bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell
Authors: Velasco Daniel Soares , Baesso Mauro Luciano , Medina Antonio Neto , Bicanic Dane Danijel , Koehorst Rob , van der Hooft Justin Johan Jozias , Bento Antonio Carlos
Published: February 2011

The frequency-domain open photoacoustic cell (OPC) approach was used to determine room temperature thermal diffusivity of skins (pericarps) from the raw tomatoes (Lycopersicon esculetum Mill.) characterized by the three different stages of ripeness (from immature-green to a mature-red). Periodically interrupted 532 nm laser radiation was used to heat the dry tomato skins, typically 10 mm in diameter and up to 68 μm thick; the modulating frequency f varied from 8 to 150 Hz. Initially, a combined OPC-model that takes into account both, the thermoelastic bending and the effect of thermal diffusion (TD), has been applied. Preliminary results showed that until at least 40 Hz, the effect of TD dominates; above this value the combined model fits the experimental data only poorly. For this reason a less complex OPC-TD approach was applied to all investigated skins instead, which predicts an exponential decrease for the amplitude of measured photoacoustic signal S with increasing f. For a specimen that is simultaneously opaque and thermally thick, S depends on f as S∼exp(−b f1/2) where b is a fitting parameter. The S versus f plot enables one to deduce the numerical value for b which, on its turn allows for the assessment of skin’s thermal diffusivity α. Thermal diffusivities obtained for the immature green, orange, and red skins (periderms) are 9.9×10−8 m2 s−1, 7.2×10−8 m2 s−1, and 4.6×10−8 m2 s−1, respectively; the uncertainty was typically 5% of the measured value.
Ground state of small mixed helium and spin-polarized tritium clusters: A quantum Monte Carlo study
Authors: Stipanović P. , Markić L. Vranješ , Boronat J. , Kežić B.
Published: February 2011

We report results for the ground-state energy and structural properties of small 4He–T↓ clusters consisting of up to four T↓ and eight 4He atoms. These results have been obtained using very well-known 4He–4He and T↓– T↓ interaction potentials and several models for the 4He– T↓ interatomic potential. All the calculations have been performed with variational and diffusion Monte Carlo methods. It takes at least three atoms to form a mixed bound state. In particular, for small clusters the binding energies are significantly affected by the precise form of the 4He– T↓ interatomic potential but the stability limits remain unchanged. The only exception is the 4He2T↓ trimer whose stability in the case of the weakest 4He– T↓ interaction potential is uncertain while it seems stable for other potentials. The mixed trimer 4He(T↓)2, a candidate for the Borromean state, is not bound. All other studied clusters are stable. Some of the weakest bound clusters can be classified as quantum halo as a consequence of having high probability of being in a classically forbidden region.
Cartesian coupled coherent states simulations: NenBr2 dissociation as a test case
Authors: Reed Stewart K. , González-Martínez Maykel L. , Rubayo-Soneira Jesús , Shalashilin Dmitrii V.
Published: February 2011

In this article, we describe coupled coherent states (CCS) simulations of vibrational predissociation of weakly bounded complexes. The CCS method is implemented in the Cartesian frame in a manner that is similar to classical molecular dynamics. The calculated lifetimes of the vibrationally excited Ne-Br2(ν) complexes agree with experiment and previous calculations. Although the CCS method is, in principle, a fully quantum approach, in practice it typically becomes a semiclassical technique at long times. This is especially true following dissociation events. Consequently, it is very difficult to converge the quantum calculations of the final Br2 vibrational distributions after predissociation and of the autocorrelation functions. However, the main advantage of the method is that it can be applied with relative ease to determine the lifetimes of larger complexes and, in order to demonstrate this, preliminary results for tetra- and penta-atomic clusters are reported.
Efficient implementation of the Hellmann–Feynman theorem in a diffusion Monte Carlo calculation
Authors: Vitiello S. A.
Published: February 2011

Kinetic and potential energies of systems of \documentclass[12pt]{minimal}\begin{document}$^4$\end{document}4He atoms in the solid phase are computed at T = 0. Results at two densities of the liquid phase are presented as well. Calculations are performed by the multiweight extension to the diffusion Monte Carlo method that allows the application of the Hellmann–Feynman theorem in a robust and efficient way. This is a general method that can be applied in other situations of interest as well.
Stability, structural, and magnetic phase diagrams of ternary ferromagnetic 3d-transition-metal clusters with five and six atoms
Authors: Guzmán-Ramírez G. , Robles J. , Vega A. , Aguilera-Granja F.
Published: February 2011

We report a theoretical investigation of free-standing \documentclass[12pt]{minimal}\begin{document}$ {\rm Fe}_{\it x} \rm {Co}_{\it y} {\rm Ni}_{\it z}$\end{document} Fe x Co y Ni z ternary clusters with x + y + z = 5 and 6. Our study is performed within density functional theory as implemented in the GAUSSIAN 03 set of programs and with the BPW91/SDD level of theory. We analyze the geometries, chemical order, local and total magnetic moments, binding energies, excess energies, and second difference in the energy in the whole range of composition, from which structural, magnetic, and stability phase diagrams are predicted for these cluster sizes. We determine the optimal stoichiometries for these clusters as regards the maximum total magnetic moment and stability.
Communication: Driven Brownian transport in eccentric septate channels
Authors: Borromeo M. , Marchesoni F. , Ghosh P. K.
Published: February 2011

