bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatigue and ferroelectric behavior of La and Zn comodified BiFeO3 thin films
Authors: Wu Jiagang , Wang John
Published: July 2010

Bi 0.90 La 0.10 Fe 0.95 Zn 0.05 O 3 (BLFZO) thin films were grown directly on Pt/TiO2/SiO2/Si(100) substrates without any buffer layer by off-axis radio frequency sputtering. The BLFZO thin film deposited at 580 °C possesses a single-phase purity, while those deposited at other temperatures exhibit a varying amount of second phases, indicating that the deposition temperature plays a critical role in the phase development of BLFZO thin films. Although La and Zn cosubstitutions lower the Curie temperature (Tc) of BiFeO3 thin films, the resulting Tc value (∼630 °C) is still much higher as compared to other lead-based or lead-free ferroelectric thin films. The BLFZO thin film exhibits a remanent polarization of 2Pr∼131.7 μC/cm2 and a coercive field of 2Ec∼496 kV/cm, in association with the improvement in electrical resistance. On the basis of the studies for frequency (1 kHz∼1 MHz) and driving field (0.8Ec∼2.0Ec) dependences, the BLFZO thin film demonstrates the desired fatigue endurance and weak frequency and driving field dependence. La and Zn cosubstitutions are shown to contribute toward the high remanent polarization and fatigue endurance.
Analysis of electrical percolation thresholds in carbon nanotube networks using the Weibull probability distribution
Authors: Pfeifer S. , Park S.-H. , Bandaru P. R.
Published: July 2010

We suggest a method for the a priori determination of the electrical percolation threshold in carbon nanotube (CNT) networks, of relevance in electronic devices, polymer composites, etc. The variability in the CNT lengths, commonly observed in practical processing and dispersion, was also considered and the resulting probability distribution function determined to be of the Weibull type. Subsequently, the predicted percolation threshold volume fractions for single-walled CNTs, ∼0.000 73 and multiwalled CNTs, ∼0.0193, were found to be in close correspondence to the experimentally determined values of 0.0011 and 0.0147, respectively.
Quasi-Newton parallel geometry optimization methods
Authors: Burger Steven K. , Ayers Paul W.
Published: July 2010

Algorithms for parallel unconstrained minimization of molecular systems are examined. The overall framework of minimization is the same except for the choice of directions for updating the quasi-Newton Hessian. Ideally these directions are chosen so the updated Hessian gives steps that are same as using the Newton method. Three approaches to determine the directions for updating are presented: the straightforward approach of simply cycling through the Cartesian unit vectors (finite difference), a concurrent set of minimizations, and the Lanczos method. We show the importance of using preconditioning and a multiple secant update in these approaches. For the Lanczos algorithm, an initial set of directions is required to start the method, and a number of possibilities are explored. To test the methods we used the standard 50-dimensional analytic Rosenbrock function. Results are also reported for the histidine dipeptide, the isoleucine tripeptide, and cyclic adenosine monophosphate. All of these systems show a significant speed-up with the number of processors up to about eight processors.
Optical spectroscopy of charge transfer transitions in multiferroic manganites, ferrites, and related insulators
Authors: Moskvin A. S. , Pisarev R. V.
Published: July 2010

The results of theoretical and experimental studies of charge transfer (CT) transitions in multiferroic manganites, ferrites, and related insulators are reviewed. Starting with a simple cluster model approach one-center p-d and two-center d-d CT transitions, their polarization properties, the role played by structural parameters, orbital mixing, and spin degree of freedom are all addressed. Optical ellipsometry data in the spectral range of 0.6–5.8eV in perovskite and hexagonal rare-earth manganites RMnO3 and in orthorhombic manganites RMn2O5 are analyzed. Two groups of iron oxides, where Fe3+ ions occupy either only octahedral positions (BiFeO3, orhoferrites RFeO3 et al.) and materials with Fe3+ ions both in octahedral and tetrahedral positions (hematite α-Fe2O3, garnets RFe5O12, lithium ferrite LiFe5O8, Ca2Fe2O5 et al.), are discussed.
Light reflection from nonlinear optical dielectric film on a bigyrotropic magnetoelectric substrate at angles close to Brewster angles
Authors: Dadoenkova Yu. S. , Lyubchanskiĭ I. L. , Lee Y. P. , Rasing Th.
Published: July 2010

Light reflection from the interface of a dielectric film, characterized by a cubic optical nonlinearity, on a bigyrotropic substrate magnetoelectric substrate is investigated theoretically. Relations are obtained for the reflection coefficient as a function of the incidence angle of the light for the main magneto-optic configurations: polar, longitudinal, and transverse. The effect of the magneto-electric and magneto-optical contributions to the electric polarization of such a biaxial structure on the polarization state of the light reflected at angles close to the Brewster angles is studied.
Asymptotic expansion of the log-partition function for a gas of interacting Brownian loops. II.
Authors: Poghosyan Suren
Published: July 2010

