bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence attribution in the UniProt Knowledgebase
Authors: Magrane Michele , Consortium UniProt
Published: April 2009

UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system and plans for its future development and enhancement will be presented.
Cardiovascular Gene Ontology Annotation Initiative
Authors: Khodiyar Varsha , Barrell Daniel , Scambler Peter , Hubank Mike , Apweiler Rolf , Talmud Philippa , Lovering Ruth
Published: April 2009

Gene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional annotation to proteins across a wide range of species ("www.geneontology.org":http://www.geneontology.org). The BHF-UCL team is funded by the British Heath Foundation to supply GO annotation specifically for human proteins involved in cardiovascular (CV) processes. This is the first time that a physiological process-centered approach has been used for human protein GO annotation. Experienced GO curators from the BHF-UCL team work alongside the bench scientists from the CV genetics group at University College London. By working in a CV dedicated environment the GO curators are able to build up their expertise in the CV field. Over 4000 proteins have been identified as being cardiovascular related and over the last 14 months, the BHF-UCL team has added 6840 Gene Ontology annotations to 603 human CV related proteins, including CDKN2A, CDKN2B, EDN2, GH1 and TERF1. In order to provide detailed annotations the BHF-UCL GO curators also initiate the development of new GO terms related to cardiovascular processes. The development of these terms, such as lipoprotein-mediated signalling, regulation of cardiac muscle hypertrophy and cardiac epithelial to mesenchymal transition, are made in collaboration with the GO editorial office and CV scientists. We will present details of the progress made in the first year of the BHF-UCL GO annotation project and the impact on microarray analysis.
Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Authors: Köhn Dagmar , Le Novère Nicolas , Knüpfer Christian
Published: April 2009

Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of models.For this purpose we propose two ontologies: The Kinetic Simulation Algorithm Ontology (KiSAO) and the TErminology for the Description of DYnamics (TEDDY). KiSAO covers algorithms used for simulation of computational models. The ontology classifies and puts into context existing simulation algorithms. For the classification, it uses several criteria such as deterministic/stochastic or spatial/nonspatial. The aim of TEDDY is to provide terms for describing and characterising dynamical behaviours, observable dynamical phenomena, and control elements of biological models and biological systems in Systems Biology and Synthetic Biology.We demonstrate how these new ontologies can extend the formalisation of models beyond structure, using the well-known repressilator model as an example. The simulation results depend pragmatically on the used algorithm: We compare the simulation results of the deterministic Livermore solver for ordinary differential equations (KiSAO:0000071) to the simulation results of the stochastic Gibson and Bruck’s next reaction method (KiSAO:0000027). The simulation results depend dynamically on the parameter setting: While parameter * (maximum number of produced proteins per promotor) is increased the modelled dynamical system undergoes a Supercritical Hopf Bifurcation (TEDDY_0000074). Below the critical value of * the system exhibits _Damped Oscillation_ (TEDDY_0000063) converging to a Stable Spiral Point (TEDDY_0000126). Above the bifurcation the system possesses a Stable _Limit Cycle_ (TEDDY_0000114), i.e. it shows Sustained Oscillation. The Negative Feedback (TEDDY_0000034) of the system is a necessary precondition for the ability of the system to oscillate.For details on KiSAO see the "MIASE project page":http://sourceforge.net/projects/miase, for details on TEDDY see the "project page":http://sourceforge.net/projects/teddyontology.
Data submission and curation for caArray, a standard based microarray data repository system
Authors: Bian X , Klemm J , Basu A , Hadfield J , Srinivasa R , Parnell T , Miller S , Mason W , Kokotov D , Duncan M , Duvall P , Gurses L , Boal T , Misquitta L , Swan D , Wysong R , Klink A , Johnson A , Fontenay G , Liu J , Colbert M , Komatsoulis G
Published: April 2009

caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG™), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG™. Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the MAGE-TAB, a spreadsheet-based format for annotating and communicating microarray data in a MIAME-compliant fashion ("http://www.mged.org/mage-tab":http://www.mged.org/mage-tab). MAGE-TAB is built on community standards – MAGE, MIAME, and Ontology. The components and work flow of MAGE-TAB files are organized in such a way which is already familiar to bench scientists and thus minimize the time and frustration of reorganizing their data before submission. The MAGE-TAB files are also structured to be machine readable so that they can be easily parsed into database. Users can control public access to experiment- and sample-level data and can create collaboration groups to support data exchange among a defined set of partners. All data submitted to caArray at NCI will go through strict curation by a group of scientists against these standards to make sure that the data are correctly annotated using proper controlled vocabulary terms and all required information are provided. Two of mostly used ontology sources are MGED ontology ("http://mged.sourceforge.net/ontologies/MGEDontology.php":http://mged.sourceforge.net/ontologies/MGEDontology.php) and NCI thesaurus ("http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do":http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). The purpose of data curation is to ensure easy comparison of results from different labs and unambiguous report of results. Data will also undergo automatic validation process before parsed into database, in which minimum information requirement and data consistency with the array designs are checked. Files with error found during validation are flagged with error message. Curators will re-examine those files and make necessary corrections before re-load the files. The iteration repeats until files are validated successfully. Data are then imported into the system and ready for access through the portal or through API. Interested parties are encouraged to review the installation package, documentation, and source code available from "http://caarray.nci.nih.gov":http://caarray.nci.nih.gov.
Standards and infrastructure for managing experimental metadata
Authors: Sansone Susanna-Assunta , Rocca-Serra Philippe
Published: April 2009

