bluuebunny/crossref_metadata_2025 huggingface dataset:
Interrelationships among Atg proteins during autophagy in Saccharomyces cerevisiae
Authors: Suzuki Kuninori , Noda Takeshi , Ohsumi Yoshinori
Published: September 2004

Macroautophagy is a bulk degradation process induced by nutrient starvation in eukaryotic cells. In Saccharomyces cerevisiae, 16 ATG genes are essential for autophagosome formation. Recently, we demonstrated that these ATG genes can be classified into three groups on the basis of localization of GFP–Atg8p/Aut7p and Atg5p/Apg5p–GFP under nutrient‐rich conditions. In this study, we analysed the intracellular localization of GFP–Atg8p, an autophagosome marker, in atg mutants under autophagy‐inducing conditions; the localization of GFP–Atg8p exhibited several distinct patterns. Subsequent analyses revealed epistatic interrelationships among Atg proteins during the process of autophagosome formation. Copyright © 2004 John Wiley & Sons, Ltd.
Effect of bone morphogenetic proteins‐4, '5 and '6 on DNA synthesis and expression of bone‐related proteins in cultured human periodontal ligament cells
Authors: Xu Wan‐Peng , Shiba Hideki , Mizuno Noriyoshi , Uchida Yuushi , Mouri Yoshihiro , Kawaguchi Hiroyuki , Kurihara Hidemi
Published: September 2004

Bone morphogenetic proteins (BMPs) have multiple functions in the development and growth of skeletal and extraskeletal tissues. Therefore, BMPs may regulate the regeneration of periodontal tissue. To investigate this issue, we examined the effects of BMP‐4, −5 and −6 on DNA synthesis and the expression of bone‐related proteins in cultures of human periodontal ligament (HPL) cells. The expression of bone‐related proteins was determined by Real‐time polymerase chain reaction and enzyme linked immunosorbent assay in cultures of HPL cells. DNA synthesis was estimated by measuring bromoderoxyuridine incorporation. It was found that BMP‐4, −5 and −6 enhanced DNA synthesis dose‐dependently. BMP‐4 and −5 increased the levels of osteopontin, BMP‐2, alkaline phosphatase and core binding factor alpha 1 mRNAs. BMP‐6 stimulated the expression of osteopontin, BMP‐2, ALPase and osteoprotegerin. These findings show that BMP‐4, −5 and −6 have different actions on the expression of bone‐related proteins and may play a role in the regeneration of periodontal tissue by promoting cell proliferation and protein expression.
A single in vivo‐selected point mutation in the active center of Toxoplasma gondii ferredoxin‐NADP+ reductase leads to an inactive enzyme with greatly enhanced affinity for ferredoxin
Authors: Thomsen-Zieger Nadine , Pandini Vittorio , Caprini Gianluca , Aliverti Alessandro , Cramer Jörg , Selzer Paul M. , Zanetti Giuliana , Seeber Frank
Published: September 2004

Electron transfer between plant‐type [2Fe–2S] ferredoxin (Fd) and ferredoxin‐NADP+ reductase (FNR) depends on the physical interaction between both proteins. We have applied a random mutagenesis approach with subsequent in vivo selection using the yeast two‐hybrid system to obtain mutants of Toxoplasma gondii FNR with higher affinity for Fd. One mutant showed a 10‐fold enhanced binding using affinity chromatography on immobilized Fd. A single serine‐to‐arginine exchange in the active site was responsible for its increased affinity. The mutant reductase was also enzymatically inactive. Homology modeling of the mutant FNR–Fd complex predicts substantial alterations of protein–FAD interactions in the active site of the enzyme with subsequent structural changes. Collectively, for the first time a point mutation in this important class of enzymes is described which leads to greatly enhanced affinity for its protein ligand.
The pCO2 variability in the midlatitude North Atlantic Ocean during a full annual cycle
Authors: Lüger Heike , Wallace Douglas W. R. , Körtzinger Arne , Nojiri Yukihiro
Published: September 2004

The results of 1 year of automated pCO2 measurements in 2002/2003 onboard the car carrier M/V Falstaff are presented and analyzed with regard to the driving forces that change the seawater pCO2 in the midlatitude North Atlantic Ocean. The pCO2 in surface seawater is controlled by thermodynamics, biology, air‐sea gas exchange, and physical mixing. Here we estimate the effects on the annual cycle of pCO2 and relate this property to parameters like SST, nitrate, and chlorophyll. On the basis of the amplitude in seawater pCO2 for all 4° × 5° grid boxes, this region can be separated into an eastern and western basin. The annual pCO2 cycle in the eastern basin (10°W–35°W) is less variable, which can be related to the two counteracting effects of temperature and biology; air‐sea gas exchange plays a minor role when using climatological MLD. In the western basin (36°W–70°W) the pCO2 amplitude is more variable and strongly follows the thermodynamic forcing, since the biological forcing (as derived from nitrate concentrations) is decreased. Biology and air‐sea exchange strongly depend on the MLD and therefore also include physical mixing effects. The pCO2 data of the analyzed region between 34°N and 52°N compare well to the Takahashi et al. [2002] climatology except for regions north of 45°N during the wintertime where the bias is significant.
Electron density in the magnetosphere
Authors: Denton R. E. , Menietti J. D. , Goldstein J. , Young S. L. , Anderson R. R.
Published: September 2004

