bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase field simulations of ferroelectric nanoparticles with different long-range-electrostatic and -elastic interactions
Authors: Wang Jie , Kamlah Marc , Zhang Tong-Yi
Published: January 2009

Two-dimensional phase field simulations of ferroelectric nanoparticles with different long-range (LR)-electrostatic and -elastic interactions and different domain wall energy densities are conducted based on the time-dependent Ginzburg–Landau equation. The phase field simulations exhibit vortex patterns of polarizations, which have purely toroidal moments of polarizations and macroscopically negligible averaged polarizations, in nanoparticles without or with weak LR-elastic interactions when LR-electrostatic interactions are fully taken into account. However, a single-domain structure without any toroidal moment of polarizations is formed in small nanoparticles if LR-electrostatic interactions are completely ignored or LR-elastic interactions are fully taken into account. The polarization gradient energy or domain wall energy density plays also an important role in the formation of polarization structure. The vortex structure transits from a multivortex structure to a single-vortex structure as the domain wall energy density increases.
Nonexponential decay laws in perturbation theory of near threshold eigenvalues
Authors: Dinu Victor , Jensen Arne , Nenciu Gheorghe
Published: January 2009

We consider a two channel model of the form Hε=[Hop00E0]+ε[0W12W210] on H=Hop⊕C. The operator Hop is assumed to have the properties of a Schrödinger operator in odd dimensions, with a threshold at zero. As the energy parameter E0 is tuned past the threshold, we consider the survival probability |⟨Ψ0,e−itHεΨ0⟩|2, where Ψ0 is the eigenfunction corresponding to eigenvalue E0 for ε=0. We find nonexponential decay laws for ε small and E0 close to zero provided that the resolvent of Hop is not at least Lipschitz continuous at the threshold zero.
Unrestricted algebraic diagrammatic construction scheme of second order for the calculation of excited states of medium-sized and large molecules
Authors: Starcke Jan Hendrik , Wormit Michael , Dreuw Andreas
Published: January 2009

An unrestricted version of the algebraic diagrammatic construction (ADC) scheme of the polarization propagator in second order perturbation theory [UADC(2)] is derived via the intermediate state representation. The accuracy of the extended UADC(2)-x approach is evaluated by comparison of computed excitation energies of 11 medium-sized radicals with their corresponding experimental literature values and with excitation energies computed at equation-of-motion-CCSD (coupled clusters singles and doubles) level of theory. Overall, our numerical tests show that UADC(2)-x exhibits an averaged mean deviation in the excitation energies of only 0.3–0.4 eV compared to experimental gas phase data. It provides thus an alternative to coupled-cluster based approaches for the calculation of excited states of medium-sized open-shell molecules.
Geometric realizations of generalized algebraic curvature operators
Authors: Gilkey P. , Nikčević S. , Westerman D.
Published: January 2009

We study the eight natural General Linear (GL) equivariant geometric realization questions for the space of generalized algebraic curvature tensors. All but one of them is solvable; a nonzero projectively flat Ricci antisymmetric generalized algebraic curvature is not geometrically realizable by a projectively flat Ricci antisymmetric torsion-free connection.
A most compendious and facile quantum de Finetti theorem
Authors: König Robert , Mitchison Graeme
Published: January 2009

In its most basic form, the finite quantum de Finetti theorem states that the reduced k-partite density operator of an n-partite symmetric state can be approximated by a convex combination of k-fold product states. Variations of this result include Renner’s “exponential” approximation by “almost-product” states, a theorem which deals with certain triples of representations of the unitary group, and the result of D’Cruz et al. [e-print quant-ph/0606139;Phys. Rev. Lett. 98, 160406 (2007)] for infinite-dimensional systems. We show how these theorems follow from a single, general de Finetti theorem for representations of symmetry groups, each instance corresponding to a particular choice of symmetry group and representation of that group. This gives some insight into the nature of the set of approximating states and leads to some new results, including an exponential theorem for infinite-dimensional systems.
Melting of defective Cu with stacking faults
Authors: Han Li-Bo , An Qi , Fu Rong-Shan , Zheng Lianqing , Luo Sheng-Nian
Published: January 2009

We conduct classical molecular dynamics simulations to investigate isobaric melting of defective Cu solids with only one type of defect: intrinsic or extrinsic stacking faults. We characterize bulk melting and nucleation of melt in terms of order parameters, liquid cluster analysis, and the mean-first-passage-time method. The stacking faults induce negligible reduction in the temperature at melting, and the amount of superheating in these defective solids is the same as the perfect solids. Both homogeneous and heterogeneous nucleations of melt are observed. The existence of the stacking faults only slightly increases the nucleation rate and the probability of nucleation at heterogeneous nucleation sites. Such observations can be attributed to the low energy of the stacking faults and the extremely high heating rates in molecular dynamics simulations. These results underscore the necessity of considering the effects of rate and defect when interpreting experimental and simulation results as regards, e.g., phase boundaries.
General moment theorems for nondistinct unrestricted partitions
Authors: Coons Michael , Kirsten Klaus
Published: January 2009

