bluuebunny/crossref_metadata_2025 huggingface dataset:
Bringing Text Miners and Biologists Closer Together
Authors: Lourenço Anália , Carneiro Sónia , Carreira Rafael , Rocha Miguel , Rocha Isabel , Ferreira Eugénio
Published: April 2009

The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do, whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from the contents of available Molecular Biology repositories, the implementation of description environments for rule specification, the implementation of dictionary- and rule-based entity recognisers, the development of flexible and extensible relationship extraction systems and the development of easy-to-use manual curation environments are of foremost importance.Our software, named @Note, aims to be a framework and a workbench for BioTM, i.e., it has been conceived for delivering end-user applications, whereas enabling collaboration with other BioTM groups. As a framework, it provides a reusable design for BioTM software systems and a set of pre-assembled software building blocks that programmers can use, extend and customise for their specific needs. As a workbench, it helps developing BioTM applications by integrating Natural Language Processing and Data Mining tools and supporting major Information Retrieval and Information Extraction processes. Moreover, it encompasses a flexible and extensible manual curation environment that enables the interaction with biologists, correcting former annotations and enhancing dictionary contents. We successfully applied @Note in the study of the stringent response on Escherichia coli, an important subject within the analysis of stress responses in bacteria. This joint effort allowed biologists to contribute to the enhancement of our manual curation environment and to identify new functionalities for the existing plug-ins and the specification of new plug-ins.
Challenges in Whole-Genome Annotation of Pyrosequenced Fungal Genomes
Authors: Kuo Alan , Grigoriev Igor
Published: April 2009

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454 sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~10k genes. ~12% of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~9% rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also, >90% of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. We conclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.
UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web
Authors: Redaschi Nicole , Consortium UniProt
Published: April 2009

The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework ("http://www.w3.org/RDF/":http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium's Semantic Web activities ("http://www.w3.org/2001/sw/":http://www.w3.org/2001/sw/) and is therefore well suited to work in a distributed and decentralized environment. The RDF data model represents arbitrary information as a set of simple statements of the form subject-predicate-object. To enable the linking of data on the Web, RDF requires that each resource must have a (globally) unique identifier. These identifiers allow everybody to make statements about a given resource and, together with the simple structure of the RDF data model, make it easy to combine the statements made by different people (or databases) to allow queries across different datasets. RDF is thus an industry standard that can make a major contribution to solve two important problems of bioinformatics: distributed annotation and data integration.
Codeword stabilized quantum codes: Algorithm and structure
Authors: Chuang Isaac , Cross Andrew , Smith Graeme , Smolin John , Zeng Bei
Published: April 2009

The codeword stabilized (CWS) quantum code formalism presents a unifying approach to both additive and nonadditive quantum error-correcting codes [IEEE Trans. Inf. Theory 55, 433 (2009)]. This formalism reduces the problem of constructing such quantum codes to finding a binary classical code correcting an error pattern induced by a graph state. Finding such a classical code can be very difficult. Here, we consider an algorithm which maps the search for CWS codes to a problem of identifying maximum cliques in a graph. While solving this problem is in general very hard, we provide three structure theorems which reduce the search space, specifying certain admissible and optimal ((n,K,d)) additive codes. In particular, we find that the re does not exist any ((7,3,3)) CWS code though the linear programming bound does not rule it out. The complexity of the CWS-search algorithm is compared with the contrasting method introduced by Aggarwal and Calderbank [IEEE Trans. Inf. Theory 54, 1700 (2008)].
Calculation of the field enhancement for a nanotube array and its emission properties
Authors: Kim Dohyung , Bourée Jean-Eric , Kim Sang Youl
Published: April 2009

In order to investigate the properties of the field enhancement factor and emission current from a nanotube array, the local electric fields on an exact tip boundary of a carbon nanotube have been calculated. The field enhancement factor of a nanotube in free space is well described by the relation 0.7×l/r, where l and r mean the length and radius of the nanotube. It has been shown that the optimum normalized spacing s/l (as referred to the length) of a square array of nanotubes to get to the maximum current density shifts toward lower values when the length of the nanotubes increases for a fixed diameter. The optimum spacing for the maximum emission current is inversely proportional to the applied electric field.
Reverberation technique for yield strength experiments at ultrahigh pressure and strain rate
Authors: DeMange P. , Colvin J. D. , Park H. S. , Pollaine S. M.
Published: April 2009