In an earlier paper [Poghosyan, S. and Zessin, H., “Asymptotic expansion of the log-partition function for a gas of interacting Brownian loops,” J. Math. Phys. 48, 093301 (2007)] we studied the asymptotic expansion of the log-partition function of a quantum gas in a bounded domain as this domain is dilated to infinity. The volume and the boundary terms of this expansion were found explicitly in terms of functional integrals. Here we obtain the third term of the expansion which in the two-dimensional case has a form of the Euler–Poincaré characteristics of the domain times a potential dependent factor given explicitly in terms of functional integrals. The analysis relies on the Feynman–Kac representation of the log-partition function and on the cluster expansion method.
Hadamard matrices from mutually unbiased bases
Authors: Diţă P.
Published: July 2010

An analytical method for getting new complex Hadamard matrices by using mutually unbiased bases and a nonlinear doubling formula is provided. The method is illustrated with the n=4 case that leads to a rich family of eight-dimensional Hadamard matrices that depend on five arbitrary parameters whose modulus is equal to unity.
Compression-compression fatigue of Pd43Ni10Cu27P20 metallic glass foam
Authors: Wang Gongyao , Demetriou Marios D. , Schramm Joseph P. , Liaw Peter K. , Johnson William L.
Published: July 2010

Compression-compression fatigue testing of metallic-glass foam is performed. A stress-life curve is constructed, which reveals an endurance limit at a fatigue ratio of about 0.1. The origin of fatigue resistance of this foam is identified to be the tendency of intracellular struts to undergo elastic and reversible buckling, while the fatigue process is understood to advance by anelastic strut buckling leading to localized plasticity (shear banding) and ultimate strut fracture. Curves of peak and valley strain versus number of cycles coupled with plots of hysteresis loops and estimates of energy dissipation at various loading cycles confirm the four stages of foam-fatigue.
Precipitation of heterogeneous nanostructures: Metal nanoparticles and dielectric nanocrystallites
Authors: Masai Hirokazu , Takahashi Yoshihiro , Fujiwara Takumi , Tokuda Yomei , Yoko Toshinobu
Published: July 2010

Heterogeneous precipitation of nanocrystallites of metallic Bi and anatase was observed in CaO–Bi2O3–B2O3–Al2O3–TiO2 glass-ceramics. Addition of AlN reduced the Bi2O3 to Bi metal nanoparticles, which were uniformly dispersed in the glass. After heat-treatment of the Bi-precipitated glass around the glass transition temperature, nanocrystalline anatase precipitated out without aggregation of the Bi metal particles. It was found that the anatase nanocrystal size was affected by the distance between a nanocrystal and a precipitated Bi nanoparticle. The glass-ceramic produced is a functional material containing a random dispersion of different types of nanoparticles with different dielectric constants.
Color tunability with temperature and pump intensity in Yb3+/Tm3+ codoped aluminosilicate glass under anti-Stokes excitation
Authors: Silva W. F. , Eliel G. S. N. , dos Santos P. V. , de Araujo M. T. , Vermelho M. V. D. , Udo P. T. , Astrath N. G. C , Baesso M. L. , Jacinto C.
Published: July 2010

Pump and thermally induced color tunabilities were demonstrated in Yb3+/Tm3+ codoped low silica calcium aluminosilicate (LSCAS) glass under anti-Stokes excitation at 1.064 μm. The effects of pump intensity and sample’s temperature on the upconversion emissions and mainly on the color tunabilities (from 800 to 480 nm) were investigated. The results revealed a 20- and a threefold reductions at 800/480 nm ratio as, respectively, the pump intensity and sample’s temperature were increased from 27 to 700 kW/cm2 and from 296 to 577 K. These behaviors with pump intensity and temperature (a strong increase of the 480 nm emission in comparison with the 800 nm one) were attributed to the several efficient processes occurring in the LSCAS system (Yb3+→Tm3+ energy-transfer processes, easy saturations of the Yb3+ and Tm3+ excited states, and radiative emissions). Besides these assigns, the temperature dependence is mainly assigned to the temperature-dependent effective absorption cross section of the ytterbium sensitizer through the so-called multiphonon-assisted anti-Stokes excitation process. Theoretical analyses and fits of the experimental data provided quantitative information.
Isomerization of nitrosomethane to formaldoxime: Energies, geometries, and frequencies from the parametric variational two-electron reduced-density-matrix method
Authors: DePrince A. Eugene , Mazziotti David A.
Published: July 2010