*See also "related poster":http://precedings.nature.com/documents/3144/version/1*Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the "MIBBI":http://www.mibbi.org project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development^1^. More than 60 groups participate in the "OBO Foundry":http://www.obofoundry.org ^2^, which coordinates the orthogonal development of ontologies such as "OBI":http://obi-ontology.org for describing experimental (meta)data. And several groups participate in the development of "ISA-Tab":http://isatab.sf.net, a tabular framework for presenting experimental metadata^3^ (analogous to "FuGE":http://fuge.sf.net, a generic data model to underpin various XML file formats^4^).We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.View the "public instance":http://www.ebi.ac.uk/bioinvindex of our ISA-based infrastructure, running at EBI, and/or "download the components":http://isatab.sf.net for your local use.*References*1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.net
An Ontology To Represent Knowledge On Animal Testing Alternatives
Authors: Wächter Thomas , Sauer Ursula , Doms Andreas , Grune Barbara , Alvers Michael , Spielmann Horst , Schroeder Michael
Published: April 2009

EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R ("www.Go3R.org":http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in the planning, authorisation and performance of animal experiments to determine the availability of alternative methods in a fast and comprehensive manner. The technical basis of this search engine is specific 3Rs expert knowledge captured within the Go3R Ontology containing 87,218 labels and synonyms. A total of 16,620 concepts were structured in 28 branches, where 1,227 concepts were newly defined to specifically describe directly 3Rs relevant knowledge. Additionally relevant headings from MeSH where referenced to reflect the topics associated with the definition of Animal Testing Alternatives. Therefore it is distinguished between thematic-defining and directly 3Rs relevant branches. In addition to the assignment of direct parent-child relationships, further relationship types were introduced to allow to model 3Rs relevant domain knowledge. Examples for such knowledge are e.g. (1) the characteristics of cell culture tests methods, which usually utilize “specific cell types” or “cell lines” and are associated with a specific “endpoint” and “endpoint detection method” or (2) named test methods like “PREDISAFE™”, which replaces an animal test namely the “eye irritation test” in rabbits and uses specific cells namely “SIRC Cells” or (3) the “Haemagglutinin-Neuraminidase Protein Assay”, which detects a protein of the “Newcastle disease virus”. Thereby, an article in which e.g. a specific 3Rs method is not explicitly mentioned could still be recognized as relevant for the specific topic searched for in an indirect manner, for example if it mentions specific cells, endpoints or endpoint detection methods, which are relevant for the respective application. The search engine Go3R with its novel ontology is already well recognized by the 3Rs community and will be further maintained and developed.
Laboratory experiments simulating solar wind driven magnetospheres
Authors: Brady P. , Ditmire T. , Horton W. , Mays M. L. , Zakharov Y.
Published: April 2009

Magnetosphere-solar wind interactions are simulated in a laboratory setting with a small permanent magnet driven by two types of supersonic plasma wind sources. The first higher speed, shorter duration plasma wind is from a laser blow-off plasma while the second longer duration, lower speed plasma wind is produced with a capacitor discharge driven coaxial electrode creating plasma jets. The stand off distance of the solar wind from the magnetosphere was measured to be 1.7±0.3 cm for the laser-produced plasma experiment and 0.87±0.03 cm for the coaxial electrode plasma experiment. The stand off distance of the plasma was calculated using data from HYADES [J. T. Larsen and S. M. Lane, J. Quant. Spectrosc. Radiat. Transf. 51, 179 (1994)] as 1.46±0.02 cm for the laser-produced plasma, and estimated for the coaxial plasma jet as rmp=0.72±0.07 cm. Plasma build up on the poles of the magnets, consistent with magnetosphere systems, was also observed.
H
3
+
+
H
2
isotopic system at low temperatures: Microcanonical model and experimental study
Authors: Hugo Edouard , Asvany Oskar , Schlemmer Stephan
Published: April 2009