A well-known result from Hardy and Ramanujan [“Aysmptotic formulae in combinatory analysis,” Proc. Lond. Math. Soc. 17, 75 (1918)] gives an asymptotic expression for the number of possible ways to express an integer as the sum of smaller integers. In this vein, we consider the general partitioning problem of writing an integer n as a sum of summands from a given sequence Λ of nondecreasing integers. Under suitable assumptions on the sequence Λ, we obtain results using associated zeta functions and saddle-point techniques. We also calculate higher moments of the sequence Λ as well as the expected number of summands. Applications are made to various sequences, including those of Barnes and Epstein types. These results are of potential interest in statistical mechanics in the context of Bose–Einstein condensation.
Kinetic models for the coordinated stepping of cytoplasmic dynein
Authors: Tsygankov Denis , Serohijos Adrian W. R. , Dokholyan Nikolay V. , Elston Timothy C.
Published: January 2009

To generate processive motion along a polymer track requires that motor proteins couple their ATP hydrolysis cycle with conformational changes in their structural subunits. Numerous experimental and theoretical efforts have been devoted to establishing how this chemomechanical coupling occurs. However, most processive motors function as dimers. Therefore a full understanding of the motor’s performance also requires knowledge of the coordination between the chemomechanical cycles of the two heads. We consider a general two-headed model for cytoplasmic dynein that is built from experimental measurements on the chemomechanical states of monomeric dynein. We explore different possible scenarios of coordination that simultaneously satisfy two main requirements of the dimeric protein: high processivity (long run length) and high motor velocity (fast ATP turnover). To demonstrate the interplay between these requirements and the necessity for coordination, we first develop and analyze a simple mechanical model for the force-induced stepping in the absence of ATP. Next we use a simplified model of dimeric dynein’s chemomechanical cycle to establish the kinetic rules that must be satisfied for the model to be consistent with recent data for the motor’s performance from single molecule experiments. Finally, we use the results of these investigations to develop a full model for dimeric dynein’s chemomechanical cycle and analyze this model to make experimentally testable predictions.
An entanglement measure for n qubits
Authors: Li Dafa , Li Xiangrong , Huang Hongtao , Li Xinxin
Published: January 2009

Coffman et al. [Phys. Rev. A 61, 052306 (2000)] introduced the residual entanglement for three qubits. In this paper, we present the entanglement measure τ(ψ) for even n qubits; for odd n qubits, we propose the residual entanglement τ(i)(ψ) with respect to qubit i and the odd n-tangle R(ψ) by averaging the residual entanglement with respect to each qubit. In this paper, we show that these measures are LU-invariant, entanglement monotones, invariant under permutations of the qubits, and multiplicative in some cases.
Bifurcations in spiral tip dynamics induced by natural convection in the Belousov–Zhabotinsky reaction
Authors: Budroni Marcello Antonio , Masia Marco , Rustici Mauro , Marchettini Nadia , Volpert Vitaly
Published: January 2009

The transition to spatial-temporal complexity exhibited by spiral waves under the effect of gravitational field in the Belousov–Zhabotinsky reaction is numerically studied on the basis of spiral tip dynamics. Successive transformations in tip trajectories are characterized as a function of the hydrodynamical parameter and attributed to a Ruelle–Takens–Newhouse scenario to chaos. The analysis describes the emergence of complexity in terms of the interplay between the evolution of the velocity field and concentration waves. In particular, (i) by mapping the tip motion in relation to some hydrodynamical pseudopotentials, the general mechanism by which the velocity field affects the tip trajectory is pointed out, and, (ii) by comparing the dynamical evolutions of local and mean properties associated with the inhomogeneous structures and to the velocity field, a surprising correlation is found. The results suggest that the reaction-diffusion-convection (RDC) coupling addresses the system to some general regimes, whose nature is imposed by the hydrodynamical contribution. More generally, RDC coupling would be formalized as the phenomenon that governs the system and drives it to chaos.
Growth and characterization of stable SrO-terminated SrTiO3 surfaces
Authors: Radovic M. , Lampis N. , Granozio F. Miletto , Perna P. , Ristic Z. , Salluzzo M. , Schlepütz C. M. , Scotti di Uccio U.
Published: January 2009

A simple technique for the growth of SrO-terminated SrTiO3 surfaces is reported. High quality SrTiO3 epitaxial films were grown by reflection high energy electron diffraction assisted pulsed laser deposition on suitably prepared NdGaO3 (110) substrates. The surface properties, analyzed within a growth/characterization multichamber ultrahigh vacuum system by photoemission spectroscopy performed on the core-level spectra of Sr and Ti, low energy electron diffraction-, scanning tunneling-, and atomic force microscopy, are fully consistent with a single Sr oxide termination. The availability of such high quality SrO-terminated SrTiO3 surfaces is of major importance for the controlled growth of oxide epilayers and interfaces.
Self-diffusion coefficient of two-center Lennard-Jones fluids: Molecular simulations and free volume theory
Authors: Nasrabad Afshin Eskandari
Published: January 2009

A comprehensive investigation is conducted to study the thermodynamics, structure, and mean free volume of rigid two-center Lennard-Jones fluids through Monte Carlo simulations. For a large number of states, the self-diffusion coefficient is computed using the following two different approaches: the equilibrium molecular dynamics simulation method and the modified Cohen–Turnbull theory. The effects of the bond elongation on different thermophysical properties are studied. The generic van der Waals theory, which has recently been extended to rigid polyatomic fluids [A. Eskandari Nasrabad and R. Laghaei, J. Chem. Phys. 125, 154505 (2006)], is used to compute the mean free volume needed in the modified Cohen–Turnbull theory. The effective site diameter is computed using the virial minimization method and the results are applied within the generic van der Waals theory. The Gibbs ensemble Monte Carlo simulation technique is applied to determine the location of the fluid phase envelope. The NVT Monte Carlo simulation method is then utilized to compute the equation of state and the correlation functions appearing in the generic van der Waals theory. It appears that the logarithm of the mean free volume versus density is almost linear at ρ>ρc independent of the bond length, which suggests a universal behavior. The self diffusion coefficient results of the modified Cohen–Turnbull theory are analyzed in detail.
Self-similarity and universality in Rayleigh–Taylor, Boussinesq turbulence
Authors: Vladimirova Natalia , Chertkov Michael
Published: January 2009