The isomerization of nitrosomethane to trans-formaldoxime is treated with the parametric variational two-electron reduced-density-matrix (2-RDM) method. In the parametric 2-RDM method, the ground-state energy is minimized with respect to a 2-RDM that is parameterized to be both size extensive and nearly N-representable. The calculations were performed with an efficient version of the 2-RDM method that we developed as an extension of the PSI3 ab initio package. Details of the implementation, which scales like configuration interaction with single and double excitations, are provided as well as a comparison of two optimization algorithms for minimizing the energy functional. The conversion of nitrosomethane to trans-formaldoxime can occur by one of two pathways: (i) a 1,3-sigmatropic hydrogen shift or (ii) two successive 1,2-sigmatropic hydrogen shifts. The parametric 2-RDM method predicts that the reaction channel involving two sequential 1,2-shifts is about 10 kcal/mol more favorable than the channel with a single 1,3-shift, which is consistent with calculations from other ab initio methods. We computed geometric parameters and harmonic frequencies for each stationary point on the reaction surfaces. Transition-state energies, geometries, and frequencies from the 2-RDM method are often more accurate than those from traditional wave function methods of a similar computational cost. Although electronic-structure methods generally agree that the 1,2-shift is more efficient, the energy ordering of the reactant nitrosomethane and the 1,2-shift intermediate formaldonitrone is unresolved in the literature. With an extrapolation to the complete-basis-set limit the parametric 2-RDM method predicts formaldonitrone to be very slightly more stable than nitrosomethane.
Terahertz time-domain-spectroscopy system based on femtosecond Yb:fiber laser and GaBiAs photoconducting components
Authors: Pačebutas V. , Bičiūnas A. , Balakauskas S. , Krotkus A. , Andriukaitis G. , Lorenc D. , Pugžlys A. , Baltuška A.
Published: July 2010

We describe a terahertz time-domain-spectroscopy system that is based on photoconductive components fabricated from low-temperature-grown GaBiAs epitaxial layers and activated by femtosecond 1.03 μm pulses emitted by an Yb:fiber laser. Experiments performed with the laser pulses of different durations have evidenced that the spectral range of the system is limited by the photoexcited carrier lifetime. The optical to terahertz conversion efficiency of the system exceeds 10−4 with the usable spectral range of about 3 THz in the case of 170 fs excitation pulses.
A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements
Authors: Chaudhury Srabanti , Makarov Dmitrii E.
Published: July 2010

Motivated by recent experimental efforts to measure the time a molecular system spends in transit between the reactants and the products of a chemical reaction, here we study the properties of the distribution of such transit times for the case of conservative dynamics on a multidimensional energy landscape. Unlike reaction rates, transit times are not invariant with respect to the order parameter (a.k.a. the experimental signal) used to monitor the progress of a chemical reaction. Nevertheless, such order parameter dependence turns out to be relatively weak. Moreover, for several model systems we find that the probability distribution of transit times can be estimated analytically, with reasonable accuracy, by assuming that the order parameter coincides with the direction of the unstable normal mode at the transition state. Although this approximation tends to overestimate the actual mean transit time measured using other order parameters, it yields asymptotically correct long-time behavior of the transit time distribution, which is independent of the order parameter.
On the microstructure of Si coimplanted with H+ and He+ ions at moderate energies
Authors: Reboh S. , Schaurich F. , Declemy A. , Barbot J. F. , Beaufort M. F. , Cherkashin N. , Fichtner P. F. P.
Published: July 2010

We report on the microstructure of silicon coimplanted with hydrogen and helium ions at moderate energies. X-ray diffraction investigations in as-implanted samples show the direct correlation between the lattice strain and implanted ion depth profiles. The measured strain is examined in the framework of solid mechanics and its physical origin is discussed. The microstructure evolution of the samples subjected to intermediate temperature annealing (350 °C) is elucidated through transmission electron microscopy. Gas-filled cavities in the form of nanocracks and spherical bubbles appear at different relative concentration, size, and depth location, depending on the total fluence. These different microstructure evolutions are connected with the surface exfoliation behavior of samples annealed at high temperature (700 °C), determining the optimal conditions for thick layer transfer. 1.5 μm thick Si films are then obtained onto glass substrates.
Visualization of droplet departure on a superhydrophobic surface and implications to heat transfer enhancement during dropwise condensation
Authors: Dietz C. , Rykaczewski K. , Fedorov A. G. , Joshi Y.
Published: July 2010

Droplet departure frequency is investigated using environmental scanning electron microscopy with implications to enhancing the rate of dropwise condensation on superhydrophobic surfaces. Superhydrophobic surfaces, formed by cupric hydroxide nanostructures, allow the condensate to depart from a surface with a tilt angle of 30° from the horizontal. The resulting decrease in drop departure size shifts the drop size distribution to smaller radii, which may enhance the heat transfer rate during dropwise condensation. The heat transfer enhancement is estimated by modifying the Rose and Le Fevre drop distribution function to account for a smaller maximum droplet size on a superhydrophobic surface.
Tunneling spectroscopy of metal-oxide-graphene structure
Authors: Zeng Caifu , Wang Minsheng , Zhou Yi , Lang Murong , Lian Bob , Song Emil , Xu Guangyu , Tang Jianshi , Torres Carlos , Wang Kang L.
Published: July 2010

