coppersensor-3 (CS3), a bright small-molecule fluorescent probe that offers the unique capability to image labile copper pools in living cells at endogenous, basal levels. We use this chemical tool in conjunction with synchotron-based microprobe X-ray fluorescence microscopy (XRFM) to discover that neuronal cells move significant pools of copper from their cell bodies to peripheral processes upon their activation. Moreover, further CS3 and XRFM imaging experiments show that these dynamic copper redistributions are dependent on calcium release, establishing a link between mobile copper and major cell signaling pathways. By providing a small-molecule fluorophore that is selective and sensitive enough to image labile copper pools in living cells under basal conditions, CS3 opens opportunities for discovering and elucidating functions of copper in living systems.
Universal noninvasive detection of solid organ transplant rejection
Authors: Snyder Thomas M. , Khush Kiran K. , Valantine Hannah A. , Quake Stephen R.
Published: March 2011

It is challenging to monitor the health of transplanted organs, particularly with respect to rejection by the host immune system. Because transplanted organs have genomes that are distinct from the recipient's genome, we used high throughput shotgun sequencing to develop a universal noninvasive approach to monitoring organ health. We analyzed cell-free DNA circulating in the blood of heart transplant recipients and observed significantly increased levels of cell-free DNA from the donor genome at times when an endomyocardial biopsy independently established the presence of acute cellular rejection in these heart transplant recipients. Our results demonstrate that cell-free DNA can be used to detect an organ-specific signature that correlates with rejection, and this measurement can be made on any combination of donor and recipient. This noninvasive test holds promise for replacing the endomyocardial biopsy in heart transplant recipients and may be applicable to other solid organ transplants.
Transcription factor Bcl11b controls selection of invariant natural killer T-cells by regulating glycolipid presentation in double-positive thymocytes
Authors: Albu Diana I. , VanValkenburgh Jeffrey , Morin Nicole , Califano Danielle , Jenkins Nancy A. , Copeland Neal G. , Liu Pentao , Avram Dorina
Published: March 2011

Invariant natural killer T cells (iNKT cells) are innate-like T cells important in immune regulation, antimicrobial protection, and anti-tumor responses. They express semi-invariant T cell receptors, which recognize glycolipid antigens. Their positive selection is mediated by double-positive (DP) thymocytes, which present glycolipid self-antigens through the noncanonical MHC class I-like molecule CD1d. Here we provide genetic and biochemical evidence that removal of the transcription factor Bcl11b in DP thymocytes leads to an early block in iNKT cell development, caused by both iNKT cell extrinsic and intrinsic defects. Specifically,Bcl11b-deficient DP thymocytes failed to supportBcl11b-sufficient iNKT precursor development due to defective glycolipid self-antigen presentation, and showed enlarged lysosomes and accumulation of glycosphingolipids. Expression of genes encoding lysosomal proteins with roles in sphingolipid metabolism and glycolipid presentation was found to be altered inBcl11b-deficient DP thymocytes. These include cathepsins and Niemann–Pick disease type A, B, and C genes. Thus, Bcl11b plays a central role in presentation of glycolipid self-antigens by DP thymocytes, and regulates directly or indirectly expression of lysosomal genes, exerting a critical extrinsic role in development of iNKT lineage, in addition to the intrinsic role in iNKT precursors. These studies demonstrate a unique and previously undescribed role of Bcl11b in DP thymocytes, in addition to the critical function in positive selection of conventional CD4 and CD8 single-positive thymocytes.