Observations of the electron density ne based on measurement of the upper hybrid resonance frequency by the Polar spacecraft Plasma Wave Instrument (PWI) are available for March 1996 to September 1997, during which time the Polar orbit sampled all MLT values three times. In a previous study, we modeled the electron density dependence along field lines as ne = ne0(Rmax/R)α, where ne0 is the equatorial electron density, Rmax ≈ LRE is the maximum geocentric radius R to any point on the field line, and α = αmodel = 8.0 − 3.0 log10ne0 + 0.28(log10ne0)2 − 0.43(Rmax/RE), for all categories of plasma (plasmasphere and plasmatrough). (In the formula for αmodel, ne0 is expressed in cm−3.) Here, we illustrate the field line dependence using several example events. We show that the plasmapause is much more evident on the large radius portion of the orbit and that at R ∼ 2 RE the electron density tends to level out at large Rmax to a constant value ∼100 cm−3. We also present an example of plasmaspheric plasma extending out to at least L ∼ 9 on the dawnside during particularly calm geomagnetic conditions (as indicated by low Kp). Then we present the average equatorial profiles of ne0 versus Rmax for plasmasphere and plasmatrough. Our average plasmasphere profile is found to have values intermediate between those based on the models of Carpenter and Anderson and Sheeley et al. The plasmatrough equatorial density ne0 scales with respect to Rmax like Rmax−3.4, but in the region for which our plasmatrough data is most reliable (L ≤ 6), it is well fit by the Rmax−4.0 scaling of Sheeley et al. or the Rmax−4.5 scaling of Carpenter and Anderson. We present a simple interpretation for the field line dependence of the density. For large ne0, such as occurs in the plasmasphere, α is close to zero on average (implying that ne is roughly constant along field lines). When ne0 decreases, so does ne at R = 2 RE, but the value there does not decrease much below 100 cm−3. (It is unclear if this value is an absolute lower density limit because most often the upper hybrid resonance emission disappears at R ∼ 2 RE because fp/fce < 1, where fp is the plasma frequency and fce is the electron cyclotron frequency.) Finally, we examined the dependence of α and the density at the equator and at R ∼ 2 RE on the average 〈Kp〉 (Kp averaged with a 3‐day timescale). There is no clear dependence of the average α − αmodel on 〈Kp〉 or on MLT. In the plasmasphere, ne0 decreases with respect to increasing 〈Kp〉.
Plastic faulting: Brittle‐like failure under high confinement
Authors: Renshaw Carl E. , Schulson Erland M.
Published: September 2004

Two distinct modes of compressive brittle‐like failure are observed in laboratory samples of rock and ice. Under low to moderate confinement, terminal failure follows microcrack growth and interaction when damage is localized along a fault oriented ∼30° to the greatest compressive stress. Under higher confinement, frictional sliding is suppressed, and sudden, localized, brittle‐like failure is not attended by a concentration of microcracks near the main fault. Also, faults that form under higher confinement are narrower and oriented ∼45° to the greatest compressive stress. We propose that these more steeply inclined faults are plastic faults whereby deformation is localized because of an instability that develops when thermal softening exceeds strain hardening. Analysis leads to a quantitative model for the shear stresses required to initiate and maintain the instability and to accommodate slip along the fault. The required stress is in general agreement with observed failure stresses from a variety of crystalline materials. Application of this model suggests that in some cases plasticity, rather than friction, limits the strength of the Earth's upper crust.
Water banks and environmental water demands: Case of the Klamath Project
Authors: Burke Susan M. , Adams Richard M. , Wallender Wesley W.
Published: September 2004

Demand for water for environmental uses, such as to provide critical habitat for endangered species, has increased competition for agricultural water supplies. In the western United States, a significant portion of these water demands is to increase in‐stream flows. Given that Endangered Species Act (ESA) requirements supersede prior appropriation rights, ESA water demands have the potential to reduce agricultural diversions, particularly in times of drought. This situation occurred in 2001 in the Klamath Basin of southern Oregon and northern California: an ESA‐related judicial ruling on the needs of several endangered fish species resulted in a major reduction in water diversions to the Klamath Reclamation Project. Using the Klamath Basin as an empirical backdrop, this study examines the potential benefits and challenges of water banks to mitigate damages to appropriative water rights holders and to provide water for environmental purposes. Results from this case study indicate that water banks are a potentially cost effective way to meet environmental needs. This study, however, illustrated several of the challenges of implementing a water bank given that modifications to the proposed bank are needed to achieve cost efficiency. Specifically, expanded trading is needed, both intraproject and interproject, to achieve the objectives of providing environmental water at minimum cost to society.
Using quasi‐linear diffusion to model acceleration and loss from wave‐particle interactions
Authors: Albert J. M.
Published: September 2004

