bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of intensity-dependent optical rotation phenomena in chiral molecules in solution
Authors: Cameron R. , Tabisz G. C.
Published: June 2007

The rotation of the plane of polarization of linearly polarized light by chiral molecules in solution is due to a forward scattering event. Ordinary optical rotation, a single-photon effect, is independent of intensity. As the light intensity is increased, other effects can appear, such as two-photon scattering or alignment of the molecule by one photon and scattering with a change of polarization by another. Both of these effects result in intensity-dependent (or nonlinear) optical rotation. A polarimeter was used to measure the nonlinear optical rotation of solutions in a heterodyne experiment. No nonlinear optical rotation was found in molecules lacking an absorption band near the laser frequency. In the three pyrimidine nucleosides studied, which do have such an absorption band, a nonlinear optical rotation was identified that was cumulative with each laser pulse. The effect persisted with a time constant that was on the order of seconds and characteristic of the molecule.
Structure and dynamics of water surrounding the poly(methacrylic acid): A molecular dynamics study
Authors: Ju Shin-Pon , Lee Wen-Jay , Huang Ching-I , Cheng Wei-Zen , Chung Yong-Ting
Published: June 2007

All-atom molecular dynamics simulations are used to study a single chain of poly(methacrylic acid) in aqueous solutions at various degrees of charge density. Through a combination of analysis on the radial distribution functions of water and snapshots of the equilibrated structure, we observe that local arrangements of water molecules, surrounding the functional groups of COO− and COOH in the chain, behave differently and correlated well to the resulting chain conformation behavior. In general, due to strong attractive interactions between water and charged COO− via the formation of hydrogen bonds, water molecules tend to form shell-like layers around the COO− groups. Furthermore, water molecules often act as a bridging agent between two neighboring COO− groups. These bridged water molecules are observed to stabilize the rodlike chain conformation that the highly charged chain reveals, as they significantly limit torsional and bending degrees of the backbone monomers. In addition, they display different dynamic properties from the bulk water. Both the resulting oxygen and hydrogen spectra are greatly shifted due to the presence of strong H-bonded interactions.
Practical error estimation in zoom-in and truncated tomography reconstructions
Authors: Xiao Xianghui , De Carlo Francesco , Stock Stuart
Published: June 2007

Synchrotron-based microtomography provides high resolution, but the resolution in large samples is often limited by the detector field of view and the pixel size. For some samples, only a small region of interest is relevant and local tomography is a powerful approach for retaining high resolution. Two methods are truncated tomography and zoom-in tomography. In this article we use existing theoretical results to estimate the error present in truncated and zoom-in tomographic reconstructions. These errors agree with the errors calculated from exact tomographic reconstructions. We argue in a heuristic manner why zoom-in tomography is superior to the truncated tomography in terms of the reconstruction error. However, the theoretical formula is not usable in practice because it requires the complete high-resolution reconstruction to be known. To solve this problem we proposed a practical method for estimating the error in zoom-in and truncated tomographies. The results using this estimation method are in very good agreement with our experimental results.
Reconstruction method of local density fluctuation for heavy ion beam probe measurements
Authors: Nakano H. , Fujisawa A. , Shimizu A. , Ohshima S. , Iguchi H. , Yoshimura Y. , Minami T.
Published: June 2007

Heavy ion beam probe (HIBP) is an excellent diagnostic to measure the density and potential fluctuations simultaneously in magnetically confined plasmas. However, it has been well known that the density fluctuation measured with the HIBP is not local but contains the fluctuations along the beam orbits. In this article, a method is proposed to evaluate local density fluctuation in the HIBP measurements by removing the well-known path integral effects. The reconstructed density fluctuation amplitude and power spectrum are shown, for example, by applying the proposed method on the density fluctuation measurement data obtained in a toroidal helical plasma, Compact Helical System.
Raman-scattering study of misfit-layered (Bi, Pb)-Sr-Co-O single crystal
Authors: Yuan S. K. , An M. , Wu Y. , Zhang Q. M. , Luo X. G. , Chen X. H.
Published: June 2007

Polarized Raman scattering measurements were performed on misfit-layered thermoelectric Bi2−xPbxSr2Co2Oy(x=0.6) single crystal from 20 K to room temperature. Four peaks were observed in the parallel polarization channel and no peaks in the cross polarization channel. One of the Raman peaks carries the asymmetric characteristic, which can be regarded as an evidence of the existence of electron-phonon coupling. Furthermore, the asymmetric parameter, proportional to the strength of electron-phonon coupling, was estimated with the asymmetric Breit–Wigner–Fano line shape. The electron-phonon coupling may play an important role in understanding the large thermoelectric power of cobalt based materials.
Excess compressibility in binary liquid mixtures
Authors: Aliotta F. , Gapiński J. , Pochylski M. , Ponterio R. C. , Saija F. , Salvato G.
Published: June 2007

Brillouin scattering experiments have been carried out on some mixtures of molecular liquids. From the measurement of the hypersonic velocities we have evaluated the adiabatic compressibility as a function of the volume fraction. We show how the quadratic form of the excess compressibility dependence on the solute volume fraction can be derived by simple statistical effects and does not imply any interaction among the components of the system other than excluded volume effects. This idea is supported by the comparison of the experimental results with a well-established prototype model, consisting of a binary mixture of hard spheres with a nonadditive interaction potential. This naive model turns out to be able to produce a very wide spectrum of structural and thermodynamic features depending on values of its parameters. An attempt has made to understand what kind of structural information can be gained through the analysis of the volume fraction dependence of the compressibility.
Adaptive explicit-implicit tau-leaping method with automatic tau selection
Authors: Cao Yang , Gillespie Daniel T. , Petzold Linda R.
Published: June 2007

