bluuebunny/crossref_metadata_2025 huggingface dataset:
Hot electron generation from intense laser irradiation of microtipped cone and wedge targets
Authors: Cho B. I. , Dyer G. M. , Kneip S. , Pikuz S. , Symes D. R. , Bernstein A. C. , Sentoku Y. , Renard-Le Galloudec N. , Cowan T. E. , Ditmire T.
Published: May 2008

X-ray production from the interaction of femtosecond laser pulses focused to relativistic intensity into re-entrant targets etched into silicon has been investigated. Kα and hard x-ray yields were compared when the laser was focused into pyramidal shaped cone targets and wedge shaped targets. Hot electron production is highest in the wedge targets irradiated with transverse polarization, though Kα is maximized with wedge targets and parallel polarization. These results are explained with particle-in-cell simulations.
Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions
Authors: Christ Clara D. , van Gunsteren Wilfred F.
Published: May 2008

A recently proposed method to obtain free energy differences for multiple end states from a single simulation of a reference state which was called enveloping distribution sampling (EDS) [J. Chem. Phys. 126, 184110 (2007)] is expanded to situations where the end state configuration space densities do not show overlap. It uses a reference state Hamiltonian suggested by Han in 1992 [Phys. Lett. A 165, 28 (1992)] in a molecular dynamics implementation. The method allows us to calculate multiple free energy differences “on the fly” from a single molecular dynamics simulation. The influence of the parameters on the accuracy and precision of the obtained free energy differences is investigated. A connection is established between the presented method and the Bennett acceptance ratio method. The method is applied to four two-state test systems (dipole inversion, van der Waals perturbation, charge inversion, and water to methanol conversion) and two multiple-state test systems [dipole inversion with five charging states and five (dis-)appearing water molecules]. Accurate results could be obtained for all test applications if the parameters of the reference state Hamiltonian were optimized according to a given algorithm. The deviations from the exact result or from an independent calculation were at most 0.6kJ∕mol. An accurate estimation of the free energy difference is always possible, independent of how different the end states are. However, the convergence times of the free energy differences are longer in cases where the end state configuration space densities do not show overlap [charge inversion, water to methanol conversion, (dis-)appearing water molecules] than in cases where the configuration space densities do show some overlap [(multiple) dipole inversion and van der Waals perturbation].
A comparative study of the Si+O2→SiO+O reaction dynamics from quasiclassical trajectory and statistical based methods
Authors: Dayou Fabrice , Larrégaray Pascal , Bonnet Laurent , Rayez Jean-Claude , Arenas Pedro Nilo , González-Lezana Tomás
Published: May 2008

The dynamics of the singlet channel of the Si+O2→SiO+O reaction is investigated by means of quasiclassical trajectory (QCT) calculations and two statistical based methods, the statistical quantum method (SQM) and a semiclassical version of phase space theory (PST). The dynamics calculations have been performed on the ground A′1 potential energy surface of Dayou and Spielfiedel [J. Chem. Phys. 119, 4237 (2003)] for a wide range of collision energies (Ec=5–400meV) and initial O2 rotational states (j=1–13). The overall dynamics is found to be highly sensitive to the selected initial conditions of the reaction, the increase in either the collisional energy or the O2 rotational excitation giving rise to a continuous transition from a direct abstraction mechanism to an indirect insertion mechanism. The product state properties associated with a given collision energy of 135meV and low rotational excitation of O2 are found to be consistent with the inverted SiO vibrational state distribution observed in a recent experiment. The SQM and PST statistical approaches, especially designed to deal with complex-forming reactions, provide an accurate description of the QCT total integral cross sections and opacity functions for all cases studied. The ability of such statistical treatments in providing reliable product state properties for a reaction dominated by a competition between abstraction and insertion pathways is carefully examined, and it is shown that a valuable information can be extracted over a wide range of selected initial conditions.
Threshold criteria for undervoltage breakdown
Authors: Cooley James E. , Choueiri Edgar Y.
Published: May 2008

The conditions under which an externally supplied pulse of electrons will induce breakdown in an undervoltaged, low-gain discharge gap are experimentally and theoretically explored. The minimum number of injected electrons required to achieve breakdown in a parallel-plate gap is measured in argon at pd values of 3–10 Torr m using ultraviolet laser pulses to photoelectrically release electrons from the cathode. This value was found to scale inversely with voltage at constant pd and with pressure within the parameter range explored. A dimensionless theoretical description of the phenomenon is formulated and numerically solved. It is found that a significant fraction of the charge on the plates must be injected for breakdown to be achieved at low gain. It is also found that fewer electrons are required as the gain due to electron-impact ionization (α process) is increased, or as the sensitivity of the α process to electric field is enhanced by increasing the gas pressure. A predicted insensitivity to ion mobility implies that the breakdown is determined during the first electron avalanche when space-charge distortion is greatest.
Ultrafast transformation of graphite to diamond: An ab initio study of graphite under shock compression
Authors: Mundy Christopher J. , Curioni Alessandro , Goldman Nir , Will Kuo I.-F. , Reed Evan J. , Fried Laurence E. , Ianuzzi Marcella
Published: May 2008

We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12km∕s (longitudinal stress>130GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.
Chiral nanopatterned surfaces as versatile enantiospecific adsorbents: A Monte Carlo model
Authors: Szabelski Paweł
Published: May 2008