We report and discuss case study simulations of the Rayleigh–Taylor instability in the Boussinesq, incompressible regime developed to turbulence. Our main focus is on a statistical analysis of density and velocity fluctuations inside of the already developed and growing in size mixing zone. Novel observations reported in the article concern self-similarity of the velocity and density fluctuations spectra inside of the mixing zone snapshot, independence of the spectra of the horizontal slice level, and universality showing itself in a virtual independence of the internal structure of the mixing zone, measured in the rescaled spatial units, of the initial interface perturbations.
Biradicalic excited states of zwitterionic phenol-ammonia clusters
Authors: Carrera A. , Nielsen I. B. , Çarçabal P. , Dedonder C. , Broquier M. , Jouvet C. , Domcke W. , Sobolewski A. L.
Published: January 2009

Phenol-ammonia clusters with more than five ammonia molecules are proton transferred species in the ground state. In the present work, the excited states of these zwitterionic clusters have been studied experimentally with two-color pump probe methods on the nanosecond time scale and by ab initio electronic-structure calculations. The experiments reveal the existence of a long-lived excited electronic state with a lifetime in the 50–100 ns range, much longer than the excited state lifetime of bare phenol and small clusters of phenol with ammonia. The ab initio calculations indicate that this long-lived excited state corresponds to a biradicalic system, consisting of a phenoxy radical that is hydrogen bonded to a hydrogenated ammonia cluster. The biradical is formed from the locally excited state of the phenolate anion via an electron transfer process, which neutralizes the charge separation of the ground state zwitterion.
Charge and spin currents in a three-terminal mesoscopic ring
Authors: Wang L. G. , Chang Kai , Chan K. S.
Published: January 2009

We theoretically investigate the charge and spin currents in a three-terminal mesoscopic ring in the presence of a uniform and nonuniform Rashba spin-orbit interaction (SOI). It is shown that a fully spin-polarized charge current and a pure spin current can be generated by tuning the probe voltages and/or the strength of the Rashba SOI. The charge and spin currents oscillate as the strength of the Rashba SOI increases induced by the spin quantum interference. The ratio of probe voltages oscillates synchronously with the pure spin current as the strength of the Rashba SOI increases in a nonuniform Rashba ring, while it remains constant in a uniform Rashba ring. We demonstrate theoretically that a three-terminal uniform Rashba ring can be used as a spin polarizer and/or spin flipper for different spin injections, and a nonuniform Rashba ring could allow us to detect the pure spin current electrically.
Optimal ion acceleration from ultrathin foils irradiated by a profiled laser pulse of relativistic intensity
Authors: Andreev A. A. , Steinke S. , Sokollik T. , Schnürer M. , Avetsiyan S. Ter , Platonov K. Yu. , Nickles P. V.
Published: January 2009

Recent investigations of relativistic laser plasmas have shown that the energy transfer from the laser field to the kinetic ion energy and therefore the attainable maximum energy of the ions increases when ultrathin targets are irradiated by laser pulse without prepulse. In this paper, the influence of the target thickness and laser pulse contrast on the energy of the accelerated ions has been studied theoretically as well as experimentally. An optimum target was searched if a real laser pulse with a certain prepulse irradiates the target.
Generalized projective synchronization in time-delayed systems: Nonlinear observer approach
Authors: Ghosh Dibakar
Published: January 2009

In this paper, we consider the projective-anticipating, projective, and projective-lag synchronization in a unified coupled time-delay system via nonlinear observer design. A new sufficient condition for generalized projective synchronization is derived analytically with the help of Krasovskii–Lyapunov theory for constant and variable time-delay systems. The analytical treatment can give stable synchronization (anticipatory and lag) for a large class of time-delayed systems in which the response system’s trajectory is forced to have an amplitude proportional to the drive system. The constant of proportionality is determined by the control law, not by the initial conditions. The proposed technique has been applied to synchronize Ikeda and prototype models by numerical simulation.
Formation and optical properties of GaSb quantum dots epitaxially grown on Si substrates using an ultrathin SiO2 film technique
Authors: Nakamura Yoshiaki , Sugimoto Tomohiro , Ichikawa Masakazu
Published: January 2009

We developed a technique for forming epitaxial GaSb quantum dots on Si substrates using ultrathin SiO2 films that contain epitaxial Ge nuclei. Unlike Volmer–Weber-type GaSb quantum dots on Si, the dot density was higher (109–1012 cm−2) and the dot size was controlled in the range of approximately 10–100 nm. The nucleation of quantum dots was initiated by trapping Ga atoms on the Ge nuclei. Photoluminescence spectroscopy measurement at 5 K revealed the quantum-confinement effect in GaSb dots causing the photoluminescence peak to be continuously blueshifted from 0.76 eV by ∼30 meV when the base length of the dots decreases from 100 to 17 nm.
Real-time studies of surface roughness development and reticulation mechanism of advanced photoresist materials during plasma processing
Authors: Pal A. R. , Bruce R. L. , Weilnboeck F. , Engelmann S. , Lin T. , Kuo M.-S. , Phaneuf R. , Oehrlein G. S.
Published: January 2009