Ultrahigh pressure and strain-rate (pressure ⪢10 GPa and strain rate ⪢105 s−1) are now attainable using high-power laser systems. A laser pulse drives a shock through a reservoir material which then unloads onto the target specimen. Laser velocimetry measurements at the back surface of the specimen are used to infer the material response. Material strength experiments have been proposed in which the pressure wave reverberates within the specimen and the cumulative resistance to compression by material strength is measured from the recorded velocimetry signature. In this work, ultrahigh pressure and strain-rate reverberation experiments are performed in tantalum, aluminum, and copper to investigate the yield strength behavior in this extreme regime. The experimental results indicate that the measurement sensitivity to yield strength is dominated by the lateral wave effects or impeded by the occurrence of spall. However, computer hydrodynamic code simulations are used to develop an experimental design based on shaping of the laser drive pulse that circumvents these difficulties. Simulations using the Steinberg–Guinan yield strength model and applying the design indicate the capability of measuring a factor-of-2 strength deviation from that predicted by the model with accuracy equal to or greater than the velocimetry measurement error.
Global phase portraits of the planar perpendicular problem of two fixed centers
Authors: Jiménez–Lara Lidia , Llibre Jaume , Vargas Martín
Published: April 2009

We study the global phase portrait of the classical problem of an electron in the electrostatic field of two protons that we assume fixed to symmetric distances on the x3 axis. The general problem can be formulated as an integrable Hamiltonian system of three degrees of freedom, but we restrict our study to the invariant planar case that is equidistant to the two fixed centers. This is a two degrees of freedom problem with two constants of motion, the energy and the angular momentum, denoted by H and C, respectively, which are independent and in involution. We describe the foliation of the four-dimensional phase space by the invariant sets of constant energy Ih and we characterize their topology. We also describe the foliation of each energy level Ih by the invariant sets Ihc, and we classify the topology of Ihc and the flow on these invariant sets. In this way we provide a global qualitative description of the motion. We also compare our results with the existing published results.
Structural and magnetic properties of (100)- and (110)-oriented epitaxial CrO2 films
Authors: Chetry K. B. , Pathak M. , LeClair P. , Gupta A.
Published: April 2009

We report the successful growth of epitaxial CrO2 (100) and CrO2 (110) films by chemical vapor deposition on TiO2 (100) and TiO2 (110) substrates, respectively. Films on TiO2 (100) follow a layer-by-layer growth mode, with smooth surfaces but significant out-of-plane compressive stress. In contrast, films on TiO2 (110) follow an islandlike growth mode and are found to be essentially strain free for even the thinnest films studied (∼35 nm). The substrate-induced stress for (100) films plays a dominant role in the evolution of the magnetic anisotropy with increasing film thickness, while (110) films show little variation in anisotropy with film thickness. As a result, the in-plane angular dependence of the saturation fields for (110) films can be understood by presuming domain wall nucleation and motion for small angles with respect to the easy axis and by coherent rotation for angles approaching the hard axis.
Magnetic properties of nickel nanowires: Effect of deposition temperature
Authors: Razeeb Kafil M. , Rhen Fernando M. F. , Roy Saibal
Published: April 2009

We have investigated the magnetic properties of electroplated nickel nanowires with very distinct nanostructures, which are obtained by simply changing the plating temperature of the electrolyte. Low temperature (40 °C) resulted in larger average grain size comparable to the diameter of the wires, whereas higher temperature (60 °C) revealed self-similar morphology composed of nanogranules. For low temperature samples, a two stage magnetization process is evident in the easy axis direction where grain size is comparable to wire diameter. In contrast, for high temperature samples, nanowires are formed by an agglomeration of particles with average diameter of about 22 nm. In this case each individual particle behaves as a single domain and thereby magnetization reversal occurs by the switching of an ensemble of randomly oriented particles and magnetization saturates quickly with applied field. In the present case, with the high density of disorder caused by the self-similar morphology of the nanogranules, we suggest that the switching mechanism of the magnetization occurs by localized coherent rotation, resulting in lower coercivity. This delineates first experimental evidence of three dimensional cooperative magnetic interactions among the nanogranules within self-similar morphology of nanowires in both parallel and perpendicular wire axes.
Band-bending effects on scanning tunneling microscope images of subsurface dopants: First-principles calculations
Authors: Hirayama Motoi , Nakamura Jun , Natori Akiko
Published: April 2009

Tip-induced band-bending (TIBB) effects on scanning tunneling microscope (STM) images have been investigated. The TIBB has an extremal value where the surface space charge layer turns from the inversion region to the depletion one with increasing dopant concentration at a fixed sample bias. Unignorable TIBB remains even for the usual degenerate semiconductor with a dopant concentration such as 1018 cm−3 for Si. The STM images for H-terminated Si(111) surfaces with dopants substituted at the subsurface have been simulated using first-principles calculations within the density functional theory. The subsurface dopants on the STM images become distinguishable more obviously in consideration of the TIBB effect, specifically for acceptors in the occupied state images and for donors in the empty state. As a result, the TIBB effect improves agreement between the experimental and the theoretical sample biases at which the dopant’s feature can be observed clearly.
Structure and elastic properties of boron suboxide at 240 GPa
Authors: Lu Y. P. , He D. W.
Published: April 2009