This paper deals with the application of the Monte Carlo simulation method for modeling of adsorption of chiral molecules on a planar surface patterned with active binding sites. The enantiomers are assumed to be rigid chains composed of four identical segments, each occupying one binding site. The energy of interaction between a segment and a binding site is characterized by εa and εb depending whether the site is active or it is inert. We demonstrate that εa>εb imposed in our previous work [J. Chem. Phys. 126, 144709 (2007)] is not a necessary condition for the separation of enantiomers form their racemate. The obtained results suggest that the major source of enantioselectivity of the surface lies in its geometrical properties. The active adsorption sites which form the chiral pattern do not have to interact stronger with the adsorbing molecules to ensure enantioseparation. In this context, the proposed chiral surface offers more flexibility in selection of the energetic properties of the binding sites. This, in practice, means wider possibilities of manipulating chemical composition of the surface.
Ion acceleration by femtosecond laser pulses in small multispecies targets
Authors: Psikal J. , Tikhonchuk V. T. , Limpouch J. , Andreev A. A. , Brantov A. V.
Published: May 2008

Ion acceleration by ultrashort intense femtosecond laser pulses (∼4×1019W∕cm2, ∼30fs) in small targets of uniform chemical composition of two ion species (protons and carbon C4+ ions) is studied theoretically via a particle-in-cell code with two spatial and three velocity components. Energy spectra of accelerated ions, the number and divergence of fast protons, are compared for various target shapes (cylinder, flat foil, curved foil) and density profiles. Dips and peaks are observed in proton energy spectra due to mutual interaction between two ion species. The simulations demonstrate that maximum energy of fast protons depends on the efficiency of laser absorption and the cross section of the hot electron cloud behind the target. A rear-side plasma density ramp can substantially decrease the energy of fast ions and simultaneously enhance their number. These results are compared with analytical estimates and with previously published experiments.
Temperature-dependent optical constants and birefringence of nematic liquid crystal 5CB in the terahertz frequency range
Authors: Pan Ru-Pin , Hsieh Cho-Fan , Pan Ci-Ling , Chen Chao-Yuan
Published: May 2008

We have measured the frequency dependence and temperature dependence of the optical constants of a liquid crystal 4′-n-pentyl-4-cyanobiphenyl (5CB) in both nematic and isotropic phases by using terahertz time-domain spectroscopy. The extinction coefficient of 5CB is less than 0.02 and without sharp absorption features in the frequency range of 0.2–1.0 THz. The extraordinary and ordinary indices of refraction at 25 °C are around 1.77 and 1.58, respectively, giving rise to a birefringence of 0.20±0.02 in this frequency range. The temperature-dependent order parameter extracted from birefringence agrees with the results from the visible region quite well.
The Einstein relation in quantum wires of III-V, ternary, and quaternary materials in the presence of light waves: Simplified theory, relative comparison, and suggestion for experimental determination
Authors: Ghatak K. P. , Bhattacharya S. , Bhowmik S. , Benedictus R. , Choudhury S.
Published: May 2008

We study the Einstein relation for the diffusivity to mobility ratio (DMR) in quantum wires (QWs) of III-V, ternary, and quaternary materials in the presence of light waves, whose unperturbed energy band structures are defined by the three band model of Kane. It has been found, taking n-InAs, n-InSb, n-Hg1−xCdxTe, n-In1−xGaxAsyP1−y lattice matched to InP as examples, that the respective DMRs exhibit decreasing quantum step dependence with the increasing film thickness, decreasing electron statistics, increasing light intensity and wavelength, with different numerical values. The nature of the variations is totally band structure dependent and is influenced by the presence of the different energy band constants. The strong dependence of the DMR on both the light intensity and the wavelength reflects the direct signature of the light waves which is in contrast as compared to the corresponding QWs of the said materials in the absence of photoexcitation. The classical equation of the DMR in the absence of any field has been obtained as a special case of the present analysis under certain limiting conditions and this is the indirect test of the generalized formalism. We have suggested an experimental method of determining the DMR in QWs of degenerate materials having arbitrary dispersion laws and our results find six applications in the field of quantum effect devices.
Adiabatic and nonadiabatic dynamics in the CH3(CD3)+HCl reaction
Authors: Retail Bertrand , Pearce Julie K. , Greaves Stuart J. , Rose Rebecca A. , Orr-Ewing Andrew J.
Published: May 2008

