bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of diamond metal-insulator-semiconductor field-effect transistors with aluminum oxide gate insulator
Authors: Hirama Kazuyuki , Miyamoto Shingo , Matsudaira Hiroki , Yamada Keisaku , Kawarada Hiroshi , Chikyo Toyohiro , Koinuma Hideomi , Hasegawa Ken , Umezawa Hitoshi
Published: March 2006

Metal-insulator-semiconductor field-effect transistors (MISFETs) with aluminum oxide as a gate insulator have been fabricated on a hydrogen-terminated diamond surface using its surface conductive layer. The aluminum oxide gate insulator was deposited on the diamond surface by the pulsed laser deposition method. The on-off ratio measured by dc was greater than five orders of magnitude, one of the best results reported for diamond FETs. The gate leak current of aluminum oxide MISFETs is three orders of magnitude less than that of conventional CaF2 MISFETs. These characteristics indicate that aluminum oxide gate insulators are suitable for high reliability power device applications of diamond MISFETs.
dc bias-induced dielectric anomalies in ⟨111⟩-oriented 0.9Pb(Mg1∕3Nb2∕3O3)–0.1PbTiO3 single crystals
Authors: Wang Jie , Jia Y. M. , Zheng R. K. , Chan Helen L. W. , Zhao X. , Luo H.
Published: March 2006

dc bias dependence of small signal dielectric response was measured on ⟨111⟩-oriented 0.9Pb(Mg1∕3Nb2∕3O3)–0.1PbTiO3 single crystals at various temperatures. It was shown that at different temperature ranges, the dielectric responses were quite different, implying different natures of the polar nanodomains. It was found that the freezing occurred effectively below freezing temperature To. Between To and Tm, the dielectric constant peak temperature, the reversible dielectric peaks under bias were explained by the mechanism of polarization rotation, revealing a possible presence of multiple polar orders in nanodomains.
High negative tunneling magnetoresistance in magnetic tunnel junctions with a ferrimagnetic CoFe–Gd electrode and a CoFe interface layer
Authors: Kaiser Christian , Parkin Stuart S. P.
Published: March 2006

Ferrimagnetic rare earth-transition metal alloys can display negatively spin polarized current and thus give rise to negative tunneling magnetoresistance in magnetic tunnel junctions. We show that a thin (∼15Å) ferromagnetic transition metal interlayer at the tunnel barrier interface can greatly enhance the negative magnetoresistance. By adjusting the relative thicknesses of the ferrimagnetic and ferromagnetic layers the coercivity can be varied by more than a hundredfold. The interface layer also significantly increases the temperature at which the device undergoes electrical breakdown.
Recombination dynamics of a 268nm emission peak in Al0.53In0.11Ga0.36N∕Al0.58In0.02Ga0.40N multiple quantum wells
Authors: Onuma T. , Keller S. , DenBaars S. P. , Speck J. S. , Nakamura S. , Mishra U. K. , Sota T. , Chichibu S. F.
Published: March 2006

Recombination dynamics of the 268nm photoluminescence (PL) peak in a quaternary Al0.53In0.11Ga0.36N∕Al0.58In0.02Ga0.40N multiple quantum well (MQW) grown on relaxed AlGaN templates were studied. Although the polarization field in the compressively strained Al0.53In0.11Ga0.36N wells was as high as 1.6MV∕cm, the value of integrated PL intensity at 300K divided by that at 8K (ηint) was as high as 1.2%. The value was similar to that obtained for the 285nm PL peak in an Al0.30Ga0.70N∕Al0.70Ga0.30N MQW (1.3%), though the AlN molar fraction in the wells was higher by a factor of 1.7. According to these results and the fact that time-resolved PL signal exhibited a stretched exponential decay shape, the improved ηint of the AlInGaN wells was attributed to a beneficial effect of the exciton localization as is the case with InGaN alloys; doping or alloying with InN was confirmed to work also on AlGaN in improving ηint to realize deep UV optoelectronic devices.
Light emission and wave guiding of quantum dots in a tube
Authors: Mendach S. , Songmuang R. , Kiravittaya S. , Rastelli A. , Benyoucef M. , Schmidt O. G.
Published: March 2006

