bluuebunny/crossref_metadata_2025 huggingface dataset:
Selection and transfer of individual plasmon-resonant metal nanoparticles
Authors: Tanaka Yoshito , Sasaki Keiji
Published: February 2010

We present a simple method for selecting a single metal nanoparticle with desired localized surface plasmon (LSP) characteristics from particle ensembles on one surface and then transferring it to another surface. The LSP of individual nanoparticles is characterized using a microspectroscopy system. An atomic force microscope mounted on the optical microscope achieves particle capture and release with the chemically modified probe.
Designed synthesis of materials for high-sensitivity geomagnetic sensors
Authors: Ding L. , Teng J. , Wang X. C. , Feng C. , Jiang Y. , Yu G. H. , Wang S. G. , Ward R. C. C.
Published: February 2010

A structure of Ta/MgO/NiFe/MgO/Ta was designed and synthesized, which combines the advantages of both tunnel magnetoresistance materials with high magnetic field sensitivity and anisotropic magnetoresistance materials with high directional sensitivity. The magnetoresistance ratio in the device with structure of Ta(5)/MgO(4)/NiFe(10)/MgO(3)/Ta(3) (thicknesses in nanometers) increases with an increase in annealing temperature, reaching a maximum value of 3.5% at 450 °C, and then decreases with a further increase in annealing temperature. Meanwhile, a high sensitivity of 2.1%/Oe is obtained. The higher magnetoresistance ratio and sensitivity come from the significant specular reflection of electrons at both interfaces due to the crystalline MgO layer together with the sharp interfaces with the NiFe layer.
High-efficiency, large-bandwidth silicon-on-insulator grating coupler based on a fully-etched photonic crystal structure
Authors: Liu Liu , Pu Minhao , Yvind Kresten , Hvam Jørn M.
Published: February 2010

A grating coupler for interfacing between single-mode fibers and photonic circuits on silicon-on-insulator is demonstrated. It consists of columns of fully etched photonic crystal holes, which are made in the same lithography and etching processes used for making the silicon-on-insulator wire waveguide. The holes have a diameter of around 143 nm, and are defined with electron-beam lithography. A peak coupling efficiency of 42% at 1550 nm and 1 dB bandwidth of 37 nm, as well as a low back reflection, are achieved. The performance of the proposed fully etched grating coupler is comparable to that based on the conventional shallowly etched grating, which needs additional fabrication steps.
Indistinguishability and interference in the coherent control of atomic and molecular processes
Authors: Gong Jiangbin , Brumer Paul
Published: February 2010

The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible “which-way” information due to quantum entanglement established in the quantum dynamics. Because quantum interference between independent pathways to the same target state occurs only when the independent pathways are indistinguishable, it is first shown that creating useful coherence between nondegenerate states of a molecule for subsequent quantum interference manipulation cannot be achieved by collisions between atoms or molecules that are prepared in momentum and energy eigenstates. Coherence can, however, be transferred from light fields to atoms or molecules. Using a particular coherent control scenario, it is shown that this coherence transfer and the subsequent coherent phase control can be readily realized by the most classical states of light, i.e., coherent states of light. It is further demonstrated that quantum states of light may suppress the extent of phase-sensitive coherent control by leaking out some which-way information while “incoherent interference control” scenarios proposed in the literature have automatically ensured the indistinguishability of multiple excitation pathways. The possibility of quantum coherence in photodissociation product states is also understood in terms of the disentanglement between photodissociation fragments. Results offer deeper insights into quantum coherence generation in atomic and molecular processes.
Hot electron transport and impact ionization in the narrow energy gap InAs1−xNx alloy
Authors: Makarovsky O. , Feu W. H. M. , Patanè A. , Eaves L. , Zhuang Q. D. , Krier A. , Beanland R. , Airey R.
Published: February 2010

We report an experimental study of hot electron dynamics in the narrow band gap dilute nitride alloy, InAs1−xNx, with x up to 0.6%. The sharp increase in the conductivity of n-type InAs1−xNx at applied electric fields above 1 kV/cm demonstrates that impact ionization dominates the hot electron dynamics. This observation, combined with the reduction in the band gap energy by the N-atoms, suggest prospects for the use of this narrow gap alloy in infrared avalanche photodiodes.
Ultrafast nanotube based diffusiophoresis nanomotors
Authors: Liu Wei , He Rongxiang , Zhu Hongwei , Hu Hao , Li Meiya , Zhao Xing-zhong
Published: February 2010

Nanomotors represent a significant step forward in nanotechnology, and prove that nanotubes and other nanostructures several hundred times smaller than the diameter of a human hair can be manipulated and assembled into true devices. In this letter, nanotubes based nanomotors are reported. The nanomotors were observed to move at a velocity of ∼0.5 m/s, which is several orders of magnitude faster than current nanomotors. Concentration difference energy was thought to provide the main motive forces to drive these nanomotors. This phenomenon which is seldom observed at macroscopic scale, is common in microscale, and can be employed to explain some motions of nano- and microscale objects.
The absorption spectrum of hydrogenated silicon carbide nanocrystals from ab initio calculations
Authors: Vörös Márton , Deák Péter , Frauenheim Thomas , Gali Adam
Published: February 2010