The existing tau-selection strategy, which was designed for explicit tau leaping, is here modified to apply to implicit tau leaping, allowing for longer steps when the system is stiff. Further, an adaptive strategy that identifies stiffness and automatically chooses between the explicit and the (new) implicit tau-selection methods to achieve better efficiency is proposed. Numerical testing demonstrates the advantages of the adaptive method for stiff systems.
Simulated surface tensions of common water models
Authors: Chen Feng , Smith Paul E.
Published: June 2007

Initial simulated values of the surface tension for the SPC/E water model have indicated excellent agreement with experiment. More recently, differing values have been obtained which are significantly lower than previous estimates. Here, we attempt to explain the differences between the previous studies and show that a variety of simulation conditions can affect the final surface tension values. Consistent values for the surface tensions of six common fixed charge water models (TIP3P, SPC, SPC/E, TIP4P, TIP5P, and TIP6P) are then determined for four temperatures between 275 and 350K. The SPC/E and TIP6P models provide the best agreement with experiment.
Two-state model based on the block-localized wave function method
Authors: Mo Yirong
Published: June 2007

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense π→π* transition for formamide upon solvation undergoes a redshift of 0.3eV, compared with the experimental data (0.40–0.5eV).
Characterization of high TC Pb(Mg1∕3Nb2∕3)O3–PbZrO3–PbTiO3 single crystals fabricated by solid state crystal growth
Authors: Zhang Shujun , Lee S. M. , Kim D. H. , Lee H. Y. , Shrout Thomas R.
Published: June 2007

Ferroelectric crystals near the morphotropic phase boundary (MPB) in the Pb(Mg1∕3Nb2∕3)O3–PbZrO3–PbTiO3 ternary system were grown using the solid state crystal growth technique. A MPB composition with a Curie temperature of ∼205°C was selected for characterization of the piezoelectric properties and temperature dependent behavior. The room temperature electromechanical coupling factors were found to be ⩾90% for k33 and ∼−87% for k32, respectively, comparable to Pb(Mg1∕3Nb2∕3)O3–PbTiO3 (PMN-PT) crystals. The coercive field, being on the order of 5kV∕cm, was found to be nearly double that of the pure PMN-PT. The temperature dependence of the piezoelectric and electromechanical properties showed temperature stability up to 160°C, expanding the temperature usage range for actuator and ultrasonic transducer applications.
Detection of nanomechanical motion by evanescent light wave coupling
Authors: De Vlaminck I. , Roels J. , Taillaert D. , Van Thourhout D. , Baets R. , Lagae L. , Borghs G.
Published: June 2007

The authors demonstrate a technique allowing sensitive nanomechanical motion detection based on the evanescent light wave coupling between two photonic nanowires. Any relative motion between the nanowires results in a change in light coupling, providing a means of registering motion. The in-plane vibrations of a 220nm×400nm×10μm nanomechanical resonator were recorded using this method. An analysis of the sensitivity reveals the potential of this integrated technique to provide fast and sensitive motion detection.
Ferromagnetic chaoite macrotubes prepared at low temperature and pressure
Authors: Li Shandong , Huang Zhigao , Lü Liya , Zhang Fengming , Du Youwei , Cai Yuanfeng , Pan Yuguan
Published: June 2007

Chaoite, a rare allotrope of carbon, is considered as a high-temperature phase abundant in circumstellar shells and is difficult to be synthesized at low temperature. However, in this study, chaoite phase was synthesized by quenching the pyrolysate of acetylene gas at low temperature and pressure. The typical morphology is a tube with 20–60μm in diameter and more than 8mm in length. Another interesting feature of these carbon macrotubes (CMTs) is the unexpected but clear intrinsic ferromagnetism. The ferromagnetism of sp-hybridized CMTs indicates that the sp-hybridized structure may be an origin of ferromagnetism.
Oxide-apertured microcavity single-photon emitting diode
Authors: Ellis D. J. P. , Bennett A. J. , Shields A. J. , Atkinson P. , Ritchie D. A.
Published: June 2007

The authors have developed a microcavity single-photon source based on a single quantum dot within a planar cavity in which wet oxidation of a high-aluminium content layer provides lateral confinement of both the photonic mode and the injection current. Lateral confinement of the optical mode in optically pumped structures produces a strong enhancement of the radiative decay rate. Using microcavity structures with doped contact layers, they demonstrate a single-photon emitting diode where current may be injected into a single dot.
Laser synchronization of a thermal explosion
Authors: Smilowitz L. , Henson B. F. , Sandstrom M. M. , Romero J. J. , Asay B. W.
Published: June 2007