Structure and elastic properties of boron suboxide at high pressure have been investigated using generalized gradient approximation within the plane-wave pseudopotential density functional theory. The elastic constants are calculated using the finite strain method. The pressure dependences of lattice parameters, elastic constants, aggregate elastic moduli, and sound velocities of boron suboxide are predicted. It is found that the most stable structure of hcp boron suboxide at zero pressure corresponds to the ratio c/a of about 2.274 and the equilibrium lattice parameters a0 and c0 are about 5.331 and 12.124 Å, respectively. The high-pressure elastic constants indicate that boron suboxide is mechanically stable up to 368 GPa. The pressure dependence of the calculated normalized volume and the aggregate elastic moduli agree well with the recent experimental results. The sound velocities along different directions for the structure of boron suboxide are obtained. It shows that the velocities of the shear wave decrease as pressure increases but those of all the longitudinal waves increase with pressure. Moreover, the azimuthal anisotropy of the compression and shear aggregate wave velocities for different pressures are predicted. They change behavior with increasing pressure around 87 GPa because of an electronic topological transition. A refined analysis has been made to reveal the high pressure elastic anisotropy in boron suboxide.
Efficient Nd3+→Yb3+ energy transfer in Nd3+,Yb3+:Gd3Ga5O12 multicenter garnet crystal
Authors: Jia Zhitai , Arcangeli Andrea , Tao Xutang , Zhang Jian , Dong Chunming , Jiang Minhua , Bonelli Lucia , Tonelli Mauro
Published: April 2009

For seeking better laser crystals with good optical properties and high efficiency, especially for application in a high power solid-state laser, Yb3+,Nd3+:Gd3Ga5O12 crystal (abbreviated as Yb,Nd:GGG below) was grown by Czochralski method. A complete optical characterization was reported including absorption and emission spectra at different temperatures and fluorescence lifetimes. Very efficient Nd3+ F43/2→Yb3+ F25/2 energy transfer was found whereas the back transfer was completely quenched at low temperature (T<200 K). From the data of Nd3+ fluorescence lifetime and emission spectrum we achieved the energy-transfer efficiency as large as 94% at 77 K and 84% at 300 K, respectively. After fitting the decay curve we got the energy-transfer microparameter with a value of 2.1×10−39 cm6 s−1 at 300 K.
Structural origin of set-reset processes in Ge15Te83Si2 glass investigated using in situ Raman scattering and transmission electron microscopy
Authors: Anbarasu M. , Asokan S. , Prusty Sudakshina , Sood A. K.
Published: April 2009

We report here that the structural origin of an easily reversible Ge15Te83Si2 glass can be a promising candidate for phase change random access memories. In situ Raman scattering studies on Ge15Te83Si2 sample, undertaken during the amorphous set and reset processes, indicate that the degree of disorder in the glass is reduced from off to set state. It is also found that the local structure of the sample under reset condition is similar to that in the amorphous off state. Electron microscopic studies on switched samples indicate the formation of nanometric sized particles of c-SiTe2 structure.
Dielectric properties of Bi1−xSrxMnO3 (x=0.40,0.50) manganites: Influence of room temperature charge order
Authors: García-Muñoz J. L. , Frontera C. , Rivas-Murias B. , Mira J.
Published: April 2009

The great tendency of Bi–Sr manganites to present charge order (CO) at very high temperatures and partial hybridization of the 6s2 lone pair with O p-orbitals makes these materials interesting as potential candidates for obtaining high dielectric constants with very small frequency dependence at room temperature. We have studied the dielectric properties of Bi1−xSrxMnO3 (x=0.40,0.50) perovskites that present CO well above room temperature (TCO∼525K). Thick (∼4mm) samples exhibit, at room and higher temperatures, high values (above 106) of the dielectric constant along a huge range of frequencies in which εr′ is nearly unvarying. The dependence on the thickness of the dielectric constant, its evolution with temperature, and the Cole–Cole diagrams evidence the influence of extrinsic effects. To properly compare the results in the two compounds, we have performed a detailed structural study using neutron and synchrotron diffraction. CO is more extended in x=0.40. The results in the two compositions allowed us to correlate CO and phase separation with the huge values of εr′ found in these systems.
Influence of the relative humidity on the properties of ferroelectric poly(vinylidene fluoride-trifluoroethylene)
Authors: Martin Bjoern , Vizdrik Gennady , Kliem Herbert
Published: April 2009