We present microphotoluminescence investigations of InAs quantum dots (QDs) integrated into self-rolling InGaAs∕GaAs strained layers. The emission signal from the QDs is redshifted due to strain relaxation and increased in intensity after the strained layers are released from the substrate and rolled up into tubes. We detect waveguided light at the tube ends, which originates from the QDs at the laser excitation spot. The possibility of integrating quantum emitters into the tube walls acting as waveguides represents a major step toward the realization of flexible high quality factor optical resonators based on rolled-up nano- and microtubes.
Structural and stoichiometric change in nitrided HfO2 grown on Ge(100) by atomic layer deposition
Authors: Chung K. B. , Whang C. N. , Cho M.-H. , Ko D.-H.
Published: March 2006

The electronic structure and stoichiometric characteristics of postnitrided HfO2 grown on Ge(100) were investigated by various physical measurements. N incorporation in HfO2 grown on Ge was strongly related to the diffusion of Ge from Ge substrate into the film by the postannealing treatment in an NH3 ambient. The diffusion of Ge into the HfO2 film was influenced by the formation of GeOx and GeOxNy in the interfacial region. The small amount of N was incorporated into the film at a nitrided temperature of 600°C, while much larger amounts of N atoms were incorporated into the interfacial layer to form GeON at a temperature of 700°C, resulting in the suppression of the diffusion of Ge into the film. However, the interfacial nitrided layer was not stably maintained during the postnitridation anneal, resulting in an enhanced interdiffusion of Ge and Hf into the film.
Terahertz microscopy of charge carriers in semiconductors
Authors: Buersgens F. , Kersting R. , Chen H.-T.
Published: March 2006

We report on the application of apertureless THz near-field microscopy for sensing charge carriers in semiconductors. This technique allows for contactless probing of electron concentrations on a micrometer scale. Experimental data and model calculations indicate that as few as about 5000 electrons can be detected in a GaAs structure.
Determination of domain wall resistance in a cobalt thin film by thickness modulation
Authors: Lee Wei-Li , Zhu Frank Q. , Chien C. L.
Published: March 2006

Inspired by a well-known fact that the magnetic coercivity of a thin film has a strong dependence on its thickness, we have fabricated a 5×60μm and 30nm thick cobalt (Co) strip with thickness modulation along its long axis. The modulation period of 700nm with a depth of 8nm was prepared by a focused ion beam. From magnetic force microscope images, we observed an induced magnetic anisotropy along the short axis of the strip. By comparing out-of-plane magnetoresistance measurements in two magnetic remnant states, we extracted a positive domain wall resistance of 0.03Ω, corresponding to 0.14% magnetoresistance (MR) in a Co thin film.
Nanoscale magnet for semiconductor spintronics
Authors: Murayama A. , Sakuma M.
Published: March 2006

A hybrid nanostructure of diluted magnetic semiconductor quantum well (DMS-QW) has been fabricated by using a ferromagnetic Co∕Pt-multilayered film with perpendicular magnetization. The nanoscale disk of DMS-QW with a diameter of 80nm was embedded in the magnetic film generating magnetic fields perpendicular to the DMS-QW plane. As a result, exciton photoluminescence with circular-polarization properties arises in a zero external field, due to the giant Zeeman effects of excitons. It indicates that the perpendicular magnetic fields applied from the Co∕Pt film align the exciton spins in the DMS nanoscale disk, acting as a nanoscale magnet for semiconductor spintronics.
Coherent 5.35μm surface emission from a GaAs-based distributed feedback quantum-cascade laser
Authors: Austerer M. , Pflügl C. , Golka S. , Schrenk W. , Andrews A. M. , Roch T. , Strasser G.
Published: March 2006

We present second-harmonic surface emission from distributed feedback GaAs∕AlGaAs quantum-cascade lasers with integrated intersubband nonlinearities. The devices show single mode fundamental and second-harmonic emission at wavelengths of 10.7 and 5.35μm, respectively. Only 5.35μm light is emitted from the surface, as the fundamental light is not coupling to radiating modes for the grating of our choice. The second-harmonic peak optical power via the surface at 78K is 150μW for a fundamental peak power of 1.1W.
Interfacial microstructure of Fe∕AlOx∕Fe magnetic tunnel junctions in high resolution
Authors: Schmitt H. , Ghafari M. , Kruk R. , Ellrich J. , Hütten A. , Schmitt L. A. , Hahn H.
Published: March 2006