The authors describe a method by which prompt ignition of thermal explosions is achieved. A convergent heating geometry is applied to a solid cylindrical explosive generating spatial temperature gradients which define a thermal ignition volume. A laser pulse is introduced via an optical fiber to apply a nonshock temperature perturbation in this volume seconds prior the normal ignition time. Explosion occurs hundreds of microseconds subsequent to this perturbation. They show that the subsequent explosive response is identical to that of a normal thermal explosion. This synchronization method enables fast radiographic imaging of nonlinear thermal explosion.
Synthesis and multiferroic properties of Bi0.8A0.2FeO3 (A=Ca,Sr,Pb) ceramics
Authors: Khomchenko V. A. , Kiselev D. A. , Vieira J. M. , Kholkin A. L. , Sá M. A. , Pogorelov Y. G.
Published: June 2007

Bi 1 − x A x Fe O 3 ceramics (A=Ca,Sr,Pb) were sintered by conventional mixed oxide route. The crystallographic structure of all samples is characterized by the rhombohedral symmetry (space group R3c). The existence of switchable ferroelectric polarization is verified by piezoresponse force microscopy that is proven to be a useful technique in semi-insulating ferroelectrics. Magnetic properties of Ca and Sr-doped ceramics are found to reproduce the antiferromagnetic behavior of undoped BiFeO3 without any enhancement of the magnetization. On the contrary, Pb-doped compound demonstrates appearance of a weak ferromagnetism. It is thus shown that Pb doping of BiFeO3 is a promising way for preparing multiferroic materials.
Tuning hole injection and charge recombination with self-assembled monolayer on silver anode in top-emitting organic light-emitting diodes
Authors: Wu Kun-Yang , Tao Yu-Tai , Huang Hung-Wei
Published: June 2007

A series of n-alkanethiol, cyano-terminated n-alkanethiol, and fluorine-substituted benzyl mercaptans were used to modify the silver anode in the fabrication of top-emitting electroluminescent devices. The efficiency of charge injection and device performance were investigated. The study shows that the size/direction of the dipole associated with the monolayer-forming molecule serves to modulate the metal work function and the charge injection barrier, whereas the alkyl chain length allows a fine tuning of charge balance in the recombination zone. A high current efficiency of ∼10.2cd∕A and a luminescence of ∼10800cd∕m2 at 200mA were achieved with the NC–C11–SH-modified devices.
Changing band offsets in copper phthalocyanine to copolymer poly(vinylidene fluoride with trifluoroethylene) heterojunctions
Authors: Xiao Jie , Sokolov Andrei , Dowben P. A.
Published: June 2007

The authors have fabricated a thin film copper phthalocyanine to crystalline ferroelectric copolymer poly(vinylidene fluoride with trifluoroethylene) heterojunction diode. The formation of a diode is expected from the band offsets between the two thin film molecular systems, as ascertained from combined photoemission and inverse photoemission studies. From the temperature and field dependence of the heterojunction, dipole interactions are implicated at the interface between copper phthalocyanine and poly(vinylidene fluoride with trifluoroethylene) and affect the band offsets and resultant diode properties.
Near-field laser parallel nanofabrication of arbitrary-shaped patterns
Authors: Guo W. , Wang Z. B. , Li L. , Whitehead D. J. , Luk’yanchuk B. S. , Liu Z.
Published: June 2007

The authors present a simple and efficient technique for laser writing of arbitrary nanopatterns across a large surface area without using projection masks. It is based on the unique near-field focusing effect of a self-assembled particle array on the surface interacting with an angular incident laser beam. The spot resolution can be down to 80nm. More than 6×106 nanolines and c-shaped uniform patterns were fabricated simultaneously over an area of 5×5mm2 by a few laser shots.
Random dipolar ferromagnetism in Co∕CoO core-shell cluster assemblies observed by electron holography
Authors: Yamamuro S. , Yamamoto K. , Peng D. L. , Hirayama T. , Sumiyama K.
Published: June 2007

The formation of large-scale ferromagnetic domains has been detected in quasi-three-dimensional random assemblies of monodisperse 6nm Co∕CoO core-shell clusters by electron holography. This is primarily attributed to the magnetic dipole interactions between these clusters, because the exchange coupling between neighboring Co cores is effectively interrupted by antiferromagnetic CoO surface layers. The magnetic field-cooled effect has been also detected by in-situ electron microscope experiment. The field-induced alignment of magnetic moments during the cooling experiment is ascribable to the exchange interactions between Co cores and CoO shells.
High piezoelectric d33 coefficient in Li-modified lead-free (Na,K)NbO3 ceramics sintered at optimal temperature
Authors: Zhao Pei , Zhang Bo-Ping , Li Jing-Feng
Published: June 2007

Li Nb O 3 -doped (Na,K)NbO3 lead-free piezoelectric ceramics were prepared by normal sintering, and the electrical properties were investigated with a special emphasis on the influence of sintering temperature. The ceramics synthesized at 1020–1080°C showed a phase transition from orthorhombic to tetragonal symmetry, which is similar to the morphtropic phase boundary (MPB). Because of such MPB-like behavior, a high piezoelectric coefficient d33 (314pC∕N) was obtained in the nominal composition 0.058LiNbO3–0.942[(Na0.535K0.480)NbO3] ceramic sintered at 1060°C; however, this high d33 value was reported previously only in the Li-modified (Na,K)NbO3-based ceramics with codopants of Ta and Sb to B site.
Syntheses of relaxor/ferroelectric superlattice thin films Pb(Sc1∕2Nb1∕2)O3∕PbTiO3 and their dielectric properties
Authors: Asanuma Shutaro , Uesu Yoshiaki , Malibert Charlotte , Kiat Jean-Michel
Published: June 2007