The electronic structure and absorption spectrum of hydrogenated silicon carbide nanocrystals (SiC NCs) have been determined by first principles calculations. We show that the reconstructed surface can significantly change not just the onset of absorption but the shape of the spectrum at higher energies. We compare our results with two recent experiments on ultrasmall SiC NCs.
Translational and rotational friction on a colloidal rod near a wall
Authors: Padding J. T. , Briels W. J.
Published: February 2010

We present particulate simulation results for translational and rotational friction components of a shish-kebab model of a colloidal rod with aspect ratio (length over diameter) L/D=10 in the presence of a planar hard wall. Hydrodynamic interactions between rod and wall cause an overall enhancement of the friction tensor components. We find that the friction enhancements to reasonable approximation scale inversely linear with the closest distance d between the rod surface and the wall, for d in the range between D/8 and L. The dependence of the wall-induced friction on the angle θ between the long axis of the rod and the normal to the wall is studied and fitted with simple polynomials in cos θ.
Cross-sectional magnetic force microscopy of MnAs/GaAs(001)
Authors: Salles B. Rache , Marangolo M. , David C. , Girard J. C.
Published: February 2010

We investigate the magnetic domain structure and stray field of MnAs/GaAs(001) thin films by magnetic force microscopy of the growth surface and of cleavage edges. The strong uniaxial magnetic anisotropy of MnAs makes the magnetic properties very similar to those of a rectangular bar magnet with constant magnetization along the easy axis direction. By analytical calculations we estimate the out-of-plane magnetic stray field component acting on electrons injected by a MnAs contact into a GaAs-based device.
Facile fabrication and biological application of tin-rich indium tin oxide nanorods
Authors: Kumar Nitin , Parajuli Omkar , Feng Man , Xu Jian , Hahm Jong-in
Published: February 2010

We demonstrate that one-dimensional indium tin oxide nanorods (ITO NRs) with high tin-incorporation ratio can be readily produced with a very good control over size and morphology using a gas-phase synthetic approach. Our current study presents a straightforward and facile growth route to synthesize ITO NRs with the atomic composition ratio of In:Sn:O (1:1:2). We further identified and assessed a promising potential application of these tin-rich InSnO2 NRs in biomolecular fluorescence assays. As-grown InSnO2 NRs showed a promising result for potential application in the fluorescence detection of protein molecules.
Multiferroic heterostructure fringe field tuning of meander line microstrip ferrite phase shifter
Authors: Geiler A. L. , Gillette S. M. , Chen Y. , Wang J. , Chen Z. , Yoon S. D. , He P. , Gao J. , Vittoria C. , Harris V. G.
Published: February 2010

Magnetic fringe fields emanating from a multiferroic heterostructure composite of Terfenol-D and lead magnesium niobate-lead titanate were utilized to actively tune a meander line microstrip ferrite phase shifter operating above ferrimagnetic resonance at C-band. Differential phase shifts of 65° were measured when tuned with an applied voltage to the multiferroic heterostructure. This demonstration of magnetoelectric field generation provides an alternative approach to tuning broadband planar microwave magnetic devices where neither strain nor direct electromagnetic coupling is experienced between device and multiferroic transducer.
Graphene mode-lockers for fiber lasers functioned with evanescent field interaction
Authors: Song Yong-Won , Jang Sung-Yeon , Han Won-Suk , Bae Mi-Kyung
Published: February 2010

Employing graphene as an intracavity passive power modulating element, we demonstrate the efficient laser pulsation in high pulse-energy regime with evanescent field interaction between the propagating light and graphene layer. Graphene is prepared by the solution based reduction of graphene oxide, and dispersed homogeneously into the water for spray onto an all-fiber substrate, side-polished fiber. With the intracavity power up to 21.41 dBm, we ensure the robust high-energy operation without any thermal damage of graphene. Resultant output pulses have center wavelength, spectral width, and repetition rate of 1561.6 nm, 1.96 nm, and 6.99 MHz, respectively.
Negative differential resistance in GaN nanowire network
Authors: Dragoman M. , Konstantinidis G. , Cismaru A. , Vasilache D. , Dinescu A. , Dragoman D. , Neculoiu D. , Buiculescu R. , Deligeorgis G. , Vajpeyi A. P. , Georgakilas A.
Published: February 2010

Negative differential resistance of gallium nitride nanowire networks deposited on an interdigitated electrode configuration patterned on a silicon dioxide/high resistivity Si substrate is experimentally demonstrated at room temperature. This effect is attributed to tunnelling between crossed gallium nitride nanowires.
Structural and compositional dependence of gadolinium-aluminum oxide for the application of charge-trap-type nonvolatile memory devices
Authors: Park Youngmin , Park Jong Kyung , Song Myeong Ho , Lim Sung Kyu , Oh Jae Sub , Joo Moon Sig , Hong Kwon , Cho Byung Jin
Published: February 2010

The structural and compositional dependence of gadolinium-aluminum oxide (GdAlO) for application to nonvolatile memory is investigated. An addition of Gd into AlO reduces the leakage current, which improves the erase window. The GdAlO film crystallizes into many different phases after annealing depending on the Gd percentage when the amount of Gd exceeds 49%. The crystallization of the GdAlO film causes a change in the band gap of the GdAlO film, resulting in a change of the retention properties. It is also found that crystallized GdAlO is more vulnerable to the generation of traps by electrical stress. The results indicate that careful optimization of the Gd percentage in GdAlO is necessary to utilize the benefit of GdAlO with minimum deterioration in the charge retention property.
Herringbone buckling patterns of anisotropic thin films on elastomeric substrates
Authors: Song J.
Published: February 2010