Magnetic tunnel junctions were prepared by deposition of a Ta-buffered Fe-AlOx-Fe trilayer on a thermally oxidized silicon wafer. In order to investigate the influence of different Fe oxides like a spinel-like phase and a spinel (Hycernite) on the tunneling magnetoresistance effect, a Fe57 tracer was deposited at the lower barrier interface. Using conversion electron Mössbauer spectroscopy the evolution of chemical, structural, and magnetic changes in the tracer was monitored starting from the as-prepared state and after several annealing steps. The nuclear probe technique enables to resolve phase formation at the interface with submonolayer resolution.
Efficient generation of green and UV light in a single PP-KTP waveguide pumped by a compact all-fiber system
Authors: Rusu M. , Rafailov E. U. , Herda R. , Okhotnikov O. G. , Saltiel S. M. , Battle P. , McNeil S. , Grudinin A. B. , Sibbett W.
Published: March 2006

We present simultaneous efficient second- (SHG) and third-harmonic generation (THG) in a single periodically-poled KTP waveguided crystal pumped by a compact femtosecond Yb-based laser in a condition of exactly phase-matched frequency doubling and nonphase-matched sum-frequency mixing processes. Internal conversion efficiency as high as 33% for SHG (532nm) and ∼2% for the cascaded THG (355nm) is reported. We believe this to be a clear experimental demonstration that strong third-harmonic can be generated in frequency doubling crystals through a nonphase-matched sum-frequency mixing process.
Photoluminescence of CdSe quantum dots and rods from buffer-layer-assisted growth
Authors: Antonov V. N. , Swaminathan P. , Soares J. A. N. T. , Palmer J. S. , Weaver J. H.
Published: March 2006

The traditional colloidal routes of fabrication of II-VI semiconductor quantum dots have been difficult to integrate with silicon technology. Here, we demonstrate that CdSe quantum dots and rods can be self-assembled and delivered in ultrahigh vacuum conditions on almost any substrate by means of buffer-layer-assisted growth (BLAG), where the buffer is thin solid Xe film. We determine the diffusivity of the particles on the buffer, and demonstrate the significance of the ionicity of the CdSe. Photoluminescence spectra are compared to the previous studies of colloidal CdSe structures. This study opens the door for the synthesis of tunable II-VI heterostructures.
Influence of the cavity on the low-temperature photoluminescence of SiGe∕Si multiquantum wells grown on a silicon-on-insulator substrate
Authors: Li C. B. , Cheng B. W. , Zuo Y. H. , Morrison A. P. , Yu J. Z. , Wang Q. M.
Published: March 2006

The influences of the cavity on the low-temperature photoluminescence of Si0.59Ge0.41∕Si multiquantum wells grown on silicon-on-insulator substrates are discussed. The positions of the modulated photoluminescence (PL) peaks not only relate to the nature of SiGe∕Si multiquantum wells, but also relate to the characteristic of the cavity. With increasing temperature, a redshift of the modulated PL peak originating from the thermo-optical effect of the cavity is observed.
Photonic band-gap structures of core-shell simple cubic crystals from holographic lithography
Authors: Moon Jun Hyuk , Yang Shu , Yang Seung-Man
Published: March 2006

We report the investigation of photonic band-gap properties of a core-shell simple cubic structure (air core with a dielectric shell) using a two-parameter level-set approach. The proposed structure can be obtained by partially backfilling high refractive index materials into a polymeric template fabricated by multibeam interference lithography. We find that the shell formation in the inverted simple cubic structure increases the complete photonic band-gap width by 10%–20% in comparison to that of a completely filled structure. The band gap between the fifth and sixth bands begins to appear at a refractive index contrast of 2.7. This study suggests the importance to investigate the core-shell formation in three-dimensional photonic crystals through backfilling, which may offer an additional control over their photonic band-gap properties.
Crossover from one- to two-dimensional space-charge-limited conduction in pentacene single crystals
Authors: Jurchescu Oana D. , Palstra Thomas T. M.
Published: March 2006