Superlattice (SL) thin films with different periods and composition ratios of Pb(Sc1∕2Nb1∕2)O3 and PbTiO3 (PT), inside and outside the morphotropic phase boundary, are synthesized by a pulsed laser deposition method. High order SL reflections are observed by x-ray diffraction, from which the SL period and correlation length are determined. The coherency of the SL structure is found to extend over the whole film in the thinner films. A maximum dielectric constant of 1800 with a dielectric loss of 0.05 is obtained in the frequency range of 1–104Hz for a SL with average composition of 25% of PT.
Elastic and electronic properties of CoFe3N, RhFe3N, and IrFe3N from first principles
Authors: Wu Zhijian , Meng Jian
Published: June 2007

First principles calculations are performed to investigate the elastic and electronic properties of MFe3N (M=Co,Rh,Ir) at Pm-3m space group. The authors’ calculation indicates that the three MFe3N phases are metallic and mechanically stable. For RhFe3N, the calculated lattice parameter of 3.826Å is in excellent agreement with the experimental value of 3.8292Å. The three phases are ferromagnetic with the calculated magnetic moments per f.u. being 8.92μB for CoFe3N, 9.04μB for RhFe3N, and 8.50μB for IrFe3N. The unusually large B∕G ratio from 2.47 for CoFe3N and 2.45 for RhFe3N to 1.81 for IrFe3N indicates that they are ductile.
Magnetic field-induced martensitic transformation and large magnetoresistance in NiCoMnSb alloys
Authors: Yu S. Y. , Ma L. , Liu G. D. , Liu Z. H. , Chen J. L. , Cao Z. X. , Wu G. H. , Zhang B. , Zhang X. X.
Published: June 2007

Magnetic field-induced martensitic transformation was realized in Ni50−xCoxMn39Sb11 alloys. The partial substitution of Co for Ni has turned the antiferromagnetically aligned Mn moments in the starting material Ni50Mn39Sb11 into a ferromagnetic ordering, raising the magnetization at room temperature from 8emu∕g for NiMnSb to ∼110emu∕g for Ni41Co9Mn39Sb11. In the same quaternary sample, a magnetization difference up to 80emu∕g was measured across the martensitic transformation, and the transformation temperature (T0=259K) could be lowered by 35K under a field of 10T. Also a magnetoresistance over 70% was observed through this field-induced transformation.
Towards controlled bottom-up architectures in organic heterostructures
Authors: de Oteyza D. G. , Krauss T. N. , Barrena E. , Sellner S. , Dosch H. , Ossó J. O.
Published: June 2007

The authors report a study on the growth of organic heterostructures based on di-indenoperylene (DIP) (p-type conduction) deposited on top of F16CuPc (n-type conduction) by real-time x-ray scattering and atomic force microscopy. Above a threshold temperature of 90°C, the formation of highly crystalline DIP islands takes place via Stranski-Krastanov growth. The temperature dependence of the growth behavior can be exploited to control the resulting morphologies, ranging from well ordered layered heterostructures to the self-organization of highly crystalline DIP islands with tunable size. This self-organization scenario of organic ambipolar nanostructures carries the potential for bottom-up growth of organic architectures for solar cell structures.
Imaging of strain in laterally overgrown GaAs layers by spatially resolved x-ray diffraction
Authors: Domagala J. Z. , Czyzak A. , Zytkiewicz Z. R.
Published: June 2007

Spatially resolved x-ray diffraction is used to analyze the strain in GaAs layers grown by liquid phase epitaxial lateral overgrowth (ELO) on SiO2-masked GaAs substrates. A downward tilt of ELO wings caused by their interaction with the mask is observed. The distribution of the tilt magnitude across the wings width is determined with micrometer-scale spatial resolution. A residual upward tilt originating from inhomogeneous Si dopant distribution in the ELO wing is found after mask removal. If a large area of the sample is studied, the technique provides precise information on the tilt of an individual wing and its distribution.
Are artificial opals non-close-packed fcc structures?
Authors: García-Santamaría F. , Braun P. V.
Published: June 2007

The authors report a simple experimental method to accurately measure the volume fraction of artificial opals. The results are modeled using several methods, and they find that some of the most common yield very inaccurate results. Both finite size and substrate effects play an important role in calculations of the volume fraction. The experimental results show that the interstitial pore volume is 4%–15% larger than expected for close-packed structures. Consequently, calculations performed in previous work relating the amount of material synthesized in the opal interstices with the optical properties may need revision, especially in the case of high refractive index materials.
Near-field microwave microscope measurements to characterize bulk material properties
Authors: Imtiaz Atif , Baldwin Thomas , Nembach Hans T. , Wallis Thomas M. , Kabos Pavel
Published: June 2007

The authors discuss near-field scanning microwave microscope measurements of the complex permittivity for bulk dielectric (fused silica), semiconductor (silicon), and metal (copper). The authors use these measurements to test existing quasistatic theoretical approach to deembed the bulk material properties from the measured data. The known quasistatic models fit the measured data well with parameters for silicon (εs=11.9, σSi=50S∕m) and fused silica (εs=3.85, tanδ=1.0×10−4). However, for copper (with σCu=5.67×107S∕m), apart from quasistatic coupling, an additional loss of 12Ω is needed to fit the data.
Stark shift of interband transitions in AlN∕GaN superlattices
Authors: Buchheim C. , Goldhahn R. , Winzer A. T. , Gobsch G. , Rossow U. , Fuhrmann D. , Hangleiter A. , Furtmayr F. , Eickhoff M.
Published: June 2007