Ultrathin films of poly(vinylidene fluoride-trifluoroethylene) copolymers were prepared by the Langmuir–Blodgett technique. These films show a hysteresis loop of the polarization versus the applied electrical field in a dry atmosphere which can be attributed to a ferroelectric phase. By increasing the relative humidity in the surrounding atmosphere, water molecules are absorbed by the samples yielding quasi-free charge carriers. These charges can fluctuate between the electrodes of the samples and build a space charge polarization superimposed to the ferroelectric polarization. Therefore, the hysteresis loops at low frequencies, where the quasi-free charges can contribute to the total polarization, are broadened and the measured remanent polarization is increased. Also, the real and the imaginary parts of the dielectric permittivity of the samples in the low frequency range are increased. Additionally, the transient decay of the retained charge is more pronounced for higher relative humidities. Furthermore, the transient desorption of the water from the polymer is measured by detection of the rapidly changed relative humidity. However, ellipsometric measurements show only a small increase in the sample thickness and no significant change in the refractive index due to the absorption of water.
Optical enhancement in nanoparticle-decorated ZnO nanorods
Authors: Lin Tzung-Hsuan , Cheng Chung-Liang , Shih Han-Yu , Chen Yang-Fang
Published: April 2009

Based on the concept of optical enhancement in nanoparticle-mediated coupling, a novel composite consisting of ZnO nanorods and ZnO nanoparticles has been synthesized and characterized. The ZnO nanoparticles can be regarded as light-coupling media to increase the absorption cross section of excitation light as well as the emission extraction efficiency due to the relaxation of momentum selection rule. With our devised ZnO nanostructures, the band gap emission of ZnO nanorods can be enhanced by up to 8.5 times. The strategy of optical enhancement provided here should be very useful in designing many other nanostructures for high efficiency optoelectronic devices.
Photoelectric performance of poly(p-phenylene vinylene)/Fe3O4 nanofiber array
Authors: Xin Y. , Huang Z. H. , Peng L. , Wang D. J.
Published: April 2009

The authors report on the assembly and photoelectric performance of poly(p-phenylene vinylene) (PPV)/Fe3O4 nanofiber array. The composite nanofibers were fabricated by electrospinning of PPV precursor/Fe3O4 nanoparticle solution, followed by thermal conversion. The Fe3O4 nanoparticles were uniformly dispersed in the PPV matrix. During the electrospinning process, magnetic fields were used to orient the nanofibers. The resulting nanofiber array was assembled directly into a photoconductor device. The photoelectric performances of the devices have been investigated, which show notable light sensitivity, good response speed, wavelength sensitivity, and reproducibility. Electrospinning is thus proposed as a simple and versatile method of fabricating one-dimensional PPV-based photoconductor devices.
Photonic band gap structures of obliquely incident electromagnetic wave propagation in a one-dimension absorptive plasma photonic crystal
Authors: Guo Bin
Published: April 2009

The photonic band gap structures of obliquely incident electromagnetic waves propagating in a one-dimension plasma photonic crystal with collision have been studied on the basis of electromagnetic theory and transfer matrix approach. The dispersion relations for both the transverse electric wave case and the transverse magnetic wave case are deduced. And the photonic band gap structures, with their function dependence on the microplasma layer density, microplasma width, collision frequency, background material dielectric constant, and incident angle, are computed. The results show that there exist two photonic band gap structures in an adsorptive plasma photonic crystal: one is a normal photonic band gap structure and the other is an absorption photonic band gap structure. Parameter dependence of the effects is calculated and discussed.
Anode pattern formation in atmospheric pressure air glow discharges with water anode
Authors: Verreycken T. , Bruggeman P. , Leys C.
Published: April 2009

Pattern formation in the anode layer at a water electrode in atmospheric pressure glow discharges in air is studied. With increasing current a sequence of different anode spot structures occurs from a constricted homogeneous spot in the case of small currents to a pattern consisting of small distinct spots for larger currents. The dependence of the number of spots on the current is (18.5+0.4N) mA with N the number of spots. The spots group together and form stripe patterns. Disappearance of the spots with increasing conductivity of the electrode seems to indicate that mechanisms of electrical nature govern the phenomenon. Similarities and differences with other experiments and models revealing pattern formation in glow discharges are discussed.
Size determination of superparamagnetic nanoparticles from magnetization curve
Authors: Chen D.-X. , Sanchez A. , Taboada E. , Roig A. , Sun N. , Gu H.-C.
Published: April 2009

The size distribution of superparamagnetic iron oxide nanoparticles in two powder samples is determined from the measured magnetization curve fitted by a core-shell model and a uniform model, both based on the Langevin function with a log-normal particle volume distribution. Different average sizes are evaluated from the fitting parameters and compared to those determined by other techniques. Conceptual discussions are presented on different models and approaches, from which the core-shell model fitting is recommended for the magnetic size determination of superparamagnetic nanoparticles.
The structure of random packings of freely jointed chains of tangent hard spheres
Authors: Karayiannis Nikos Ch. , Foteinopoulou Katerina , Laso Manuel
Published: April 2009