Current research has reemphasized the importance of cyclotron resonant wave particle interactions for radiation belt electrons. Whistler mode hiss, chorus, and EMIC waves can act in combination to cause acceleration and loss of radiation belt electrons at greater rates than previously appreciated. These processes can be described by quasi‐linear theory, but calculating quasi‐linear diffusion coefficients is computationally demanding. Recent advances have been made in computing bounce averaged quasi‐linear pitch angle, energy, and mixed diffusion coefficients for hiss and EMIC in the high density plasmasphere; this paper outlines generalization of these techniques for chorus waves, prevalent in the low density region outside the plasmasphere. These coefficients are associated with a two‐dimensional diffusion equation whose numerical solution by finite differencing methods requires care, for reasons having to do with the relation between the mixed and other diffusion coefficients, as discussed.
Dependence of the lateral ion transport on the driving frequency in nematic liquid crystal displays
Authors: Stojmenovik G. , Vermael S. , Neyts K. , Asselt R. van , Verschueren A. R. M.
Published: September 2004

The presence of ions in a liquid crystal (LC) influences the transmission characteristics of LC displays. These ions follow the electric field perpendicular to the electrodes and move back and forth under the influence of the ac field. Because of their charge, they can distort the electric field, which leads to transmission changes. Recently it was discovered that due to the LC anisotropy, ion motion parallel with the plane of the electrodes (perpendicular to the electric field) is also possible, even without lateral fields. After driving a pixel for a long time, the ions will accumulate at one pixel edge, which leads to unwanted image artifacts. In this paper, we investigate the frequency dependence of the lateral ion transport in twisted nematic liquid crystal displays at high and low ion concentrations, different ion mobilities, and LC rotational viscosities, for a fixed voltage just above the LC threshold.
Anomalous magnetoresistance in NiMnGa thin films
Authors: Golub Vladimir O. , Vovk Andriy Ya. , Malkinski Leszek , O’Connor Charles J. , Wang Zhenjun , Tang Jinke
Published: September 2004

The origin of anomalous negative magnetoresistance and its temperature dependence in polycrystalline Ni–Mn–Ga films prepared by pulse laser deposition was studied. The investigation of structural, transports, magnetic, and ferromagnetic resonance properties of the films suggests contributions of different mechanisms in magnetotransport. At low magnetic fields the main contribution to magnetoresistance is due to the transport between the areas with different orientation of magnetic moments, while at high fields it is an electron scattering of in spin-disordered areas.
Nonohmic behavior of SnO2-MnO polycrystalline ceramics. II. Analysis of admittance and dielectric spectroscopy
Authors: Orlandi M. O. , Bomio M. R. D. , Longo E. , Bueno P R.
Published: September 2004

An analysis of the admittance and dielectric response of SnO2·MnO-based varistors in the frequency range from 100Hz to 15MHz and a temperature range from 293–573K allowed the formation of electronic transitions in space-charge regions to be characterized as a function of the Nb2O5 dopant concentration in SnO2·MnO polycrystalline-based ceramics. This analysis revealed that the formation of trapping states in space-charge regions was indirectly dependent on the concentration of Nb2O5 as a result of a microstructural modification, as discussed in Part I of this paper. Moreover, the presence of type I SnO2-SnO2 grain boundaries, which are thin and Mn rich, was found to favor the formation of space-charge regions in this kind of device. In the systems in question, oxygen vacancies or MnSn′-like defects were suggested as the source of trap states situated ∼0.49eV below the conduction band. The samples were also found to display very dissimilar dielectric responses in terms of the power law exponents of the peak loss, which were attributed to the influence of the conductance terms of type-II junctions whose frequency cannot be separated from the trapping relaxation process. As a result, Mott-Schottky plots could not be constructed for the SnO2·MnO-based systems studied here.
Polymer dielectric treatment using ultraviolet-ozone: A photoelectron spectroscopy and ellipsometric porosimetry study
Authors: Toan Le Quoc , Whelan C. M. , Struyf H. , Vanhaelemeersch S. , Azioune A. , Louette P. , Pireaux J.-J. , Maex K.
Published: September 2004

Ultraviolet-ozone (UV-O3) treatment of polyarylene, a semiconductor dielectric polymer, has been characterized using contact angle measurements, x-ray photoelectron spectroscopy, spectroscopic ellipsometry (SE), and ellipsometric porosimetry. Significant modification of the film surface composition is already observed after a short exposure time (30s). Longer treatment time leads to further increase in oxygen concentration and formation of an oxidized surface layer and densification of the film as evidenced by solvent adsorption data. Results obtained from SE indicate few changes in optical parameters, thickness, and refractive index (RI) of the film, up to 5min of UV-O3 treatment. Increasing the exposure time further leads to a substantial change in film thickness and an increase in RI. The same trend was observed for porous polyarylene but to a stronger extent. A dense layer at the porous polymer surface is only formed after 20min of treatment. Under these conditions, the optical properties of the material are strongly modified, with a substantial thickness shrinkage and increase in RI.
Intermolecular association in liquid N-methylacetamide as studied by x-ray scattering
Authors: Trabelsi Sahbi , Nasr Salah
Published: September 2004