Highly ordered herringbone buckling patterns have been observed in stiff thin films on elastomeric substrates under an equibiaxial compression. Existing mechanics models assume the thin film to be isotropic, which does not agree with recent experiments of single crystal thin films (e.g., silicon) on elastomeric substrates, where the film has cubic symmetry with anisotropic material properties. A theoretical model for herringbone buckling patterns of anisotropic thin films on elastomeric substrates is developed in this paper. The prediction of the buckling directions agrees well with experiments. The approximation of the use of isotropic material properties is also analyzed.
Spatial distribution of two-dimensional electron gas in a ZnO/Mg0.2Zn0.8O heterostructure probed with a conducting polymer Schottky contact
Authors: Nakano M. , Tsukazaki A. , Ueno K. , Gunji R. Y. , Ohtomo A. , Fukumura T. , Kawasaki M.
Published: February 2010

A ZnO/Mg0.2Zn0.8O heterostructure was characterized at T=2 K through capacitance measurements with using a conducting polymer, poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS), as a Schottky contact. The Nyquist diagram, which is the trajectory curve of the complex impedance vector, appeared to be an excellent semicircular shape, implying that the PEDOT:PSS/ZnO/Mg0.2Zn0.8O junction can be described with an equivalent single RC parallel circuit. Capacitance-voltage characteristics elucidate the existence of a two-dimensional electron gas, where 1019 cm−3 electrons are confined within 5 nm at the ZnO/Mg0.2Zn0.8O heterointerface.
Transport in organic semiconductors in large electric fields: From thermal activation to field emission
Authors: Worne J. H. , Anthony J. E. , Natelson D.
Published: February 2010

Understanding charge transport in organic semiconductors in large electric fields is relevant to many applications. We present transport measurements in organic field-effect transistors based on poly(3-hexylthiophene) and 6,13-bis(triisopropyl-silylethynyl) (TIPS) pentacene with short channels, from room temperature down to 4.2 K. Near 300 K transport in both systems is well described by thermally assisted hopping with Poole–Frenkel-type enhancement of the mobility. At low temperatures and large gate voltages, transport in both materials becomes nearly temperature independent, crossing over into field-driven tunneling. These data, particularly in TIPS-pentacene, show that great caution must be exercised when considering more exotic (e.g., Tomonaga–Luttinger liquid) interpretations of transport.
Negative differential resistance and rectifying behaviors in phenalenyl molecular device with different contact geometries
Authors: Fan Zhi-Qiang , Chen Ke-Qiu
Published: February 2010

The electronic transport properties in phenalenyl molecular device are studied by using nonequilibrium Green’s functions in combination with the density-functional theory. The results show that the electronic transport properties are strongly dependent on the contact geometry. The negative differential resistance behavior with large peak to valley ratio is observed when the molecule contacts the Au electrodes through two second-nearest sites or one second-nearest site and one third-nearest site, while the rectifying performance is observed only when the molecule contacts the Au electrodes through one second-nearest site and one third-nearest site. The mechanisms are proposed for these phenomena.
Gyrotropic photonic crystal waveguide switches
Authors: Wu Z. , Levy Miguel , Fratello V. J. , Merzlikin A. M.
Published: February 2010

Functional photonic crystals fabricated in iron garnet films are shown to provide magnetically-controllable optical switching. Transverse-electric and transverse-magnetic stop band separation in conjunction with optical gyrotropy are utilized to selectively block and transmit near-infrared light in waveguide geometries. Geometrical birefringence allows the simultaneous low- and high-birefringence in different modes necessary to create band gap separation and effective magneto-optic gyrotropy in a single device.
Low-voltage indium gallium zinc oxide thin film transistors on paper substrates
Authors: Lim Wantae , Douglas E. A. , Norton D. P. , Pearton S. J. , Ren F. , Heo Young-Woo , Son S. Y. , Yuh J. H.
Published: February 2010

We have fabricated bottom-gate amorphous (α-) indium-gallium-zinc-oxide (InGaZnO4) thin film transistors (TFTs) on both paper and glass substrates at low processing temperature (≤100 °C). As a water and solvent barrier layer, cyclotene (BCB 3022–35 from Dow Chemical) was spin-coated on the entire paper substrate. TFTs on the paper substrates exhibited saturation mobility (μsat) of 1.2 cm2 V−1 s−1, threshold voltage (VTH) of 1.9 V, subthreshold gate-voltage swing (S) of 0.65 V decade−1, and drain current on-to-off ratio (ION/IOFF) of ∼104. These values were only slightly inferior to those obtained from devices on glass substrates (μsat∼2.1 cm2 V−1 s−1, VTH∼0 V, S∼0.74 V decade−1, and ION/IOFF=105–106). The uneven surface of the paper sheet led to relatively poor contact resistance between source-drain electrodes and channel layer. The ability to achieve InGaZnO TFTs on cyclotene-coated paper substrates demonstrates the enormous potential for applications such as low-cost and large area electronics.
Interface induced band gap reduction and electron transfer in semiconducting carbon nanotube
Authors: Hossain M. Zubaer
Published: February 2010