The scattering dynamics leading to the formation of Cl (P3∕22) and Cl* (P1∕22) products of the CH3+HCl reaction (at a mean collision energy ⟨Ecoll⟩=22.3kcalmol−1) and the Cl (P3∕22) products of the CD3+HCl reaction (at ⟨Ecoll⟩=19.4kcalmol−1) have been investigated by using photodissociation of CH3I and CD3I as sources of translationally hot methyl radicals and velocity map imaging of the Cl atom products. Image analysis with a Legendre moment fitting procedure demonstrates that, in all three reactions, the Cl∕Cl* products are mostly forward scattered with respect to the HCl in the center-of-mass (c.m.) frame but with a backward scattered component. The distributions of the fraction of the available energy released as translation peak at ft=0.31–0.33 for all the reactions, with average values that lie in the range ⟨ft⟩=0.42–0.47. The detailed analysis indicates the importance of collision energy in facilitating the nonadiabatic transitions that lead to Cl* production. The similarities between the c.m.-frame scattering and kinetic energy release distributions for Cl and Cl* channels suggest that the nonadiabatic transitions to a low-lying excited potential energy surface (PES) correlating to Cl* products occur after passage through the transition state region on the ground-state PES. Branching fractions for Cl* are determined to be 0.14±0.02 for the CH3+HCl reaction and 0.20±0.03 for the CD3+HCl reaction. The difference cannot be accounted for by changes in collision energy, mass effects, or vibrational excitation of the photolytically generated methyl radical reagents and instead suggests that the low-frequency bending modes of the CD3H or CH4 coproduct are important mediators of the nonadiabatic couplings occurring in this reaction system.
Dynamics of the F2 reaction with the simplest π-bonding molecule
Authors: Lu Yu-Ju , Xie Tingxian , Fang Jing-Wen , Shao Hua-Chieh , Lin Jim J.
Published: May 2008

The reaction of F2+C2H4 has been investigated with crossed molecular beam experiments and high level ab initio calculations. For a wide range of collision energies up to 11kcal∕mol, only one reaction channel could be observed in the gas phase. The primary products of this channel were identified as F+CH2CH2F. The experimental reaction threshold of collision energy was determined to be 5.5±0.5kcal∕mol. The product angular distribution was found to be strongly backward, indicating that the reaction time scale is substantially shorter than rotation. The calculated transition state structure suggests an early barrier; such dynamics is consistent with the small product kinetic energy release measured in the experiment. All experimental results consistently support a rebound reaction mechanism, which is suggested by the calculation of the intrinsic reaction coordinate. This work provides a clear and unambiguous description of the reaction dynamics, which may help to answer the question why the same reaction produces totally different products in the condensed phase.
Phase, shape, and architecture of SF6 and SF6∕CO2 aerosol particles: Infrared spectra and modeling of vibrational excitons
Authors: Firanescu George , Luckhaus David , Signorell Ruth
Published: May 2008

Information on the phase, shape, and architecture of pure SF6 and mixed SF6∕CO2 aerosol particles is extracted from experimental infrared spectra by comparison with predictions from quantum mechanical exciton calculations. The radius of the particles lies around 50nm. The following extensions to our previous vibrational exciton model are included: (i) To account for the many degrees of freedom of degenerate vibrational bands of aerosol particles, we take a time-dependent approach to calculate infrared absorption spectra directly from the dipole autocorrelation function. (ii) In addition to the dipole-dipole interaction, dipole-induced dipole terms are included to account for the high polarizability of SF6 and CO2. We find SF6 aerosol particles with a cubiclike shape directly after their formation and a change in the shape toward elongated particles with increasing time. Our microscopic model reveals that the cubic-to-monoclinic phase transition at 96K found in the bulk cannot be observed with infrared spectroscopy because the two phases show almost identical spectra. Infrared spectra of two-component SF6∕CO2 particles with core-shell structure show characteristic split absorption bands for the shell. By contrast, homogeneously mixed SF6∕CO2 particles lead to broad infrared bands for both the core and the shell. The molecular origin of these various spectral features is uncovered by the analysis of the vibrational eigenfunctions.
Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian
Authors: Kormann Katharina , Holmgren Sverker , Karlsson Hans O.
Published: May 2008

Several different numerical propagation techniques for explicitly time-dependent Hamiltonians are discussed and compared, with the focus on models of pump-probe experiments. The quality of the rotating wave approximation is analyzed analytically, and we point out under which circumstances the modeling becomes inaccurate. For calculations with the fully time-dependent Hamiltonian, we show that for multistate systems, with either time or space dependence in the interstate coupling, the fourth order truncated Magnus expansion can be reformulated so that no commutators appear. Our results show that the split-operator method should only be used when low accuracy is acceptable. For accurate and efficient time stepping, the Magnus-Lanczos approach appears to be the best choice.
A new method to calculate Franck–Condon factors of multidimensional harmonic oscillators including the Duschinsky effect
Authors: Chang Jia-Lin
Published: May 2008

Calculations of Franck–Condon factors are crucial for interpreting vibronic spectra of molecules and studying nonradiative processes. We have developed a new method for calculating Franck–Condon factors of multidimensional harmonic oscillators including the Duschinsky effect. Closed-form formulas of two-, three-, and four-dimensional Franck–Condon factors were derived straightforwardly by using the properties of Hermite polynomials and Gaussian integrals. This new method was applied to study the photoelectron spectra of H2O+(B̃B22) and D2O+(B̃B22), whose equilibrium geometries and harmonic vibrational frequencies were calculated by using the coupled cluster singles and doubles with perturbative triples [CCSD(T)] method together with the basis sets of 6-311++G(3df,2pd) and aug-cc-pVTZ. The adiabatic ionization energies were computed by using the CCSD(T) method extrapolated to the complete basis set limit with aug-cc-pVXZ (X=D,T,Q,5). It was found that the simulated photoelectron spectra were mainly composed of ν2 progressions and the combination bands of ν1 and ν2, whereas pure ν1 transitions should be too weak to be observable, contrary to the literature reports. It was also found that the first discernible peak in the experimental photoelectron spectra did not correspond to the adiabatic transition. The adiabatic ionization energies of H2O+(B̃B22) and D2O+(B̃B22) are proposed to be 16.78 and 16.83eV, about 0.40 and 0.58eV lower than the best experimental values, respectively. Conversely, the calculated ionization energies are in agreement with the proposed values within 0.02eV.
Ab initio study of the optical phonons in one-dimensional antiferromagnet Ca2CuO3
Authors: Hoang Nam Nhat , Nguyen Thu Hang , Nguyen Chau
Published: May 2008