We report the crossover from one- to two-dimensional space-charge-limited conduction in pentacene single crystals with planar contacts. The space charge is confined to the in-plane longitudinal direction for L∕h⩽15, with L the contact separation and h the sample thickness. For L∕h>250 the space charge is dominated by the transverse component of the electric field.
Influence of acoustic phonon confinement on electron mobility in ultrathin silicon on insulator layers
Authors: Donetti L. , Gámiz F. , Rodriguez N. , Jimenez F. , Sampedro C.
Published: March 2006

We show the importance of acoustic phonon confinement in ultrathin silicon-on-insulator inversion layers by comparing electron mobility calculated by the Monte Carlo method assuming a bulk acoustic phonon model (the usual procedure) with that obtained by using a confined acoustic phonon model developed in this work. Both freestanding and rigid boundary conditions are taken into account for the evaluation of the confined phonon dispersion in a three-layer structure. Mobility reductions of 30% are observed for silicon thicknesses of around 5–10nm when the confined acoustic phonon model is used.
Low temperature transport behavior and Kondo scattering in dilute Mn-doped NaγCo1−xMnxO2
Authors: Zhang Jincang , Zhang Zaiqing , Xu Yan , Jing Chao , Cao Shixun , Zhao Yonggang
Published: March 2006

We studied the low temperature transport behavior and its dependence on applied magnetic field for dilute Mn-doped NaγCo1−xMnxO2 (x=0, 0.03, 0.07, 0.1). Strikingly, a resistivity minimum was discovered for all the doped samples at low temperatures and was weakly dependent on the external magnetic field. Combining with the susceptibility measurements, the results prove the coexistence of Kondo scattering and possibly enhanced electron-electron (e-e) interaction induced by dilute Mn doping. This signature of e-e interaction may reflect a typical characteristic of strong correlation systems.
High Curie temperatures in (Ga,Mn)N from Mn clustering
Authors: Hynninen Teemu , Raebiger Hannes , von Boehm J. , Ayuela Andrés
Published: March 2006

The effect of microscopic Mn cluster distribution on the Curie temperature (TC) of (Ga,Mn)N is studied using density-functional calculations together with the mean field approximation. We find that the calculated TC depends crucially on the microscopic cluster distribution, which can explain the abnormally large variations in experimental TC values from a few K to well above room temperature. The partially dimerized Mn2-Mn1 distribution is found to give the highest TC>500K, and in general, the presence of the Mn2 dimer has a tendency to enhance TC. The lowest TC values close to zero are obtained for the Mn4-Mn1 and Mn4-Mn3 distributions.
Combinatorial approach to morphology studies of epitaxial thin films
Authors: Suljovrujić E. , Mićić M. , Demic S. , Srdanov V. I.
Published: March 2006

Described is the application of a combinatorial physical vapor deposition (CPVD) method for studying the growth dynamics of epitaxial films. The CPVD method takes advantage of the angle-dependent evaporation rate from a point source to produce thin film libraries whose deposition rate changes continuously for a factor of 50 across a 70-mm long-substrate. The link between the deposition rate and the resulting thin film morphology was made by spatially correlated absorption and atomic force microscopy measurements. It is shown that the growth of tryphenyldiamine derivate on a silica surface proceeds by three-dimensional growth of isolated islands which, at some critical coverage, coalesce to form uniform amorphous film. While the critical coverage of such films depends on the deposition rate in the 0.015–0.4nm∕s region, the particle size distribution function does not.
Formation of flat, relaxed Si1−xGex alloys on Si(001) without buffer layers
Authors: Hong S. , Kim H.-W. , Bae D. K. , Song S. C. , Lee G.-D. , Yoon E. , Kim C. S. , Foo Y. L. , Greene J. E.
Published: March 2006

Atomically flat, fully strained Si1−xGex layers with thicknesses ranging from 40 to 240nm were grown on Si(001) at 450°C by ultrahigh-vacuum chemical vapor deposition and subjected to annealing at 1000°C for 20min to induce relaxation. In order to minimize surface diffusion during annealing and thereby inhibit strain-induced roughening in favor of misfit dislocation formation, SiO2 capping layers are deposited prior to annealing. The overall process results in smooth, relaxed alloy layers without the necessity of using several-μm-thick compositionally graded buffer layers.
Correlation between grain and grain-boundary critical current densities in ex situ coated conductors with variable YBa2Cu3O7−δ layer thickness
Authors: Palau A. , Puig T. , Obradors X. , Feenstra R. , Gapud A. A.
Published: March 2006