State-to-state thermal rate coefficients for reactions of all H3++H2 isotopic variants are derived and compared to new experimental data. The theoretical data are also sought for astrochemical modeling of cold environments (<50K). The rates are calculated on the basis of a microcanonical approach using the Langevin model and the conservation laws of mass, energy, angular momentum, and nuclear spin. Full scrambling of all five nuclei during the collision is assumed for the calculations and alternatively partial dynamical restrictions are considered. The ergodic principle of the collision is employed in two limiting cases, neglecting (weak ergodic limit) or accounting for explicit degeneracies of the reaction mechanisms (strong ergodic limit). The resulting sets of rate coefficients are shown to be consistent with the detailed balance and thermodynamical equilibrium constants. Rate coefficients, k(T), for the deuteration chain of H3+ with HD as well as H2D+∕H3+ equilibrium ratios have been measured in a variable temperature 22-pole ion trap. In particular, the D2H++HD→D3++H2 rate coefficient indicates a change in reaction mechanism when going to higher temperatures. The good overall agreement between experiment and theory encourages the use of the theoretical predictions for astrophysical modeling.
Tailoring the work function of indium tin oxide electrodes in electrophosphorescent organic light-emitting diodes
Authors: Sharma Asha , Hotchkiss Peter J. , Marder Seth R. , Kippelen Bernard
Published: April 2009

We investigate the use of organic surface modifiers based on phosphonic acid anchoring groups that react with the surface of indium tin oxide (ITO) in order to modify its work function, surface energy, and the charge injection in organic multilayer electrophosphorescent devices. The phosphonic acid surface modifiers, possessing different substituting groups, are found to tune the work function of ITO in the range of 4.40–5.40 eV. These surface modifiers have been tested as an interfacial layer between the ITO anode and hole transport layers (HTL) that are either processed from the vapor phase or from solution. The use of this interfacial layer with a solution-processible HTL results in high quantum and luminous efficiencies of 20.6% and 68 cd/A at 100 cd/m2 (17.5% and 60 cd/A at 1000 cd/m2). The enhanced performance of the devices incorporating phosphonic acid modifiers could be associated with an improved charge injection and a better compatibility with the hydrophobic nature of the organic layer. The performance of these devices is also compared to that of devices in which ITO is modified with other well-known techniques such as air plasma treatment or the use of a layer of poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate).
Coupling light from an organic light emitting diode (OLED) into a single-mode waveguide: Toward monolithically integrated optical sensors
Authors: Ramuz Marc , Bürgi Lukas , Stanley Ross , Winnewisser Carsten
Published: April 2009

Evanescent coupling is used to couple light from a polymer light emitting diode (PLED) into a planar single-mode waveguide. The PLED is monolithically integrated on top of the waveguide in a stacked configuration. Due to the waveguide’s proximity, the emission zone of the PLED and the waveguide modes overlap substantially, so that the PLED can directly excite the modes. An additional spacer layer between PLED and waveguide is shown to improve the coupling efficiency by about a factor of 5. For iridium-based diodes PLED-to-waveguide coupling efficiencies of as high as 3.2% have been obtained.
Effect of oxygen concentration on nanoindentation-induced phase transformations in ion-implanted amorphous silicon
Authors: Ruffell S. , Vedi J. , Bradby J. E. , Williams J. S. , Haberl B.
Published: April 2009

The effect of the local oxygen concentration in ion-implanted amorphous Si (a-Si) on nanoindentation-induced phase transformations has been investigated. Implantation of oxygen into the a-Si films has been used to controllably introduce an approximately constant concentration of oxygen, ranging from ∼1018 to ∼1021 cm−3, over the depth range of the phase transformed zones. Nanoindentation was performed under conditions that ensure a phase transformed zone composed completely of Si-III/XII in the nominally oxygen-free a-Si. The effect of the local oxygen concentration has been investigated by analysis of the unloading curves, Raman microspectroscopy, and cross-sectional transmission electron microscopy (XTEM). The formation of Si-III/XII is suppressed with increasing oxygen concentration, favoring a greater volume of a-Si within the zones. The Raman microspectroscopy and XTEM verify that the volume of Si-III/XII decreases with increasing O concentration. With the smaller volumes of Si-III/XII, the pop-out normally observed on load versus penetration depth curves during unloading decreases in magnitude, becoming more kinklike and is barely discernable at high concentrations of oxygen. The probability of forming any high pressure phases is reduced from 1 to ∼0.1 for a concentration of 1021 cm−3. We suggest that the bonding of O with Si reduces the formation of Si-III/XII during unloading through a similar mechanism to that of oxygen-retarded solid phase crystallization of a-Si.
Synthesis of ultrathin carbon films by direct current filtered cathodic vacuum arc
Authors: Zhang H.-S. , Komvopoulos K.
Published: April 2009

