bluuebunny/crossref_metadata_2025_split huggingface dataset:
i‐Patch: Interprotein contact prediction using local network information
Authors: Hamer Rebecca , Luo Qiang , Armitage Judith P. , Reinert Gesine , Deane Charlotte M. 
Published: June 2010

AbstractBiological processes are commonly controlled by precise protein‐protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i‐Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i‐Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i‐Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i‐Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i‐Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes. Proteins 2010. © 2010 Wiley‐Liss, Inc.
CAPRI targets T29–T42: Proving ground for new docking procedures
Authors: Eisenstein Miriam , Ben‐Shimon Avraham , Frankenstein Ziv , Kowalsman Noga 
Published: June 2010

AbstractThe critical assessment of protein interactions (CAPRI) experiment provides a unique opportunity for unbiased assessment of docking procedures. The recent CAPRI targets T29–T42 entailed docking of bound, unbound, and modeled structures, presenting a wide range of prediction difficulty. We submitted accurate predictions for targets T40, T41, and T42, a good prediction for T32 and acceptable predictions for T29 and T34. The accuracy of our docking results generally matched the prediction difficulty; hence, docking of modeled proteins produced less accurate results. However, there were interesting exceptions: an accurate prediction was submitted for the dimer of modeled tetratricopeptide repeat (T42) and only an acceptable prediction for the bound/unbound case T29. The ensembles of docking models produced in the scans included an acceptable or better prediction for every target. We show here that our recently developed postscan reevaluation procedure, which tests propensity and solvation measures of the whole interface and the interface core, successfully distinguished these predictions from false docking models. For enzyme–inhibitor targets, we show that the distance of the interface from the enzyme's centroid ranked high native like docking models. Also, for one case we demonstrate that docking of an ensemble of conformers produced by normal modes analysis can improve the accuracy of the prediction. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent
Authors: Kannan Srinivasaraghavan , Zacharias Martin 
Published: June 2010

AbstractComparative or homology modeling of a target protein based on sequence similarity to a protein with known structure is widely used to provide structural models of proteins. Depending on the target‐template similarity these model structures may contain regions of limited structural accuracy. In principle, molecular dynamics (MD) simulations can be used to refine protein model structures and also to model loop regions that connect structurally conserved regions but it is limited by the currently accessible simulation time scales. A recently developed biasing potential replica exchange (BP‐REMD) method was used to refine loops and complete decoy protein structures at atomic resolution including explicit solvent. In standard REMD simulations several replicas of a system are run in parallel at different temperatures allowing exchanges at preset time intervals. In a BP‐REMD simulation replicas are controlled by various levels of a biasing potential to reduce the energy barriers associated with peptide backbone dihedral transitions. The method requires much fewer replicas for efficient sampling compared with T‐REMD. Application of the approach to several protein loops indicated improved conformational sampling of backbone dihedral angle of loop residues compared to conventional MD simulations. BP‐REMD refinement simulations on several test cases starting from decoy structures deviating significantly from the native structure resulted in final structures in much closer agreement with experiment compared to conventional MD simulations. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Structure of the ATP‐binding domain of Plasmodium falciparum Hsp90
Authors: Corbett Kevin D. , Berger James M. 
Published: June 2010

AbstractHsp90 is an important cellular chaperone and attractive target for therapeutics against both cancer and infectious organisms. The Hsp90 protein from the parasite Plasmodium falciparum, the causative agent of malaria, is critical for this organism's survival; the anti‐Hsp90 drug geldanamycin is toxic to P. falciparum growth. We have solved the structure of the N‐terminal ATP‐binding domain of P. falciparum Hsp90, which contains a principal drug‐binding pocket, in both apo and ADP‐bound states at 2.3 Å resolution. The structure shows that P. falciparum Hsp90 is highly similar to human Hsp90, and likely binds agents such as geldanamycin in an identical manner. Our results should aid in the structural understanding of Hsp90‐drug interactions in P. falciparum, and provide a scaffold for future drug‐discovery efforts. Proteins 2010; © 2010 Wiley‐Liss, Inc.
Microstructure characterization of high‐purity aluminum processed by dynamic severe plastic deformation
Authors: Dirras Guy , Chauveau Thierry , Abdul‐Latif Akrum , Ramtani Salah , Bui Quang‐Hien 
Published: June 2010