We analyze the structure of dense random packings of freely jointed chains of tangent hard spheres as a function of concentration (packing density) with particular emphasis placed on the behavior in the vicinity of their maximally random jammed (MRJ) state. Representative configurations over the whole density range are generated through extensive off-lattice Monte Carlo simulations on systems of average chain lengths ranging from N=12 to 1000 hard spheres. Several measures of order are used to quantitatively describe either local structure (sphere arrangements and bonded geometry) or global behavior (chain conformations and statistics). In addition, the employed measures are used to elucidate the effect of connectivity on structure, by comparing monatomic and chain assemblies of hard spheres at the MRJ state.
Comments on “The Euclidean gravitational action as black hole entropy, singularities, and space-time voids” [J. Math. Phys. 49, 042501 (2008)]
Authors: Mitra Abhas
Published: April 2009

We point out that the space-time void inferred by Castro [J. Math. Phys. 49, 042501 (2008)] results from his choice of a discontinuous radial gauge. Further since the integration constant α0=2M0 (G=c=1) occurring in the vacuum Hilbert/Schwarzschild solution of a neutral “point mass” is zero [Arnowitt et al., in Gravitation: An Introduction to Current Research, edited by L. Witten (Wiley, New York, 1962), Chap. 7, p. 227; also Phys. Rev. Lett. 4, 375 (1960). A. Mitra, Adv. Space Res. 38, 2917 (2006); Proceedings of the XIth Marcel-Grossmann Conference on General Relativity (World Scientific, Singapore, 2008), Vol. 3, p. 1968], Castro’s gauge reduces to the well behaved and physical Hilbert gauge. Physically this means that true Hilbert/Schwarzschild black holes have unique gravitational mass M=0. Accordingly, the unphysical space-time void inferred by Castro is actually nonexistent.
Accurately determining single molecule trajectories of molecular motion on surfaces
Authors: Claytor Kevin , Khatua Saumyakanti , Guerrero Jason M. , Tcherniak Alexei , Tour James M. , Link Stephan
Published: April 2009

This paper presents a method for simultaneously determining multiple trajectories of single molecules from sequential fluorescence images in the presence of photoblinking. The tracking algorithm is computationally nondemanding and does not assume a model for molecular motion, which allows one to determine correct trajectories even when a distribution of movement speeds is present. We applied the developed procedure to the important problem of monitoring surface motion of single molecules under ambient conditions. By limiting the laser exposure using sample scanning confocal microscopy, long-time trajectories have been extracted without the use of oxygen scavengers for single fluorescent molecules. Comparison of the experimental results to simulations showed that the smallest diffusion constants extracted from the trajectories are limited by detector shot noise giving error in locating the positions of the individual molecules. The simulations together with the single molecule trajectories and distributions of diffusion constants allowed us therefore to distinguish between mobile and immobile molecules. Because the analysis algorithm only requires a time series of images, the procedure presented here can be used in conjunction with various imaging methodologies to study a wide range of diffusion processes.
Resonant spin-filtering in cobalt decorated nanotubes
Authors: Blase X. , Margine E. R.
Published: April 2009

We study by means of first-principles calculations within the Landauer formalism the transport properties of carbon nanotubes filled with cobalt clusters. We show that in the limit of small cluster sizes, a significant spin polarization of the incoming π−π∗ wave packets can be obtained on a large energy range around the Fermi level. However, in the limit of increasing cluster size, both the spin polarization and total conductance decrease dramatically, suggesting that strategies to limit the diffusion of magnetic adatoms must be found for applications in spintronics.
The symmetric quartic map for trajectories of magnetic field lines in elongated divertor tokamak plasmas
Authors: Jones Morgin , Wadi Hasina , Ali Halima , Punjabi Alkesh
Published: April 2009

The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in divertor tokamaks can be any coordinates for which a transformation to (ψt,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψt is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct the symmetric quartic map such that the only parameter that determines magnetic geometry is the elongation of the separatrix surface. The poloidal flux inside the separatrix, the safety factor as a function of normalized minor radius, and the magnetic perturbation from the symplectic discretization are all held constant, and only the elongation is κ varied. The width of stochastic layer, the area, and the fractal dimension of the magnetic footprint and the average radial diffusion coefficient of magnetic field lines from the stochastic layer; and how these quantities scale with κ is calculated. The symmetric quartic map gives the correct scalings which are consistent with the scalings of coordinates with κ. The effects of m=1, n=±1 internal perturbation with the amplitude that is expected to occur in tokamaks are calculated by adding a term [H. Ali, A. Punjabi, A. H. Boozer, and T. Evans, Phys. Plasmas 11, 1908 (2004)] to the symmetric quartic map. In this case, the width of stochastic layer scales as 0.35 power of κ. The area of the footprint is roughly constant. The average radial diffusion coefficient of field lines near the X-point scales linearly with κ. The low mn perturbation changes the quasisymmetric structure of the footprint, and reorganizes it into a single, large scale, asymmetric structure. The symmetric quartic map is combined with the dipole map [A. Punjabi, H. Ali, and A. H. Boozer, Phys. Plasmas 10, 3992 (2003)] to calculate the effects of magnetic perturbation from a current carrying coil. The coil position and coil current coil are constant. The dipole perturbation enhances the magnetic shear. The width of the stochastic layer scales exponentially with κ. The area of the footprint decreases as the κ increases. The radial diffusion coefficient of field lines scales exponentially with κ. The dipole perturbation changes the topology of the footprint. It breaks up the toroidally spiraling footprint into a number of separate asymmetric toroidal strips. Practical applications of the symmetric quartic map to elongated divertor tokamak plasmas are suggested.
Bulk resonance absorption induced by relativistic effects in laser-plasma interaction
Authors: Ding Wen-Jun , Sheng Z.-M. , Zhang J. , Yu M. Y.
Published: April 2009