Filtered cathodic vacuum arc was used to synthesize ultrathin carbon films on silicon substrates. The depth profiles, near-surface chemical composition, fractions of tetrahedral (sp3) and trigonal (sp2) carbon atom hybridizations, roughness, and hardness of the carbon films were determined from Monte Carlo (T-DYN) simulations and x-ray reflectivity (XRR), x-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and surface force microscopy (SFM) measurements, respectively. Films of thickness of only a few nanometers possessed smaller sp3 fractions than much thicker films. The effective hardness was found to depend on the sp3 fraction and silicon-carbon composition profile. The formation of different carbon atom bonds, film growth mechanisms, and optimum process conditions for synthesizing ultrathin carbon films are interpreted in the context of T-DYN, XRR, XPS, AFM, and SFM results and surface bombardment, adsorption, and diffusion mechanisms.
Orientational ordering in solid C60 fullerene-cubane
Authors: Verberck Bart , Vliegenthart Gerard A. , Gompper Gerhard
Published: April 2009

We study the structure and phase behavior of fullerene-cubane C60⋅C8H8 by Monte Carlo simulation. Using a simple potential model capturing the icosahedral and cubic symmetries of its molecular constituents, we reproduce the experimentally observed phase transition from a cubic to an orthorhombic crystal lattice and the accompanying rotational freezing of the C60 molecules. We elaborate a scheme to identify the low-temperature orientations of individual molecules and to detect a pattern of orientational ordering similar to the arrangement of C60 molecules in solid C60. Our configuration of orientations supports a doubled periodicity along one of the crystal axes.
Variational symplectic algorithm for guiding center dynamics and its application in tokamak geometry
Authors: Qin Hong , Guan Xiaoyin , Tang William M.
Published: April 2009

A variational symplectic integrator for the guiding center motion of charged particles in general magnetic fields is developed to enable accurate long-time simulation studies of magnetized plasmas. Instead of discretizing the differential equations of the guiding center motion, the action of the guiding center motion is discretized and minimized to obtain the iteration rules for advancing the dynamics. The variational symplectic integrator conserves exactly a discrete Lagrangian symplectic structure and globally bounds the numerical error in energy by a small number for all simulation time steps. Compared with standard integrators, such as the fourth order Runge–Kutta method, the variational symplectic integrator has superior numerical properties over long integration time. For example, in a two-dimensional tokamak geometry, the variational symplectic integrator is able to guarantee the accuracy for both the trapped and transit particle orbits for arbitrarily long simulation time. This is important for modern large-scale simulation studies of fusion plasmas where it is critical to use algorithms with long-term accuracy and fidelity. The variational symplectic integrator is expected to have a wide range of applications.
Numerical investigation of the stability of bubble train flow in a square minichannel
Authors: Öztaskin Murat C. , Wörner Martin , Soyhan Hakan S.
Published: April 2009

The stability of a train of equally sized and variably spaced gas bubbles that move within a continuous wetting liquid phase through a straight square minichannel is investigated numerically by a volume-of-fluid method. The flow is laminar and cocurrent upward and driven by a pressure gradient and buoyancy. The simulations start from fluid at rest with two identical bubbles placed on the axis of the computational domain, the size of the bubbles being comparable to that of the channel. In vertical direction, periodic boundary conditions are used. These result in two liquid slugs of variable length, depending on the initial bubble-to-bubble distance. The time evolution of the length of both liquid slugs during the simulation indicates if the bubble train flow is “stable” (equal terminal length of both liquid slugs) or “unstable” (contact of both bubbles). Several cases are considered, which differ with respect to bubble size, domain size, initial bubble shape, and separation. All cases lead to axisymmetric bubbles with the capillary number in the range of 0.11–0.23. The results show that a recirculation pattern develops in the liquid slug when its length exceeds a critical value that is about 10%–20% of the channel width. If a recirculation pattern exists in both liquid slugs, then the bubble train flow is stable. When there is a recirculation pattern in one liquid slug and a bypass flow in the other, the bubble train flow may be stable or not depending on the local flow field in the liquid slugs close to the channel centerline. These results suggest that a general criterion for the stability of bubble train flow cannot be formulated in terms of the capillary and Reynolds number only, but must take into account the length of the liquid slug.
Intense laser-plasma interactions: New frontiers in high energy density physics
Authors: Norreys P. A. , Beg F. N. , Sentoku Y. , Silva L. O. , Smith R. A. , Trines R. M. G. M.
Published: April 2009