In eccentric septate channels the pores connecting adjacent compartments are shifted off-axis, either periodically or randomly, so that straight trajectories parallel to the axis are not allowed. Driven transport of a Brownian particle in such a channel is characterized by a strong suppression of the current and its dispersion. For large driving forces, both quantities approach an asymptotic value, which can be analytically approximated in terms of the stationary distribution of the particle exit times out of a single channel compartment.
Numerical failure analysis of current-confined-path current perpendicular-to-plane giant magnetoresistance spin-valve read sensors under high current density
Authors: Zeng Ding Gui , Chung Kyung-Won , Ha Jae-Geun , Bae Seongtae
Published: February 2011

Thermomigration (TM)-induced failures occurred in the current-confined-path (CCP) current perpendicular-to-the plane (CPP) giant magnetoresistance spin valve (GMR SV) read sensors with Cu nanopillar metal paths (∼5 nm in diameter) operating at a high current density (J>2×107 A/cm2) have been numerically studied to explore the magnetic and electrical stability. The Cu interdiffusion (migration) from nanopillars into adjacent magnetic layers (e.g., CoFe) due to thermally induced mass transport was found to be the main physical reason for the magnetic failures of CCP-CPP GMR SV read sensors including the change in interlayer coupling and the reduction in exchange bias field as well as MR. Furthermore, it was numerically verified that the TM-induced failures are more dominant than the electromigration-induced failures at the higher current density beyond J=6×107 A/cm2 in the CCP-CPP GMR SV read sensors. However, all the numerical calculation results demonstrated in this study clearly suggest that these undesirable electrical and magnetic failures occurred in the CCP-CPP GMR SV read sensors can be improved by tuning the path density, the purity (electrical resistivity), and the uniformity of Cu nanopillar metal paths.
Dependence on diameter and growth direction of apparent strain to failure of Si nanowires
Authors: Steighner M. S. , Snedeker L. P. , Boyce B. L. , Gall K. , Miller D. C. , Muhlstein C. L.
Published: February 2011

Previous studies of the mechanical properties of Si nanowires have not shown the size-dependent strengths that are expected for this prototypical brittle material. A potential source of the ambiguity in the literature is the development of tensile stresses during the large (nonlinear) deflections that were present during the flexure tests. In this work we show that size-dependent strengths can be observed in Si nanowires when they are evaluated using uniaxial tension loading conditions. Si nanowires with diameters ranging from 268 to 840 nm were fabricated using the vapor-liquid-solid method and were strained to failure in vacuum using a micromachined load frame. The smallest nanowires were the strongest but the magnitude of the size effect suggests that the flaw populations in Si nanowires are orientation-dependent.
Solvent-free coarse-grained lipid model for large-scale simulations
Authors: Noguchi Hiroshi
Published: February 2011

A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction between particles. A bilayer structure is formed by orientation-dependent (tilt and bending) potentials. In this model, the membrane properties (bending rigidity, line tension of membrane edge, area compression modulus, lateral diffusion coefficient, and flip-flop rate) can be varied over broad ranges. The stability of the bilayer membrane is investigated via droplet-vesicle transition. The rupture of the bilayer and worm-like micelle formation can be induced by an increase in the spontaneous curvature of the monolayer membrane.
Ab initio chemical kinetics for reactions of ClO with Cl2O2 isomers
Authors: Zhu R. S. , Lin M. C.
Published: February 2011

The mechanisms for the reactions of ClO with ClOClO, ClOOCl, and ClClO2 have been investigated at the CCSD(T)/6–311+G(3df)//PW91PW91/6–311+G(3df) level of theory. The rate constants for their low energy channels have been calculated by statistical theory. The results show that the main products for the reaction of ClO with ClOClO are ClOCl + ClOO, which can be produced readily by ClO abstracting the terminal O atom from ClOClO. This process occurs without an intrinsic barrier, with the predicted rate constant: k (ClO + ClOClO) = 7.26 × 10−10 T−0.15 × exp (−40/T) cm3molecule−1s−1 for 200–1500 K. For the reactions of ClO + ClOOCl and ClClO2, the lowest abstraction barriers are 7.2 and 7.3 kcal/mol, respectively, suggesting that these two reactions are kinetically unimportant in the Earth's stratosphere as their rate constants are less than 10−14 cm3molecule−1s−1 below 700 K. At T = 200–1500 K, the computed rate constants can be represented by k (ClO+ ClOOCl) = 1.11 × 10 −14 T 0.87 exp (−3576/T) and k (ClO+ ClClO2) = 4.61 × 10−14 T0.53 exp (−3588/T) cm3molecule−1s−1. For these systems, no experimental or theoretical kinetic data are available for comparison.
Effects of continuum breakdown on hypersonic aerothermodynamics for reacting flow
Authors: Holman Timothy D. , Boyd Iain D.
Published: February 2011

This study investigates the effects of continuum breakdown on the surface aerothermodynamic properties (pressure, stress, and heat transfer rate) of a sphere in a Mach 25 flow of reacting air in regimes varying from continuum to a rarefied gas. Results are generated using both continuum [computational fluid dynamics (CFD)] and particle [direct simulation Monte Carlo (DSMC)] approaches. The DSMC method utilizes a chemistry model that calculates the backward rates from an equilibrium constant. A preferential dissociation model is modified in the CFD method to better compare with the vibrationally favored dissociation model that is utilized in the DSMC method. Tests of these models are performed to confirm their validity and to compare the chemistry models in both numerical methods. This study examines the effect of reacting air flow on continuum breakdown and the surface properties of the sphere. As the global Knudsen number increases, the amount of continuum breakdown in the flow and on the surface increases. This increase in continuum breakdown significantly affects the surface properties, causing an increase in the differences between CFD and DSMC. Explanations are provided for the trends observed.
Suppression of the Ag/Si surface conductivity transition temperature by organic adsorbates
Authors: Song F. , Gammelgaard L. , Hofmann Ph. , Wells J. W.
Published: February 2011