Surface roughness development of photoresist (PR) films during low pressure plasma etching has been studied using real-time laser light scattering from photoresist materials along with ellipsometric and atomic force microscopy (AFM) characterization. We show that evolution of the intensity of light scattered from a film surface can be used to study the development of surface roughness for a wide range of roughness starting from subnanometer to few hundred nanometers. Laser light scattering in combination with ellipsometry and AFM is also used to study the reticulation mechanism of 193 and 248 nm PRs during argon plasma processing. We employ a three-layer model (modified layer, rough layer, and bulk film) of the modified PR surface (193 and 248 nm PRs) to simulate and understand the behavior of ellipsometric Ψ-Δ trajectories. Bruggeman’s effective medium approximation is employed to study the roughness that develops on the surface after reticulation. When the glass transition temperature of the organic materials is reached during Ar plasma processing, the PR films reticulate and roughness develops rapidly. Roughness development is more pronounced for 248 nm PR than for 193 nm PR. Simulation of Ψ-Δ shows that the growth of roughness is accompanied by strong expansion in the materials, which is stronger for 248 nm PR than 193 nm PR. The leading factors responsible for reticulation are found to be compressive stress that develops in the modified surface layer as it is created along with strong molecular chain motion and expansion of the material when the temperature is increased past the glass transition temperature. Reticulation leads to a significantly different surface morphology for 248 nm PR as compared to 193 nm PR and can be related to differences in molecular structure and composition leading to different responses when a modified surface layer is formed by ion bombardment accompanying plasma etching.
Free-molecular heat transfer of vibrating cantilever and bridges
Authors: Martin Michael James , Houston Brian H.
Published: January 2009

Vibrating cantilever and bridge structures for micro- and nanodevices are characterized by high frequencies and length scales below the continuum limit. Free-molecular heat transfer equations are used to estimate the heat transfer from structures vibrating at high frequencies. The heat transfer is computed for a cantilever cross section as a function of a frequency and amplitude of vibration. These results are then integrated across the mode shape of cantilever and bridge structures to give a net heat transfer for the system. In micro- and nanodevices, the effect of frequency on the heat transfer is strongest for devices operating at cryogenic temperatures and extremely high frequencies. In mesoscale devices, the effect of frequency can be seen for devices with amplitudes on the order of microns and frequencies in the kilohertz region.
Charge transfer rates in organic semiconductors beyond first-order perturbation: From weak to strong coupling regimes
Authors: Nan Guangjun , Wang Linjun , Yang Xiaodi , Shuai Zhigang , Zhao Yi
Published: January 2009

Semiclassical Marcus electron transfer theory is often employed to investigate the charge transport properties of organic semiconductors. However, quite often the electronic couplings vary several orders of magnitude in organic crystals, which goes beyond the application scope of semiclassical Marcus theory with the first-order perturbative nature. In this work, we employ a generalized nonadiabatic transition state theory (GNTST) [Zhao et al., J. Phys. Chem. A 110, 8204 (2004)], which can evaluate the charge transfer rates from weak to strong couplings, to study charge transport properties in prototypical organic semiconductors: quaterthiophene and sexithiophene single crystals. By comparing with GNTST results, we find that the semiclassical Marcus theory is valid for the case of the coupling <10 meV for quaterthiophene and <5 meV for sexithiophene. It is shown that the present approach can be applied to design organic semiconductors with general electronic coupling terms. Taking oligothiophenes as examples, we find that our GNTST-calculated hole mobility is about three times as large as that from the semiclassical Marcus theory. The difference arises from the quantum nuclear tunneling and the nonperturbative effects.
Disorder accumulation and recovery in gold-ion irradiated 3C-SiC
Authors: Jiang W. , Weber W. J. , Lian J. , Kalkhoran N. M.
Published: January 2009

A single-crystal 3C-SiC film on a Si/SiO2/Si (separation by implantation of oxygen ) substrate was irradiated in different areas at 156 K with Au2+ ions to low fluences. The disorder profiles as a function of dose on both the Si and C sublattices have been determined in situ using a combination of 0.94 MeV D+ Rutherford backscattering spectrometry and nuclear reaction analysis in channeling geometry along the ⟨100⟩, ⟨110⟩, and ⟨111⟩ axes. The results indicate that for the same damage state, the level of disorder on the Si sublattice in 3C-SiC follows a decreasing order along the ⟨111⟩, ⟨100⟩, and ⟨110⟩ axes, while that on the C sublattice shows comparable values. Similar levels of Si and C disorder are observed along the ⟨111⟩ axis over the applied dose range. However, the level of C disorder is higher than that of Si disorder along all axes at low doses. The amount of disorder recovery during thermal annealing depends on the sublattice (Si or C) and crystallographic orientation. Room-temperature recovery occurs for both sublattices in 3C-SiC irradiated to a dose of 0.047 dpa or lower. Significant recovery is observed along all directions during thermal annealing at 600 K. The results are discussed and compared to those for 6H-SiC and 4H-SiC under similar irradiation conditions.
Transition to complete synchronization in phase-coupled oscillators with nearest neighbor coupling
Authors: El-Nashar Hassan F. , Muruganandam Paulsamy , Ferreira Fernando F. , Cerdeira Hilda A.
Published: January 2009