Resonance absorption in relativistic laser-plasma interaction is studied via two-dimensional particle-in-cell simulation. As the laser intensity increases from the linear regime, the absorption rate first decreases due to relativistic modulation of the electron plasma oscillations excited at the mode conversion layer. However, the trend reverses after a critical intensity. The reversal can be attributed to the fact that the relativistic critical layer depends on the local intensity of the laser pulse, so that instead of occurring in a thin layer, resonance absorption occurs in a plasma bulk region, leading absorption rate increase. The reflected-light spectrum also shows broadening and splitting of the harmonics at high laser intensities, which can be attributed to critical-surface oscillations driven by the laser ponderomotive force.
Resonantly enhanced selective photochemical etching of GaN
Authors: Trichas E. , Kayambaki M. , Iliopoulos E. , Pelekanos N. T. , Savvidis P. G.
Published: April 2009

Wavelength dependent photochemical etching of GaN films reveals a strong resonant enhancement of the photocurrent at the GaN gap, in close agreement with the excitonic absorption profile of GaN. The corresponding etching rate of GaN strongly correlates with the measured photocurrent. No photocurrent, nor etching is observed for AlGaN films under same excitation conditions. The method could pave the way to the development of truly selective etching of GaN on AlGaN for the fabrication of nitride based optoelectronic devices.
Direct visualization of three-step magnetization reversal of nanopatterned spin-valve elements using off-axis electron holography
Authors: He Kai , Smith David J. , McCartney Martha R.
Published: April 2009

The remanent states and magnetization reversal mechanisms for nanopatterned Co/Cu/Py (Py=Permalloy) spin-valve elements with slotted-ring shapes have been studied using off-axis electron holography. The hysteresis loops of individual elements were quantitatively determined for slots parallel to the applied field, indicating that three identifiably separate steps occurred during reversal. Magnetization configurations at each stage were directly visualized, suggesting that Co and Py layers undergo coherent switching from onion state to flux-closure state and finally to reverse onion state. The effective loop rotation direction for the Py layer was clockwise.
Magnetic-field cycling instrumentation for dynamic nuclear polarization-nuclear magnetic resonance using photoexcited triplets
Authors: Kagawa Akinori , Negoro Makoto , Takeda Kazuyuki , Kitagawa Masahiro
Published: April 2009

To advance static solid-state NMR with hyperpolarized nuclear spins, a system has been developed enabling dynamic nuclear polarization (DNP) using electron spins in the photoexcited triplet state with X-band microwave apparatus, followed by static solid-state nuclear magnetic resonance (NMR) experiments using the polarized nuclear-spin system with a goniometer. In order to perform the DNP and NMR procedures in different magnetic fields, the DNP system and the NMR system are spatially separated, between which the sample can be shuttled while its orientation is controlled in a reproducible fashion. We demonstrate that the system developed in this work is operational for solid-state NMR with hyperpolarized nuclear-spin systems in static organic materials, and also discuss the application of our system.
Numerical approach to time-dependent quantum transport and dynamical Kondo transition
Authors: Zheng Xiao , Jin Jinshuang , Welack Sven , Luo Meng , Yan YiJing
Published: April 2009

An accurate and efficient numerical approach is developed for the transient electronic dynamics of open quantum systems at low temperatures. The calculations are based on a formally exact hierarchical equations of motion quantum dissipation theory [J. S. Jin et al., J. Chem. Phys. 128, 234703 (2008)]. We propose a hybrid scheme that combines the Matsubara expansion technique and a frequency dispersion treatment to account for reservoir correlation functions. The new scheme not just admits various forms of reservoir spectral functions but also greatly reduces the computational cost of the resulting hierarchical equations, especially in the low temperature regime. Dynamical Kondo effects are obtained and the cotunneling induced Kondo transitions are resolved in the transient current in response to time-dependent external voltages.
Assembly dynamics of two-β sheets revealed by molecular dynamics simulations
Authors: Xu Weixin , Ping Jiang , Li Weifeng , Mu Yuguang
Published: April 2009