The dependence of the percolative critical current density at low magnetic fields on YBa2Cu3O7−δ (YBCO) layer thickness is studied by comparing grain, JcG, and grain-boundary, JcGB, critical current densities for a series of ex situ processed YBCO films on a RABiTS template. Both critical current densities decrease as a function of thickness and the values of JcG and JcGB show a clear correlation which suggests the existence of an interaction between Abrikosov–Josephson vortices on the grain boundaries and Abrikosov vortices in the bulk of the grains. This opens the possibility to improve JcGB by optimizing the pinning capabilities of the grains.
Could the relaxed and the O-deficient CrO2(100) surface retain half-metallicity?
Authors: Hong Feng , Che J. G.
Published: March 2006

We report the results of a first principles study on the clean and the reduced CrO2(100) surface. It is shown that both surfaces retain the half-metallicity because they share a common feature: the surface Cr atom also behaves like an isolated ion. Thus, the half-metallicity of the CrO2 surfaces can be qualitatively understood by a simple model based on Hund’s rule.
High-detectivity quantum-dot infrared photodetectors grown by metalorganic chemical-vapor deposition
Authors: Szafraniec J. , Tsao S. , Zhang W. , Lim H. , Taguchi M. , Quivy A. A. , Movaghar B. , Razeghi M.
Published: March 2006

A mid-wavelength infrared photodetector based on InGaAs quantum dots buried in an InGaP matrix and deposited on a GaAs substrate was demonstrated. Its photoresponse at T=77K was measured to be around 4.7μm with a cutoff at 5.5μm. Due to the high peak responsivity of 1.2A∕W and low dark-current noise of the device, a specific peak detectivity of 1.1×1012cmHz1∕2W−1 was achieved at −0.9V bias.
Surface band bending of a-plane GaN studied by scanning Kelvin probe microscopy
Authors: Chevtchenko S. , Ni X. , Fan Q. , Baski A. A. , Morkoç H.
Published: March 2006

We report the value of surface band bending for undoped, a-plane GaN layers grown on r-plane sapphire by metalorganic vapor phase epitaxy. The surface potential was measured directly by ambient scanning Kelvin probe microscopy. The upward surface band bending of GaN films grown in the [112¯0] direction was found to be 1.1±0.1V. Because polarization effects are not present on a-plane GaN, we attribute such band bending to the presence of charged surface states. We have modeled the surface band bending assuming a localized level of surface states in the band gap on the surface. It should be noted that the band bending observed for a-plane layers is comparable to that obtained on polar c-plane layers, and both a-plane and c-plane GaN films with similar surface treatments demonstrate comparable band bending behavior, indicating that charged surface states dominate band banding in both cases.
Dynamic longitudinal-optical phonon decay via transient electron-phonon interactions in low-temperature-grown GaAs
Authors: Yee K. J. , Lee D. , Liu X. , Dobrowolska M. , Furdyna J. K. , Lee K. G. , Kim D. S. , Lim Y. S.
Published: March 2006

We present results on dynamic decay of coherent longitudinal-optical phonons in a low-temperature-grown GaAs. We show that the observed behavior originates from transient electron-phonon scatterings which reflect the depletion of carriers from the surface via carrier trapping and diffusion processes. The electron longitudinal-optical (LO)-phonon scattering rate of around 8.6×10−18ps−1cm3 is obtained from the excitation density dependence of the scattering rate.
Tunable stop-band hollow waveguide Bragg reflectors with tapered air core for adaptive dispersion-compensation
Authors: Sakurai Yasuki , Matsutani Akihiro , Koyama Fumio
Published: March 2006