We investigate synchronization in a Kuramoto-like model with nearest neighbor coupling. Upon analyzing the behavior of individual oscillators at the onset of complete synchronization, we show that the time interval between bursts in the time dependence of the frequencies of the oscillators exhibits universal scaling and blows up at the critical coupling strength. We also bring out a key mechanism that leads to phase locking. Finally, we deduce forms for the phases and frequencies at the onset of complete synchronization.
Field emission properties of Si tip arrays coated with N-doped SrTiO3 thin films at different substrate temperature
Authors: Bian H. J. , Chen X. F. , Pan J. S. , Zhu W. , Sun Chang Q.
Published: January 2009

The effect of substrate temperature (TS) on the behavior of field emission, microstructure, optical band gap, and the surface energy of N-doped SrTiO3 thin films coated on silicon tip arrays has been examined in detail. Results indicate that the TS dominates the chemical states of nitrogen added to the sputtered SrTiO3 films and hence the observations. At the critical temperature of 600 °C, nitrogen atoms incorporate into the oxide film with sp-hybridization features. The generation of the nonbonding lone pair states narrows the optical band gap and the lone pair induced antibonding dipoles lower the threshold field for electron emission substantially. At lowered TS, molecular adsorption of nitrogen dominates. Contact angle measurements further evidence for the presence of antibonding dipole states at the surfaces which is responsible for the adsorbate-induced surface stress.
The importance of the photonic mode density in bioassays based on evanescent optical waves
Authors: Sato Akihiro , Menges Bernhard , Knoll Wolfgang
Published: January 2009

We have determined limits of detection (LODs) of DNA hybridization using an optical detection by two different method, i.e., surface plasmon fluorescence spectroscopy (SPFS) and optical waveguide fluorescence spectroscopy (OWFS), however, an identical sensor. Both techniques have a similar detection principle using the enhanced electromagnetic field to excite fluorophores and to monitor DNA hybridization in real-time with high sensitivity. Firstly, the detection of DNA hybridization was conducted by SPFS and the LOD value was found to be 2.0pM (2.0×10−12mol∕L). The same study was further conducted by OWFS, and a LOD of 170fM (1.7×10−13mol∕L) and 100fM (1×10−13mol∕L) was achieved for TM1 and TE0 modes, respectively, indicating that an improvement of the LOD of one order of magnitude is possible with OWFS. Furthermore, the photonic mode density at resonance of each mode was calculated, and these values are reflected in the LOD values. The present study illustrates the potential of OWFS as biosensor applications being able to detect in real-time even trace amounts of analyte.
Adsorption of hydrogen on boron-doped graphene: A first-principles prediction
Authors: Zhou Y. G. , Zu X. T. , Gao F. , Nie J. L. , Xiao H. Y.
Published: January 2009

The doping effects of boron on the atomic adsorption of hydrogen on graphene have been investigated using density functional theory calculations. The hydrogen adsorption energies and electronic structures have been considered for pristine and B-doped graphene with the adsorption of hydrogen on top of carbon or boron atom. It is found that the B-doping forms an electron-deficient structure and decreases the hydrogen adsorption energy dramatically. For the adsorption of hydrogen on top of other sites, similar results have also been found. These results indicate that the hydrogen storage capacity is improved by the doping of B atom.
Annealing effects on faceting of InAs∕GaAs(001) quantum dots
Authors: Placidi E. , Della Pia A. , Arciprete F.
Published: January 2009

The aspect ratio and faceting evolution of quantum dots grown at 500°C were studied as a function of postgrowth annealing temperature. We show that faceting and aspect ratio strictly depend on growth conditions. The evolution toward {136} and {137} facets is kinetically limited and occurs under different experimental conditions. Furthermore long annealing procedures lead to the occurrence of low aspect ratio domes different from those forming at higher growth temperatures.
Studies of turbulence and transport in Alcator C-Mod H-mode plasmas with phase contrast imaging and comparisons with GYRO
Authors: Lin L. , Porkolab M. , Edlund E. M. , Rost J. C. , Fiore C. L. , Greenwald M. , Lin Y. , Mikkelsen D. R. , Tsujii N. , Wukitch S. J.
Published: January 2009

Recent advances in gyrokinetic simulation of core turbulence and associated transport requires an intensified experimental effort to validate these codes using state of the art synthetic diagnostics to compare simulations with experimental data. A phase contrast imaging (PCI) diagnostic [M. Porkolab, J. C. Rost, N. Basse et al., IEEE Trans. Plasma Sci. 34, 229 (2006)] is used to study H-mode plasmas in Alcator C-Mod [M. Greenwald, D. Andelin, N. Basse et al., Nucl. Fusion 45, S109 (2005)]. The PCI system is capable of measuring density fluctuations with high temporal (2kHz–5MHz) and wavenumber (0.5–55cm−1) resolution. Recent upgrades have enabled PCI to localize the short wavelength turbulence in the electron temperature gradient range and resolve the direction of propagation (i.e., electron versus ion diamagnetic direction) of the longer wavelength turbulence in the ion temperature gradient (ITG) and trapped electron mode range. The studies focus on plasmas before and during internal transport barrier formation in an enhanced Dα H-mode plasma assisted with ion cyclotron resonance frequency heating. Nonlinear GYRO simulations have also been performed [J. Candy and R. E. Waltz, Phys. Rev. Lett. 91, 045001 (2003)] and the predicted fluctuation is compared against experimental measurements through a synthetic PCI diagnostic method. The simulated fluctuations from GYRO agree with experimental measurements in the ITG regime. GYRO also shows good agreement in transport predictions with experimental measurements after reducing the ion temperature gradient (∼15%) and adding E×B shear suppression, all within the experimental uncertainty.
Memory effects in photoinduced femtosecond magnetization rotation in ferromagnetic GaMnAs
Authors: Wang J. , Cotoros I. , Chemla D. S. , Liu X. , Furdyna J. K. , Chovan J. , Perakis I. E.
Published: January 2009