We present temperature dependent nanoscale four-contact conductance measurements performed on a submonolayer coverage of cobalt phthalocyanine on Si(111)–(3×3)Ag. The presence of the organic adsorbates suppresses the reversible Ag/Si surface phase transition temperature and reduces the magnitude of the accompanying switching of the surface conductance. The absence of an observable Kondo effect is also discussed in terms of the reported electron transfer between the Ag/Si surface and the Co2+ ion.
Hydration of hydrophobic biological porphyrins
Authors: Guizado T. R. Cuya , Louro S. R. W. , Anteneodo C.
Published: February 2011

Explicit solvent, single solute molecular dynamics simulations of protoporphyrin IX and its \documentclass[12pt]{minimal}\begin{document}${\rm Fe}^{2+}$\end{document} Fe 2+ complex (heme) in water were performed. The relation of solute–solvent was examined through the spatial distribution functions of water molecules around the centroid of the porphyrin ring. A detailed description of the time-averaged structure of water surrounding the solutes as well as of its fluctuations is presented.
Experimental characterization of hexaferrite ceramics from 100 GHz to 1 THz using vector network analysis and terahertz-time domain spectroscopy
Authors: Yang Bin , Wang Xinke , Zhang Yan , Donnan Robert S.
Published: February 2011

Gyrotropic, magnetically-hard hexaferrite ceramics, are a very promising material for deployment as quasioptical nonreciprocal devices at high frequencies (⪢90 GHz). In this paper, a quasioptical measurement bench driven by a vector-network analyzer and a terahertz (THz) time domain spectroscopy measurement system are used in conjunction to characterize a thin (2.02 mm thickness) hexaferrite plate for two orthogonal states of beam polarization. From these data, the intrinsic circular-polarization transmittance for each state (or case), of polarization, left and right, is computed. Inherent magneto-optical constants of the plate over the range of 100 GHz to 1 THz are then determined. Analysis reveals low attenuation of the hexaferrite ceramics over millimeter and submillimeter wave bands.
The role of temperature in nucleation processes
Authors: ter Horst J. H. , Bedeaux D. , Kjelstrup S.
Published: February 2011

Heat and mass transfers are coupled processes, also in nucleation. In principle, a nucleating cluster would have a different temperature compared to the surrounding supersaturated old phase because of the heat release involved with attaching molecules to the cluster. In turn a difference in temperature across the cluster surface is a driving force for the mass transfer to and from the cluster. This coupling of forces in nonisothermal nucleation is described using mesoscopic nonequilibrium thermodynamics, emphasizing measurable heat effects. An expression was obtained for the nonisothermal nucleation rate in a one-component system, in the case where a temperature difference exists between a cluster distribution and the condensed phase. The temperature is chosen as a function of the cluster size only, while the temperature of the condensed phase is held constant by a bath. The generally accepted expression for isothermal stationary nucleation is contained as a limiting case of the nonisothermal stationary nucleation rate. The equations for heat and mass transport were solved for stationary nucleation with the given cluster distribution and with the temperature controlled at the boundaries. A factor was defined for these conditions, determined by the heat conductivity of the surrounding phase and the phase transition enthalpy, to predict the deviation between isothermal and nonisothermal nucleation. For the stationary state described, the factor appears to give small deviations, even for primary nucleation of droplets in vapor, making the nonisothermal rate smaller than the isothermal one. The set of equations may lead to larger and different thermal effects under different boundary conditions, however.
Protein folding in a reverse micelle environment: The role of confinement and dehydration
Authors: Martinez Anna Victoria , DeSensi Susan C. , Dominguez Laura , Rivera Eva , Straub John E.
Published: February 2011

Characterization of the molecular interactions that stabilize the folded state of proteins including hydrogen bond formation, solvation, molecular crowding, and interaction with membrane environments is a fundamental goal of theoretical biophysics. Inspired by recent experimental studies by Gai and co-workers, we have used molecular dynamics simulations to explore the structure and dynamics of the alanine-rich AKA2 peptide in bulk solution and in a reverse micelle environment. The simulated structure of the reverse micelle shows substantial deviations from a spherical geometry. The AKA2 peptide is observed to (1) remain in a helical conformation within a spherically constrained reverse micelle and (2) partially unfold when simulated in an unconstrained reverse micelle environment, in agreement with experiment. While aqueous solvation is found to stabilize the N- and C-termini random coil portions of the peptide, the helical core region is stabilized by significant interaction between the nonpolar surface of the helix and the aliphatic chains of the AOT surfactant. The results suggest an important role for nonpolar peptide–surfactant and peptide–lipid interactions in stabilizing helical geometries of peptides in reverse micelle environments.
Photoelectron spectroscopic study of the E⊗e Jahn–Teller effect in the presence of a tunable spin–orbit interaction. I. Photoionization dynamics of methyl iodide and rotational fine structure of CH3I+ and CD3I+
Authors: Grütter M. , Michaud J. M. , Merkt F.
Published: February 2011