We present the cluster-model ab initio study of the optical phonons in the one-dimensional antiferromagnet Ca2CuO3 based on the Hartree–Fock self-consistent field calculation with the 3-21G basis set. The obtained results showed very good agreement with the observed data. The Cu–O bands generally showed lower shifts in Ca2CuO3 than in pure CuO and were primarily composed of the vibrations of the oxygen in static host lattice, whereas the Cu movements only happened in the collective lattice vibrations. An almost complete classification of the forbidden phonons is presented.
A phenomenological model for the reliability of GaAs based heterojunction bipolar transistors
Authors: Lee C. P. , Chau F. , Lin B. , Kretschmar M. , Ma W.
Published: May 2008

We present a phenomenological model for the lifetime prediction of GaAs based heterojunction bipolar transistors (HBTs). Both thermal activation process and recombination enhanced defect generation process were considered phenomenologically. At high stress temperatures, the lifetime of the transistor is determined by the thermal activation process and is independent of the stress current. But at low stress temperatures, the device’s lifetime is controlled by the recombination enhanced defect generation process and is dependent on the stress current. The model has been used to fit experimental data, and very reasonable agreement was obtained. The model is valid for all stress temperatures and stress currents. It provides a good guideline for projecting HBTs lifetimes using accelerated stress test.
Determining the stress tensor in strained semiconductor structures by using polarized micro-Raman spectroscopy in oblique backscattering configuration
Authors: Ossikovski Razvigor , Nguyen Quang , Picardi Gennaro , Schreiber Joachim
Published: May 2008

We present a characterization technique for the determination of the stress tensor as well as of the crystallographic orientation of strained semiconductor structures. The technique is based on a polarized oblique incidence micro-Raman experiment in a backscattering configuration. A methodology relating the stress-induced frequency shifts and linewidths of the phonon peak to the stress tensor components within the adopted experimental configuration was developed. The method consists in monitoring the variations of the stress-sensitive peak frequencies and linewidths while rotating stepwise the sample about its normal. The practical application of the technique is illustrated on a Si∕SiGe sample microelectronic structure demonstrating a full plane stress tensor determination.
Terahertz detection mechanism of inexpensive sensitive glow discharge detectors
Authors: Rozban D. , Kopeika N. S. , Abramovich A. , Farber E.
Published: May 2008

The detection mechanism of glow discharge plasma, which is derived from direct current gas breakdown, in neon indicator lamps was investigated in the terahertz and microwave regimes. Such devices exhibit high sensitivity to terahertz radiation. Experimental setups at 10, 100, and 250GHz were carried out and analyzed. The analysis of the experimental results shows that the dominant mechanism of the glow discharge detector (GDD) in these regimes is enhanced cascade ionization. Furthermore, the responsivity at 10GHz decreases with the increase in the dc bias current between the electrodes, while the responsivity at 100 and 250GHz increases with the dc current. This is attributed to electron-neutral atom collision frequency (ν) of the GDD being tens of gigahertz and its increasing with dc bias current according to dc field increase.
On a class of damped vibration problems with obstacles and without direct variational structures
Authors: Wu Xian
Published: May 2008

The main purpose of this paper is to study the following damped vibration problems: −ẍ=q(x)∣ẋ∣2+f(t), with x(0)−x(2π)=ẋ(0)−ẋ(2π)=0, x(t)⩾0, ∀t∊R and ẋ(t0−)=−ẋ(t0+), if x(t0)=0, where ẋ(t0−)=limt→t0−0ẋ(t) and ẋ(t0+)=limt→t0+0ẋ(t). The variational sets are given and some multiplicity results of periodic solutions satisfying the presented equations are obtained.
Ultrahard diamond indenter prepared from nanopolycrystalline diamond
Authors: Sumiya H. , Harano K. , Irifune T.
Published: May 2008

Knoop indenters were prepared from nanopolycrystalline diamonds (NPDs) synthesized by direct conversion sintering from graphite under high pressure and high temperature. Owing to the fine structure (grain size: 10–100nm) of NPD, high-accuracy sharp edges could be formed at the indenter tips. The indentation tests demonstrated that the NPD indenter can form normal (measurable) indentations on NPD samples without fracture or chipping even at high temperatures of up to 1000°C, while conventional indenters made of single-crystal diamonds break easily above 600°C. This suggests that the NPD indenter has greater potential in high-temperature hardness tests than the conventional single-crystal diamond indenters.
Measurement of deep states in hole doped organic semiconductors
Authors: Ray Debdutta , Narasimhan K. L.
Published: May 2008