We report a photoinduced femtosecond change in the magnetization direction in the ferromagnetic semiconductor GaMnAs, which allows for the detection of a four-state magnetic memory on the femtosecond time scale. The temporal profile of the magnetization exhibits a discontinuity that reveals two distinct temporal regimes, marked by the transition from a carrier-mediated nonthermal regime within the first 200 fs to a thermal, lattice-heating picosecond regime.
A modified commercial scanner as an image plate for table-top optical applications
Authors: Casado-Rojo S. , Lorenzana H. E. , Cáceres M. , Baonza V. G.
Published: January 2009

A reliable, accurate, and inexpensive optical detector for table-top applications is described here. Based on a commercial high resolution office scanner coupled to a projection plate, the detector offers a large image plate surface, allowing recording of sizeable images without systematic errors associated with coupling optics aberrations. Several tests on distance-dependent and steady interference patterns are presented and discussed. The extension to other types of optical measurements by substituting the projection plate is proposed.
Nonlinear optical properties of graphene oxide in nanosecond and picosecond regimes
Authors: Liu Zhibo , Wang Yan , Zhang Xiaoliang , Xu Yanfei , Chen Yongsheng , Tian Jianguo
Published: January 2009

The nonlinear optical properties of graphene oxide (GO) were investigated at 532 nm in nanosecond and picosecond regimes. Results show that two-photon absorption dominates nonlinear absorption process of GO in the case of picosecond pulses, while excited state nonlinearities play an important role in the case of nanosecond pulses. Additionally, we compared nonlinear optical properties of three different dimensional carbon-based materials (two-dimensional graphene, one-dimensional carbon nanotube, and zero-dimensional fullerene) in nanosecond and picosecond regimes, respectively. The nonlinear mechanism of GO is distinctly different from nonlinear scattering of carbon nanotube and excited state nonlinearity of fullerene.
Epitaxial SmCo5 thin films with perpendicular anisotropy
Authors: Seifert M. , Neu V. , Schultz L.
Published: January 2009

Epitaxial SmCo5 thin films with strong perpendicular magnetic anisotropy have been developed by pulsed laser deposition on heated Ru buffered Al2O3(0001) substrates. Pole figure measurements on thicker films reveal the existence of two epitaxial variants, 30° in-plane rotated to each other, which reduces to a single epitaxial relation for smaller film thickness. The presence of a single SmCo5 phase with perpendicular direction of the c-axis is established by multiple peak analysis of x-ray data in pole figure geometry and is confirmed by a numerical fit of hysteresis measurements, which results in an anisotropy constant of Ku=7.6 MJ/m3.
B profile alteration by annealing in reactive ambients
Authors: Pawlak B. J. , Cowern N. E. B. , Vandervorst W.
Published: January 2009

Suppression or stimulation of B diffusion and activation in Si (coimplanted with F) has been investigated by anneals in a N2 ambient enriched with H2 or O2. The H2 rich ambient leads to B desorption and therefore stimulated diffusion toward the surface, thus effectively reducing indiffusion. Annealing in an O2 rich ambient promotes deeper B diffusion by injection of Si interstitials. The impact of these ambients can further be modulated by combining the B implant with a shallow or deep F coimplant acting as Si interstitial trap. Deep F coimplant and H2 rich ambient offer attractive B diffusion and activation.
Optical modulation of near-infrared photoluminescence from lead sulfide quantum dots in glasses
Authors: Liu Chao , Kwon Yong Kon , Heo Jong
Published: January 2009

The authors report the modulation of photoluminescence intensity from lead sulfide quantum dots using two laser beams with different wavelengths. Photoluminescence from lead sulfide quantum dots in glasses was reversibly switched between the “bright” and “dark” states and degree of darkening to 16% of the initial intensity was realized. Changes in the photoluminescence were insensitive to temperature but strongly dependent on the power densities of the modulating laser beam. This efficient optical modulation has potential for optical switching and memory device applications.
Electronic structure of In2O3 from resonant x-ray emission spectroscopy
Authors: Piper L. F. J. , DeMasi A. , Cho S. W. , Smith K. E. , Fuchs F. , Bechstedt F. , Körber C. , Klein A. , Payne D. J. , Egdell R. G.
Published: January 2009

The valence and conduction band structures of In2O3 have been measured using a combination of valence band x-ray photoemission spectroscopy, O K-edge resonant x-ray emission spectroscopy, and O K-edge x-ray absorption spectroscopy. Excellent agreement is noted between the experimental spectra and O 2p partial density of states calculated within hybrid density functional theory. Our data are consistent with a direct band gap for In2O3.
Dynamics of gold nanoparticles in a polymer melt
Authors: Grabowski Christopher A. , Adhikary Bijoy , Mukhopadhyay Ashis
Published: January 2009