A structural investigation of liquid N methylacetamide was performed at 308 K using x-ray scattering. To extract the molecular form factor F1(q), the geometry of the conformer which has been found in the crystal is considered. The intermolecular structure function DM(q) is interpreted in terms of H-bonding interactions. The crystal N⋯O distance is taken into accounted and the number of H bond(s) is assumed to be, respectively, equal to one and two. The liquid structure can be described by a linear dimer or chainlike trimer similar to the ones existing in the crystal. The structure factors SM(q) extracted from these clusters fairly agree with the experimental one beyond q=2.5 Å−1.
Evolution of dislocation structure in the heat affected zone of a nickel-based single crystal
Authors: Barabash O. M. , Horton J. A. , Babu S. S. , Vitek J. M. , David S. A. , Park J. W. , Ice G. E. , Barabash R. I.
Published: September 2004

Using polychromatic microbeam synchrotron diffraction together with electron and optical microscopy, we studied dislocation structure changes of Ni—based single crystal superalloy during impulse heating up to the melting temperature. It is shown that the distribution of the thermal gradient is not monotonic. The maximum value of the thermal gradient is observed in the heat affected zone near the fusion line. Depending on the temperature, the formation of dislocation is accompanied by the partial or complete dissolution of γ′ particles in the matrix. Dislocations form and multiply due to thermal gradients, and their arrangement correlates with temperature gradient field and with the dissolution and reprecipitation of γ′ particles.
High-pressure Raman spectroscopy of diamond anvils to 250GPa: Method for pressure determination in the multimegabar pressure range
Authors: Akahama Yuichi , Kawamura Haruki
Published: September 2004

The first-order Raman spectra of diamond anvils used in a gasketed high-pressure cell have been measured at pressure up to 250GPa. The high-frequency edge of the Raman band, which corresponds to the Raman shift of the culet face, is represented by a function of pressure in the sample chamber up to 250GPa. The dependence is almost independent on loading conditions. The application of the pressure dependence for pressure determination up to the multimegabars pressure region is proposed.
Effect of in situ CdCl2 treatment on spray deposited CdTe∕CdS heterostructure
Authors: Krishna K. Vamsi , Dutta V.
Published: September 2004

CdTe thin films have been deposited without and with in situ CdCl2 treatment using spray pyrolysis technique. Scanning electron microscopy studies show enhanced grain growth in the presence of CdCl2. Glancing incidence angle x-ray diffraction is used to observe the microstructural changes of CdTe∕CdS heterostructure at different depths by changing the incident angle. Spraying of CdCl2 on CdS prior to CdTe deposition promotes S diffusion throughout CdTe film and also Te diffusion into CdS. There is an associated change in the microstress of the CdTe film at different layers. The films without CdCl2 treatment show compressive microstress varying from −98to−158MPa with increasing incident angle. CdCl2 spray during CdTe deposition leads to compressive microstress varying from −98MPa at the interface to −19MPa near the surface and CdCl2 spray prior to CdTe deposition leads to a mildly tensile stress (+20to+40MPa). Photoluminescence spectra for CdTe films with the in situ treatment show a reduction in the band gap due to S diffusion as well as the reduction in the defect band intensity. An in situ CdCl2 treatment results in less surface oxidation compared to ex situ process, as seen from x-ray photoelectron spectroscopy study. A shift of ∼200meV in the Fermi energy towards the valence band is also observed in valence band spectra after the in situ CdCl2 treatment.
Fluctuation theorem and Onsager reciprocity relations
Authors: Andrieux D. , Gaspard P.
Published: September 2004

The Onsager and higher-order reciprocity relations are derived from a fluctuation theorem for nonequilibrium reactions ruled by the chemical master equation. The fluctuation theorem is obtained for the generating function of the macroscopic fluxes between chemiostats maintaining the system in a nonequilibrium steady state. The macroscopic affinities associated with the fluxes are identified by graph theory. The Yamamoto–Zwanzig formulas for the reaction constants are also derived from the fluctuation theorem.
Evaluation of back-side secondary ion mass spectrometry for boron diffusion in silicon and silicon-on-insulator substrates
Authors: Yeo K. L. , Wee A. T. S. , Chong Y. F.
Published: September 2004

We present a study on the redistribution of boron in (100) crystalline silicon and silicon-on-insulator (SOI) substrates after rapid thermal processing (RTP). The use of SOI back-side secondary ion mass spectrometry (SIMS) technique in obtaining an accurate diffusion profile is also investigated. Our results show that the boron diffusion profiles (using conventional frontside SIMS) do not deviate in any of the two types of substrates after RTP with a soak time of 30sec, indicating that the insulating effect of SOI substrate does not enhance the diffusion of boron. Since the profile obtained by the back-side SIMS technique is always shallower than that of front-side SIMS, it is deduced that the back-side SIMS technique gives a better representation of the real profile.
Transverse characterization of tapered photonic crystal fibers
Authors: Mägi E. C. , Steinvurzel P. , Eggleton B. J.
Published: September 2004