In this paper, we report on the electrical properties of hole doped N,N′-diphenyl-N,N′-bis(3-methylphenyl)-(1,1′-biphenyl)-4,4′-diamine and tris(8-hydroxyquinoline) aluminum. Tetrafluorotetracyanoquinodimethane is used as the dopant. From the frequency dependence of the capacitance measurements, we show that deep levels dominate the capacitance. From the frequency and bias dependence, we estimate the density of deep levels above the Fermi level to be about 1017 cm−3. These states presumably arise due to polarization and Coulomb energy fluctuations.
Strain-induced ferromagnetism enhancement in Co:ZnO films
Authors: Liu X. J. , Song C. , Zeng F. , Pan F. , He B. , Yan W. S.
Published: May 2008

The structural and ferromagnetic properties of Zn0.95Co0.05O films grown on Si and LiNbO3 (LNO) substrates have been studied as a function of thickness (15–900 nm). The structural characterizations indicate that the c-axis lattice constant and Co–O bond length slightly decrease with the increase in film thickness, implying the progressive relaxation of the tensile strain. The magnetic measurements show that a larger strain can result in an enhancement of room temperature ferromagnetism. The thinnest films (15 nm) with the largest lattice strains possess the highest saturated magnetic moments, i.e., 5.52 and 2.96μB/Co in Co:ZnO/LNO and Co:ZnO/Si films, respectively. As the film becomes thicker, the saturated ferromagnetism rapidly decreases, which is about two orders of magnitude smaller than that of the 15-nm-thick film when its thickness is 900 nm. The enhancement of ferromagnetism in Co:ZnO films originates from the combination of enlarged Co–O bond length and increased defect amount induced by strain.
Microwave dielectric properties of graded barium strontium titanate films
Authors: Cole M. W. , Weiss C. V. , Ngo E. , Hirsch S. , Coryell L. A. , Alpay S. P.
Published: May 2008

Compositionally graded barium strontium titanate (BaxSr1−xTiO3 or BST) multilayers (5mol% MgO doped and undoped) were prepared via metallo-organic solution deposition on Pt–Si substrates and characterized electrically at 0.5, 5, and 10GHz. For the undoped BST multilayers, the small-signal dielectric response, tunability, and the loss tangent at 10GHz were 261, 25% at 1778kV∕cm, and 0.078, respectively. On the other hand, the Mg-doped BST multilayers displayed a significant improvement in the loss characteristics at 10GHz (0.039) but the dielectric response and its tunability were lower (189 and 15%, respectively, at 1778kV∕cm).
Localized electrical characterization of the giant permittivity effect in CaCu3Ti4O12 ceramics
Authors: Fiorenza Patrick , Lo Nigro Raffaella , Bongiorno Corrado , Raineri Vito , Ferarrelli Matthew C. , Sinclair Derek C. , West Anthony R.
Published: May 2008

Nanoscale imaging of the electrical properties of CaCu3Ti4O12 ceramics has been performed using scanning impedance microscopy. Two kinds of electrical inhomogeneity are detected, namely, depletion layers at grain boundaries and calcium titanate inclusions, both of which are more resistive than the bulk of the grains. Energy filtered transmission electron microscopy was used to estimate the chemical composition of the inclusions.
Efficient photovoltaic device fashioned of highly aligned multilayers of electrospun TiO2 nanowire array with conjugated polymer
Authors: Shim Hee-Sang , Na Seok-In , Nam Sang Hoon , Ahn Hyo-Jin , Kim Hae Jin , Kim Dong-Yu , Kim Won Bae
Published: May 2008

We report here a simple and easy method of fabricating arranged inorganic nanowire architecture via electrospinning method equipped with a devised collector and demonstrate hybrid photovoltaic cells that are fashioned of planar-aligned TiO2 nanowire architectures such as uniaxially aligned nanowires and multiple layers of cross-aligned nanowire arrays with poly[2-methoxy, 5-(2′-ethyl-hexyloxy)-1,4-phenylenevinylene]. The power conversion efficiency can be significantly improved by at least 70% under 1sun condition depending on the degree of aligning TiO2 nanowire arrays through enhancing charge collection and transport rate, as well as facilitating the polymer infiltration as compared to a randomly collected TiO2 nanowire electrode.
Existence and asymptotic stability for the semilinear wave equation with boundary damping and source term
Authors: Park Jong Yeoul , Ha Tae Gab
Published: May 2008

In this paper, we consider the semilinear wave equation with boundary conditions. This work is devoted to prove the existence of solutions and uniform decay rates of the wave equation with boundary damping and source term.
Abnormal phase transition and magnetic properties in Cu, Fe co-doped In2O3 nanocrystals
Authors: Chu Dewei , Zeng Yu-Ping , Jiang Dongliang
Published: May 2008

Fe, Cu co-doped In2O3 nanocrystals were synthesized by a coprecipitation method. Phase analyses revealed that Fe ions have high solubility (up to 15.4at.%) in the In2O3 matrix, while the Cu ions strongly restrain In2O3 phase transition from cubic to hexagonal. Raman spectroscopy shows that by adding Cu ions, the defect concentration increases. The samples show no evidence of ferromagnetism by additional Cu doping, indicating that Cu content might be a key point to realize room temperature ferromagnetism in Fe doped In2O3.
Effects of visible and synchrotron x-ray radiation on the growth of silver nanoplates on n-GaAs wafers: A comparative study
Authors: Sun Yugang , Yan Hanfei , Wu Xiaohua
Published: May 2008