Ab initio study of a carbon nanotube-SiO2 interface reveals that the energetic preference for the nanotube to bind on particular sites on the O-terminated surface differs substantially from that on the Si-terminated surface. Besides, the chemical reactivity at the interface leads to electron-transfer from the nanotube to the dielectric substrate, and distorts the nanotube’s homogeneous distribution of electrons. The interaction also initiates substantial reduction in the band gap of the nanotube, as it approaches the surface.
Genomic code for
Sox10
activation reveals a key regulatory enhancer for cranial neural crest
Authors: Betancur Paola , Bronner-Fraser Marianne , Sauka-Spengler Tatjana
Published: February 2010

The neural crest is a multipotent, stem cell-like population that migrates extensively in the embryo and forms a wide array of derivatives, ranging from neurons to melanocytes and cartilage. Analyses of the gene regulatory network driving neural crest development revealed
Sox10
as one of the earliest neural crest-specifying genes, cell-autonomously driving delamination and directly regulating numerous downstream effectors and differentiation gene batteries. In search of direct inputs to the neural crest specifier module, we dissected the chick
Sox10
genomic region and isolated two downstream regulatory regions with distinct spatiotemporal activity. A unique element, Sox10E2 represents the earliest-acting neural crest
cis
-regulatory element, critical for initiating
Sox10
expression in newly formed cranial, but not vagal and trunk neural crest. A second element, Sox10E1, acts in later migrating vagal and trunk crest cells. Deep characterization of Sox10E2 reveals Sox9, Ets1, and cMyb as direct inputs mediating enhancer activity. ChIP, DNA-pull down, and gel-shift assays demonstrate their direct binding to the Sox10E2 enhancer in vivo, whereas mutation of their corresponding binding sites, or inactivation of the three upstream regulators, abolishes both reporter and endogenous
Sox10
expression. Using
cis
-regulatory analysis as a tool, our study makes critical connections within the neural crest gene regulatory network, thus being unique in establishing a direct link of upstream effectors to a key neural crest specifier.
ArabidopsisIWS1 interacts with transcription factor BES1 and is involved in plant steroid hormone brassinosteroid regulated gene expression
Authors: Li Lei , Ye Huaxun , Guo Hongqing , Yin Yanhai
Published: February 2010

Plant steroid hormones, brassinosteroids (BRs), regulate essential growth and developmental processes. BRs signal through membrane-localized receptor BRI1 and several other signaling components to regulate the BES1 and BZR1 family transcription factors, which in turn control the expression of hundreds of target genes. However, knowledge about the transcriptional mechanisms by which BES1/BZR1 regulate gene expression is limited. By a forward genetic approach, we have discovered thatArabidopsis thalianaInteract-With-Spt6 (AtIWS1), an evolutionarily conserved protein implicated in RNA polymerase II (RNAPII) postrecruitment and transcriptional elongation processes, is required for BR-induced gene expression. Loss-of-function mutations inAtIWS1lead to overall dwarfism inArabidopsis, reduced BR response, genome-wide decrease in BR-induced gene expression, and hypersensitivity to a transcription elongation inhibitor. Moreover, AtIWS1 interacts with BES1 both in vitro andin vivo.Chromatin immunoprecipitation experiments demonstrated that the presence of AtIWS1 is enriched in transcribed as well as promoter regions of the target genes under BR-induced conditions. Our results suggest that AtIWS1 is recruited to target genes by BES1 to promote gene expression during transcription elongation process. Recent genomic studies have indicated that a large number of genes could be regulated at steps after RNAPII recruitment; however, the mechanisms for such regulation have not been well established. The study therefore not only establishes an important role for AtIWS1 in plant steroid–induced gene expression but also suggests an exciting possibility that IWS1 protein can function as a target for pathway-specific activators, thereby providing a unique mechanism for the control of gene expression.
Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor–dependent signaling pathways in renal collecting duct cells
Authors: Rinschen Markus M. , Yu Ming-Jiun , Wang Guanghui , Boja Emily S. , Hoffert Jason D. , Pisitkun Trairak , Knepper Mark A.
Published: February 2010

Vasopressin’s action in renal cells to regulate water transport depends on protein phosphorylation. Here we used mass spectrometry–based quantitative phosphoproteomics to identify signaling pathways involved in the short-term V2-receptor–mediated response in cultured collecting duct cells (mpkCCD) from mouse. Using Stable Isotope Labeling by Amino acids in Cell culture (SILAC) with two treatment groups (0.1 nM dDAVP or vehicle for 30 min), we carried out quantification of 2884 phosphopeptides. The majority (82%) of quantified phosphopeptides did not change in abundance in response to dDAVP. Analysis of the 273 phosphopeptides increased by dDAVP showed a predominance of so-called “basophilic” motifs consistent with activation of kinases of the AGC family. Increases in phosphorylation of several known protein kinase A targets were found. In addition, increased phosphorylation of targets of the calmodulin-dependent kinase family was seen, including autophosphorylation of calmodulin-dependent kinase 2 at T286. Analysis of the 254 phosphopeptides decreased in abundance by dDAVP showed a predominance of so-called “proline-directed” motifs, consistent with down-regulation of mitogen-activated or cyclin-dependent kinases. dDAVP decreased phosphorylation of both JNK1/2 (T183/Y185) and ERK1/2 (T183/Y185; T203/Y205), consistent with a decrease in activation of these proline-directed kinases in response to dDAVP. Both ERK and JNK were able to phosphorylate residue S261of aquaporin-2 in vitro, a site showing a decrease in phosphorylation in response to dDAVP in vivo. The data support roles for multiple vasopressin V2-receptor–dependent signaling pathways in the vasopressin signaling network of collecting duct cells, involving several kinases not generally accepted to regulate collecting duct function.
Close association of RNA polymerase II and many transcription factors with Pol III genes
Authors: Raha Debasish , Wang Zhong , Moqtaderi Zarmik , Wu Linfeng , Zhong Guoneng , Gerstein Mark , Struhl Kevin , Snyder Michael
Published: February 2010