We propose a tunable stop-band hollow waveguide Bragg reflector with a variable tapered air core for an adjustable dispersion-compensation device. The tapered air-core structure gives us chirped Bragg reflection. The precise control of tapered air-core thickness and angle enables us to achieve the dynamic tuning of both stop-band width and center wavelength of Bragg reflection. We demonstrate center-wavelength tuning of 20.1nm corresponding to 1.3% of propagation constant change and stop-band expansion up to 5nm. Also, we demonstrate dispersion tuning operation either in negative or positive dispersion ranges with delay-time difference of about 10ps.
Spin-Hall effect in a diffusive two-dimensional electron system with spin-orbit coupling under an in-plane magnetic field
Authors: Lin Q. , Liu S. Y. , Lei X. L.
Published: March 2006

It is shown that a finite spin-Hall current can be induced by applying an in-plane magnetic field in a diffusive two-dimensional electron system with the Rashba and Dresselhaus spin-orbit couplings subjected to a dc electric field. The spin-Hall conductivity depends not only on the strength and direction of the magnetic field, but also strongly depends on the form of the scattering potential. It can be negative or positive in the case of remote impurity scattering, but essentially positive in the case of short-range scattering.
COMP-angiopoietin-1 promotes wound healing through enhanced angiogenesis, lymphangiogenesis, and blood flow in a diabetic mouse model
Authors: Cho Chung-Hyun , Sung Hoon-Ki , Kim Kyung-Tae , Cheon Hyae Gyeong , Oh Goo Taeg , Hong Hyo Jeong , Yoo Ook-Joon , Koh Gou Young
Published: March 2006

Microvascular dysfunction is a major cause of impaired wound healing seen in diabetic patients. Therefore, reestablishment of structural and functional microvasculature could be beneficial to promote wound healing in these patients. Angiopoietin-1 (Ang1) is a specific growth factor functioning to generate a stable and functional vasculature through the Tie2 and Tie1 receptors. Here we determined the effectiveness of cartilage oligomeric matrix protein (COMP)-Ang1, a soluble, stable, and potent form of Ang1, on promotion of healing in cutaneous wounds of diabetic mice. An excisional full-thickness wound was made in the dorsal side of the tail of diabetic (
db
/
db
) mice, and mice were then treated systemically with adenovirus (Ade) encoding COMP-Ang1 or with control virus encoding β-gal (Ade-β-gal) or treated topically with recombinant COMP-Ang1 protein or BSA. Time course observations revealed that mice treated with Ade-COMP-Ang1 or COMP-Ang1 protein showed accelerated wound closure and epidermal and dermal regeneration, enhanced angiogenesis and lymphangiogenesis, and higher blood flow in the wound region compared with mice treated with control virus or BSA. COMP-Ang1 promotion of wound closure and angiogenesis was not dependent on endothelial nitric oxide synthase or inducible nitric oxide synthase alone. Taken together, these findings indicate that COMP-Ang1 can promote wound healing in diabetes through enhanced angiogenesis, lymphangiogenesis, and blood flow.
Microparadigms: Chains of collective reasoning in publications about molecular interactions
Authors: Rzhetsky Andrey , Iossifov Ivan , Loh Ji Meng , White Kevin P.
Published: March 2006

We analyzed a very large set of molecular interactions that had been derived automatically from biological texts. We found that published statements, regardless of their verity, tend to interfere with interpretation of the subsequent experiments and, therefore, can act as scientific “microparadigms,” similar to dominant scientific theories [Kuhn, T. S. (1996)
The Structure of Scientific Revolutions
(Univ. Chicago Press, Chicago)]. Using statistical tools, we measured the strength of the influence of a single published statement on subsequent interpretations. We call these measured values the momentums of the published statements and treat separately the majority and minority of conflicting statements about the same molecular event. Our results indicate that, when building biological models based on published experimental data, we may have to treat the data as highly dependent-ordered sequences of statements (i.e., chains of collective reasoning) rather than unordered and independent experimental observations. Furthermore, our computations indicate that our data set can be interpreted in two very different ways (two “alternative universes”): one is an “optimists’ universe” with a very low incidence of false results (<5%), and another is a “pessimists’ universe” with an extraordinarily high rate of false results (>90%). Our computations deem highly unlikely any milder intermediate explanation between these two extremes.
Analysis of internal loops within the RNA secondary structure in almost quadratic time
Authors: Ogurtsov Aleksey Y. , Shabalina Svetlana A. , Kondrashov Alexey S. , Roytberg Mikhail A.
Published: March 2006

Motivation: Evaluating all possible internal loops is one of the key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available runs in time O(L3), L is the length of the RNA.