A simple and effective approach has been developed to grow silver (Ag) nanoplates on n-type gallium arsenide (GaAs) wafers through a reaction between the wafers themselves and aqueous solutions of silver nitrate at room temperature [Sun and Wiederrecht, Small 3, 1964 (2007)]. In this letter, the effect of green laser irradiation, which can efficiently excite the valence band of a GaAs substrate to form electron-hole pairs in the shallow surface region (<3μm), on the growth of Ag nanoplates is studied. Illumination with the laser significantly depresses the growth of Ag nanoplates. In comparison, the influence of synchrotron x-rays, which can excite the deep core levels of elements and deeply penetrate (>50μm) into GaAs lattices, on the growth of Ag nanoplates is also studied. The results indicate that the excited deep core levels can relax into electron-hole pairs in the band edges to induce similar effects to that of the green laser except that the larger area around the x-ray beam is affected to inhibit the growth of Ag nanoplates.
Excitation and photoluminescence polarization anisotropy of single CdSe nanowires
Authors: Lan Aidong , Giblin Jay , Protasenko Valdimir , Kuno Masaru
Published: May 2008

Excitation/emission polarization anisotropies (ρexc∕emm) of single CdSe nanowires (NWs) were studied for their size, frequency, and dielectric environment dependencies. Single NW optical experiments show strong ρexc dielectric environment dependencies for both thick and thin NWs in agreement with classical dielectric contrast models. Furthermore, no excitation frequency sensitivities were seen for both thick and thin wires, in air and under poly(methyl methacrylate) (PMMA). Moderate radial dependencies were also found for NWs embedded in PMMA. Complementary emission anisotropy measurements yielded significant radial and dielectric environment sensitivities with statistically smaller ρemm values than ρexc. A moderate ρemm frequency dependence was observed for thin NWs in PMMA.
Dynamic voltage-current characteristics for a water jet plasma arc
Authors: Yang Jiaxiang , Lan Sheng , Xu Zuoming
Published: May 2008

A virtual instrument technology is used to measure arc current, arc voltage, dynamic V-I characteristics, and nonlinear conductance for a cone-shaped water jet plasma arc under ac voltage. Experimental results show that ac arc discharge mainly happens in water vapor evaporated from water when heated. However, due to water’s cooling effect and its conductance, arc conductance, reignition voltage, extinguish voltage, and current zero time are very different from those for ac arc discharge in gas work fluid. These can be valuable to further studies on mechanism and characteristics of plasma ac discharge in water, and even in gas work fluid.
Cross-polarized excitons in carbon nanotubes
Authors: Kilina Svetlana , Tretiak Sergei , Doorn Stephen K. , Luo Zhengtang , Papadimitrakopoulos Fotios , Piryatinski Andrei , Saxena Avadh , Bishop Alan R.
Published: May 2008

Polarization of low-lying excitonic bands in finite-size semiconducting single-walled carbon nanotubes (SWNTs) is studied by using quantum-chemical methodologies. Our calculations elucidate properties of cross-polarized excitons, which lead to the transverse optical absorption of nanotubes and presumably couple to intermediate-frequency modes recently observed in resonance Raman excitation spectroscopy. We identify up to 12 distinct excitonic transitions below the second fundamental band associated with the
E
22
van Hove singularity. Calculations for several chiral SWNTs distinguish the optically active “bright” excitonic band polarized parallel to the tube axis and several optically “weak” cross-polarized excitons. The rest are optically (near) forbidden “dark” transitions. An analysis of the transition density matrices related to excitonic bands provides detailed information about delocalization of excitonic wavefunction along the tube. Utilization of the natural helical coordinate system accounting for the tube chirality allows one to disentangle longitudinal and circumferential components. The distribution of the transition density matrix along a tube axis is similar for all excitons. However, four parallel-polarized excitons associated with the
E
11
transition are more localized along the circumference of a tube, compared with others related to the
E
12
and
E
21
cross-polarized transitions. Calculated splitting between optically active parallel- and cross-polarized transitions increases with tube diameter, which compares well with experimental spectroscopic data.
Force-induced growth of adhesion domains is controlled by receptor mobility
Authors: Smith Ana-Sunčana , Sengupta Kheya , Goennenwein Stefanie , Seifert Udo , Sackmann Erich
Published: May 2008

In living cells, adhesion structures have the astonishing ability to grow and strengthen under force. Despite the rising evidence of the importance of this phenomenon, little is known about the underlying mechanism. Here, we show that force-induced adhesion-strengthening can occur purely because of the thermodynamic response to the elastic deformation of the membrane, even in the absence of the actively regulated cytoskeleton of the cell, which was hitherto deemed necessary. We impose pN-forces on two fluid membranes, locally pre-adhered by RGD-integrin binding. One of the binding partners is always mobile whereas the mobility of the other can be switched on or off. Immediate passive strengthening of adhesion structures occurs in both cases. When both binding partners are mobile, strengthening is aided by lateral movement of intact bonds as a transient response to force-induced membrane-deformation. By extending our microinterferometric technique to the suboptical regime, we show that the adhesion, as well as the resistance to force-induced de-adhesion, is greatly enhanced when both, rather than only one, of the binding partners are mobile. We formulate a theory that explains our observations by linking the macroscopic shape deformation with the microscopic formation of bonds, which further elucidates the importance of receptor mobility. We propose this fast passive response to be the first-recognition that triggers signaling events leading to mechanosensing in living cells.
Identification of innate immunity genes and pathways using a comparative genomics approach
Authors: Alper Scott , Laws Rebecca , Lackford Brad , Boyd Windy A. , Dunlap Paul , Freedman Jonathan H. , Schwartz David A.
Published: May 2008