The high-resolution single-photon pulsed-field-ionization zero-kinetic-energy photoelectron spectra of the \documentclass[12pt]{minimal}\begin{document}$\tilde{\rm {X}}^+$\end{document}X̃+ 2\documentclass[12pt]{minimal}\begin{document}$\rm {E_{3/2}}\leftarrow \tilde{\rm {X}}\, ^1{\rm A}_1$\end{document}E3/2←X̃1A1 transition of CH3I and CD3I have been recorded. The spectral resolution of better than 0.15 cm−1 enabled the observation of the rotational structure. CH3I+ and CD3I+ are subject to a weak \documentclass[12pt]{minimal}\begin{document}$\rm {E}\otimes \rm {e}$\end{document}E⊗e Jahn–Teller effect and strong spin–orbit coupling. The treatment of the rovibronic structure of the photoelectron spectra in the corresponding spin double group, \documentclass[12pt]{minimal}\begin{document}$\rm {C_{3v}^2(M)}$\end{document}C3v2(M), including the effects of the spin–orbit interaction and the vibrational angular momentum, allowed the reproduction of the experimentally observed transitions with spectroscopic accuracy. The relevant spin–orbit and linear Jahn–Teller coupling parameters of the \documentclass[12pt]{minimal}\begin{document}$\tilde{\rm {X}}^+$\end{document}X̃+ ground state were derived from the analysis of the spectra of the two isotopomers, and improved values were obtained for the adiabatic ionization energies [\documentclass[12pt]{minimal}\begin{document}${E_{\rm {I}}(\rm {CH}_3\rm {I})}/hc =76931.35(20)$\end{document}EI( CH 3I)/hc=76931.35(20) cm−1 and \documentclass[12pt]{minimal}\begin{document}${E_{\rm {I}}(\rm {CD}_3\rm {I})}/hc=76957.40(20)$\end{document}EI( CD 3I)/hc=76957.40(20) cm−1] and the rotational constants of the cations. Rovibronic photoionization selection rules were derived for transitions connecting neutral states following Hund's-case-(b)-type angular momentum coupling and ionic states following Hund's-case-(a)-type coupling. The selection rules, expressed in terms of the angular momentum projection quantum number P, account for all observed transitions and provide an explanation for the nonobservation of several rotational sub-bands in the mass-analyzed threshold-ionization spectra of \documentclass[12pt]{minimal}\begin{document}$\rm {CH}_3\rm {I}$\end{document} CH 3I and \documentclass[12pt]{minimal}\begin{document}$\rm {CD}_3\rm {I}$\end{document} CD 3I reported recently by Lee et al. [J. Chem. Phys. 128, 044310 (2008)].
Spin-filter and Fano antiresonant effect in conductance through a zigzaglike polymer device: Nonequilibrium Green's function approach
Authors: Fu Hua-Hua , Yao Kai-Lun
Published: February 2011

Electronic transport through a quasi-one-dimensional zigzaglike polymer device is theoretically studied by means of the nonequilibrium Green's function approach. In this system, the main zigzag chain consists of carbon atoms and is attached with side radicals at its next-near-neighbor sites. The results show that a zero point of the linear conductance spectrum occurs due to the Fano antiresonance induced by the electron hoppings between the main chain and the side radicals, which leads to the fact that the linear conductance spectrum displays an insulating band around the antiresonant point. The increase in the polymer size makes both edges of the insulating band to become steep rapidly, which makes the insulating band approach to be a well-defined one. The formation of the dimer along the main chain enhances the insulating band width but much suppresses the electronic transport through the device. Moreover, if the many-body effect due to the electron interaction is taken into account, the antiresonance effect and the well-defined insulating band remain. As a result, a well spin-polarized window appears as the spin splitting occurred by applying an external magnetic field. These results strongly propose that there is a new way for the organic polymer to be applied as a spin-filter.
Measurement of depth and energy of buried trap states in dielectric films by single electron tunneling force spectroscopy
Authors: Johnson J. P. , Winslow D. W. , Williams C. C.
Published: February 2011

Electronic trap states in dielectric materials critically influence the reliability and performance of electronic devices. A method to characterize such states with atomic scale spatial resolution is presented. The method is based on tunneling charge measurements, performed at different voltages and tip-sample gaps, and a tunneling model. When combined with previously demonstrated two-dimensional trap state imaging, this method will provide for three-dimensional imaging of electronic defect states in dielectrics with atomic scale spatial resolution.
Enhancement of tetragonality and role of strontium vacancies in heterovalent doped SrTiO3
Authors: Tkach A. , Almeida A. , Moreira J. Agostinho , Correia T. M. , Chaves M. R. , Okhay O. , Vilarinho P. M. , Gregora I. , Petzelt J.
Published: February 2011

The effect of Sr vacancies on the behavior of strontium titanate with trivalent dopants (La3+, Gd3+, and Y3+) substituting Sr2+ ions is reported. A remarkable shift of the antiferrodistortive transition temperature Ta is revealed by Raman spectroscopy for just a small content of dopant. It is shown that a unique linear dependence of Ta versus tolerance factor is obtained when Sr-vacancies are taken into account. A vacancy size value of ∼1.54 Å is estimated, which is ∼7% larger than Sr2+ radius. This size difference enables explaining the unexpected increase of lattice parameter with increasing Bi3+ content in Sr1−1.5xBixTiO3.
Room temperature writing of electrically conductive and insulating zones in silicon by nanoindentation
Authors: Ruffell S. , Sears K. , Bradby J. E. , Williams J. S.
Published: February 2011