We demonstrate the tapering of photonic crystal fibers to create an all-silica two-dimensional photonic crystal with a submicron pitch and holes smaller than 200nm. We characterize the fundamental partial band gaps of this structure as a function of the taper diameter by probing the fiber in the transverse geometry along both symmetry axes. In tapering the fiber, we are able to shift the fundamental partial gap from the midinfrared to 1100nm, corresponding to a reduction in diameter by 2.5 times. A complete description of the tapering process is provided. We produced a number of tapers that either maintained the cross-sectional aspect ratio or collapse the holes relative to the photonic crystal structure. From these, we show that the strength of the band gap can be continuously varied by collapsing the holes. For tapers which maintain the cross-sectional aspect ratio, we show that there is a good correlation between the experiment and the band-structure calculations.
Fabrication of exchange-coupled α-Fe∕L1-FePd nanocomposite isolated particles
Authors: Kawamura Junichi , Sato Kazuhisa , Hirotsu Yoshihiko
Published: September 2004

Oriented nanocomposite particles of α-Fe and ordered L10-FePd have been fabricated by electron-beam deposition and successive postdeposition annealing at temperatures higher than 773K. High-resolution transmission electron microscopy, nanobeam electron diffraction, and nanobeam elemental analysis indicated that two regions composed of α-Fe and L10-FePd coexisted in each nanoparticle separated by a diffuse boundary. Magnetic hysteresis measurements using a superconducting quantum interference device magnetometer showed a gradual increase in the saturation magnetization with increasing volume ratio of the α-Fe region, whereas the coercivity decreased with the volume of α-Fe. There were no obvious steps in each magnetization curve. These results indicated the existence of an exchange coupling between the α-Fe and L10-FePd crystallites connected coherently with each other within the nanoparticles. The effects of the α-Fe region size on hard magnetic properties are also discussed.
Theoretical investigation on electron transport through an organic molecule: Effect of the contact structure
Authors: Nara Jun , Geng W. T. , Kino Hiori , Kobayashi Nobuhiko , Ohno Takahisa
Published: September 2004

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.
Electrical transport in ZnO1−δ films: Transition from band-gap insulator to Anderson localized insulator
Authors: Tiwari Ashutosh , Jin C. , Narayan J. , Park M.
Published: September 2004

We have thoroughly investigated the effect of oxygen nonstoichiometry on the electrical transport characteristics of ZnO1−δ films. These films were grown on optical grade quartz substrates by using a pulsed laser deposition technique. In order to alter the amount of oxygen nonstoichiometry (δ), oxygen partial pressure during the film growth was systematically varied from 102Torrto10−5Torr. Qualitative estimates about the amount of oxygen nonstoichiometry in these films were made using Raman Spectroscopy data. High resolution electrical resistivity and thermoelectric power measurements were performed in the temperature range 12–300K. A detailed analysis of electrical transport data showed a transition from band-gap insulating state (for the films prepared at high oxygen environments) to Anderson localized insulating state (for the films prepared at lower oxygen environments).
Time-dependent electron tunneling through time-dependent tunnel barriers
Authors: Gribnikov Z. S. , Haddad G. I.
Published: September 2004

A plane electron wave incident on a tunnel-transparent potential barrier formed by the potential V(x,t)=V0(x)+V1(x)cosωt generates, in addition to the usual stationary transmitted and reflected stationary waves, also “transmitted” and “reflected” electron waves oscillating with the same frequency ω. The transmitted oscillating wave can serve as the basis for transit-time microwave generators oscillating in the terahertz range. (Such oscillators are ballistic analogs of the tunnel-emission transit-time diode oscillators suggested almost half a century ago.) In the special case of a rectangular potential barrier, we describe the dependence of a small transmitted oscillating wave amplitude on the frequency ω and the value of V1(x). We consider two forms of V1(x): (1) homogeneous oscillation of the height of the rectangular barrier and (2) V1(x)=aδ(x−x1) [where δ(x) is the Dirac delta function and 0<x1<w; w is the barrier thickness]. For sufficiently high frequencies ω determined by the time for tunneling, a much higher emission of the transmitted oscillating wave takes place in comparison with the results of quasistatic calculations.
Defect structure studies of bulk and nano-indium-tin oxide
Authors: González G. B. , Mason T. O. , Quintana J. P. , Warschkow O. , Ellis D. E. , Hwang J.-H. , Hodges J. P. , Jorgensen J. D.
Published: September 2004

The defect structure of bulk and nano-indium-tin oxide was investigated by a combination of experimental techniques, including high-resolution synchrotron x-ray diffraction, extended x-ray absorption fine structure, and time-of-flight neutron diffraction on powder specimens. The structural results include atomic positions, cation distributions, and oxygen interstitial populations for oxidized and reduced materials. These structural parameters were correlated with theoretical calculations and in situ electrical conductivity and thermopower measurements as well as existing defect models, with special reference to the model of Frank and Köstlin [G. Frank and H. Köstlin, Appl. Phys. A 27, 197 (1982)].
Trapping of excitons at chemical defects in polyethylene
Authors: Ceresoli D. , Tosatti E. , Scandolo S. , Santoro G. , Serra S.
Published: September 2004