The assembly dynamics of two β sheets with different initial separation distances are explored by multiple all-atom molecular dynamics simulations with the presence of explicit water solvent. The β sheet is composed of seven identical peptides in an antiparallel fashion. The peptide sequence is the 20–29 segment of human Islet amyloid polypeptide. Our simulations show that the assembly occurs not only in the lateral direction but also along the longitudinal direction, which provides a new insight into the assembly pathway at the early stage of fibril elongation. Based on Poisson–Boltzmann free energy analysis and quasiharmonic configuration entropy estimation, the entropic contribution is found to play an important role in the longitudinal assembly. Moreover, a possible oligomeric state with cyclic form is suggested based on one assembly model found in the simulations, illustrating the polymorphic nature of aggregation of the amyloidogenic peptide.
Nondestructive detection of hidden chemical compounds with laser Compton-scattering gamma rays
Authors: Hayakawa Takehito , Ohgaki Hideaki , Shizuma Toshiyuki , Hajima Ryoichi , Kikuzawa Nobuhiro , Minehara Eisuke , Kii Toshiteru , Toyokawa Hiroyuki
Published: April 2009

A nondestructive assay method for measuring a shielded chemical compound has been proposed. The chemical compound is measured by using a nuclear resonance fluorescence (NRF) measurement technique with an energy tunable laser Compton-scattering (LCS) γ-ray source. This method has an advantage that hidden materials can be detected through heavy shields such as iron plates of a thickness of several centimeters. A detection of a chemical compound of melamine, C3H6N6, shielded by 15-mm-thick iron and 4-mm-thick lead plates is demonstrated. The NRF γ-rays of C12 and N14 of the melamine are measured by using the LCS γ-rays of the energies of up to 5.0 MeV. The observed ratio (C12/N14)exp=0.39±0.12 is consistent with (C/N)melamine=0.5.
Numerical results for the Ar and CF4 mixture gas in a dual frequency capacitively coupled plasma using a hybrid model
Authors: Bi Zhen-Hua , Dai Zhong-Ling , Xu Xiang , Li Zhi-Cheng , Wang You-Nian
Published: April 2009

A one dimensional hybrid model has been proposed to study the Ar and CF4 mixture gas in a dual-frequency (DF) capacitively coupled plasma. To achieve the more precise spatiotemporal distributions of the electric field and ions flux, the ion momentum equations are adopted instead of the drift-diffusion model with the effective electric field approximation. By adjusting DF sources, the evolutions of ions densities, ion energy distributions, and ion angular distributions are obtained and the modulation effects are discussed. Finally, the comparison between the simulation and experimental result shows that the hybrid model could qualitatively describe the characteristic of the mixtures in less time, which will be more promising in two dimensional and three dimensional simulations.
Temperature-dependent photoluminescence and electron field emission properties of AlN nanotip arrays
Authors: Ji X. H. , Zhang Q. Y. , Lau S. P. , Jiang H. X. , Lin J. Y.
Published: April 2009

Large-scale single-crystalline AlN nanotip arrays have been fabricated via a facile catalysis-free approach using AlCl3 powder and NH3 as starting materials. These nanotips exhibit an intense broad ultraviolet emission centered at 3.28 eV. The field emission features a notable electron current with a low turn-on field. The turn-on and threshold electric field are found to decrease substantially from 7.7 to 3.9 V/μm and 7.9 to 4.1 V/μm, respectively, while the estimated field enhancement factor increases from 483 to 1884 with increasing the ambient-temperature from room temperature to 573 K. The dependence of the photoluminescence and electron field emission with temperature and the possible mechanism involved has systematically been investigated and thus discussed.
Depth resolution of piezoresponse force microscopy
Authors: Johann Florian , Ying Yongjun J. , Jungk Tobias , Hoffmann Ákos , Sones Collin L. , Eason Robert W. , Mailis Sakellaris , Soergel Elisabeth
Published: April 2009

Given that a ferroelectric domain is generally a three dimensional entity, the determination of its area as well as its depth is mandatory for full characterization. Piezoresponse force microscopy (PFM) is known for its ability to map the lateral dimensions of ferroelectric domains with high accuracy. However, no depth profile information has been readily available so far. Here, we have used ferroelectric domains of known depth profile to determine the dependence of the PFM response on the depth of the domain, and thus effectively the depth resolution of PFM detection.
Organic/inorganic hybrid solar cells with vertically oriented ZnO nanowires
Authors: Liu Junpeng , Wang Shanshan , Bian Zuqiang , Shan Meina , Huang Chunhui
Published: April 2009