Conventional silicon devices are fabricated in the diamond cubic phase of silicon, so-called Si-I. Other phases of silicon such as Si-XII and Si-III can be formed under pressure applied by nanoindentation and these phases are metastable at room temperature and pressure. We demonstrate in this letter that such phases exhibit different electrical properties to normal (diamond cubic) silicon and exploit this to perform maskless, room temperature, electrical patterning of silicon by writing both conductive and insulating zones directly into silicon substrates by nanoindentation. Such processing opens up a number of potentially new applications without the need for high temperature processing steps.
Numerical investigation of elongated drops in a microfluidic T-junction
Authors: Afkhami S. , Leshansky A. M. , Renardy Y.
Published: February 2011

We present a combined numerical and asymptotic approach for modeling droplets in microchannels. The magnitude of viscous forces relative to the surface tension force is characterized by a capillary number, Ca, which is assumed to be small. The numerical results successfully capture existing asymptotic solutions for the motion of drops in unconfined and confined flows; examples include the analytic Stokes flow solution for a two-dimensional inviscid bubble placed in an unbounded parabolic flow field and asymptotic formulas for slender bubbles and drops in confined flows. An extensive investigation of the accuracy of the computations is presented to probe the efficacy of the methodology and algorithms. Thereafter, numerical simulations are presented for droplet breakup in a symmetric microfluidic T-junction. The results are shown to support a proposed mechanism for breakup, driven by a pressure drop in a narrow gap between the droplet and the outer channel wall, which was formally derived in the limit Ca1/5⪡1 [A. M. Leshansky and L. M. Pismen, “Breakup of drops in a microfluidic T junction,” Phys. Fluids 21, 023303 (2009)].
Electrically controlled hydrophobicity in a surface modified nanoporous carbon
Authors: Kim Taewan , Lu Weiyi , Lim Hyuck , Han Aijie , Qiao Yu
Published: February 2011

Conventional surface treatments lead to constant surface morphologies and properties. Here we show that as the inner surfaces of a nanoporous carbon are modified by 16-mercaptohexadecanoic acid through a two-step grafting process, due to the flexibility of the surface chains, the end groups can be repelled by negative surface charges and attracted by positive surface charges. Thus, the surface wettability is controlled electrically. The effective solid-liquid interfacial tension in the nanopores is analyzed in a pressure induced infiltration experiment.
Determining ferroelectric polarity at the nanoscale
Authors: LeBeau James M. , D’Alfonso Adrian J. , Wright Nicholas J. , Allen Leslie J. , Stemmer Susanne
Published: February 2011

Position averaged convergent beam electron diffraction (PACBED) in scanning transmission electron microscopy is shown to be capable of determining the direction of ferroelectric polarity at the nanoscale. We show that PACBED patterns of ferroelectric materials such as PbTiO3 and BaTiO3 are sensitive to both unit cell distortion and the absolute direction of polarity within the unit cell. It is shown that the polarity can be determined even in cases where real-space high-resolution transmission electron microscopy would not be capable of resolving the atomic displacements. The method is applied to determine the direction of polarization in an epitaxial BaTiO3 film.
Epitaxial integration of ferromagnetic correlated oxide LaCoO3 with Si (100)
Authors: Posadas A. , Berg M. , Seo H. , de Lozanne A. , Demkov A. A. , Smith D. J. , Kirk A. P. , Zhernokletov D. , Wallace R. M.
Published: February 2011

We have grown epitaxial strained LaCoO3 on (100)-oriented silicon by molecular beam epitaxy using a relaxed epitaxial SrTiO3 buffer layer. Superconducting quantum interference device magnetization measurements show that, unlike the bulk material, the ground state of the strained LaCoO3 on silicon is ferromagnetic with a TC of 85 K. First principles calculations suggest that a ferromagnetic ground state can be stabilized in LaCoO3 by a sufficiently large biaxial tensile strain with the transition accompanied by a partial untilting of the CoO6 octahedra.
Bandgap tailoring of rutile TiO2(110) via surface patterning with electron cyclotron resonance sputtering
Authors: Majumder Subrata , Paramanik D. , Solanki V. , Bag B. P. , Varma Shikha
Published: February 2011

Crystalline TiO2 nanodots have been formed on single crystal rutile TiO2(110) surfaces via ion beam sputtering method by utilizing Ar ion beams from electron cyclotron resonance source. Nearly five times enhancement in absorbance of visible light, ∼5 times increase in luminescence, and ∼0.1 eV narrowing of bandgap are observed for nanodot-patterned surfaces, in the absence of any dopant material. Formation of crystalline rutile TiO2 nanodots and development of Ti interstitials on the TiO2(110) surface, after ion beam sputtering, are responsible for these observations. Results suggest that these nanodot-patterned rutile TiO2 surfaces can become effective photocatalysts.
Surface properties for rarefied circular jet impingement on a flat plate
Authors: Khasawneh Khaleel , Liu Hongli , Cai Chunpei
Published: February 2011