The e1h1, e1h2, and e1h3 transitions of AlN∕GaN superlattices with different well widths were detected by electroreflectance measurements in dependence on the externally applied voltage. The quantum confined Stark effect of several tens of meV is observed, whose energy shift increases for larger well widths. The experimental results agree with quantum mechanical calculations at the Brillouin zone center. For well widths of 2.3 and 1.4nm an intrinsic electric field strength in the wells of 5.04 and 6.07MV∕cm is calculated.
(111)-textured Mn-substituted BiFeO3 thin films on SrRuO3∕Pt∕Ti∕SiO2∕Si structures
Authors: Singh S. K. , Menou N. , Funakubo H. , Maruyama K. , Ishiwara H.
Published: June 2007

(111)-textured 5%-Mn-substituted BiFeO3 (BFMO) thin films were fabricated on (111)-oriented SrRuO3(SRO)∕Pt∕Ti∕SiO2∕Si structures by chemical solution deposition. X-ray diffraction analyses (θ-2θ and pole figures) confirmed that SRO and BFMO films were highly (111) textured. High-resolution x-ray diffraction reciprocal space mapping showed that the crystal structure of the BFMO films was a rhombohedrally distorted perovskite structure. Transmission electron microscopy cross section images revealed that BFMO films were composed of columnar grains epitaxially aligned on the SRO grains. The remanent polarization of approximately 70μC∕cm2 and coercive field of approximately 300kV∕cm were observed at 900kV∕cm applied electric field in the (111)-textured BFMO thin films.
Electrical and ultraviolet photoresponse properties of quasialigned ZnO nanowires/p-Si heterojunction
Authors: Ghosh R. , Basak D.
Published: June 2007

The authors report on the electrical and ultraviolet (UV) photoresponse properties of quasialigned ZnO nanowires (NWs)∕p-Si heterojunction grown by a low-temperature solvothermal technique. The current-voltage characteristic of a single ZnO NW∕p-Si junction measured by a scanning tunneling microscope shows a rectifying behavior with a rectification ratio IF∕IR of 33 at 5V. The current transport is dominated by the recombination-tunneling mechanism for 0.4V<V<1.5V while by the space-charge-limited current conduction beyond 1.5V. The heterojunction is sensitive to the UV light with the faster rise and decay time constants of 360 and 280ms, respectively.
Dimensional crossover of thermal conductance in nanowires
Authors: Wang Jian , Wang Jian-Sheng
Published: June 2007

Dimensional dependence of thermal conductance at low temperatures in nanowires is studied using the nonequilibrium Green’s function method. The authors’ calculation shows a smooth dimensional crossover of thermal conductance in nanowire from one-dimensional to three-dimensional behavior with the increase of diameters. The results are consistent with the experimental findings that the temperature dependence of thermal conductance at low temperature for diameters from tens to hundreds of nanometers will be close to the Debye law. The calculation also suggests that universal thermal conductance is only observable in nanowires with small diameters. They also find that the interfacial thermal conductance across Si and Ge nanowires is much lower than the corresponding value in bulk materials.
Infrared spectra of organic monolayer films in a standing wave measured by photon-trap spectroscopy
Authors: Egashira Kazuhiro , Terasaki Akira , Kondow Tamotsu
Published: June 2007

Photon-trap spectroscopy, a generalized scheme of cavity ringdown spectroscopy, is applied to measure an infrared spectrum of the C–H stretching vibration of alkylsiloxane monolayer films grafted on a silicon substrate. A continuous-wave laser beam is introduced into a high-finesse Fabry-Pérot cavity containing the substrate placed exactly normal to the light beam to minimize optical losses. The lifetime of the light trapped in the cavity is measured to detect optical absorption sensitively. The results show clear dependence of the absorbance on the location of the monolayers with respect to a standing wave formed in the cavity; the absorbance is practically zero when the monolayers on both the surfaces are adjusted at nodes, whereas it is maximized at antinodes. The present experiment is materialized on the basis of the principles established by our previous study [Terasaki et al., J. Opt. Soc. Am. B 22, 675 (2005)].
Energy barriers from ferromagnetic contacts to semiconducting polymers
Authors: Campbell I. H. , Crone B. K.
Published: June 2007

The authors present built-in potential, current-voltage (I-V), and electroluminescence-voltage (EL-V) measurements of as deposited and plasma oxidized ferromagnetic metal/polymer/Ca light-emitting diode structures. They specifically considered Co, Fe, Ni, and a Ni:Fe alloy in contact with poly[2-methoxy,5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene] and poly (9,9-dioctylfluorene). Built-in potential measurements showed that the oxidized films had hole Schottky barriers corresponding closely to the pristine metal work function, whereas the as deposited films had barriers 0.65–0.95eV larger. Plasma oxidation improved hole injection, consistent with the reduced energy barriers, as demonstrated by I-V and EL-V measurements. These results enable design of spin based organic electronic devices.
Optical amplification of the resonance of a bimetal silicon cantilever
Authors: Ono Takahito , Yoshida Shinya , Kawai Yusuke , Esashi Masayoshi
Published: June 2007