The unique density of states of graphene at the device level is probed via tunneling spectroscopy of macroscopic metal-oxide-graphene structures. Local conductance minima from electrons tunneling into the graphene Dirac point are observed in the dI/dV spectra of both the single-junction and dual-junction configurations. Nonequally-spaced Landau levels, including the hallmark n=0 level, are observed in the presence of a magnetic field. Linear energy-momentum dispersion near the Dirac point, as well as the Fermi velocity, is extracted from both experiments. Local potential fluctuations and interface defects significantly influence these fine physical features, leading to peak broadening and anomalies comparing to the results from the ultra sharp scanning tunneling microscope tip. This study provides important implications for potential tunneling-based graphene devices in the future.
General decay for a nonlinear beam equation with weak dissipation
Authors: Park Jong Yeoul , Park Sun Hye
Published: July 2010

In this paper, we investigate the influence of dissipation on decay properties of the solutions for a quasilinear beam equation with nonlinear weak dissipation.
First-principles theories for anharmonic lattice vibrations
Authors: Hirata So , Keçeli Murat , Yagi Kiyoshi
Published: July 2010

Size-extensive generalizations of the vibrational self-consistent field (VSCF), vibrational Møller–Plesset perturbation (VMP), and vibrational coupled-cluster (VCC) methods are made to anharmonic lattice vibrations of extended periodic systems on the basis of a quartic force field (QFF) in delocalized normal coordinates. Copious terms in the formalisms of VSCF that have nonphysical size dependence are identified algebraically and eliminated, leading to compact and strictly size-extensive equations. This “quartic” VSCF method (qVSCF) thus defined has no contributions from cubic force constants and alters only the transition energies of the underlying harmonic-oscillator reference from a subset of quartic force constants. It also provides a way to evaluate an anharmonic correction to the lattice structure due to cubic force constants of a certain type. The second-order VMP and VCC methods in the QFF based on the qVSCF reference are shown to account for anharmonic effects due to all cubic and quartic force constants in a size-extensive fashion. These methods can be readily extended to a higher-order truncated Taylor expansion of a potential energy surface in normal coordinates. An algebraic proof of the lack of size-extensivity in the vibrational configuration-interaction method is also presented.
Isothermal Magnetic Advection: Creating functional fluid flows for heat and mass transfer
Authors: Solis Kyle J. , Martin James E.
Published: July 2010

Natural convection has been of interest for over a century due to its rich nonlinear dynamics and applications to heat transfer. However, convection occurs only when both gravity and a destabilizing thermal gradient exist. We have discovered a unique class of vigorous, emergent fluid flows that have the full functionality of natural convection but can be stimulated regardless of gravity or thermal gradients, simply by subjecting a platelet suspension to certain time-dependent biaxial magnetic fields of modest strength. This enigmatic phenomenon may facilitate cooling in microgravity environments and in other circumstances where convection fails.
Demonstration of homojunction ZnTe solar cells
Authors: Tanaka Tooru , Yu Kin M. , Stone Peter R. , Beeman Jeffrey W. , Dubon Oscar D. , Reichertz Lothar A. , Kao Vincent M. , Nishio Mitsuhiro , Walukiewicz Wladek
Published: July 2010

We report on the proof of photovoltaic activity of homojunction ZnTe solar cells in which n-ZnTe layers are fabricated by thermal diffusion of Al into p-ZnTe at several diffusion times to control the junction depth. An open circuit voltage of approximately 0.9 V was obtained under 1× sun AM1.5G condition in all solar cells, independent of diffusion times, while a short circuit current dropped down with increasing the diffusion time due to an increased light absorption in heavily defective Al-diffused layer. These fundamental results provide a basis for future development of intermediate band solar cells based on ZnTe materials.
Dynamical growth behavior of copper clusters during electrodeposition
Authors: Hsu Pei-Cheng , Chu Yong , Yi Jae-Mock , Wang Cheng-Liang , Wu Syue-Ren , Hwu Y. , Margaritondo G.
Published: July 2010

Ultrahigh resolution full-field transmission x-ray microscopy enabled us to observe detailed phenomena during the potentiostatic copper electrodeposition on polycrystalline gold. We detected two coexisting cluster populations with different sizes. Their growth behaviors are different, with a shape transitions only occurring for large clusters. These differences influence the micromorphology and general properties of the overlayer.
Low temperature differential thermoacoustic Stirling engine
Authors: Biwa Tetsushi , Hasegawa Daichi , Yazaki Taichi
Published: July 2010

To what extent can we lower the critical temperature ratio (CTR) necessary to start a thermoacoustic engine? We present an experimental method for predicting the CTR before the temperature ratio arrives at it using quality factor measurements. Based on the experimental quality factors, we tried to decrease the CTR of a thermoacoustic Stirling engine consisting of a looped tube and a branch resonator. Installation of the multiple regenerators at suitable positions can markedly enhance acoustic power production while overcoming energy dissipation. Results show that the CTR is decreased from 1.76 to 1.19 using five differentially heated regenerators.
Functionalized multiwall carbon nanotubes incorporated polymer/fullerene hybrid photovoltaics
Authors: Nismy N. A. , Adikaari A. A. D. T. , Silva S. R. P.
Published: July 2010