Transcription of the eukaryotic genomes is carried out by three distinct RNA polymerases I, II, and III, whereby each polymerase is thought to independently transcribe a distinct set of genes. To investigate a possible relationship of RNA polymerases II and III, we mapped their in vivo binding sites throughout the human genome by using ChIP-Seq in two different cell lines, GM12878 and K562 cells. Pol III was found to bind near many known genes as well as several previously unidentified target genes. RNA-Seq studies indicate that a majority of the bound genes are expressed, although a subset are not suggestive of stalling by RNA polymerase III. Pol II was found to bind near many known Pol III genes, including tRNA, U6, HVG, hY, 7SK and previously unidentified Pol III target genes. Similarly, in vivo binding studies also reveal that a number of transcription factors normally associated with Pol II transcription, including c-Fos, c-Jun and c-Myc, also tightly associate with most Pol III-transcribed genes. Inhibition of Pol II activity using α-amanitin reduced expression of a number of Pol III genes (e.g., U6, hY, HVG), suggesting that Pol II plays an important role in regulating their transcription. These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression.
Centromere-localized breaks indicate the generation of DNA damage by the mitotic spindle
Authors: Guerrero Astrid Alonso , Gamero Mercedes Cano , Trachana Varvara , Fütterer Agnes , Pacios-Bras Cristina , Díaz-Concha Nuria Panadero , Cigudosa Juan Cruz , Martínez-A. Carlos , van Wely Karel H. M.
Published: February 2010

Most carcinomas present some form of chromosome instability in combination with spindle defects. Numerical instability is likely caused by spindle aberrations, but the origin of breaks and translocations remains elusive. To determine whether one mechanism can bring about both types of instability, we studied the relationship between DNA damage and spindle defects. Although lacking apparent repair defects, primary
Dido
mutant cells formed micronuclei containing damaged DNA. The presence of centromeres showed that micronuclei were caused by spindle defects, and cell cycle markers showed that DNA damage was generated during mitosis. Although the micronuclei themselves persisted, the DNA damage within was repaired during S and G2 phases. DNA breaks in
Dido
mutant cells regularly colocalized with centromeres, which were occasionally distorted. Comparable defects were found in
APC
mutant cell lines, an independent system for spindle defects. On the basis of these results, we propose a model for break formation in which spindle defects lead to centromere shearing.
Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome
Authors: Amemiya Chris T. , Powers Thomas P. , Prohaska Sonja J. , Grimwood Jane , Schmutz Jeremy , Dickson Mark , Miyake Tsutomu , Schoenborn Michael A. , Myers Richard M. , Ruddle Francis H. , Stadler Peter F.
Published: February 2010

The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a “living fossil.” An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth
Latimeria menadoensis
. Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species.
Intrinsic reactivity and driving force dependence in concerted proton–electron transfers to water illustrated by phenol oxidation
Authors: Bonin Julien , Costentin Cyrille , Louault Cyril , Robert Marc , Routier Mathilde , Savéant Jean-Michel
Published: February 2010

Three experimental techniques, laser flash photolysis, redox catalysis, and stopped-flow, were used to investigate the variation of the oxidation rate constant of phenol in neat water with the driving force offered by a series of electron acceptors. Taking into account a result previously obtained with a low–driving force electron acceptor thus allowed scanning more than half an electron-volt driving force range. Variation of the rate constant with pH showed the transition between a direct phenol oxidation reaction at low pH, where the rate constant does not vary with pH, and a stepwise reaction involving the prior deprotonation of phenol by OH
-
, characterized by a unity-slope variation. Analyses of the direct oxidation kinetics, based on its variation with the driving force and on the determination of H/D isotope effects, ruled out a stepwise mechanism in which electron transfer is followed by the deprotonation of the initial cation radical at the benefit of a pathway in which proton and electron are transferred concertedly. Derivation of the characteristics of counterdiffusion in termolecular reactions allowed showing that the concerted process is under activation control. It is characterized by a remarkably small reorganization energy, in line with the electrochemical counterpart of the reaction, underpinning the very peculiar behavior of water as proton acceptor when it is used as the solvent.
Calculation of the magnetization oscillation frequency in a nanostructured synthetic ferrimagnet
Authors: Lee Jong Min , Lee K-J , Lim S H
Published: February 2010