Hybrid photovoltaic (PV) devices based on copper-phthalocyanine and fullerene combined with ZnO nanowire array as direct charge transport paths were fabricated. The optimized device with ZnO nanowire has a more than fourfold increase in PV performance than the device without nanowire. The former has an open circuit voltage of 0.46 V, a short circuit current of 3.86 mA/cm2, a fill factor of 0.30, and a power conversion efficiency of 0.53%. The hybrid device based on ZnO nanowires with improved PV performance suggests a way for fabrication of PV device with more exciton dissociation interface area and continuous carrier transport paths.
Sustainable Urban Form and Residential Development Viability
Authors: Jones Colin , Leishman Chris , MacDonald Charlotte
Published: April 2009

Arguments about sustainable urban form have generally been in normative terms without recourse to its practicality. The paper shows that the essential elements of urban form are outcomes of real estate markets. The focus of the research is to examine the economic sustainability constraints to the adaptation of the existing urban form via housing market development viability. To address the task a number of econometric models are linked together to estimate spatial patterns of viability in five cities. The results demonstrate a substantial difference between cities that can be attributed not to urban form per se but to socioeconomic factors. This demonstrates that in practice it is impossible to divorce the physical structure of cities from their economic and social structure. Viability is also influenced strongly by public policy through the location of social housing. The research suggests that a driving force/constraint for development viability is the level of neighbourhood house prices. Large swathes of negative viability are found even without accounting for the additional costs of brownfield development, suggesting that there are major constraints to the reconfiguration of housing markets in some cities in a piecemeal way.
The Everyday and the Episodic: The Spatial and Political Impacts of Urban Informality
Authors: Kudva Neema
Published: April 2009

Informality, understood either as an economic sector or as a form of shelter and service provision, dominates Southern cities, even as disciplinary divides dominate the study of informality and its impacts. The author seeks to move beyond these divides by focusing on the production of urban space under different structural conditions in two Indian cities, Delhi and Ahmedabad. Using a Lefebvrian theoretical framework, the author examines existing literature to unpack the mutually constitutive political and spatial practices of informality. The segregated spaces thus produced can be linked to a politics of informality that includes not just everyday resistance and creeping encroachments to achieve gains, but also episodic moments of open protest, collective mobilization, and violence. In highlighting these impacts, production of space theories also open up the question of generating knowledge for new sites of resistance.
Students in Cities: A Preliminary Analysis of Their Patterns and Effects
Authors: Munro Moira , Turok Ivan , Livingston Mark
Published: April 2009

This paper adds to a growing literature on the impacts of the growth in student numbers in the UK, by focusing explicitly on their spatial residential patterns and impacts on labour markets in cities. It shows that students are typically highly residentially concentrated and statistically the population of students shows a high degree of segregation from nonstudents. Turnover within student neighbourhoods is argued to be sufficiently high to cause significant neighbourhood and community disruption in many cities. Students are also shown to have very distinct labour-market characteristics, being highly concentrated within particular sectors and types of occupation. Here too they have the potential for wider impacts, including displacement effects in relation to other local young people from entry-level jobs and increasing the flexibilisation of working practices. Students are also distinctive in apparently being able to find work if they wish to, although the evidence suggests that this is probably marginally easier in more buoyant labour markets. There is much unexplained variation between cities, though, which suggests the need for more detailed local work.
‘Going Away to Uni’: Mobility, Modernity, and Independence of English Higher Education students
Authors: Holdsworth Clare
Published: April 2009

Recent changes in English higher education (HE) admissions policies and financial support have sought to increase diversity among university entrants. It is anticipated that, as more young people from different backgrounds choose to go to university, a greater proportion will choose to study at local higher education institutions (HEIs), rather than move away. I review the evidence for a trend to more localised study among English HE students. Analysis of admissions data shows that HE expansion has been concomitant with less interregional student mobility. However, despite the fact that a smaller proportion of students are moving away to university, the expectation that going to university means moving away continues to shape students' experiences of and attitudes to university life. I unpack the taken-for-granted assumptions about student mobility and transitions to independence and adulthood. Drawing on analysis of interview data with students, I explore how assumptions about student mobilities are socially and culturally coconstituted and how student mobility has become established as an elite practice within English HE.
Urban Politics and the Production of Capital Mobility in the United States
Authors: Pendras Mark
Published: April 2009

In the quest to explain changing urban political economic conditions over the past thirty years urban researchers have naturalized capital mobility, to the point where challenging the mobility of capital appears either impossible, undesirable, or both. In this paper I aim to denaturalize capital mobility and to repoliticize the relationship between capital and place through a critical legal geographic investigation of corporate mobility rights in the United States. The overall goal is to help urban researchers to think critically about the politics of capital mobility and to ensure that the legal principles enabling capital mobility remain open to challenge from alternative political perspectives.