In this paper, we investigate rarefied jet gas flows out of a circular exit impinging on a vertical flat plate. We employ a constraint relation about the velocity components of gas particles leaving a nozzle exit point and arriving at a given spatial point outside the nozzle. This relation leads to several analytical expressions for collisionless flow property distributions on the plate surface, including density, slip-velocity, temperature, pressure, shear stress, and heat flux. Numerical simulation results obtained with the direct simulation Monte Carlo method validate the analytical collisionless flow solutions. The impingement properties on the plate surface are accurate when the Knudsen number is large.
Simulation of low frequency Buneman instability of a current-driven plasma by particle in cell method
Authors: Niknam A. R. , Komaizi D. , Hashemzadeh M.
Published: February 2011

The nonlinear dynamics of low frequency Buneman instability in a current-driven cold unmagnetized plasma are studied using particle in cell simulation. Simulations of the Buneman instability show that the electron density profile has sharp peaks and the amplitude of the peaks changes with time. Also, the nonlinear evolution of this instability and saturation time is investigated by the time variation of the electric potential energy in the plasma. Moreover, the electron trapping phenomena and the formation of phase space electron holes are presented by considering the phase space diagram and electron distribution function. Finally, the ion mass effect on saturation time is investigated and it is found that the saturation time increases by increasing the ion mass and the saturation level is not very sensitive to the ion mass.
Real-time direct observation of Li in LiCoO2 cathode material
Authors: Huang Rong , Hitosugi Taro , Findlay Scott D. , Fisher Craig A. J. , Ikuhara Yumi H. , Moriwake Hiroki , Oki Hideki , Ikuhara Yuichi
Published: February 2011

The direct observation of light elements such as Li is a challenge even for state-of-the-art electron microscopy techniques because such elements scatter electrons only weakly. Using the annular bright field scanning transmission electron microscopy imaging technique, we have simultaneously visualized columns of Li, O, and Co ions in the lithium-ion battery cathode material LiCoO2, which is one of the most important cathode materials for industrial applications. The annular bright field image exhibits a good signal-to-noise ratio and the image contrast is not reversed as the specimen thickness changes. The direct visualization of light elements in real time with this method represents an important breakthrough in characterizing the active materials in solid-state electrochemical devices.
A novel method for determining the M-band fraction in laser-driven gold hohlraums
Authors: Li Yongsheng , Huo Wen Yi , Lan Ke
Published: February 2011

A novel method is proposed for determining the M-band (2–4 keV) fraction in laser-driven gold (Au) hohlraums, based on our study on the responses of x-ray ablative shock waves to Au M-band radiation flux in aluminum (Al) and titanium (Ti). Due to their different opacity properties, the velocity of shock wave in Al decreases as the M-band fraction, while increases in Ti. The scaling relation of radiation temperature with shock velocity and M-band fraction is given for Al and Ti materials. Our method provides a complementary means in determining the M-band fraction in a hohlraum.
Transition from relaxor to ferroelectric-like phase in poly(vinylideneflouride-trifluoroethylene-chloroflouroethylene) terpolymer ultrathin films
Authors: Wang J. L. , Yuan S. Z. , Tian L. , Meng X. J. , Sun J. L. , Chu J. H.
Published: February 2011

The poly(vinylidenefluoride-trifluoroethylene-chlorofluoroethylene) terpolymer (56.2/36.3/7.5, mol %) films from 1.6 to 10 nm in thickness were prepared by the Langmuir–Blodgett method. The dielectric and ferroelectric properties of the terpolymer films were investigated. The phase transition of the films of less 3.2 nm in thickness exhibits a ferroelectric-like nature, which is inconsistent with the bulk terpolymers. The peak of the permittivity is at ∼360 K, which is much higher than the thick terpolymer films and it is independent on frequency. Both polarization-electric field and capacitance-voltage curves show a ferroelectric-like characteristic, which is confirmed by piezoresponse force microscopy, suggesting the presence of all-trans molecular conformation.
High-resolution multi-MeV x-ray radiography using relativistic laser-solid interaction
Authors: Courtois C. , Edwards R. , Compant La Fontaine A. , Aedy C. , Barbotin M. , Bazzoli S. , Biddle L. , Brebion D. , Bourgade J. L. , Drew D. , Fox M. , Gardner M. , Gazave J. , Lagrange J. M. , Landoas O. , Le Dain L. , Lefebvre E. , Mastrosimone D. , Pichoff N. , Pien G. , Ramsay M. , Simons A. , Sircombe N. , Stoeckl C. , Thorp K.
Published: February 2011

When high intensity (≥1019 W cm−2) laser light interacts with matter, multi-MeV electrons are produced. These electrons can be utilized to generate a MeV bremsstrahlung x-ray emission spectrum as they propagate into a high-Z solid target positioned behind the interaction area. The short duration (<10 ps) and the small diameter (<500 μm) of the x-ray pulse combined with the MeV x-ray spectrum offers an interesting alternative to conventional bremsstrahlung x-ray sources based on an electron accelerator used to radiograph dense, rapidly moving objects. In experiments at the Omega EP laser, a multi-MeV x-ray source is characterized consistently with number of independent diagnostics. An unfiltered x-ray dose of approximately 2 rad in air at 1 m and a source diameter of less than 350 μm are inferred. Radiography of a complex and high area density (up to 61 g/cm2) object is then performed with few hundred microns spatial resolution.
Kinetic linear model of the interaction of helical magnetic perturbations with cylindrical plasmas
Authors: Ivanov Ivan B. , Heyn Martin F. , Kasilov Sergei V. , Kernbichler Winfried
Published: February 2011