Gold nanoparticles are used as a luminescent contrast agent to study size-dependent dynamics in polymer matrix. The experiments measured the diffusion coefficient of particles in poly(butyl methacrylate) melt by tracking their motion within a diffraction-limited focus of a laser with 150 fs pulses at 800 nm. Our results indicate that for unentangled polymers, when the particle radius (R) is greater than the gyration radius (Rg) of the chain, the Stokes–Einstein relation can accurately predict particle dynamics. For longer chains, if the entanglement mesh length is larger than R, the particle diffuses ∼250 times faster than predicted by the Stokes–Einstein relation.
A role for NANOG in G1 to S transition in human embryonic stem cells through direct binding of CDK6 and CDC25A
Authors: Zhang Xin , Neganova Irina , Przyborski Stefan , Yang Chunbo , Cooke Michael , Atkinson Stuart P. , Anyfantis George , Fenyk Stefan , Keith W. Nicol , Hoare Stacey F. , Hughes Owen , Strachan Tom , Stojkovic Miodrag , Hinds Philip W. , Armstrong Lyle , Lako Majlinda
Published: January 2009

In this study, we show that NANOG, a master transcription factor, regulates S-phase entry in human embryonic stem cells (hESCs) via transcriptional regulation of cell cycle regulatory components. Chromatin immunoprecipitation combined with reporter-based transfection assays show that the C-terminal region of NANOG binds to the regulatory regions of CDK6 and CDC25A genes under normal physiological conditions. Decreased CDK6 and CDC25A expression in hESCs suggest that both CDK6 and CDC25A are involved in S-phase regulation. The effects of NANOG overexpression on S-phase regulation are mitigated by the down-regulation of CDK6 or CDC25A alone. Overexpression of CDK6 or CDC25A alone can rescue the impact of NANOG down-regulation on S-phase entry, suggesting that CDK6 and CDC25A are downstream cell cycle effectors of NANOG during the G1 to S transition.
Golgi targeting of Drosophila melanogaster β4GalNAcTB requires a DHHC protein family–related protein as a pilot
Authors: Johswich Anita , Kraft Benjamin , Wuhrer Manfred , Berger Monika , Deelder André M. , Hokke Cornelis H. , Gerardy-Schahn Rita , Bakker Hans
Published: January 2009

Drosophila melanogaster β4GalNAcTB mutant flies revealed that this particular N-acetylgalactosaminyltransferase is predominant in the formation of lacdiNAc (GalNAcβ1,4GlcNAc)-modified glycolipids, but enzymatic activity could not be confirmed for the cloned enzyme. Using a heterologous expression cloning approach, we isolated β4GalNAcTB together with β4GalNAcTB pilot (GABPI), a multimembrane-spanning protein related to Asp-His-His-Cys (DHHC) proteins but lacking the DHHC consensus sequence. In the absence of GABPI, inactive β4GalNAcTB is trapped in the endoplasmic reticulum (ER). Coexpression of β4GalNAcTB and GABPI generates the active enzyme that is localized together with GABPI in the Golgi. GABPI associates with β4GalNAcTB and, when expressed with an ER retention signal, holds active β4GalNAcTB in the ER. Importantly, treatment of isolated membrane vesicles with Triton X-100 disturbs β4GalNAcTB activity. This phenomenon occurs with multimembrane-spanning glycosyltransferases but is normally not a property of glycosyltransferases with one membrane anchor. In summary, our data provide evidence that GABPI is required for ER export and activity of β4GalNAcTB.
The nuclear export factor Xpo1p targets Mad1p to kinetochores in yeast
Authors: Scott Robert J. , Cairo Lucas V. , Van de Vosse David W. , Wozniak Richard W.
Published: January 2009

Nuclear pore complexes (NPCs) mediate all nucleocytoplasmic traffic and provide docking sites for the spindle assembly checkpoint (SAC) protein Mad1p. Upon SAC activation, Mad1p is recruited onto kinetochores and rapidly cycles between NPCs and kinetochores. We examined the mechanism of Mad1p movement onto kinetochores and show that it is controlled by two components of the nuclear transport machinery, the exportin Xpo1p and Ran–guanosine triphosphate (GTP). Mad1p contains a nuclear export signal (NES) that is recognized by Xpo1p. The NES, Xpo1p, and RanGTP are all required for Mad1p recruitment onto kinetochores in checkpoint-activated cells. Consistent with this function, Xpo1p also accumulates on kinetochores after SAC activation. We have also shown that Xpo1p and RanGTP are required for the dynamic cycling of Mad1p between NPCs and kinetochores in checkpoint-arrested cells. These results reveal an important function for Xpo1p in mediating intranuclear transport events and identify a signaling pathway between kinetochores and NPCs.
Lamin B1 controls oxidative stress responses via Oct-1
Authors: Malhas Ashraf N. , Lee Chiu Fan , Vaux David J.
Published: January 2009

Interaction of lamins with chromatin and transcription factors regulate transcription. Oct-1 has previously been shown to colocalize partly with B-type lamins and is essential for transcriptional regulation of oxidative stress response genes. Using sequential extraction, co-immunoprecipitation (IP), fluorescence loss in photobleaching, and fluorescence resonance energy transfer, we confirm Oct-1–lamin B1 association at the nuclear periphery and show that this association is lost in Lmnb1Δ/Δ cells. We show that several Oct-1–dependent genes, including a subset involved in oxidative stress response, are dysregulated in Lmnb1Δ/Δ cells. Electrophoretic mobility shift assay and chromatin IP reveal that Oct-1 binds to the putative octamer-binding sequences of the dysregulated genes and that this activity is increased in cells lacking functional lamin B1. Like Oct1−/− cells, Lmnb1Δ/Δ cells have elevated levels of reactive oxygen species and are more susceptible to oxidative stress. Sequestration of Oct-1 at the nuclear periphery by lamin B1 may be a mechanism by which the nuclear envelope can regulate gene expression and contribute to the cellular response to stress, development, and aging.
The SH3 domains of two PCH family members cooperate in assembly of the Schizosaccharomyces pombe contractile ring
Authors: Roberts-Galbraith Rachel H. , Chen Jun-Song , Wang Jianqiu , Gould Kathleen L.
Published: January 2009