Multiwall carbon nanotubes are introduced into poly(3-hexylthiophene) and [6,6] phenyl C61 butyric acid methyl fullerene, bulk heterojunction organic photovoltaic devices. Utilization of nanotubes requires chemical modifications for compatibility with solution processable photovoltaics. Better dispersions of carbon nanotubes in organic solvents are achieved by acid functionalization of tubes. Pristine and acid treated multiwall carbon nanotubes have been incorporated into the photoactive layer and better results in fill factors of 62% and efficiency of 2.3% are achieved under Air Mass 1.5 Global illumination through the use of acid treated nanotubes.
Transform between the permeability and permittivity in the close-packed Ni nanoparticles
Authors: Zhang X. F. , Guan P. F. , Dong X. L.
Published: July 2010

We report an anomalously electromagnetic resonance in a simple Ni nanoparticle/paraffin system. The resonance, caused by the near-field interaction of nanoparticles, appears at ∼16 GHz as decreasing the interparticle distance down to ∼11 nm. It is associated with an unusual energy transfer from the permeability to permittivity, resulting in the enhanced dielectric and weakened magnetic attenuations. These experimental results can be well modeled by a numerical simulation, evidencing the enhanced electrical filed distribution as decreasing the interaction distance. This study enables us to first realize the permeability-to-permittivity transform of electromagnetic wave in nanocomposites.
High numerical aperture microlens arrays of close packing
Authors: Wu Dong , Wu Si-Zhu , Niu Li-Gang , Chen Qi-Dai , Wang Rui , Song Jun-Feng , Fang Hong-Hua , Sun Hong-Bo
Published: July 2010

Closed-packed high numerical aperture (NA) microlens arrays (MLA) are highly desirable for high resolution imaging and high signal-to-noise-ratio detection in micro-optical and integrated optical applications. However, realization of such devices remains technically challenging. Here, we report high quality fabrication of curved surfaces and MLAs by taking the full advantage of surface self-smoothing effect by creating highly reproducible voxels and by adopting an equal-arc scanning strategy. MLA of approximately 100% fill ratio and NA of 0.46, much greater than those ever reported, 0.13, is demonstrated, whose excellent optical performance was approved by the sharp focusing and high resolution imaging.
Structural and thermal properties of MnSi single crystal
Authors: Tite T. , Shu G. J. , Chou F. C. , Chang Y.-M.
Published: July 2010

Polarized Raman spectroscopy of MnSi single crystal was carried out to characterize its phonons, crystal structure, and thermal stability. The Raman spectra show correct Raman selection rules and consistence with those of the other transition metal silicide compounds. The MnSi thermal stability and phase transformation is investigated by monitoring the evolution of Raman spectrum as a function of the laser intensity, in which three compositions, MnSi, MnSiO3, and Mn5Si3, can be identified. The involved oxidation reaction is then proposed and verified by performing the thermogravimetric and x-ray diffraction analysis.
InGaN staircase electron injector for reduction of electron overflow in InGaN light emitting diodes
Authors: Ni X. , Li X. , Lee J. , Liu S. , Avrutin V. , Özgür Ü. , Morkoç H. , Matulionis A. , Paskova T. , Mulholland G. , Evans K. R.
Published: July 2010

Ballistic and quasiballistic electron transport across the active InGaN layer are shown to be responsible for electron overflow and electroluminescence efficiency droop at high current levels in InGaN light emitting diodes both experimentally and by first-order calculations. An InGaN staircase electron injector with step-like increased In composition, an “electron cooler,” is proposed for an enhanced thermalization of the injected hot electrons to reduce the overflow and mitigate the efficiency droop. The experimental data show that the staircase electron injector results in essentially the same electroluminescence performance for the diodes with and without an electron blocking layer, confirming substantial electron thermalization. On the other hand, if no InGaN staircase electron injector is employed, the diodes without the electron blocking layer have shown significantly lower (three to five times) electroluminescence intensity than the diodes with the blocking layer. These results demonstrate a feasible method for the elimination of electron overflow across the active region, and therefore, the efficiency droop in InGaN light emitting diodes.
Few-layer epitaxial graphene grown on vicinal 6H–SiC studied by deep ultraviolet Raman spectroscopy
Authors: Kisoda Kenji , Kamoi Susumu , Hasuike Noriyuki , Harima Hiroshi , Morita Kouhei , Tanaka Satoru , Hashimoto Akihiro
Published: July 2010

Few layer epitaxial graphenes (1.8–3.0 layers) grown on vicinal 6H–SiC (0001) were characterized by deep ultraviolet Raman spectroscopy. Shallow penetration depth of the probe laser enabled us to observe G-peak of graphene without subtraction of the SiC substrate signal from observed spectra. The G-peak was greatly shifted to higher frequency compared to that of graphite due to in-plane compressive stress deriving from the substrate. The frequency shift decreased with the number of graphene layers because of stress relaxation from layer to layer. Our experiment suggests that the stress is completely relaxed within five to six graphene layers.
Polariton parametric oscillation in a single micropillar cavity
Authors: Ferrier Lydie , Pigeon Simon , Wertz Esther , Bamba Motoaki , Senellart Pascale , Sagnes Isabelle , Lemaître Aristide , Ciuti Cristiano , Bloch Jacqueline
Published: July 2010