AbstractFine‐grained aluminum (700–1000 nm) was processed by dynamic severe plastic deformation of coarse‐grained (3 mm) pure aluminum (99.999 wt.%). The resulting microstructure was characterized by transmission electron microscopy (TEM) and X‐ray profile analyses. It is observed that the grain size determined by TEM departs from measurements made by X‐ray profile analysis. In the latter case, the average crystallite size determined over the global crystallographic or on the deformation‐induced texture components, namely {123} 〈 751 〉, {100} 〈 011〉, and {223} 〈 154 〉, yields similar values (∼225 nm). By contrast, the dislocation density determined on these texture components is about two times higher than the one measured on the global texture. The difference might be related to the specificities of the induced crystallographic texture.
Reflectance anisotropy spectra of CdTe(001) surfaces
Authors: Vázquez‐Nava R. A. , Arzate N. , Mendoza B. S. 
Published: June 2010

AbstractWe present first‐principles calculations of reflectance anisotropy spectra (RAS) of the more common CdTe(001) surface reconstructions: Te‐terminated $(2 \times 1)$ and Cd‐terminated $(2 \times 1)$ and c$(2 \times 2)$. The last two reconstructions with a Cd coverage of half atomic layers. Calculations have been performed by using the density‐functional formalism within the local‐density approximation + scissors corrections. The electron–ion interaction has been modeled by ab initio, relativistic norm‐conserving pseudopotentials. We have also calculated RAS spectra using a semi‐empirical tight binding method (SETB) within a ${\rm sp}^3 {\rm s}^*$ basis. We show RAS of each surface reconstruction and compare our theoretical results with experimental results reported in the literature and we found a good agreement between experimental and theoretical spectra for the $(2 \times 1)$ reconstructions.
Enhanced back and forward scattering in the reflection of light from weakly rough random metal surfaces
Authors: Simonsen Ingve 
Published: June 2010

AbstractThe scattering of light from a weakly rough random silver surface characterized by a double rectangular power spectrum is studied by numerical simulations. This power spectrum can support both the enhanced back and forward scattering phenomena, which for weakly rough surfaces, are both related to the excitation of surface plasmon polaritons. Here we review these phenomena and present new results from a numerical study of the dependence of the diffuse scattering on the amplitudes (γi, i = 1, 2) of the two rectangular portions of the power spectrum. It is found that there exist an optimal range of ratios, γ2/γ1, over which forward scattering peaks can be observed. By just changing the correlations along the interface, while keeping all other parameters like roughness, polarization, and angle of incidence unchanged, the fraction of the incident light that is scattered diffusely can be as large as 16%, while for other parameters as small as 1%. Moreover, a change in the correlation function only, can result in a 3.5 times increase in the amount of light that is absorbed at the weakly rough metal interface (σ = 10 nm).
Synchrotron infrared spectroscopic ellipsometry for characterization of biofunctional surfaces
Authors: Sun Guoguang , Rosu Dana Maria , Zhang Xin , Hovestädt Marc , Pop Simona , Schade Ulrich , Aulich Dennis , Gensch Michael , Ay Bernhard , Holzhütter Hermann‐Georg , Zahn Dietrich R. T. , Esser Norbert , Volkmer Rudolf , Rappich Jörg , Hinrichs Karsten 
Published: June 2010