Theoretical equations were derived for the resonance frequency of magnetization oscillation in a nanostructured synthetic ferrimagnet in the framework of a single domain model. The theoretical equations, which are applicable to various magnetization alignments including a spin flop, were then tested using a micromagnetic simulation in both the macrospin and microspin models. Excellent agreement was obtained between the results of the theoretical prediction and micromagnetic simulation in the macrospin model over the entire range of applied magnetic fields, confirming the validity of the theoretical equations derived in this study. The agreement between the results from the theoretical prediction and the micromagnetic simulation in the microspin model was not excellent, particularly in the acoustic mode, showing a substantial deviation from the ideal single domain behaviour. However, good agreement was obtained by decreasing the magnetization component in the thickness direction by 10% of that in the single domain state. This suggests that the magnetization deviates slightly from the single domain state as the magnetization moves out of the film plane during a magnetization oscillation.
Optical and electrical characterizations of cerium oxide thin films
Authors: Chiu Fu-Chien , Lai Chih-Ming
Published: February 2010

The optical dielectric function of cerium oxide (CeO2) was characterized by the spectroscopic ellipsometry (SE) technique using the Kramers–Kronig relation and the Tauc–Lorentz (TL) dispersion model. Experimental results showed that the bandgap energy and refractive index at 632.8 nm of CeO2 are about 3.23 ± 0.05 eV and 2.33 ± 0.08, respectively. Based on the optical properties, the electrical conduction mechanisms in CeO2 thin films are determined to be Schottky emission in a medium electric field (0.5–1.6 MV cm−1) from 350 to 500 K and Poole–Frenkel emission in a high electric field (>2.36 MV cm−1) from 450 to 500 K. Accordingly, the conduction band offsets between Al and CeO2 and the trap energy level are about 0.62 ± 0.01 eV and 1.53 ± 0.01 eV, respectively.
Proton-implanted optical channel waveguides in Nd : YAG laser ceramics
Authors: Tan Yang , Chen Feng
Published: February 2010

We report on the fabrication of optical channel waveguides in Nd : YAG ceramics by multi-energy proton implantation at a total dose of 8 × 1016 ions cm−2. The modal distribution of the guided modes obtained from numerical calculation was in good agreement with the experimental result. The propagation loss of the waveguide was determined to be ∼4 dB cm−1 after post-annealing up to 400 °C in air. Confocal micro-photoluminescence experiments have revealed relevant changes in the Nd spectroscopic properties in the waveguide's active volume. These changes include line broadening and shifting as well as a clear luminescence quenching, which were attributed to the strong structural modifications induced by the high-dose proton implantation.
Charge storage characteristics of high density Mo nanocrystal embedded in silicon oxide and silicon nitride
Authors: Lin Chao-Cheng , Chang Ting-Chang , Tu Chun-Hao , Chen Shih-Ching , Hu Chih-Wei , Sze Simon M , Tseng Tseung-Yuen , Chen Sheng-Chi , Lin Jian-Yang
Published: February 2010

We investigated the formation and charge storage characteristics of Mo nanocrystals in silicon oxide and in silicon nitride by rapid thermal annealing of oxygen- and nitrogen-incorporated Mo and Si mixed layers. A high density of Mo nanocrystal (6 × 1012 cm−2) was formed in the nitrogen-incorporated layer. Electrical analyses indicated that the memory window of the Mo nanocrystal embedded in the nitride is larger than that in the oxide. A reliability test showed that the Mo nanocrystal in the nitride has better reliability than the Mo nanocrystal in the oxide, which was explained by an electrical field simulation.
Electron-beam generated copper plasma: formation and cross-field propagation
Authors: Majumder A , Sahu G K , Thakur K B , Mago V K
Published: February 2010

In an evaporator, when a high-energy continuous electron beam impinges a copper target, it generates an atomic beam. It is observed that plasma is formed. The primary and the backscattered electrons from the surface of the target produce copper plasma by electron-impact ionization of the atoms. The plasma is of low temperature, weakly ionized and is present in a weak transverse magnetic field. The magnetic field is used to bend the electrons from the gun. The plasma flows in a direction that is perpendicular to the target surface and transverse to the magnetic field. The plasma expansion is weakly collisional. It decays along the flow direction due to cross-field diffusion.
Time resolved optical emission spectroscopy of an HPPMS coating process
Authors: Theiß S , Bibinov N , Bagcivan N , Ewering M , Awakowicz P , Bobzin K
Published: February 2010

This paper deals with the time resolved optical emission spectroscopy of a high power pulse magnetron sputtering (HPPMS) physical vapour deposition coating process. With an industrial coating unit CC800/9 HPPMS (CemeCon AG, Würselen) a (Cr,Al,Si)N coating was deposited. During the coating process, an absolute calibrated Echelle spectrometer (ESA-3000) measured the intensities of the spectral lines of chromium (Cr), aluminium (Al) and molecular bands of nitrogen (N2). Time resolved measurements enable us to calculate different parameters such as the average velocity of sputtered Al and Cr atoms or the internal plasma parameters electron density n
e and electron temperature kT
e with a time resolution of 20 µs. With these parameters, we determine the ionization rates of Al, Cr, Ar and Kr atoms and the deposition densities of Al and Cr atoms. Thus simulated deposition densities of 1.75 × 1020 m−2 s−1 for chromium and 1.7 × 1022 m−2 s−1 for aluminium are reached.
Theoretical and experimental determination of gas and electron temperatures for gas discharges in Ne and He mixtures with copper, bromine, hydrogen and strontium
Authors: Temelkov K A , Vuchkov N K , Freijo-Martin I , Ekov R P
Published: February 2010