Results: We propose a new algorithm for evaluating internal loops, its run-time is O(M*log2L), M<L2 is a number of possible nucleotide pairings. We created a software tool Afold which predicts the optimal secondary structure of RNA molecules of lengths up to 28 000 nt, using a computer with 2 Gb RAM. We also propose algorithms constructing sets of conditionally optimal multi-branch loop free (MLF) structures, e.g. the set that for every possible pairing (x, y) contains an optimal MLF structure in which nucleotides x and y form a pair. All the algorithms have run-time O(M*log2L).

Availability: Executables of Afold software tool, precompiled for Linux and Windows, are available at .

Contact:  MRoytberg@impb.psn.ru

Supplementary information:
An effective structure learning method for constructing gene networks
Authors: Chen Xue-wen , Anantha Gopalakrishna , Wang Xinkun
Published: March 2006

Motivation: Bayesian network methods have shown promise in gene regulatory network reconstruction because of their capability of capturing causal relationships between genes and handling data with noises found in biological experiments. The problem of learning network structures, however, is NP hard. Consequently, heuristic methods such as hill climbing are used for structure learning. For networks of a moderate size, hill climbing methods are not computationally efficient. Furthermore, relatively low accuracy of the learned structures may be observed. The purpose of this article is to present a novel structure learning method for gene network discovery.

Results: In this paper, we present a novel structure learning method to reconstruct the underlying gene networks from the observational gene expression data. Unlike hill climbing approaches, the proposed method first constructs an undirected network based on mutual information between two nodes and then splits the structure into substructures. The directional orientations for the edges that connect two nodes are then obtained by optimizing a scoring function for each substructure. Our method is evaluated using two benchmark network datasets with known structures. The results show that the proposed method can identify networks that are close to the optimal structures. It outperforms hill climbing methods in terms of both computation time and predicted structure accuracy. We also apply the method to gene expression data measured during the yeast cycle and show the effectiveness of the proposed method for network reconstruction.

Contact:  xwchen@ku.edu
WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks
Authors: Lee Dong-Yup , Yun Choamun , Cho Ayoun , Hou Bo Kyeng , Park Sunwon , Lee Sang Yup
Published: March 2006

Summary: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.

Availability: WebCell is accessible at or .

Contact:  leesy@kaist.ac.kr
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier
Authors: Yousef Malik , Nebozhyn Michael , Shatkay Hagit , Kanterakis Stathis , Showe Louise C. , Showe Michael K.
Published: March 2006

Motivation: Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we describe a new technique, which is applicable across several species, for predicting miRNA genes. This technique is based on machine learning, using the Naïve Bayes classifier. It automatically generates a model from the training data, which consists of sequence and structure information of known miRNAs from a variety of species.

Results: Our study shows that the application of machine learning techniques, along with the integration of data from multiple species is a useful and general approach for miRNA gene prediction. Based on our experiments, we believe that this new technique is applicable to an extensive range of eukaryotes' genomes. Specific structure and sequence features are first used to identify miRNAs followed by a comparative analysis to decrease the number of false positives (FPs). The resulting algorithm exhibits higher specificity and similar sensitivity compared to currently used algorithms that rely on conserved genomic regions to decrease the rate of FPs.

Availability: The BayesMiRNAfind program is available at

Contact:  showe@wistar.org

Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of viable circular permutants using a graph theoretic approach
Authors: Paszkiewicz Konrad H. , Sternberg Michael J. E. , Lappe Michael
Published: March 2006

Motivation: In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting regions where a protein can be split to form a viable circular permutant. Circular permutants are a powerful experimental tool to probe folding mechanisms and more recently have been used to design split enzyme reporter proteins.

Results: We test our method on an extensive set of experiments carried out on dihydrofolate reductase in which circular permutants were constructed for every amino acid position in the sequence, together with partial data from studies on other proteins. Results show that closeness is capable of correctly identifying significantly more residues which are suitable for circular permutation than solvent accessibility. This has potential implications for the design of successful split enzymes having particular importance for the development of protein–protein interaction screening methods and offers new perspectives on protein folding. More generally, the method illustrates the success with which graph-theoretic measures encapsulate the variety of long and short range interactions between residues during the folding process.