AbstractThe structural and thickness homogeneity of different biofunctional surfaces after coating an Au substrate was studied by infrared spectroscopic ellipsometry (IRSE). Monolayer coverage was achieved by washing the samples in aqueous solution. A selected cysteine‐modified CHL peptide and an anti‐glutathione S‐transfer (GST) antibody produced a characteristic change in the IR ellipsometric spectra after peptide and antibody adsorption, confirming the biosensing ability of this technique. IR ellipsometric mapping at the synchrotron storage ring BESSY II in Berlin allowed laterally resolved characterization of the protein films. The IR ellipsometric tanΨ and Δ maps revealed that the protein films are inhomogeneous in structure and thickness after adsorption of the peptide and antibody. The absolute thickness of the protein films varied considerably by up to 3 to 7 nm. We also studied cytosine films with different thicknesses (d = 58 nm and 125 nm) and a guanine film (d = 84 nm). For the two cytosine films the synchrotron spectra revealed that the thicker film in particular was rather homogeneous in thickness but inhomogeneous in structure. For the guanine film the shape of vibrational bands in the ellipsometric spectra correlated with anisotropic molecular orientations.
a ‐plane AlN and AlGaN growth on r ‐plane sapphire by MOVPE
Authors: Miyagawa Reina , Miyake Hideto , Hiramatsu Kazumasa 
Published: June 2010

AbstractThe growth of a‐plane (11‐20) AlN and AlGaN on r‐plane (1‐102) sapphire has been investigated with the aim of application to LEDs and LDs in the deep ultra‐violet region. a‐plane AlN and AlGaN were grown on r‐plane sapphire by low‐pressure metalorganic vapor phase epitaxy (LP‐MOVPE). The crystalline quality and surface morphology of a‐plane AlN were optimized at a growth temperature of 1250 °C with the off‐angle of r‐plane sapphire between ‐1° and +1°, and a‐plane AlGaN grown on the AlN layer using ‐0.45°‐off r‐plane sapphire as a substrate exhibited high crystalline quality. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Performance and reliability of ultraviolet‐C pseudomorphic light emitting diodes on bulk AlN substrates
Authors: Grandusky James , Cui Yongjie , Gibb Shawn , Mendrick Mark , Schowalter Leo 
Published: June 2010

AbstractLow dislocation density, epitaxial layers of AlxGa1–xN are grown pseudomorphically on native AlN substrates prepared from high quality, bulk crystals. In addition to low dislocation density, they are atomically smooth and can be doped n‐type to obtain sheet resistances < 200 Ohms/sq/μm. These layers are used as templates for the growth of high quality multiple quantum well (MQW) structures and ultraviolet (UV) light emitting diodes (LED). The pseudomorphic growth and atomically smooth surfaces are achieved for a full device structure. Previously we have demonstrated the high optical quality of these structures through temperature dependant photoluminescence measurements and X‐ray diffraction. Recently full device structures have been fabricated and packaged. These devices, with emission wavelength between 250 nm and 280 nm show linear increase in output power as a function of current up to 150 mA in thermal equilibrium. Additionally output powers up to 1.3 mW have been achieved at 258 nm at 400 mA drive current. Reliability of the devices has been measured for 1000 hours with expected lifetimes greater than 3000 hours for input currents up to 150 mA (with an average current density of approximately 150 A/cm2). (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Combination of short‐range periodicity and interfacial stress effects on valence band scheme in strained MQW (GaN/AlGaN)n
Authors: Emura Shuichi , Tani Hironobu , Kin Masane , Zhou Yi‐Kai , Hasegawa Shigehiko , Asahi Hajime 
Published: June 2010

AbstractWe observed intense photoluminescence from the GaN well layers of the multi‐quantum well consisting of GaN and Al0.24Ga0.76N with various thicknesses (about 0.8, 1.6, 2.4 nm) of the GaN well layers. The peak position of the photoluminescence largely shifts towards the higher energy and the peak intensity becomes strong enormously with the decreasing of the GaN well‐layer thickness. We qualitatively discuss on the effects of the interfacial stress (strain) and the induced dielectric polarization in addition to the short‐range periodicity to elucidate the observed phenomena instead of the usual explanation based on an internal electric field effect, that seems to be too intuitive and of little physical logic. The band scheme alteration is also discussed with the observed phenomena of the photoluminescence in connection with the above argument. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lateral patterning of GaN polarity using wet etching process
Authors: Fukuhara Yujiro , Katayama Ryuji , Onabe Kentaro 
Published: June 2010