This letter reports a photothermal transducer consisting of an ultrathin Au∕Si bimetal cantilever that functions as a resonator having a total thickness of 45nm and a quality factor of ∼12000. Due to its high-quality factor and small volume, this transducer is sensitive to the photothermal effect and its thermal response frequency is comparatively high. The authors demonstrated that the irradiation of a weak laser beam can enhance the transducer’s response due to the nonlinear photothermal effect. Mechanical frequency-modulated detection of modulated light is demonstrated using this bimetal transducer.
Origin of colossal dielectric response of CaCu3Ti4O12 studied by using CaTiO3∕CaCu3Ti4O12∕CaTiO3 multilayer thin films
Authors: Mitsugi Masakazu , Asanuma Shutaro , Uesu Yoshiaki , Fukunaga Mamoru , Kobayashi Wataru , Terasaki Ichiro
Published: June 2007

To elucidate the origin of the colossal dielectric response (CDR) of CaCu3Ti4O12 (CCTO), multilayer thin films of CCTO interposed in insulating CaTiO3 (CTO) were synthesized using a pulsed laser deposition technique. The capacitance C of CTO/CCTO/CTO films with different layer thicknesses is measured. After removing the capacitance of CTO by extrapolating C to zero CTO thickness, the real part of dielectric constant of CCTO is estimated to be 329–435, which is much smaller than the reported value for CCTO thin films. This fact indicates that the CDR of CCTO is extrinsic and originates from an internal barrier layer capacitor.
Spatialising Participatory Approaches: The Contribution of Geography to a Mature Debate
Authors: Kesby Mike
Published: June 2007

This paper explores the contribution that geographers can make to debates about the nature and utility of participatory approaches. It argues for a constructive reconciliation between these approaches and the growing poststructural critique of participation. Through an examination of the similarities and entanglements between power and empowerment it highlights the centrality of geographical issues to understanding how participation works and how its resources might be distanciated beyond the arenas of participatory projects to produce empowering effects elsewhere.
Chromosomal periodicity of evolutionarily conserved gene pairs
Authors: Wright Matthew A. , Kharchenko Peter , Church George M. , Segrè Daniel
Published: June 2007

Chromosomes are compacted hundreds of times to fit in the cell, packaged into dynamic folds whose structures are largely unknown. Here, we examine patterns in gene locations to infer large-scale features of bacterial chromosomes. Specifically, we analyzed >100 genomes and identified thousands of gene pairs that display two types of evolutionary correlations: a tendency to co-occur and a tendency to be located close together in many genomes. We then analyzed the detailed distribution of these pairs in
Escherichia coli
and found that genes in a pair tend to be separated by integral multiples of 117 kb along the genome and to be positioned in a 117-kb grid of genomic locations. In addition, the most pair-dense locations coincide with regions of intense transcriptional activity and the positions of top transcribed and conserved genes. These patterns suggest that the
E. coli
chromosome may be organized into a 117-kb helix-like topology that localizes a subset of the most essential and highly transcribed genes along a specific face of this structure. Our approach indicates an evolutionarily maintained preference in the spacing of genes along the chromosome and offers a general comparative genomics framework for studying chromosome structure, broadly applicable to other organisms.
Functional MRI of the zebra finch brain during song stimulation suggests a lateralized response topography
Authors: Voss Henning U. , Tabelow Karsten , Polzehl Jörg , Tchernichovski Ofer , Maul Kristen K. , Salgado-Commissariat Delanthi , Ballon Douglas , Helekar Santosh A.
Published: June 2007

Electrophysiological and activity-dependent gene expression studies of birdsong have contributed to the understanding of the neural representation of natural sounds. However, we have limited knowledge about the overall spatial topography of song representation in the avian brain. Here, we adapt the noninvasive functional MRI method in mildly sedated zebra finches (
Taeniopygia guttata
) to localize and characterize song driven brain activation. Based on the blood oxygenation level-dependent signal, we observed a differential topographic responsiveness to playback of bird's own song, tutor song, conspecific song, and a pure tone as a nonsong stimulus. The bird's own song caused a stronger response than the tutor song or tone in higher auditory areas. This effect was more pronounced in the medial parts of the forebrain. We found left–right hemispheric asymmetry in sensory responses to songs, with significant discrimination between stimuli observed only in the right hemisphere. This finding suggests that perceptual responses might be lateralized in zebra finches. In addition to establishing the feasibility of functional MRI in sedated songbirds, our results demonstrate spatial coding of song in the zebra finch forebrain, based on developmental familiarity and experience.
Chemical cues induce consumer-specific defenses in a bloom-forming marine phytoplankton
Authors: Long Jeremy D. , Smalley Gabriela W. , Barsby Todd , Anderson Jon T. , Hay Mark E.
Published: June 2007