In a previous paper we studied an injected electron-hole pair in crystalline polyethylene (PE) and found that the exciton becomes weakly self-trapped in a narrow interchain pocket comprised between two gauche defects. Despite the large energy stored in the trapped excitation, there did not appear to be a direct nonradiative channel for electron-hole recombination. Actual polyethylene systems of practical use are, however, neither crystalline nor pure. To understand the fate of an electron-hole pair in the impure case, we studied by ab initio simulations the evolution of an exciton trapped on three common chemical defects found in polyethylene: a grafted carbonyl (C=O); an intrachain vinyl group (C=C); a grafted carboxyl (COOH). Ab initio simulations lead to predict three different outcomes: trapping, nonradiative recombination, and homolitic bond-breaking, respectively. This suggests that extrinsic self-trapping of electron-hole pairs over chemical defects inside the quasicrystalline fraction of PE could be relevant for electrical damage in high-voltage cables.
A model for fatigue in ferroelectric thin films based on trapping of carriers at interfacial states
Authors: Le Rhun G. , Poullain G. , Bouregba R.
Published: September 2004

Experimental data on fatigue in the Metal∕Ferroelectric∕Metal thin film structures are reported. A model is proposed based on the trapping and the releasing of the free carriers in the band-gap states located at the interfaces between the electrodes and the ferroelectric film. Fits of the experimental data with the plots calculated from the model show very good agreement. In particular, the fatigue dependence on both the frequency and the magnitude of the applied voltage is well reproduced by the model. Saturation of fatigue for a large number of cycles is also predicted.
Relaxation modes in glass forming meta-toluidine
Authors: Carpentier L. , Decressain R. , Descamps M.
Published: September 2004

The dynamics in supercooled meta-toluidine was studied using dielectric relaxation, modulated differential scanning calorimetry, proton spin-lattice relaxation times, and viscosity measurements. The combination of these different techniques has clearly shown a large decoupling of the relaxation modes whose origin is attributed to the formation of clusters via the NH2 bonding. This decoupling starts at a temperature also corresponding to a change of the dynamical behavior from a high temperature Arrhenius evolution to a Vogel-Fulcher-Tamman low temperature evolution.
Vicinal fluorine-fluorine coupling constants: Fourier analysis
Authors: San Fabián J. , Westra Hoekzema A. J. A.
Published: September 2004

Stereochemical dependences of vicinal fluorine-fluorine nuclear magnetic resonance coupling constants (3JFF) have been studied with the multiconfigurational self-consistent field in the restricted active space approach, with the second-order polarization propagator approximation (SOPPA), and with density functional theory. The SOPPA results show the best overall agreement with experimental couplings. The relationship with the dihedral angle between the coupled fluorines has been studied by Fourier analysis, the result is very different from that of proton-proton couplings. The Fourier coefficients do not resemble those of a typical Karplus equation. The four nonrelativistic contributions to the coupling constants of 1,2-difluoroethane configurations have been studied separately showing that up to six Fourier coefficients are required to reproduce the calculated values satisfactorily. Comparison with Fourier coefficients for matching hydrogen fluoride dimer configurations suggests that the higher order Fourier coefficients (Cn⩾3) originate mainly from through-space Fermi contact interaction. The through-space interaction is the main reason JFF3 do not follow the Karplus equation.
Quantum process tomography of the quantum Fourier transform
Authors: Weinstein Yaakov S. , Havel Timothy F. , Emerson Joseph , Boulant Nicolas , Saraceno Marcos , Lloyd Seth , Cory David G.
Published: September 2004

The results of quantum process tomography on a three-qubit nuclear magnetic resonance quantum information processor are presented and shown to be consistent with a detailed model of the system-plus-apparatus used for the experiments. The quantum operation studied was the quantum Fourier transform, which is important in several quantum algorithms and poses a rigorous test for the precision of our recently developed strongly modulating control fields. The results were analyzed in an attempt to decompose the implementation errors into coherent (overall systematic), incoherent (microscopically deterministic), and decoherent (microscopically random) components. This analysis yielded a superoperator consisting of a unitary part that was strongly correlated with the theoretically expected unitary superoperator of the quantum Fourier transform, an overall attenuation consistent with decoherence, and a residual portion that was not completely positive—although complete positivity is required for any quantum operation. By comparison with the results of computer simulations, the lack of complete positivity was shown to be largely a consequence of the incoherent errors which occurred over the full quantum process tomography procedure. These simulations further showed that coherent, incoherent, and decoherent errors can often be identified by their distinctive effects on the spectrum of the overall superoperator. The gate fidelity of the experimentally determined superoperator was 0.64, while the correlation coefficient between experimentally determined superoperator and the simulated superoperator was 0.79; most of the discrepancies with the simulations could be explained by the cummulative effect of small errors in the single qubit gates.
Crossed beams study of the reaction CH21+C2H2→C3H3+H
Authors: Floyd Davis H. , Shu Jinian , Peterka Darcy S. , Ahmed Musahid
Published: September 2004