A review is presented here of a number of invited papers presented at the 2008 American Physical Society April meeting [held jointly with High Energy Density Physics/High Energy Density Laboratory Astrophysics (HEDP/HEDLA) Conference] devoted to intense laser-matter interactions. They include new insights gained from wave-kinetic theory into laser-wakefield accelerators and drift wave turbulence interacting with zonal flows in magnetized plasmas; interactions with cluster media for the generation of radiative blast waves; fast electron energy transport in cone-wire targets; numerical investigations into Weibel instability in electron-positron-ion plasmas and the generation of gigabar pressures with thin foil interactions.
Stellar explosions, instabilities, and turbulence
Authors: Drake R. P. , Kuranz C. C. , Miles A. R. , Muthsam H. J. , Plewa T.
Published: April 2009

It has become very clear that the evolution of structure during supernovae is centrally dependent on the pre-existing structure in the star. Modeling of the pre-existing structure has advanced significantly, leading to improved understanding and to a physically based assessment of the structure that will be present when a star explodes. It remains an open question whether low-mode asymmetries in the explosion process can produce the observed effects or whether the explosion mechanism somehow produces jets of material. In any event, the workhorse processes that produce structure in an exploding star are blast-wave driven instabilities. Laboratory experiments have explored these blast-wave-driven instabilities and specifically their dependence on initial conditions. Theoretical work has shown that the relative importance of Richtmyer–Meshkov and Rayleigh–Taylor instabilities varies with the initial conditions and does so in ways that can make sense of a range of astrophysical observations.
Frontiers of the physics of dense plasmas and planetary interiors: Experiments, theory, and applications
Authors: Fortney J. J. , Glenzer S. H. , Koenig M. , Militzer B. , Saumon D. , Valencia D.
Published: April 2009

Recent developments of dynamic x-ray characterization experiments of dense matter are reviewed, with particular emphasis on conditions relevant to interiors of terrestrial and gas giant planets. These studies include characterization of compressed states of matter in light elements by x-ray scattering and imaging of shocked iron by radiography. Several applications of this work are examined. These include the structure of massive “super-Earth” terrestrial planets around other stars, the 40 known extrasolar gas giants with measured masses and radii, and Jupiter itself, which serves as the benchmark for giant planets.
Theoretical study of the electronic states of CuCl2
Authors: Zou Wenli , Boggs James E.
Published: April 2009

The electronic states of the CuCl2 molecule are studied by several theoretical methods. We report geometries, excitation energies, vibrational frequencies, rotational constants, and transition dipole moments. With the purpose to describe the correlation energy accurately enough, a set of diffuse secondary 3d′ orbitals is introduced, thus resulting in a large active space of 21 electrons in 17 orbitals. By restricting the active space and selecting dominant configurations, the results of the general multireference second-order perturbation theory with this large active space agree very well with the experimental ones. It is found that the so-called Π2u state is asymmetric linear and the Σ2u+ state is bent at the minima on their adiabatic potential energy surfaces, whereas the other five gerade states are centrosymmetric linear. After including the spin-orbit coupling, the (I)Π2g3/2–(I)Π2g1/2 splitting is computed to be 415 cm−1, in excellent agreement with the experimental value of about 480 cm−1.
Determination of energy band gap of nanocrystalline SbSI using diffuse reflectance spectroscopy
Authors: Nowak M. , Kauch B. , Szperlich P.
Published: April 2009

Twelve methods of determining energy band gap (Eg) of semiconductors using diffuse reflectance spectroscopy have been applied in investigations of sonochemically produced antimony sulfoiodide (SbSI) consisting of nanowires. It has been proved that the best method of determining Eg is based on simultaneous fitting of many mechanisms of absorption to the spectral dependence of Kubelka–Munk function evaluated from the diffuse reflectance data. It allows determining the values of indirect forbidden Eg, the Urbach energy, and the constant absorption/scattering of the examined semiconductor.
Self collimation of ultrasound in a three-dimensional sonic crystal
Authors: Soliveres Ester , Espinosa Víctor , Pérez-Arjona Isabel , Sánchez-Morcillo Víctor J. , Staliunas Kestutis
Published: April 2009

We present the experimental demonstration of self-collimation (subdiffractive propagation) of an ultrasonic beam inside a three-dimensional (3D) sonic crystal. The crystal is formed by two crossed steel cylinders structures in a woodpilelike geometry disposed in water. Measurements of the 3D field distribution show that a narrow beam, which diffractively spreads in the absence of the sonic crystal, is strongly collimated in propagation inside the crystal, demonstrating the 3D self-collimation effect.
A one-dimensional dipole lattice model for water in narrow nanopores
Authors: Köfinger Jürgen , Hummer Gerhard , Dellago Christoph
Published: April 2009