The linear kinetic model of the interaction of helical rotating magnetic perturbations (resonant and nonresonant) with a tokamak plasma developed in [M. F. Heyn et al., Nucl. Fusion 46, S159 (2006)] is extended by a Galilean invariant collision operator and a different finite Larmor radius expansion scheme of particle current density. The model is applied to study the plasma screening effect on resonant magnetic perturbations and the resulting torques acting on the plasma at various orders of Larmor radius expansion.
Experimental validation of strong directional selectivity in nonsymmetric metallic gratings with a subwavelength slit
Authors: Cakmakyapan Semih , Caglayan Humeyra , Serebryannikov Andriy E. , Ozbay Ekmel
Published: February 2011

Strong directional selectivity is theoretically predicted and experimentally validated at the microwave frequencies in the beaming regime for a single subwavelength slit in nonsymmetric metallic gratings with double-side corrugations. The operation regime can be realized at a fixed angle of incidence when the surface-plasmon assisted transmission is significant within a narrow range of observation angles, if illuminating one of the grating interfaces, and tends to vanish for all observation angles, if illuminating the opposite interface. The studied effect is connected with asymmetry (nonreciprocity) in the beaming that occurs if the surface plasmon properties are substantially different for the two interfaces being well isolated from each other.
Chaotic emission and tunable self-sustained pulsations in a two-section Fabry–Perot quantum dot laser
Authors: Mesaritakis Charis , Argyris Apostolos , Simos Christos , Simos Hercules , Kapsalis Alexandros , Krestnikov Igor , Syvridis Dimitris
Published: February 2011

We present an experimental study on the intrinsic instabilities of a two electrode InAs/InGaAs Fabry–Perot quantum dot laser in the absence of optical feedback. By individually controlling the current injected in each electrode, different regimes of operation are allowed including tunable self-sustained pulsations and coherence collapse resulting to possible chaotic emission. The origin of these effects does not resign in the presence of optical feedback but is associated to the carrier dynamics of the quantum dot device. A numerical analysis on the time traces collected from the device reveals high complexity output in terms of correlation dimension.
Stressed crops emit more methane despite the mitigating effects of elevated carbon dioxide
Authors: Qaderi Mirwais M. , Reid David M.
Published: January 2011

Recent studies using single environmental variables show that under aerobic conditions terrestrial plants can emit methane (CH4). However, the effects of multiple environmental factors – as components of global climate change – on aerobic CH4 emissions have been little studied. We examined the combined effects of temperature, carbon dioxide (CO2) and watering regime on CH4 emissions from six commonly cultivated crop species: faba bean, sunflower, pea, canola, barley and wheat. Plants were grown from seeds in controlled-environment growth chambers under two temperature regimes (24°C day/20°C night and 30°C day/26°C night), two CO2 concentrations (380 and 760 µmol mol–1) and two watering regimes (well watered and water stressed). Plants were grown first under 24/20°C for 1 week from sowing, and then placed under experimental conditions for a further week. After the specified time, plant growth, gas exchange and CH4 emission rates were determined. Our results revealed that higher temperature and water stress significantly enhance CH4 emissions from plants, whereas elevated CO2 had the opposite effect and partially reverses the promotive effects of these factors. We suggest that the despite the mitigating effects of rising atmospheric CO2, CH4 emission may be higher in the face of ongoing global climate change in warmer and drier environments.
TBR1 directly represses
Fezf2
to control the laminar origin and development of the corticospinal tract
Authors: Han Wenqi , Kwan Kenneth Y. , Shim Sungbo , Lam Mandy M. S. , Shin Yurae , Xu Xuming , Zhu Ying , Li Mingfeng , Šestan Nenad
Published: February 2011

The corticospinal (CS) tract is involved in controlling discrete voluntary skilled movements in mammals. The CS tract arises exclusively from layer (L) 5 projection neurons of the cerebral cortex, and its formation requires L5 activity of
Fezf2
(
Fezl
,
Zfp312
). How this L5-specific pattern of
Fezf2
expression and CS axonal connectivity is established with such remarkable fidelity had remained elusive. Here we show that the transcription factor TBR1 directly binds the
Fezf2
locus and represses its activity in L6 corticothalamic projection neurons to restrict the origin of the CS tract to L5. In
Tbr1
null mutants, CS axons ectopically originate from L6 neurons in a
Fezf2
-dependent manner. Consistently, misexpression of
Tbr1
in L5 CS neurons suppresses
Fezf2
expression and effectively abolishes the CS tract. Taken together, our findings show that TBR1 is a direct transcriptional repressor of
Fezf2
and a negative regulator of CS tract formation that restricts the laminar origin of CS axons specifically to L5.
Dual interaction of factor H with C3d and glycosaminoglycans in host–nonhost discrimination by complement
Authors: Kajander Tommi , Lehtinen Markus J. , Hyvärinen Satu , Bhattacharjee Arnab , Leung Elisa , Isenman David E. , Meri Seppo , Goldman Adrian , Jokiranta T. Sakari
Published: February 2011