Thermal conductivities of binary gas systems are calculated on the basis of 12-6 Lennard-Jones and rigid sphere inter-atomic interaction approximations for the case of gas discharges in He and Ne with small admixtures of copper, bromine, hydrogen and strontium. Assuming that the gas temperature varies only in the radial direction and using the calculated thermal conductivities, an analytical solution of the steady-state heat conduction equation is found for two discharge tube constructions. Two cases of uniform and non-uniform power input are considered. For both cases the average gas temperature is found by averaging the radial gas temperature distribution over the radius. Measurement of the relative intensities of some He and Ne spectral lines, originating from different upper levels, has enabled us to determine the average electron temperature.
Experimental determination and simulation of the angular distribution of the metal flux during magnetron sputter deposition
Authors: Horkel M , Van Aeken K , Eisenmenger-Sittner C , Depla D , Mahieu S , Leroy W P
Published: February 2010

To understand the film growth during magnetron sputter deposition a detailed knowledge of the flux of sputtered species from the target towards the substrate is vital. One important parameter is the angular distribution of the impinging neutral target atoms on the substrate, since it is responsible for, for example, self-shadowing effects. The determination of the angular distribution of the metal flux at an arbitrary point in the deposition chamber is achieved by a pinhole camera, where the information of the angular distribution is converted into a thickness profile. This paper describes the construction of such a pinhole camera which is capable of differential pumping, the determination of the angular distribution for a wide variety of target materials, and which can easily be inserted into a deposition chamber. The angular distributions of different materials (Cu, W, Al, Ti, Mg) at different parameters (pressure, lateral position and vertical position) are experimentally determined and compared with simulations obtained from a newly developed Monte Carlo code. It was also investigated whether parameters derived from the angular distribution are related to the degree of thermalization of the impinging particles.
Substrate-regulated morphology of graphene
Authors: Li Teng , Zhang Zhao
Published: February 2010

We delineate a general theoretical framework to determine the substrate-regulated graphene morphology through energy minimization. We then apply such a framework to study the graphene morphology on a substrate with periodic surface grooves. Depending on the substrate surface roughness and the graphene–substrate interfacial bonding energy, the equilibrium morphology of graphene ranges from (1) closely conforming to the substrate, to (2) remaining flat on the substrate. Interestingly, in certain cases, the graphene morphology snaps between the above two limiting states. Our quantitative results envision a promising strategy to precisely control the graphene morphology over large areas. The rich features of the substrate-regulated graphene morphology (e.g. the snap-through instability) can potentially lead to new design concepts of functional graphene device components.
Response of magnetron sputtered AlN films to controlled atmosphere annealing
Authors: Jose Feby , Ramaseshan R , Dash S , Bera S , Tyagi A K , Raj Baldev
Published: February 2010

The present investigation deals with the examination of the response of amorphous AlN films to post-deposition annealing environments such as high vacuum (HV) and nitrogen atmosphere (NA). The c/a ratio values from GIXRD for both cases are around 1.602. The XPS profile of NA-AlN shows a deficiency of nitrogen on the surface, whereas the oxygen impurity level is negligible in the case of NA compared with HV. The PL spectra substantiate the nitrogen vacancies in NA-AlN. The amorphous AlN exhibits a nanoindentation hardness of 18 GPa.
Chemically deposited Sb2S3 thin films for optical recording
Authors: Shaji S , Arato A , O'Brien J J , Liu J , Castillo G Alan , Palma M I Mendivil , Roy T K Das , Krishnan B
Published: February 2010

Laser induced changes in the properties of Sb2S3 thin films prepared by chemical bath deposition are described in this paper. Sb2S3 thin films of thickness 550 nm were deposited from a solution containing SbCl3 and Na2S2O3 at 27 °C for 5 h. These thin films were irradiated by a 532 nm continuous wave laser beam under different conditions at ambient atmosphere. X-ray diffraction analysis showed amorphous to polycrystalline transformation due to laser exposure of these thin films. Morphology and composition of these films were described. Optical properties of these films before and after laser irradiation were analysed. The optical band gap of the material was decreased due to laser induced crystallization. The results obtained confirm that there is further scope for developing this material as an optical recording media.
Spectral tuning of near-field radiative heat flux between two thin silicon carbide films
Authors: Francoeur Mathieu , Mengüç M Pinar , Vaillon Rodolphe
Published: February 2010