Blooms of the phytoplanktonPhaeocystiscan comprise 85% of total production and generate major biogeochemical signals across broad oceanic regions. The success ofPhaeocystismay result from its ability to change size by many orders of magnitude when it shifts from small cells of 4–6 μm to large colonies of up to 30,000 μm in diameter. Single cells are consumed by ciliates but not copepods, whereas colonies are consumed by copepods but not ciliates. We demonstrate that chemical cues associated with each of these grazers induce consumer-specific, but opposing, morphological transformations in the bloom-forming speciesPhaeocystis globosa. Chemical cues from grazing copepods suppress colony formation by a significant 60–90%, a response that should be adaptive because copepods feed four times more on colonies versus solitary cells. In contrast, chemical cues from grazing ciliates enhance colony formation by >25%, a response that should be adaptive because ciliates grow three times faster when fed solitary cells versus colonies. Because size-selective predation fundamentally alters community structure and ecosystem function, this chemically cued shift may redirect energy and nutrients from food webs supporting fisheries to those fueling detrital pathways, thus potentially altering ecosystem-level processes such as productivity, carbon storage, and nutrient release.
Small-molecule-mediated rescue of protein function by an inducible proteolytic shunt
Authors: Pratt Matthew R. , Schwartz Edmund C. , Muir Tom W.
Published: June 2007

Controlling protein function through posttranslational manipulations has emerged as an attractive complementary technology to existing genetic systems. Often these methods involve developing pharmacological agents to probe protein function without the need to generate a unique compound for each protein family. One common strategy uses small molecules that act as chemical inducers of dimerization by mediating the interaction of two proteins. Herein we report the use of a chemical inducer of dimerization for the development of a posttranslational technology for the manipulation of protein function. This system, split ubiquitin for the rescue of function (SURF), places the complementation of genetically split ubiquitin under the control of rapamycin-induced dimerization of FK506-binding protein and FKBP12-rapamycin-binding protein. Before complementation a “degron” dooms a protein of interest for destruction by the proteasome. Addition of rapamycin results in a proteolytic shunt away from degradation by inducing ubiquitin complementation and cleavage of the protein of interest from the degron. Importantly, the native protein is rescued. We characterized this system with firefly luciferase and went on to apply it to members of three important classes of proteins: proteases (caspase-3), kinases (v-Src), and transcription factors (Smad3). This general strategy should allow for inducible rescue of a variety of proteins in such a way that their native structure and function are maintained.
Genome sequencing reveals complex secondary metabolome in the marine actinomycete
Salinispora tropica
Authors: Udwary Daniel W. , Zeigler Lisa , Asolkar Ratnakar N. , Singan Vasanth , Lapidus Alla , Fenical William , Jensen Paul R. , Moore Bradley S.
Published: June 2007

Recent fermentation studies have identified actinomycetes of the marine-dwelling genus
Salinispora
as prolific natural product producers. To further evaluate their biosynthetic potential, we sequenced the 5,183,331-bp
S. tropica
CNB-440 circular genome and analyzed all identifiable secondary natural product gene clusters. Our analysis shows that
S. tropica
dedicates a large percentage of its genome (≈9.9%) to natural product assembly, which is greater than previous
Streptomyces
genome sequences as well as other natural product-producing actinomycetes. The
S. tropica
genome features polyketide synthase systems of every known formally classified family, nonribosomal peptide synthetases, and several hybrid clusters. Although a few clusters appear to encode molecules previously identified in
Streptomyces
species, the majority of the 17 biosynthetic loci are novel. Specific chemical information about putative and observed natural product molecules is presented and discussed. In addition, our bioinformatic analysis not only was critical for the structure elucidation of the polyene macrolactam salinilactam A, but its structural analysis aided the genome assembly of the highly repetitive
slm
loci. This study firmly establishes the genus
Salinispora
as a rich source of drug-like molecules and importantly reveals the powerful interplay between genomic analysis and traditional natural product isolation studies.
Calreticulin and Hsp90 stabilize the human insulin receptor and promote its mobility in the endoplasmic reticulum
Authors: Ramos Rowena R. , Swanson Andrea J. , Bass Joseph
Published: June 2007

Elimination of misfolded membrane proteins in the endoplasmic reticulum (ER) affects cell survival and growth and can be triggered by either local physiologic events or disease-associated mutations. Regulation of signaling receptor degradation involves both cytosolic and ER luminal molecular chaperones, but the mechanisms and timing of this process remain uncertain. Here we report that calreticulin (CRT) and Hsp90 exert distinct effects on the stability and cell surface levels of native and misfolded forms of the human insulin receptor (hIR) and a human variant found in type A insulin resistance. CRT was unique in stabilizing the disease variant and in augmenting hIR expression when glycolysis was abrogated. Effects of Hsp90 were independent of receptor tyrosine phosphorylation and did not change levels of downstream signaling kinases. Live cell imaging revealed that movement of the hIR through the ER was accelerated by misfolding or by overexpression of either CRT or Hsp90. Together, our results indicate that both CRT and Hsp90 control expression of hIR at its earliest maturation stages and modulate its movement within the ER before either degradation or cell surface expression.
Two type III effector genes of
Xanthomonas oryzae
pv.
oryzae
control the induction of the host genes
OsTFIIA
γ
1
and
OsTFX1
during bacterial blight of rice
Authors: Sugio Akiko , Yang Bing , Zhu Tong , White Frank F.
Published: June 2007