AbstractA lateral patterning of GaN polarity using wet etching process is demonstrated. The lattice polarity of a GaN film is examined by RHEED, KOH etching, micro‐Raman scattering and Kelvin force microscopy investigations. We have confirmed the high crystal quality of the lattice‐polarity inverted GaN heterostructure fabricated by the all‐wet process. The difference between the surface potentials of the N‐polar and Ga‐polar GaN regions originates from the inversion of the direction of the spontaneous polarization as deduced from the fact that the piezoelectric polarization is negligible compared with the spontaneous polarization. The KOH etching result is consistent with the above mentioned result. This work is the first and direct demonstration for the successful fabrication of the polarity‐inverted GaN heterostructure by an all‐wet process. We suggest the feasibility of the convenient all wet process for the fabrication of the quasi‐phase‐matched waveguides and photonic crystals for efficient nonlinear frequency conversion (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gate‐recessed normally‐off GaN‐on‐ Si HEMT using a new O2‐BCl3 digital etching technique
Authors: Burnham Shawn D. , Boutros Karim , Hashimoto Paul , Butler Colleen , Wong Danny W.S. , Hu Ming , Micovic Miroslav 
Published: June 2010

AbstractA new, semi‐self‐limiting, digital etch process using separate oxygen (O2) and boron trichloride (BCl3) plasmas to sequentially remove layers of material from AlGaN/GaN high electron mobility transistors (HEMTs) on the order of a few angstroms per cycle is presented. This novel digital or atomic layer etching (ALE) technique was used for the conversion of AlGaN/GaN HEMT devices from depletion mode (normally‐on operation) to enhancement mode (normally‐off operation). For a fixed BCl3 time of 60 sec per cycle, the etch rate per cycle was increased from 1.4 nm/cycle to 2.5 nm/cycle by increasing the O2 time per cycle from zero to 15 seconds, and remained fairly constant with higher O2 time per cycle for a self‐limiting etch process. Two GaN‐on‐Si wafers from the same CVD growth were processed side‐by‐side using the device layout and process steps, except for the depletion‐to‐enhancement conversion step, to compare ALE and fluorine treatment. The ALE‐processed had a peak gm of 250 mS/mm, 67% higher than the fluorine‐treatment process. The ALE process resulted in a threshold voltage variation of +/‐ 150 mV across the 3 inch wafer (σ = 63 mV), which was less than half of that of the fluorine‐treatment wafer. The three‐terminal breakdown voltage of the ALE‐processed wafer exceeded 1100 V, which is the first demonstration of such a high voltage device using GaN‐on‐Si and a gate recess technique, and the drain leakage current was in the μA/mm range at 1100 V. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The study on Schottky contact between Ti and GaSe
Authors: Huang Wen‐Chang , Horng Chia‐Tsung , Chen Yu‐Min , Chen Chien‐Chou 
Published: June 2010

AbstractA new Schottky contact, Ti/p‐GaSe was presented at this study. It shows an effective barrier height of 1.01 eV with an ideality factor of 2.8 and a reverse leakage current density of 3.8×10‐7 A/cm2 at a reverse voltage of 4 V was measured after rapid thermal annealing at 350 °C for 30 s. The capacitance‐voltage measurement was also used to evaluate the diode characteristics. The annealed diodes also showed linear relationship at the capacitance‐voltage (C‐2‐V) plotting. The formation of TiGaSe2 was observed by X‐ray diffraction analysis after the diode was annealed at 250 °C for 30 s. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Transport, magnetic and structural properties of bulk In2‐xFexO3
Authors: Fahed C. , Qadri S. B. , Kim H. , Piqué A. , Miller M. , Mahadik N. A. , Rao M. V. , Osofsky M. 
Published: June 2010

AbstractBulk samples of In2‐xFexO3 were synthesized for x ≤ 0.40 in a body‐centered cubic phase. Their structural, transport and magnetic properties were investigated as a function of composition. The lattice parameters of the solid solutions decrease with increasing Fe‐content. The electrical data showed reduced conductivities for higher Fe compositions. The magnetic measurements showed paramagnetic behavior for x values of 0.1 and 0.2, and a small degree of ferromagnetism for x = 0.4. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Room‐temperature ferromagnetism in V‐doped GaN thin films grown by MOCVD
Authors: Souissi M. , Schmerber G. , Derory A. , El Jani B. 
Published: June 2010