We demonstrate parametric oscillation of discrete polariton states in a single squared GaAs/GaAlAs micropillar cavity. Resonantly exciting a selected polariton mode with a continuous wave pump laser, parametric oscillation is evidenced on the two neighbored modes (signal and idler). Abrupt switch-off of the device is observed under high excitation. We present comprehensive results concerning the power-dependence of the energy and linewidth of the emission resonances as well as their far-field patterns. Quantum Monte Carlo calculations give a quantitative understanding of the physics of this micro-optical parametric oscillator involving fully confined discrete polariton modes.
Whispering-gallery-mode terahertz pulse propagation on a curved metallic plate
Authors: Mendis Rajind , Mittleman Daniel M.
Published: July 2010

We demonstrate terahertz (THz) pulse propagation on a cylindrical aluminum plate, with low loss and negligible dispersion via transverse-electric type whispering gallery (WG) modes. We observe an apparent superluminal effect where the group velocity is greater than c, and explain this phenomenon by means of a plane-wave description of the WG modes. The propagation loss is dominated by the diffraction loss due to unbounded lateral spreading, with a negligible ohmic-loss contribution. Both experimental and theoretical results indicate a total loss as low as 2.6 dB/m at a frequency of 0.47 THz.
Generation of two-color continuous variable quantum entanglement at 0.8 and 1.5 μm
Authors: Li Yongmin , Guo Xiaomin , Bai Zengliang , Liu Chunchun
Published: July 2010

Two-color continuous variable quantum entanglement at 0.8 and 1.5 μm was experimentally demonstrated by using an above-threshold optical parametric oscillator based on a periodically poled KTiOPO4 crystal. The system presented here has potential applications in future quantum information networks, e.g., it can be used to made a connection between a quantum memory device based on alkaline atoms and a quantum communication device based on telecommunication optical fibers.
Alternating matter motion in photoinduced mass transport driven and enhanced by light polarization in amorphous chalcogenide films
Authors: Trunov M. L. , Lytvyn P. M. , Dyachyns’ka O. M.
Published: July 2010

We present direct measurements of the kinetics of surface relief gratings (SRGs) formation in amorphous As20Se80 thin films observed in real time by in situ atomic force microscopy. SRGs are induced in different holographic schemes of recording using near band-gap light and enhanced additionally by light polarized orthogonally to the recording beams. We demonstrate that the direction of mass transport depends on the polarization of additional light and recording pattern and can be driven by their modulation. Additional light triggers a giant mass transport and accelerates SRG formation while increasing it in height up to the order of the film thickness.
Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins
Authors: Kruglik Sergei G. , Yoo Byung-Kuk , Franzen Stefan , Vos Marten H. , Martin Jean-Louis , Negrerie Michel
Published: July 2010

We investigated the ultrafast structural transitions of the heme induced by nitric oxide (NO) binding for several heme proteins by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We probed the heme iron motion by the evolution of the iron-histidine Raman band intensity after NO photolysis. Unexpectedly, we found that the heme response and iron motion do not follow the kinetics of NO rebinding. Whereas NO dissociation induces quasi-instantaneous iron motion and heme doming (< 0.6 ps), the reverse process results in a much slower picosecond movement of the iron toward the planar heme configuration after NO binding. The time constant for this primary domed-to-planar heme transition varies among proteins (∼30 ps for myoglobin and its H64V mutant, ∼15 ps for hemoglobin, ∼7 ps for dehaloperoxidase, and ∼6 ps for cytochrome
c
) and depends upon constraints exerted by the protein structure on the heme cofactor. This observed phenomenon constitutes the primary structural transition in heme proteins induced by NO binding.
RNAi screen for telomerase reverse transcriptase transcriptional regulators identifies HIF1α as critical for telomerase function in murine embryonic stem cells
Authors: Coussens Matthew , Davy Philip , Brown Lancer , Foster Christopher , Andrews William H. , Nagata Melissa , Allsopp Richard
Published: July 2010