To reveal regulators of innate immunity, we used RNAi assays to monitor the immune response when genes are inhibited in
Caenorhabditis elegans
and mouse macrophages. Genes that altered innate immune responsiveness in
C. elegans
were validated in murine macrophages, resulting in the discovery of 11 genes that regulate the innate immune response in both systems and the subsequent identification of a protein interaction network with a conserved role in innate immunity regulation. We confirmed the role of four of these 11 genes in antimicrobial gene regulation using available mutants in
C. elegans
. Several of these genes (
acy-1
,
tub-2
, and
tbc-1
) also regulate susceptibility to the pathogen
Pseudomonas aeruginosa
. These genes may prove critical to understanding host defense and represent potential therapeutic targets for infectious and immunological diseases.
Alternative splicing: A missing piece in the puzzle of intron gain
Authors: Tarrío Rosa , Ayala Francisco J. , Rodríguez-Trelles Francisco
Published: May 2008

Spliceosomal introns, a hallmark of eukaryotic gene organization, were an unexpected discovery. After three decades, crucial issues such as when and how introns first appeared in evolution remain unsettled. An issue yet to be answered is how intron positions arise
de novo
. Phylogenetic investigations concur that intron positions continue to emerge, at least in some lineages. Yet genomic scans for the sources of introns occupying new positions have been fruitless. Two alternative solutions to this paradox are: (
i
) formation of new intron positions halted before the recent past and (
ii
) it continues to occur, but through processes different from those generally assumed. One process generally dismissed is intron sliding—the relocation of a preexisting intron over short distances—because of supposed associated deleterious effects. The puzzle of intron gain arises owing to a pervasive operational definition of introns, which sees them as precisely demarcated segments of the genome separated from the neighboring nonintronic DNA by unmovable limits. Intron homology is defined as position homology. Recent studies of pre-mRNA processing indicate that this assumption needs to be revised. We incorporate recent advances on the evolutionarily frequent process of alternative splicing, by which exons of primary transcripts are spliced in different patterns, into a new model of intron sliding that accounts for the diversity of intron positions. We posit that intron positional diversity is driven by two overlapping processes: (
i
) background process of continuous relocation of preexisting introns by sliding and (
ii
) spurts of extensive gain/loss of new intron sequences.
EGF Transregulates Opioid Receptors through EGFR-mediated GRK2 Phosphorylation and Activation
Authors: Chen Yuejun , Long Hui , Wu Ziyan , Jiang Xi , Ma Lan
Published: May 2008

G protein–coupled receptor (GPCR) kinases (GRKs) are key regulators of GPCR function. Here we demonstrate that activation of epidermal growth factor receptor (EGFR), a member of receptor tyrosine kinase family, stimulates GRK2 activity and transregulates the function of G protein–coupled opioid receptors. Our data showed that EGF treatment promoted DOR internalization induced by DOR agonist and this required the intactness of GRK2-phosphorylation sites in DOR. EGF stimulation induced the association of GRK2 with the activated EGFR and the translocation of GRK2 to the plasma membrane. After EGF treatment, GRK2 was phosphorylated at tyrosyl residues. Mutational analysis indicated that EGFR-mediated phosphorylation occurred at GRK2 N-terminal tyrosyl residues previously shown as c-Src phosphorylation sites. However, c-Src activity was not required for EGFR-mediated phosphorylation of GRK2. In vitro assays indicated that GRK2 was a direct interactor and a substrate of EGFR. EGF treatment remarkably elevated DOR phosphorylation in cells expressing the wild-type GRK2 in an EGFR tyrosine kinase activity–dependent manner, whereas EGF-stimulated DOR phosphorylation was greatly decreased in cells expressing mutant GRK2 lacking EGFR tyrosine kinase sites. We further showed that EGF also stimulated internalization of μ-opioid receptor, and this effect was inhibited by GRK2 siRNA. These data indicate that EGF transregulates opioid receptors through EGFR-mediated tyrosyl phosphorylation and activation of GRK2 and propose GRK2 as a mediator of cross-talk from RTK to GPCR signaling pathway.
A Multicomponent Assembly Pathway Contributes to the Formation of Acentrosomal Microtubule Arrays in InterphaseDrosophilaCells
Authors: Rogers Gregory C. , Rusan Nasser M. , Peifer Mark , Rogers Stephen L.
Published: May 2008