The reaction of electronically excited singlet methylene (1CH2) with acetylene (C2H2) was studied using the method of crossed molecular beams at a mean collision energy of 3.0 kcal/mol. The angular and velocity distributions of the propargyl radical (C3H3) products were measured using single photon ionization (9.6 eV) at the advanced light source. The measured distributions indicate that the mechanism involves formation of a long-lived C3H4 complex followed by simple C-H bond fission producing C3H3+H. This work, which is the first crossed beams study of a reaction involving an electronically excited polyatomic molecule, demonstrates the feasibility of crossed molecular beam studies of reactions involving CH21.
Vibronic coupling and double excitations in linear response time-dependent density functional calculations: Dipole-allowed states of N2
Authors: Neugebauer Johannes , Baerends Evert Jan , Nooijen Marcel
Published: September 2004

The present study serves two purposes. First, we evaluate the ability of present time-dependent density functional response theory (TDDFRT) methods to deal with avoided crossings, i.e., vibronic coupling effects. In the second place, taking the vibronic coupling effects into account enables us, by comparison to the configuration analysis in a recent ab initio study [J. Chem. Phys. 115, 6438 (2001)], to identify the neglect of double excitations as the prime cause of limited accuracy of these linear response based TDDFRT calculations for specific states. The “statistical averaging of (model) orbital potentials (SAOP)” Kohn–Sham potential is used together with the standard adiabatic local-density approximation (ALDA) for the exchange-correlation kernel. We use the N2 molecule as prototype, since the TDDFRT/SAOP calculations have already been shown to be accurate for the vertical excitations, while this molecule has a well-studied, intricate vibronic structure as well as significant double excitation nature in the lowest Πu1 state at elongated bond lengths. A simple diabatizing scheme is employed to obtain a diabatic potential energy matrix, from which we obtain the absorption spectrum of N2 including vibronic coupling effects. Considering the six lowest dipole allowed transitions of Σu+4 and Πu1 symmetry, we observe a good general agreement and conclude that avoided crossings and vibronic coupling can indeed be treated satisfactorily on the basis of TDDFRT excitation energies. However, there is one state for which the accuracy of TDDFRT/ALDA clearly breaks down. This is the state for which the ab initio calculations find significant double excitation character. To deal with double excitation character is an important challenge for time-dependent density functional theory.
A framework model based on the Smoluchowski equation in two reaction coordinates
Authors: Schumaker Mark F. , Watkins David S.
Published: September 2004

The general form of the Smoluchowski equation in two reaction coordinates is obtained as the diffusion limit of a random walk on an infinite square grid using transition probabilities that satisfy detailed balance at thermodynamic equilibrium. The diffusion limit is then used to construct a generalization of the single-particle model to two reaction coordinates. The state space includes a square on which diffusion takes place and an isolated empty state. Boundary conditions on opposite sides of the square correspond to transitions between the empty state and the square. The two-dimensional (2D) model can be reduced to a 1D single-particle model by adiabatic elimination. A finite element solution of the 2D boundary value problem is described. The method used to construct the 2D model can be adapted to state spaces that have been constructed by other authors to model K+ conduction through gramicidin, proton conduction through dioxolane-linked gramicidin, and chloride conduction through the bacterial H+−Cl− antiporter.
Single molecule kinetics. I. Theoretical analysis of indicators
Authors: Witkoskie James B. , Cao Jianshu
Published: September 2004

Single molecule experiments reveal intriguing phenomenon in chemical and biological systems. Several indicators of complex dynamics, including “intensity” correlations, “event” correlations, and characteristic functions have been proposed, but extraction of information from these indicators can be difficult since these indicators only observe certain characteristics of the system. Generally, for systems that follow Poisson kinetics, all of these indicators contain similar information about the relaxation times of the system and the connections between different relaxation times, but the information is convoluted in different ways so the strength of various indicators is system specific. The paper discusses the theoretical implications and information content of various data analysis methods for single molecule experiments and demonstrates the relationships between indicators. Under certain conditions, common indicators contain all available information about systems with Poisson kinetics between degenerate states, but extraction of this information is generally not numerically feasible. The paper also discusses practical issues associated with these analyses, which motivates a numerical study based on Bayes’ formula in the companion paper [J. Witkoskie and J. S. Cao, J. Chem. Phys. 121, 6373 (2004), following paper].
Gigahertz actuator of multiwall carbon nanotube encapsulating metallic ions: molecular dynamics simulations
Authors: Kang Jeong Won , Hwang Ho Jung
Published: September 2004

This paper demonstrates a gigahertz actuator based on multiwall carbon nanotubes (CNT) encapsulating metallic ions using classical molecular-dynamics simulations. Our results for a vacant CNT oscillator were in good agreement with the results obtained from previous experiments, theories, and simulations. Encapsulated potassium ions accelerated by an applied external electric field could initialize a gigahertz actuator composed of a 7K+@CNT oscillator, in which a CNT encapsulates seven potassium ions. The energetics and operation of a vacant CNT oscillator were similar to those of the 7K+@CNT oscillator except for the binding energies, the correlated collisions, and the mass increase caused by the encapsulated ions. Since the total mass of the 7K+@CNT oscillator was slightly higher than that of the vacant CNT oscillator, the frequency of the vacant CNT oscillator was slightly higher than the frequency of the 7K+@CNT oscillator. The correlated collisions between the ions or between the CNT and the ions slightly affected the oscillation dynamics, such as restoring force and frequency.
Determination of the band gap depth profile of the penternary Cu(In(1−X)GaX)(SYSe(1−Y))2 chalcopyrite from its composition gradient
Authors: Bär M. , Bohne W. , Röhrich J. , Strub E. , Lindner S. , Lux-Steiner M. C. , Fischer Ch.-H. , Niesen T. P. , Karg F.
Published: September 2004