We present a recently developed one-dimensional dipole lattice model that accurately captures the key properties of water in narrow nanopores. For this model, we derive three equivalent representations of the Hamiltonian that together yield a transparent physical picture of the energetics of the water chain and permit efficient computer simulations. In the charge representation, the Hamiltonian consists of nearest-neighbor interactions and Coulomb-like interactions of effective charges at the ends of dipole ordered segments. Approximations based on the charge picture shed light on the influence of the Coulomb-like interactions on the structure of nanopore water. We use Monte Carlo simulations to study the system behavior of the full Hamiltonian and its approximations as a function of chemical potential and system size and investigate the bimodal character of the density distribution occurring at small system sizes.
Diffusion mechanism and the thermal stability of fluorine ions in GaN after ion implantation
Authors: Wang M. J. , Yuan L. , Chen K. J. , Xu F. J. , Shen B.
Published: April 2009

The diffusion mechanisms of fluorine ions in GaN are investigated by means of time-of-flight secondary ion mass spectrometry. Instead of incorporating fluorine ions close to the sample surface by fluorine plasma treatment, fluorine ion implantation with an energy of 180 keV is utilized to implant fluorine ions deep into the GaN bulk, preventing the surface effects from affecting the data analysis. It is found that the diffusion of fluorine ions in GaN is a dynamic process featuring an initial out-diffusion followed by in- diffusion and the final stabilization. A vacancy-assisted diffusion model is proposed to account for the experimental observations, which is also consistent with results on molecular dynamic simulation. Fluorine ions tend to occupy Ga vacancies induced by ion implantation and diffuse to vacancy rich regions. The number of continuous vacancy chains can be significantly reduced by a dynamic thermal annealing process. As a result, strong local confinement and stabilization of fluorine ions can be obtained in GaN crystal, suggesting excellent thermal stability of fluorine ions for device applications.
Stability properties of free-electron laser in Raman regime with thermal electron beam
Authors: Chakhmachi A. , Maraghechi B.
Published: April 2009

In the context of kinetic theory an expression for the growth rate of a free-electron laser, under the weak resonance instability condition, for full dispersion relation has been obtained. The space-charge potential is included in the analysis and the expression for growth rate reduces to that of the Compton regime under the low density condition. With the assumption of a spread in the longitudinal momentum in the form of a Gaussian distribution function, the effect of the thermal electron beam on the growth rate is studied. The results are compared to another linear theory, a computer simulation, and an experiment.
Magnetic properties of single crystalline Co nanowire arrays with different diameters and orientations
Authors: Huang X. H. , Li G. H. , Dou X. C. , Li L.
Published: April 2009

Single crystalline Co nanowire arrays with different diameters and orientations were grown within porous anodic alumina membranes by a pulsed electrodeposition technique and the magnetic properties of the nanowire were systematically studied. It was found that the magnetization behavior of the Co nanowire arrays is anisotropic and their magnetic properties can be effectively modulated through tuning either the diameter or the orientation of the nanowires. The magnetic properties of the Co nanowires were discussed qualitatively by using the classical magnetization theory and single domain model.
Deposition of silicon dioxide films using an atmospheric pressure microplasma jet
Authors: Raballand V. , Benedikt J. , Hoffmann S. , Zimmermann M. , von Keudell A.
Published: April 2009

Organic and inorganic silicon dioxide films have been deposited by means of an atmospheric pressure microplasma jet. Tetramethylsilane (TMS), oxygen, and hexamethyldisiloxane (HMDSO) are injected into argon as plasma forming gases. In the case of TMS injection, inorganic films are deposited if an admixture of oxygen is used. In the case of HMDSO injection, inorganic films can be deposited at room temperature even without any oxygen admixture: at low HMDSO flow rates [<0.1 SCCM (SCCM denotes cubic centimeters per minute at STP),<32 ppm], the SiOxHz films contain no carbon and exhibit oxygen-to-silicon ratio close to 2 according to x-ray photoelectron spectroscopy. At high HMDSO flow rates (>0.1 SCCM,>32 ppm), SiOxCyHz with up to 21% of carbon are obtained. The transition from organic to inorganic film is confirmed by Fourier transform infrared spectroscopy. The deposition of inorganic SiO2 films from HMDSO without any oxygen admixture is explained by an ion-induced polymerization scheme of HMDSO.
Effect of interfacial roughness correlation on diffuse scattering intensity in a neutron supermirror
Authors: Maruyama R. , Yamazaki D. , Ebisawa T. , Soyama K.
Published: April 2009