AbstractV‐doped GaN thin films were grown on c‐sapphire substrate by metal organic chemical vapour deposition method (MOCVD). We have used vanadium tetrachloride (VCl4) to intentionally incorporate vanadium (V) during the crystal growth of GaN. X‐ray diffraction measurements revealed no secondary phase in the samples.Magnetic experiments using superconducting quantum interference device (SQUID) showed clear hysteresis loop in magnetization versus applied field (M –H) curves for V‐doped GaN films. The ferromagnetic behavior was evidenced at 300 K, implying the Curie temperature to be over 300 K. Strong and broad blue‐luminescent band (centered at 2.6 eV) is induced by the V doping in GaN. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
RF‐plasma assisted PLD growth of Zn3N2 thin films
Authors: Ayouchi Rachid , Casteleiro Catarina , Santos Luis , Schwarz Reinhard 
Published: June 2010

AbstractPolycrystalline Zn3N2 films were prepared on sapphire and quartz substrates by reactive pulsed laser ablation of a metallic zinc target in a nitrogen plasma atmosphere using a frequency‐doubled Nd:YAG laser, assisted by a 13.56 MHz radio‐frequency (RF) plasma. The morphological, structural and optical properties are studied by Scanning Electron Microscopy, X‐ray diffraction, transmittance and ellipsometric spectroscopy. SEM revealed a very smooth and crack‐free film surface. X‐ray diffraction indicates that the Zn3N2 films deposited at 400 °C substrate temperature are cubic in structure with no preferred orientation. The lattice constant has been estimated to be a = 0.97 nm. The absorption coefficient is deduced from the transmission spectra, and its dependence on photon energy is examined to determine the optical band gap. Refractive index and film thickness are deduced from spectroscopic ellipsometry measurements. Zn3N2 is determined to be a n‐type semiconductor with a direct band gap of 3.2 eV. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of SnO2:F thin films deposited by an economic spray pyrolysis technique
Authors: Memarian Nafiseh , Rozati Seyed Mohammad , Elamurugu Elangovan , Fortunato Elvira 
Published: June 2010

AbstractFluorine doped tin oxide (FTO) semiconductor thin films were deposited on glass substrates using spray pyrolysis technique and the effect of fluorine (F‐) doping (varying 0‐30 at%) is explored. X‐ray diffraction studies confirmed the tetragonal structure with polycrystalline nature. The crystallinity of undoped films is enhanced with the increase in F‐doping. The films doped with 25 at% F show a strong orientation along (101) plane. The grain size of the undoped films (214 nm) is increased with the increase in F‐doping level to reach a maximum of 415 nm (25 at% F). A minimum sheet resistance of ∼5.4 Ω/□ obtained for the 30 at% F doped films is among the lowest reported values. The average visible transmittance (400‐700 nm) of the undoped films (61.4%) is increased with the increasing F‐doping to reach a maximum of 74.5% (25 at%. F). The films doped with 25 at.% F showed high value of figure of merit (4.55 × 10‐3 Ω‐1). The obtained results authenticate the influence of F‐doping on the properties of the deposited films. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Zn1‐xMgxO thin films deposited by spray pyrolysis
Authors: Sahal M. , Marí B. , Mollar M. , Manjón F. J. 
Published: June 2010

AbstractThis work reports on an analysis of the chemical composition, structural, and optical properties of Mg‐doped zinc oxide (ZMO) thin films with Mg concentration up to 54 at.% and prepared by the spray pyrolysis technique from acetate precursors. Chemical analysis show that the [Mg]/[Zn] ratio incorporated into the films is higher than that present in the starting solution. X‐ray diffraction, Raman scattering, and transmission measurements show that all samples exhibit a single phase wurtzite structure with a transmittance above 70% in the visible range. Increasing Mg content leads to an increase of the band gap energy from 3.23 in pure ZnO to 3.57 eV in films with 54 at% of Mg content. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)