In animal cells, centrosomes nucleate microtubules that form polarized arrays to organize the cytoplasm. Drosophila presents an interesting paradox however, as centrosome-deficient mutant animals develop into viable adults. To understand this discrepancy, we analyzed behaviors of centrosomes and microtubules in Drosophila cells, in culture and in vivo, using a combination of live-cell imaging, electron microscopy, and RNAi. The canonical model of the cycle of centrosome function in animal cells states that centrosomes act as microtubule-organizing centers throughout the cell cycle. Unexpectedly, we found that many Drosophila cell-types display an altered cycle, in which functional centrosomes are only present during cell division. On mitotic exit, centrosomes disassemble producing interphase cells containing centrioles that lack microtubule-nucleating activity. Furthermore, steady-state interphase microtubule levels are not changed by codepleting both γ-tubulins. However, γ-tubulin RNAi delays microtubule regrowth after depolymerization, suggesting that it may function partially redundantly with another pathway. Therefore, we examined additional microtubule nucleating factors and found that Mini-spindles, CLIP-190, EB1, or dynein RNAi also delayed microtubule regrowth; surprisingly, this was not further prolonged when we codepleted γ-tubulins. Taken together, these results modify our view of the cycle of centrosome function and reveal a multi-component acentrosomal microtubule assembly pathway to establish interphase microtubule arrays in Drosophila.
High-Resolution Crystal Structure and In Vivo Function of a Kinesin-2 Homologue inGiardia intestinalis
Authors: Hoeng J. C. , Dawson S. C. , House S. A. , Sagolla M. S. , Pham J. K. , Mancuso J. J. , Löwe J. , Cande W. Z.
Published: May 2008

A critical component of flagellar assembly, the kinesin-2 heterotrimeric complex powers the anterograde movement of proteinaceous rafts along the outer doublet of axonemes in intraflagellar transport (IFT). We present the first high-resolution structures of a kinesin-2 motor domain and an ATP hydrolysis–deficient motor domain mutant from the parasitic protist Giardia intestinalis. The high-resolution crystal structures of G. intestinalis wild-type kinesin-2 (GiKIN2a) motor domain, with its docked neck linker and the hydrolysis-deficient mutant GiKIN2aT104N were solved in a complex with ADP and Mg2+at 1.6 and 1.8 Å resolutions, respectively. These high-resolution structures provide unique insight into the nucleotide coordination within the active site. G. intestinalis has eight flagella, and we demonstrate that both kinesin-2 homologues and IFT proteins localize to both cytoplasmic and membrane-bound regions of axonemes, with foci at cell body exit points and the distal flagellar tips. We demonstrate that the T104N mutation causes GiKIN2a to act as a rigor mutant in vitro. Overexpression of GiKIN2aT104N results in significant inhibition of flagellar assembly in the caudal, ventral, and posterolateral flagellar pairs. Thus we confirm the conserved evolutionary structure and functional role of kinesin-2 as the anterograde IFT motor in G. intestinalis.
The Involvement of the Tyrosine Kinase c-Src in the Regulation of Reactive Oxygen Species Generation Mediated by NADPH Oxidase-1
Authors: Gianni Davide , Bohl Ben , Courtneidge Sara A. , Bokoch Gary M.
Published: May 2008

NADPH oxidase (Nox) family enzymes are one of the main sources of cellular reactive oxygen species (ROS), which have been shown to function as second messenger molecules. To date, seven members of this family have been reported, including Nox1-5 and Duox1 and -2. With the exception of Nox2, the regulation of the Nox enzymes is still poorly understood. Nox1 is highly expressed in the colon, and it requires two cytosolic regulators, NoxO1 and NoxA1, as well as the binding of Rac1 GTPase, for its activity. In this study, we investigate the role of the tyrosine kinase c-Src in the regulation of ROS formation by Nox1. We show that c-Src induces Nox1-mediated ROS generation in the HT29 human colon carcinoma cell line through a Rac-dependent mechanism. Treatment of HT29 cells with the Src inhibitor PP2, expression of a kinase-inactive form of c-Src, and c-Src depletion by small interfering RNA (siRNA) reduce both ROS generation and the levels of active Rac1. This is associated with decreased Src-mediated phosphorylation and activation of the Rac1-guanine nucleotide exchange factor Vav2. Consistent with this, Vav2 siRNA that specifically reduces endogenous Vav2 protein is able to dramatically decrease Nox1-dependent ROS generation and abolish c-Src-induced Nox1 activity. Together, these results establish c-Src as an important regulator of Nox1 activity, and they may provide insight into the mechanisms of tumor formation in colon cancers.
Identification of OBO nonalignments and its implications for OBO enrichment
Authors: Bada Michael , Hunter Lawrence
Published: May 2008

Motivation: Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are based on the added formal definitions and that reflect nonalignments between the linked terms. However, these projects require that these definitions be necessary and sufficient, a strong requirement that often does not hold. If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences.

Results: We describe a methodology by which we have identified over 1900 instances of nonredundant nonalignments between terms from the Gene Ontology (GO) biological process (BP), cellular component (CC) and molecular function (MF) ontologies, Chemical Entities of Biological Interest (ChEBI) and the Cell Type Ontology (CL). Many of the 39.8% of these nonalignments whose object terms are more atomic than the subject terms are not currently examined in other ontology-enrichment projects due to the fact that the necessary and sufficient conditions required for the inferences are not currently examined. Analysis of the ratios of nonalignments to assertions from which the nonalignments were identified suggests that BP–MF, BP–BP, BP–CL and CC–CC terms are relatively well-aligned, while ChEBI–MF, BP–ChEBI and CC–MF terms are relatively not aligned well. We propose four ways to resolve an identified nonalignment and recommend an analogous implementation of our methodology in ontology-enrichment tools to identify types of nonalignments that are currently not detected.

Availability: The nonalignments discussed in this article may be viewed at http://compbio.uchsc.edu/Hunter_lab/Bada/nonalignments_2008_03_06.html. Code for the generation of these nonalignments is available upon request.

Contact:  mike.bada@uchsc.edu