Schizosaccharomyces pombe cdc15 homology (PCH) family members participate in many cellular processes by bridging the plasma membrane and cytoskeleton. Their F-BAR domains bind and curve membranes, whereas other domains, typically SH3 domains, are expected to provide cytoskeletal links. We tested this prevailing model of functional division in the founding member of the family, Cdc15, which is essential for cytokinesis in S. pombe, and in the related PCH protein, Imp2. We find that the distinct functions of Imp2 and Cdc15 are SH3 domain independent. However, the Cdc15 and Imp2 SH3 domains share an essential role in recruiting proteins to the contractile ring, including Pxl1 and Fic1. Together, Pxl1 and Fic1, a previously uncharacterized C2 domain protein, add structural integrity to the contractile ring and prevent it from fragmenting during division. Our data indicate that the F-BAR proteins Cdc15 and Imp2 contribute to a single biological process with both distinct and overlapping functions.
Bone morphogenetic protein 2 induces pulmonary angiogenesis via Wnt–β-catenin and Wnt–RhoA–Rac1 pathways
Authors: de Jesus Perez Vinicio A. , Alastalo Tero-Pekka , Wu Jenny C. , Axelrod Jeffrey D. , Cooke John P. , Amieva Manuel , Rabinovitch Marlene
Published: January 2009

Mutations in bone morphogenetic protein (BMP) receptor II (BMPRII) are associated with pulmonary artery endothelial cell (PAEC) apoptosis and the loss of small vessels seen in idiopathic pulmonary arterial hypertension. Given the low penetrance of BMPRII mutations, abnormalities in other converging signaling pathways may be necessary for disease development. We hypothesized that BMPRII supports normal PAEC function by recruiting Wingless (Wnt) signaling pathways to promote proliferation, survival, and motility. In this study, we report that BMP-2, via BMPRII-mediated inhibition of GSK3-β, induces β-catenin (β-C) accumulation and transcriptional activity necessary for PAEC survival and proliferation. At the same time, BMP-2 mediates phosphorylated Smad1 (pSmad1) or, with loss of BMPRII, pSmad3-dependent recruitment of Disheveled (Dvl) to promote RhoA–Rac1 signaling necessary for motility. Finally, using an angiogenesis assay in severe combined immunodeficient mice, we demonstrate that both β-C– and Dvl-mediated RhoA–Rac1 activation are necessary for vascular growth in vivo. These findings suggest that the recruitment of both canonical and noncanonical Wnt pathways is required in BMP-2–mediated angiogenesis.
Sustained activation of STAT5 is essential for chromatin remodeling and maintenance of mammary-specific function
Authors: Xu Ren , Nelson Celeste M. , Muschler John L. , Veiseh Mandana , Vonderhaar Barbara K. , Bissell Mina J.
Published: January 2009

Epithelial cells, once dissociated and placed in two-dimensional (2D) cultures, rapidly lose tissue-specific functions. We showed previously that in addition to prolactin, signaling by laminin-111 was necessary to restore functional differentiation of mammary epithelia. Here, we elucidate two additional aspects of laminin-111 action. We show that in 2D cultures, the prolactin receptor is basolaterally localized and physically segregated from its apically placed ligand. Detachment of the cells exposes the receptor to ligation by prolactin leading to signal transducers and activators of transcription protein 5 (STAT5) activation, but only transiently and not sufficiently for induction of milk protein expression. We show that laminin-111 reorganizes mammary cells into polarized acini, allowing both the exposure of the prolactin receptor and sustained activation of STAT5. The use of constitutively active STAT5 constructs showed that the latter is necessary and sufficient for chromatin reorganization and β-casein transcription. These results underscore the crucial role of continuous laminin signaling and polarized tissue architecture in maintenance of transcription factor activation, chromatin organization, and tissue-specific gene expression.
Mitochondrial degeneration and not apoptosis is the primary cause of embryonic lethality in ceramide transfer protein mutant mice
Authors: Wang Xin , Rao Raghavendra Pralhada , Kosakowska-Cholody Teresa , Masood M. Athar , Southon Eileen , Zhang Helin , Berthet Cyril , Nagashim Kunio , Veenstra Timothy K. , Tessarollo Lino , Acharya Usha , Acharya Jairaj K.
Published: January 2009

Ceramide transfer protein (CERT) functions in the transfer of ceramide from the endoplasmic reticulum (ER) to the Golgi. In this study, we show that CERT is an essential gene for mouse development and embryonic survival and, quite strikingly, is critical for mitochondrial integrity. CERT mutant embryos accumulate ceramide in the ER but also mislocalize ceramide to the mitochondria, compromising their function. Cells in mutant embryos show abnormal dilation of the ER and degenerating mitochondria. These subcellular changes manifest as heart defects and cause severely compromised cardiac function and embryonic death around embryonic day 11.5. In spite of ceramide accumulation, CERT mutant mice do not die as a result of enhanced apoptosis. Instead, cell proliferation is impaired, and expression levels of cell cycle–associated proteins are altered. Individual cells survive, perhaps because cell survival mechanisms are activated. Thus, global compromise of ER and mitochondrial integrity caused by ceramide accumulation in CERT mutant mice primarily affects organogenesis rather than causing cell death via apoptotic pathways.