Neutron supermirrors are increasingly important devices for transporting, bending, and focusing neutron beams. Reflected neutrons from a supermirror are divided into specular and off-specular (diffuse) components. Suppression of the diffuse component is important since it reduces the signal-to-noise ratio, a serious problem when a supermirror is used in a focusing system for purposes such as small angle scattering measurements. The diffuse intensity can be decreased by more than one order of magnitude by adopting NiC/Ti multilayers instead of conventional Ni/Ti multilayers. In order to obtain insight into the mechanism that controls the diffuse intensity from a supermirror, the crystal structure of Ni and NiC monolayers and the interface structure of Ni/Ti and NiC/Ti multilayers were investigated. The crystallite size in the NiC monolayer was found to be smaller than that in the Ni monolayer by a factor of 4.1 by x-ray diffraction measurement. The interface structure of the Ni/Ti and NiC/Ti multilayers was observed by neutron reflectivity and diffuse intensity measurements. For the NiC/Ti multilayer, the lateral correlation length was smaller by a factor of 3.6 than for the Ni/Ti multilayer, whereas the vertical correlation length was greater by a factor exceeding 25. Diffuse intensity calculations based on the distorted wave Born approximation revealed that these differences explain the difference between the diffuse intensity of the Ni/Ti and NiC/Ti supermirrors. This study demonstrated that a multilayer with a large vertical correlation length and a small lateral correlation length effectively suppresses the diffuse intensity from a supermirror.
S
-band relativistic magnetron operation with an active plasma cathode
Authors: Hadas Y. , Sayapin A. , Kweller T. , Krasik Ya. E.
Published: April 2009

Results of experimental research on a relativistic S-band magnetron with a ferroelectric plasma source as a cathode are presented. The cathode plasma was generated using a driving pulse (∼3 kV, 200 ns) applied to the ferroelectric cathode electrodes via inductive decoupling prior to the beginning of an accelerating pulse (200 kV, 150 ns) delivered by a linear induction accelerator. The magnetron and generated microwave radiation parameters obtained for the ferroelectric plasma cathode and the explosive emission plasma were compared. It was shown that the application of the ferroelectric plasma cathode allows one to avoid a time delay in the appearance of the electron emission to achieve a better matching between the magnetron and linear induction accelerator impedances and to increase significantly (∼30%) the duration of the microwave pulse with an ∼10% increase in the microwave power. The latter results in the microwave radiation generation being 30% more efficient than when the explosive emission cathode is used, where efficiency does not exceed 20%.
Coupled magnetostatic and electromagnetic oscillations in hexaferrite-dielectric heterostructures
Authors: Popov Maksym A. , Zavislyak Igor V. , Srinivasan Gopalan , Zagorodnii Volodymyr V.
Published: April 2009

The observation of coupled magnetostatic-electromagnetic oscillations over 60–75 GHz in strontium hexaferrite-quartz structures is reported. Data on frequencies of the modes have been obtained as a function of the bias magnetic field and quantitatively analyzed for two cases: when ferrite or quartz is in contact with waveguide wall. Mode repulsion is observed over a 50% wider frequency range for the case of ferrite in contact with the metal than for the case when quartz is in contact with the metal waveguide. A model is developed for the coupled oscillations and theoretical mode frequencies are in very good agreement with the data. Estimated Q-factor for the coupled modes shows significant and unique variation with the bias magnetic field in the mode repulsion region.
A physics-based model of electrical conduction decrease with time in amorphous Ge2Sb2Te5
Authors: Boniardi M. , Redaelli A. , Pirovano A. , Tortorelli I. , Ielmini D. , Pellizzer F.
Published: April 2009

The time-stability of the electrical characteristics of chalcogenide materials is one of the most important issues for their use in nonvolatile solid state memory applications. In particular the electrical conduction of the glassy phase evolves with time due to two different physical phenomena: the crystallization and the so-called low conductivity drift. Despite the physics of crystallization having been extensively studied in literature, the latter is mainly described by phenomenological relationships, and its physical comprehension is still under discussion. In this paper we study the amorphous phase low-field conductivity drift and its dependence on the temperature experienced by the device. We developed an experimental procedure able to separate the reversible change in the electrical conductivity with temperature due to the material semiconductorlike behavior from the nonreversible one related to the drift mechanism. A drift model explaining such nonreversible conductivity change as a band diagram modification is also provided and calibrated on experimental data. The present work finally introduces alternative metrics for drift quantification that can be useful in order to compare different materials.
The optical and vibrational properties of dominant defects in undoped ZnO: A first-principles study
Authors: Hu J. , Pan B. C.
Published: April 2009