In various types of stem cells, including embryonic stem (ES) cells and hematopoietic stem cells, telomerase functions to ensure long-term self-renewal capacity via maintenance of telomere reserve. Expression of the catalytic component of telomerase, telomerase reverse transcriptase (Tert), which is essential for telomerase activity, is limiting in many types of cells and therefore plays an important role in establishing telomerase activity levels. However, the mechanisms regulating expression of Tert in cells, including stem cells, are presently poorly understood. In the present study, we sought to identify genes involved in the regulation of Tert expression in stem cells by performing a screen in murine ES (mES) cells using a shRNA expression library targeting murine transcriptional regulators. Of 18 candidate transcriptional regulators of Tert expression identified in this screen, only one candidate, hypoxia inducible factor 1 alpha (Hif1α), did not have a significant effect on mES cell morphology, survival, or growth rate. Direct shRNA-mediated knockdown of Hif1α expression confirmed that suppression of Hif1α levels was accompanied by a reduction in both Tert mRNA and telomerase activity levels. Furthermore, gradual telomere attrition was observed during extensive proliferation of Hif1α-targeted mES cells. Switching Hif1α-targeted mES cells to a hypoxic environment largely restored Hif1α levels, as well as Tert expression, telomerase activity levels, and telomere length. Together, these findings suggest a direct effect of Hif1α on telomerase regulation in mES cells, and imply that Hif1α may have a physiologically relevant role in maintenance of functional levels of telomerase in stem cells.
11-Deoxycortisol is a corticosteroid hormone in the lamprey
Authors: Close David A. , Yun Sang-Seon , McCormick Stephen D. , Wildbill Andrew J. , Li Weiming
Published: July 2010

Corticosteroid hormones are critical for controlling metabolism, hydromineral balance, and the stress response in vertebrates. Although corticosteroid hormones have been well characterized in most vertebrate groups, the identity of the earliest vertebrate corticosteroid hormone has remained elusive. Here we provide evidence that 11-deoxycortisol is the corticosteroid hormone in the lamprey, a member of the agnathans that evolved more than 500 million years ago. We used RIA, HPLC, and mass spectrometry analysis to determine that 11-deoxycortisol is the active corticosteroid present in lamprey plasma. We also characterized an 11-deoxycortisol receptor extracted from sea lamprey gill cytosol. The receptor was highly specific for 11-deoxycortisol and exhibited corticosteroid binding characteristics, including DNA binding. Furthermore, we observed that 11-deoxycortisol was regulated by the hypothalamus–pituitary axis and responded to acute stress. 11-Deoxycortisol implants reduced sex steroid concentrations and up-regulated gill Na+, K+-ATPase, an enzyme critical for ion balance. We show here that 11-deoxycortisol functioned as both a glucocorticoid and a mineralocorticoid in the lamprey. Our findings indicate that a complex and highly specific corticosteroid signaling pathway evolved at least 500 million years ago with the arrival of the earliest vertebrate.
Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama
Authors: Crawford Andrew J. , Lips Karen R. , Bermingham Eldredge
Published: July 2010

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen,
Batrachochytrium dendrobatidis
. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.
Prolonged activation of NMDA receptors promotes dephosphorylation and alters postendocytic sorting of GABA
B
receptors
Authors: Terunuma Miho , Vargas Karina J. , Wilkins Megan E. , Ramírez Omar A. , Jaureguiberry-Bravo Matías , Pangalos Menelas N. , Smart Trevor G. , Moss Stephen J. , Couve Andrés
Published: July 2010

Slow and persistent synaptic inhibition is mediated by metabotropic GABA
B
receptors (GABA
B
Rs). GABA
B
Rs are responsible for the modulation of neurotransmitter release from presynaptic terminals and for hyperpolarization at postsynaptic sites. Postsynaptic GABA
B
Rs are predominantly found on dendritic spines, adjacent to excitatory synapses, but the control of their plasma membrane availability is still controversial. Here, we explore the role of glutamate receptor activation in regulating the function and surface availability of GABA
B
Rs in central neurons. We demonstrate that prolonged activation of NMDA receptors (NMDA-Rs) leads to endocytosis, a diversion from a recycling route, and subsequent lysosomal degradation of GABA
B
Rs. These sorting events are paralleled by a reduction in GABA
B
R-dependent activation of inwardly rectifying K
+
channel currents. Postendocytic sorting is critically dependent on phosphorylation of serine 783 (S783) within the GABA
B
R2 subunit, an established substrate of AMP-dependent protein kinase (AMPK). NMDA-R activation leads to a rapid increase in phosphorylation of S783, followed by a slower dephosphorylation, which results from the activity of AMPK and protein phosphatase 2A, respectively. Agonist activation of GABA
B
Rs counters the effects of NMDA. Thus, NMDA-R activation alters the phosphorylation state of S783 and acts as a molecular switch to decrease the abundance of GABA
B
Rs at the neuronal plasma membrane. Such a mechanism may be of significance during synaptic plasticity or pathological conditions, such as ischemia or epilepsy, which lead to prolonged activation of glutamate receptors.
Physically grounded approach for estimating gene expression from microarray data
Authors: McMullen Patrick D. , Morimoto Richard I. , Amaral Luís A. Nunes
Published: July 2010