Xanthomonas oryzae
pv.
oryzae
strain PXO99
A
induces the expression of the host gene
Os8N3
, which results in increased host susceptibility to bacterial blight of rice. Here, we show that PXO99
A
affects the expression of two additional genes in a type III secretion system-dependent manner, one encoding a bZIP transcription factor (
OsTFX1
) and the other the small subunit of the transcription factor IIA located on chromosome 1 (
OsTFIIA
γ
1
). Induction of
OsTFX1
and
OsTFIIA
γ
1
depended on the type III effector genes
pthXo6
and
pthXo7
, respectively, both encoding two previously undescribed members of the transcription activator-like (TAL) effector family.
pthXo7
is strain-specific and may reflect adaptation to the resistance mediated by xa5, an allele of
OsTFIIA
γ
5
encoding a second form of the TFIIA small subunit on chromosome 5 of rice. The loss of
pthXo6
resulted in reduced pathogen virulence, and ectopic expression of
OsTFX1
abrogated the requirement for
pthXo6
for full virulence.
X. oryzae
pv.
oryzae
therefore modulates the expression of multiple host genes using multiple TAL effectors from a single strain, and evidence supports the hypothesis that expression of the associated host genes contributes to host susceptibility to disease.
Structural basis for streptogramin B resistance in
Staphylococcus aureus
by virginiamycin B lyase
Authors: Korczynska Magdalena , Mukhtar Tariq A. , Wright Gerard D. , Berghuis Albert M.
Published: June 2007

The streptogramin combination therapy of quinupristin–dalfopristin (Synercid) is used to treat infections caused by bacterial pathogens, such as methicillin-resistant
Staphylococcus aureus
and vancomycin-resistant
Enterococcus faecium
. However, the effectiveness of this therapy is being compromised because of an increased incidence of streptogramin resistance. One of the clinically observed mechanisms of resistance is enzymatic inactivation of the type B streptogramins, such as quinupristin, by a streptogramin B lyase, i.e., virginiamycin B lyase (Vgb). The enzyme catalyzes the linearization of the cyclic antibiotic via a cleavage that requires a divalent metal ion. Here, we present crystal structures of Vgb from
S. aureus
in its apoenzyme form and in complex with quinupristin and Mg
2+
at 1.65- and 2.8-Å resolution, respectively. The fold of the enzyme is that of a seven-bladed β-propeller, although the sequence reveals no similarity to other known members of this structural family. Quinupristin binds to a large depression on the surface of the enzyme, where it predominantly forms van der Waals interactions. Validated by site-directed mutagenesis studies, a reaction mechanism is proposed in which the initial abstraction of a proton is facilitated by a Mg
2+
-linked conjugated system. Analysis of the Vgb–quinupristin structure and comparison with the complex between quinupristin and its natural target, the 50S ribosomal subunit, reveals features that can be exploited for developing streptogramins that are impervious to Vgb-mediated resistance.
Divergent ecological effects of oceanographic anomalies on terrestrial ecosystems of the Mexican Pacific coast
Authors: Caso Margarita , González-Abraham Charlotte , Ezcurra Exequiel
Published: June 2007

Precipitation pulses are essential for the regeneration of drylands and have been shown to be related to oceanographic anomalies. However, whereas some studies report increased precipitation in drylands in northern Mexico during El Niño years, others report increased drought in the southern drylands. To elucidate the effect of oceanographic/atmospheric anomalies on moisture pulses along the whole Pacific coast of Mexico, we correlated the average Southern Oscillation Index values with total annual precipitation for 117 weather stations. We also analyzed this relationship for three separate rainfall signals: winter-spring, summer monsoon, and fall precipitation. The results showed a distinct but divergent seasonal pattern: El Niño events tend to bring increased rainfall in the Mexican northwest but tend to increase aridity in the ecosystems of the southern tropical Pacific slope. The analysis for the separated rainfall seasons showed that El Niño conditions produce a marked increase in winter rainfall above 22° latitude, whereas La Niña conditions tend to produce an increase in the summer monsoon-type rainfall that predominates in the tropical south. Because these dryland ecosystems are dependent on rainfall pulses for their renewal, understanding the complex effect of ocean conditions may be critical for their management in the future. Restoration ecology, grazing regimes, carrying capacities, fire risks, and continental runoff into the oceans could be predicted from oceanographic conditions. Monitoring the coupled atmosphere–ocean system may prove to be important in managing and mitigating the effects of large-scale climatic change on coastal drylands in the future.
The two-pore channel
TPK1
gene encodes the vacuolar K
+
conductance and plays a role in K
+
homeostasis
Authors: Gobert Anthony , Isayenkov Stanislav , Voelker Camilla , Czempinski Katrin , Maathuis Frans J. M.
Published: June 2007

The
Arabidopsis thaliana
genome contains five genes that encode two pore K
+
(TPK) channels. The most abundantly expressed isoform of this family, TPK1, is expressed at the tonoplast where it mediates K
+
-selective currents between cytoplasmic and vacuolar compartments. TPK1 open probability depends on both cytoplasmic Ca
2+
and cytoplasmic pH but not on the tonoplast membrane voltage. The channel shows intrinsic rectification and can be blocked by Ba
2+
, tetraethylammonium, and quinine. TPK1 current was found in all shoot cell types and shows all of the hallmarks of the previously described vacuolar K (VK) tonoplast channel characterized in guard cells. Characterization of TPK1 loss-of-function mutants and TPK1-overexpressing plants shows that TPK1 has a role in intracellular K
+
homeostasis affecting seedling growth at high and low ambient K
+
levels. In stomata, TPK1 function is consistent with vacuolar K
+
release, and removal of this channel leads to slower stomatal closure kinetics. During germination, TPK1 contributes to the radicle development through vacuolar K
+
deposition to provide expansion growth or in the redistribution of essential minerals.