Studying native defects in semiconductors is of crucial importance for understanding the nature of defects as well as for controlling the quality of the as-grown materials. In this work, we present theoretical studies on the electronic structures, optical and vibrational properties of the dominant defects (VO, HO and VZn) in nominally undoped wurtzite ZnO. We find that the imaginary parts of dielectric functions and absorption coefficient arising from these defects show different features. Typically, the existence of VO in bulk ZnO makes it transparent for visible light but not for violet light. For the cases of both HO and VZn, there are strong infrared absorptions. On the other hand, the vibrational frequencies associated with these defects are calculated, from which some typical vibrational modes relevant to the defects are revealed.
Tzitzeica solitons versus relativistic Calogero–Moser three-body clusters
Authors: Nimmo J. J. C. , Ruijsenaars S. N. M.
Published: April 2009

We establish a connection between the hyperbolic relativistic Calogero–Moser systems and a class of soliton solutions to the Tzitzeica equation (also called the Dodd–Bullough–Zhiber–Shabat–Mikhailov equation). In the 6N-dimensional phase space Ω of the relativistic systems with 2N particles and N antiparticles, there exists a 2N-dimensional Poincaré-invariant submanifold ΩP corresponding to N free particles and N bound particle-antiparticle pairs in their ground state. The Tzitzeica N-soliton tau functions under consideration are real valued and obtained via the dual Lax matrix evaluated in points of ΩP. This correspondence leads to a picture of the soliton as a cluster of two particles and one antiparticle in their lowest internal energy state.
Capillary filling in centrifugally actuated microfluidic devices with dynamically evolving contact line motion
Authors: Chakraborty Debapriya , Gorkin Robert , Madou Marc , Kulinsky Lawrence , Chakraborty Suman
Published: April 2009

In the present work, we analyze the capillary filling dynamics in centrifugally actuated microfluidic platforms with dynamically evolving contact line motion for wetting fluids. Special attention is devoted to estimate the effects of variable hydraulic resistances over different flow regimes. Dynamics of the meniscus advancement within the rotating microchannel turns out to be typically nonlinear, in tune with the relative instantaneous strengths of the capillary forces, centrifugal forces, and viscous resistances. Detailed dynamical characteristics of the meniscus evolution are obtained from the approximate semianalytical and full-scale numerical solutions, and are found to agree well with the experimental findings on lab-on-a-compact disk arrangements.
Thermoelectric properties of bismuth based cobalt-rhodium oxides with hexagonal (Co,Rh)O2 layers
Authors: Okada Satoshi , Sakai Akihiro , Kanno Tsutomu , Yotsuhashi Satoshi , Adachi Hideaki
Published: April 2009

We have investigated the thermoelectric properties of Co and Rh mixed solid solutions Bi1.7Ba2(Co1−zRhz)2Oα (0≤z≤1) with hexagonal (Co,Rh)O2 layers. Partial substitution of Rh for Co in the hexagonal layers resulted in higher electric resistivity than in Bi1.7Ba2Co2Oα and Bi1.7Ba2Rh2Oα endmembers. We believe this to be due to the uneven charge distribution by the difference in ionic energy between Co and Rh. Thermal conductivity in Co/Rh mixed Bi1.7Ba2(Co0.5Rh0.5)2Oα showed lower values than those of endmembers. However, owing to its high resistivity, the thermoelectric performance of Bi1.7Ba2(Co0.5Rh0.5)2Oα did not exceed the values of endmembers at room temperature.
Studies on metal/n-GaAs Schottky barrier diodes: The effects of temperature and carrier concentrations
Authors: Mangal Sutanu , Banerji P.
Published: April 2009

Metal/Semiconductor Schottky diodes were fabricated to study the effect of temperature and carrier concentrations on diode parameters, such as ideality factor and barrier heights. The diodes were formed on the epitaxial layers of metal organic chemical vapor deposition (MOCVD) grown n-GaAs with metals such as Al, Pd, and Zn–Pd deposited onto n-GaAs by thermal evaporation technique. Trimethyl gallium and AsH3 were used as Ga and As precursors, respectively, to grow GaAs on semi-insulating GaAs substrates at 600 °C and H2S was used for n-type doping in a horizontal reactor atmospheric pressure MOCVD system. The Schottky diodes were characterized by forward bias current-voltage measurements in the temperature range 130–300 K and capacitance-voltage measurement at room temperature and diode parameters such as ideality factor and barrier height have been evaluated. It is found that the Schottky barrier height decreases with decrease in temperature while the ideality factor increases. It is also observed that the barrier height increases linearly with the applied forward bias voltage and the rate of change of barrier height with voltage increases for higher carrier concentration of the semiconductor. The carrier concentration of n-GaAs was chosen in the regime 1×1016–8.2×1016 cm−3 so that the depletion region extends inside the semiconductor and the diode can be used as a III–V photovoltaic device.