A simple model is introduced which determines the optical band-gap energy Eg for penternary Cu(In(1−X)GaX)(SYSe(1−Y))2 (CIGSSe) alloys from its Ga∕(Ga+In) ratio as well as from its S∕(S+Se) ratio. In order to verify the model the depth dependent composition of a CIGSSe sample was revealed by elastic recoil detection analysis. Applying the model, the concentration profiles were transferred in an Eg profile. Finally, these values were compared with optical band-gap energies, which were obtained directly by independent characterization methods.
Comment on “Probing the sulfur polymerization transition in situ with Raman spectroscopy” [J. Chem. Phys. 118, 8460 (2003)]
Authors: Steudel Ralf , Eckert Bodo
Published: September 2004

Recently Kalampounias, Andrikopoulos, and Yannopoulos [J. Chem. Phys. 118, 8460 (2003)] reported the temperature dependent polymer content of liquid elemental sulfur in the temperature region 120–300 °C as determined by in situ Raman spectroscopy. At all temperatures the polymer contents obtained are considerably higher than the well established experimental data determined by quenching-extraction procedures. We show that the method employed by Kalampounias, Andrikopoulos, and Yannopoulos underestimates the presence of rings other than S8, which most probably are responsible for the reported higher polymer contents, especially in the low temperature region.
Polaron-exciton model of resonance energy transfer
Authors: Markvart T. , Greef R.
Published: September 2004

It is shown that Förster’s expression for the electronic energy transfer rate can be recast in a form predicted for exciton motion that interacts strongly with molecular vibrations. Using a simple model based on the Kennard-Stepanov theory, Förster’s expression for the spectral overlap is shown to be of a thermally activated form, as obtained previously by multiphonon theory. In contrast, the high-frequency internal vibrations contribute a factor which results from tunneling through a potential barrier between potential curves in the configuration coordinate diagram. We thus show that resonance energy transfer is equivalent to phonon-assisted hopping of a trapped excitonic polaron.
Shearing of nanoscopic bridges in two-component thin liquid layers between chemically patterned walls
Authors: Hemming C. J. , Patey G. N.
Published: September 2004

Bridge phases associated with a phase transition between two liquid phases occur when a two-component liquid mixture is confined between chemically patterned walls. In the bulk the liquid mixture with components A, B undergoes phase separation into an A-rich phase and a B-rich phase. The walls bear stripes attractive to A. In the bridge phase A-rich and B-rich regions alternate. Grand canonical Monte Carlo studies are performed with the alignment between stripes on opposite walls varied. Misalignment of the stripes places the nanoscopic liquid bridges under shear strain. The bridges exert a Hookean restoring force on the walls for small displacements from equilibrium. As the strain increases there are deviations from Hooke’s law. Eventually there is an abrupt yielding of the bridges. Molecular dynamics simulations show the bridges form or disintegrate on time scales which are fast compared to wall motion and transport of molecules into or from the confined space. Some interesting possible applications of the phenomena are discussed.
Ab initio study of the electronic spectrum of peroxyacetyl nitrate
Authors: Francisco Joseph S. , Li Yumin
Published: September 2004

A theoretical study of the ground and excited states of peroxyacetyl nitrate (PAN), CH3C(O)OONO2, has been carried out using high level ab initio molecular orbital methods. The ground state geometry and vibrational frequencies are calculated using the coupled-cluster method. The vertical excitation energies for the lowest three excited states are calculated using the complete active space self-consistent field method along with the multireference internally contracted configuration interaction method. These results are compared with vertical excitation energies calculated with the coupled cluster equation of motion method. The calculation provides relevant insight into the origin of PAN absorption in the UV wavelength region from 200 to 300 nm. The nature of the electron transitions for these excited states is discussed.
Peculiar magnetic and electrical properties near structural percolation in metal-insulator granular layers
Authors: Sousa J. B. , Santos J. A. M. , Silva R. F. A. , Teixeira J. M. , Ventura J. , Araújo J. P. , Freitas P. P. , Cardoso S. , Pogorelov Yu. G. , Kakazei G. N. , Snoeck E.
Published: September 2004

We study CoFe∕Al2O3 multilayers, varying from granular to continuous structure with CoFe nominal thickness (10Å⩽t⩽18Å). Structural percolation takes place at t=tc≈18Å, changing from activated to metallic conductance. A sharp anomaly in ac coercivity of magneto-optical Kerr effect and in magnetization M by superconducting quantum interferometer device is found at t=t*≈17Å, interpreted as transition from superferromagnetism (by dipolar coupled CoFe clusters) to exchange ferromagnetism. Onset at t=t* of anisotropic magnetoresistance (AMR) is attributed to skew scattering of bandlike electrons within giant fractal clusters. These structures may cause the observed Barkhausen noises in M and AMR at t≈t*, disappearing at t>t*.