The alternative pathway of complement is important in innate immunity, attacking not only microbes but all unprotected biological surfaces through powerful amplification. It is unresolved how host and nonhost surfaces are distinguished at the molecular level, but key components are domains 19–20 of the complement regulator factor H (FH), which interact with host (i.e., nonactivator surface glycosaminoglycans or sialic acids) and the C3d part of C3b. Our structure of the FH19–20:C3d complex at 2.3-Å resolution shows that FH19–20 has two distinct binding sites, FH19 and FH20, for C3b. We show simultaneous binding of FH19 to C3b and FH20 to nonactivator surface glycosaminoglycans, and we show that both of these interactions are necessary for full binding of FH to C3b on nonactivator surfaces (i.e., for target discrimination). We also show that C3d could replace glycosaminoglycan binding to FH20, thus providing a feedback control for preventing excess C3b deposition and complement amplification. This explains the molecular basis of atypical hemolytic uremic syndrome, where mutations on the binding interfaces between FH19–20 and C3d or between FH20 and glycosaminoglycans lead to complement attack against host surfaces.
DNA phosphorothioation is widespread and quantized in bacterial genomes
Authors: Wang Lianrong , Chen Shi , Vergin Kevin L. , Giovannoni Stephen J. , Chan Simon W. , DeMott Michael S. , Taghizadeh Koli , Cordero Otto X. , Cutler Michael , Timberlake Sonia , Alm Eric J. , Polz Martin F. , Pinhassi Jarone , Deng Zixin , Dedon Peter C.
Published: February 2011

Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of thedndgenes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity ofdndgene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison ofdndgenes and PT sequence contexts strongly supports the horizontal transfer ofdndgenes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.
Cystic fibrosis transmembrane conductance regulator with a shortened R domain rescues the intestinal phenotype of

CFTR
−/−

mice
Authors: Ostedgaard Lynda S. , Meyerholz David K. , Vermeer Daniel W. , Karp Philip H. , Schneider Lindsey , Sigmund Curt D. , Welsh Michael J.
Published: February 2011

Gene transfer could provide a novel therapeutic approach for cystic fibrosis (CF), and adeno-associated virus (AAV) is a promising vector. However, the packaging capacity of AAV limits inclusion of the full-length cystic fibrosis transmembrane conductance regulator (CFTR) cDNA together with other regulatory and structural elements. To overcome AAV size constraints, we recently developed a shortened CFTR missing the N-terminal portion of the R domain (residues 708–759, CFTRΔR) and found that it retained regulated anion channel activity in vitro. To test the hypothesis that CFTRΔR could correct in vivo defects, we generated

CFTR
−/−

mice bearing a transgene with a fatty acid binding protein promoter driving expression of human CFTRΔR in the intestine (

CFTR
−/−
;TgΔR

). We found that intestinal crypts of

CFTR
−/−
;TgΔR

mice expressed CFTRΔR and the intestine appeared histologically similar to that of WT mice. Moreover, like full-length
CFTR
transgene, the
CFTRΔR
transgene produced CFTR Cl
−
currents and rescued the

CFTR
−/−

intestinal phenotype. These results indicate that the N-terminal part of the CFTR R domain is dispensable for in vivo intestinal physiology. Thus, CFTRΔR may have utility for AAV-mediated gene transfer in CF.
Presenilin 2 modulates endoplasmic reticulum (ER)–mitochondria interactions and Ca
2+
cross-talk
Authors: Zampese Enrico , Fasolato Cristina , Kipanyula Maulilio J. , Bortolozzi Mario , Pozzan Tullio , Pizzo Paola
Published: February 2011

Presenilin mutations are the main cause of familial Alzheimer's disease (FAD). Presenilins also play a key role in Ca
2+
homeostasis, and their FAD-linked mutants affect cellular Ca
2+
handling in several ways. We previously have demonstrated that FAD-linked presenilin 2 (PS2) mutants decrease the Ca
2+
content of the endoplasmic reticulum (ER) by inhibiting sarcoendoplasmic reticulum Ca
2+
-ATPase (SERCA) activity and increasing ER Ca
2+
leak. Here we focus on the effect of presenilins on mitochondrial Ca
2+
dynamics. By using genetically encoded Ca
2+
indicators specifically targeted to mitochondria (aequorin- and GFP-based probes) in SH-SY5Y cells and primary neuronal cultures, we show that overexpression or down-regulation of PS2, but not of presenilin 1 (PS1), modulates the Ca
2+
shuttling between ER and mitochondria, with its FAD mutants strongly favoring Ca
2+
transfer between the two organelles. This effect is not caused by a direct PS2 action on mitochondrial Ca
2+
-uptake machinery but rather by an increased physical interaction between ER and mitochondria that augments the frequency of Ca
2+
hot spots generated at the cytoplasmic surface of the outer mitochondrial membrane upon stimulation. This PS2 function adds further complexity to the multifaceted nature of presenilins and to their physiological role within the cell. We also discuss the importance of this additional effect of FAD-linked PS2 mutants for the understanding of FAD pathogenesis.
Quantitative trait prediction based on genetic marker-array data, a simulation study
Authors: Yip Wai-ki , Lange Christoph
Published: February 2011

Motivation: Using simulation studies for quantitative trait loci (QTL), we evaluate the prediction quality of regression models that include as covariates single-nucleotide polymorphism (SNP) genetic markers which did not achieve genome-wide significance in the original genome-wide association study, but were among the SNPs with the smallest P-value for the selected association test. We compare the results of such regression models to the standard approach which is to include only SNPs that achieve genome-wide significance. Using mean square prediction error as the model metric, our simulation results suggest that by using the coefficient of determination (R2) value as a guideline to increase or reduce the number of SNPs included in the regression model, we can achieve better prediction quality than the standard approach. However, important parameters such as trait heritability, the approximate number of QTLs, etc. have to be determined from previous studies or have to be estimated accurately.

Contact:  wkyip@hsph.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.