High-throughput technologies, including gene-expression microarrays, hold great promise for the systems-level study of biological processes. Yet, challenges remain in comparing microarray data from different sources and extracting information about low-abundance transcripts. We demonstrate that these difficulties arise from limitations in the modeling of the data. We propose a physically motivated approach for estimating gene-expression levels from microarray data, an approach neglected in the microarray literature. We separately model the noises specific to sample amplification, hybridization, and fluorescence detection, combining these into a parsimonious description of the variability sources in a microarray experiment. We find that our model produces estimates of gene expression that are reproducible and unbiased. While the details of our model are specific to gene-expression microarrays, we argue that the physically grounded modeling approach we pursue is broadly applicable to other molecular biology technologies.
Contrasting plant diversification histories within the Andean biodiversity hotspot
Authors: Pennington R. Toby , Lavin Matt , Särkinen Tiina , Lewis Gwilym P. , Klitgaard Bente B. , Hughes Colin E.
Published: July 2010

The Andes are the most species-rich global biodiversity hotspot. Most research and conservation attention in the Andes has focused on biomes such as rain forest, cloud forest, and páramo, where much plant species diversity is the hypothesized result of rapid speciation associated with the recent Andean orogeny. In contrast to these mesic biomes, we present evidence for a different, older diversification history in seasonally dry tropical forests (SDTF) occupying rain-shadowed inter-Andean valleys. High DNA sequence divergence in
Cyathostegia mathewsii
, a shrub endemic to inter-Andean SDTF, indicates isolation for at least 5 million years of populations separated by only
ca
. 600 km of high cordillera in Peru. In conjunction with fossil evidence indicating the presence of SDTF in the Andes in the late Miocene, our data suggest that the disjunct small valley pockets of inter-Andean SDTF have persisted over millions of years. These forests are rich in endemic species but massively impacted, and merit better representation in future plans for science and conservation in Andean countries.
Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase
Authors: Vaithiyalingam Sivaraja , Warren Eric M. , Eichman Brandt F. , Chazin Walter J.
Published: July 2010

DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-Å resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C–RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.
Time-resolved luminescence resonance energy transfer imaging of protein–protein interactions in living cells
Authors: Rajapakse Harsha E. , Gahlaut Nivriti , Mohandessi Shabnam , Yu Dan , Turner Jerrold R. , Miller Lawrence W.
Published: July 2010

Förster resonance energy transfer (FRET) with fluorescent proteins permits high spatial resolution imaging of protein–protein interactions in living cells. However, substantial non-FRET fluorescence background can obscure small FRET signals, making many potential interactions unobservable by conventional FRET techniques. Here we demonstrate time-resolved microscopy of luminescence resonance energy transfer (LRET) for live-cell imaging of protein–protein interactions. A luminescent terbium complex, TMP-Lumi4, was introduced into cultured cells using two methods: (
i
) osmotic lysis of pinocytic vesicles; and (
ii
) reversible membrane permeabilization with streptolysin O. Upon intracellular delivery, the complex was observed to bind specifically and stably to transgenically expressed
Escherichia coli
dihydrofolate reductase (eDHFR) fusion proteins. LRET between the eDHFR-bound terbium complex and green fluorescent protein (GFP) was detected as long-lifetime, sensitized GFP emission. Background signals from cellular autofluorescence and directly excited GFP fluorescence were effectively eliminated by imposing a time delay (10 μs) between excitation and detection. Background elimination made it possible to detect interactions between the first PDZ domain of ZO-1 (fused to eDHFR) and the C-terminal YV motif of claudin-1 (fused to GFP) in single microscope images at subsecond time scales. We observed a highly significant (
P
 < 10
-6
), six-fold difference between the mean, donor-normalized LRET signal from cells expressing interacting fusion proteins and from control cells expressing noninteracting mutants. The results show that time-resolved LRET microscopy with a selectively targeted, luminescent terbium protein label affords improved speed and sensitivity over conventional FRET methods for a variety of live-cell imaging and screening applications.
Mapping the first stages of mesoderm commitment during differentiation of human embryonic stem cells
Authors: Evseenko Denis , Zhu Yuhua , Schenke-Layland Katja , Kuo Jeffrey , Latour Brooke , Ge Shundi , Scholes Jessica , Dravid Gautam , Li Xinmin , MacLellan W. Robb , Crooks Gay M.
Published: July 2010

Our understanding of how mesodermal tissue is formed has been limited by the absence of specific and reliable markers of early mesoderm commitment. We report that mesoderm commitment from human embryonic stem cells (hESCs) is initiated by epithelial-to-mesenchymal transition (EMT) as shown by gene expression profiling and by reciprocal changes in expression of the cell surface proteins, EpCAM/CD326 and NCAM/CD56. Molecular and functional assays reveal that the earliest CD326
−
CD56
+
cells, generated from hESCs in the presence of activin A, BMP4, VEGF, and FGF2, represent a multipotent mesoderm-committed progenitor population. CD326
−
CD56
+
progenitors are unique in their ability to generate all mesodermal lineages including hematopoietic, endothelial, mesenchymal (bone, cartilage, fat, fibroblast), smooth muscle, and cardiomyocytes, while lacking the pluripotency of hESCs. CD326
−
CD56
+
cells are the precursors of previously reported, more lineage-restricted mesodermal progenitors. These findings present a unique approach to study how germ layer specification is regulated and offer a promising target for tissue engineering.