Spectral distributions of radiative heat flux between two thin silicon carbide films separated by sub-wavelength distances in vacuum are analysed. An analytical expression for the near-field flux between two layers of finite thicknesses in terms of film reflection and transmission coefficients is derived for the first time. The resulting equation clearly shows the resonant modes of thermal emission, absorption and the cross-coupling of surface phonon-polaritons (SPhPs) between the layers. When the films are of the same thickness, the resonant frequencies maximizing near-field thermal emission almost match those of absorption. The small discrepancies, due to SPhP coupling between the films, lead to loss of spectral coherence affecting mostly the low frequency mode. The flux profiles also show that splitting of the resonance into two distinct frequencies happens when the ratio thickness of the film over the separation gap is less than unity. When the thickness of one film increases relative to the other, spectral distributions of flux are significantly altered due to an important mismatch between the resonant frequencies of high emission and absorption. This modification of the near-field flux is mostly due to weaker SPhP coupling within the layer of increasing thickness. Based on an asymptotic analysis of the dispersion relation, an approximate approach is proposed to predict the resonant modes maximizing the flux between two films, which can be potentially extended to multiple thin layers. The outcome of this work would allow tailoring near-field radiative heat transfer, and can eventually be used to design customized nanostructures for energy harvesting applications.
The K-shell Auger electron spectrum of gadolinium obtained using neutron capture in a solid state device
Authors: Schultz David , Blasy Bryan , Santana Juan Colon , Young Chris , Petrosky J C , McClory J W , LaGraffe D , Brand J I , Tang Jinke , Wang Wendong , Schemm N , Balkir S , Bauer M , Ketsman I , Fairchild R W , Losovyj Ya B , Dowben P A
Published: February 2010

Highly doped or alloyed Gd2O3 in HfO2 films form heterojunction diodes with silicon. Single neutron capture events can be identified with a Hf0.85Gd0.15O1.93 to n-type silicon heterojunction. With long pulse integration times and suppression of the smaller pulses, there is agreement between the key pulse height spectral features and those predicted by Monte Carlo simulations. The latter align very well with the decay channels of the Gd following neutron capture, particularly those involving the Gd K-shell Auger electron resonances.
Cosmic chronometers: constraining the equation of state of dark energy. I: H(z) measurements
Authors: Daniel Stern  , Raul Jimenez  , Licia Verde  , Marc Kamionkowski  , S. Adam Stanford
Published: February 2010

We present new determinations of the cosmic expansion history from
red-envelope galaxies. We have obtained for this purpose high-quality
spectra with the Keck-LRIS spectrograph of red-envelope galaxies
in 24 galaxy clusters in the redshift range 0.2 < z < 1.0. We
complement these Keck spectra with high-quality, publicly available
archival spectra from the SPICES and VVDS surveys. We improve over
our previous expansion history measurements in Simon et al. (2005)
by providing two new determinations of the expansion history: H(z) = 97±62 km sec−1 Mpc−1 at z ≃ 0.5 and H(z) = 90±40 km sec−1 Mpc−1 at z ≃ 0.9. We discuss
the uncertainty in the expansion history determination that arises
from uncertainties in the synthetic stellar-population models. We
then use these new measurements in concert with cosmic-microwave-background
(CMB) measurements to constrain cosmological parameters, with a
special emphasis on dark-energy parameters and constraints to the
curvature. In particular, we demonstrate the usefulness of direct
H(z) measurements by constraining the dark-energy equation of
state parameterized by w
0 and w

a
and allowing for arbitrary
curvature. Further, we also constrain, using only CMB and H(z)
data, the number of relativistic degrees of freedom to be 4±0.5 and their total mass to be < 0.2 eV, both at 1σ.
Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments
Authors: Kirchner Marc , Timm Wiebke , Fong Peying , Wangemann Philine , Steen Hanno
Published: February 2010

Motivation: Mass spectrometry (MS) has become the method of choice for protein/peptide sequence and modification analysis. The technology employs a two-step approach: ionized peptide precursor masses are detected, selected for fragmentation, and the fragment mass spectra are collected for computational analysis. Current precursor selection schemes are based on data- or information-dependent acquisition (DDA/IDA), where fragmentation mass candidates are selected by intensity and are subsequently included in a dynamic exclusion list to avoid constant refragmentation of highly abundant species. DDA/IDA methods do not exploit valuable information that is contained in the fractional mass of high-accuracy precursor mass measurements delivered by current instrumentation.

Results: We extend previous contributions that suggest that fractional mass information allows targeted fragmentation of analytes of interest. We introduce a non-linear Random Forest classification and a discrete mapping approach, which can be trained to discriminate among arbitrary fractional mass patterns for an arbitrary number of classes of analytes. These methods can be used to increase fragmentation efficiency for specific subsets of analytes or to select suitable fragmentation technologies on-the-fly. We show that theoretical generalization error estimates transfer into practical application, and that their quality depends on the accuracy of prior distribution estimate of the analyte classes. The methods are applied to two real-world proteomics datasets.

Availability: All software used in this study is available from http://software.steenlab.org/fmf

Contact:  hanno.steen@childrens.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning
Authors: Wu Chia-Chin , Asgharzadeh Shahab , Triche Timothy J. , D'Argenio David Z.
Published: February 2010

Motivation: Three major problems confront the construction of a human genetic network from heterogeneous genomics data using kernel-based approaches: definition of a robust gold-standard negative set, large-scale learning and massive missing data values.

Results: The proposed graph-based approach generates a robust GSN for the training process of genetic network construction. The RVM-based ensemble model that combines AdaBoost and reduced-feature yields improved performance on large-scale learning problems with massive missing values in comparison to Naïve Bayes.

Contact:  dargenio@bmsr.usc.edu

Supplementary information:  Supplementary material is available at Bioinformatics online.