Contact:  konrad.paszkiewicz@imperial.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
CAFE: a computational tool for the study of gene family evolution
Authors: De Bie Tijl , Cristianini Nello , Demuth Jeffery P. , Hahn Matthew W.
Published: March 2006

Summary: We present CAFE (Computational Analysis of gene Family Evolution), a tool for the statistical analysis of the evolution of the size of gene families. It uses a stochastic birth and death process to model the evolution of gene family sizes over a phylogeny. For a specified phylogenetic tree, and given the gene family sizes in the extant species, CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss (quantified by a p-value) and identify which branches cause the p-value to be small for significant families.

Availability: Software is available from

Contact:  mwh@indiana.edu
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
Authors: Wainreb Gilad , Haspel Nurit , Wolfson Haim J. , Nussinov Ruth
Published: March 2006

Motivation: Secondary-Structure Guided Superposition tool (SSGS) is a permissive secondary structure-based algorithm for matching of protein structures and in particular their fragments. The algorithm was developed towards protein structure prediction via fragment assembly.

Results: In a fragment-based structural prediction scheme, a protein sequence is cut into building blocks (BBs). The BBs are assembled to predict their relative 3D arrangement. Finally, the assemblies are refined. To implement this prediction scheme, a clustered structural library representing sequence patterns for protein fragments is essential. To create a library, BBs generated by cutting proteins from the PDB are compared and structurally similar BBs are clustered. To allow structural comparison and clustering of the BBs, which are often relatively short with flexible loops, we have devised SSGS. SSGS maintains high similarity between cluster members and is highly efficient. When it comes to comparing BBs for clustering purposes, the algorithm obtains better results than other, non-secondary structure guided protein superimposition algorithms.

Availability: SSGS is available for download at

Contact:  ruthn@ncifcrf.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
Proteomic Analysis of Seed Filling in Brassica napus. Developmental Characterization of Metabolic Isozymes Using High-Resolution Two-Dimensional Gel Electrophoresis
Authors: Hajduch Martin , Casteel Jill E. , Hurrelmeyer Katherine E. , Song Zhao , Agrawal Ganesh Kumar , Thelen Jay J.
Published: March 2006

Brassica napus (cultivar Reston) seed proteins were analyzed at 2, 3, 4, 5, and 6 weeks after flowering in biological quadruplicate using two-dimensional gel electrophoresis. Developmental expression profiles for 794 protein spot groups were established and hierarchical cluster analysis revealed 12 different expression trends. Tryptic peptides from each spot group were analyzed in duplicate using matrix-assisted laser desorption ionization time-of-flight mass spectrometry and liquid chromatography-tandem mass spectrometry. The identity of 517 spot groups was determined, representing 289 nonredundant proteins. These proteins were classified into 14 functional categories based upon the Arabidopsis (Arabidopsisthaliana) genome classification scheme. Energy and metabolism related proteins were highly represented in developing seed, accounting for 24.3% and 16.8% of the total proteins, respectively. Analysis of subclasses within the metabolism group revealed coordinated expression during seed filling. The influence of prominently expressed seed storage proteins on relative quantification data is discussed and an in silico subtraction method is presented. The preponderance of energy and metabolic proteins detected in this study provides an in-depth proteomic view on carbon assimilation in B. napus seed. These data suggest that sugar mobilization from glucose to coenzyme A and its acyl derivative is a collaboration between the cytosol and plastids and that temporal control of enzymes and pathways extends beyond transcription. This study provides a systematic analysis of metabolic processes operating in developing B. napus seed from the perspective of protein expression. Data generated from this study have been deposited into a web database (http://oilseedproteomics.missouri.edu) that is accessible to the public domain.
Recruitment of Novel Calcium-Binding Proteins for Root Nodule Symbiosis in Medicago truncatula
Authors: Liu Junqi , Miller Susan S. , Graham Michelle , Bucciarelli Bruna , Catalano Christina M. , Sherrier D. Janine , Samac Deborah A. , Ivashuta Sergey , Fedorova Maria , Matsumoto Peter , Gantt J. Stephen , Vance Carroll P.
Published: March 2006

Legume rhizobia symbiotic nitrogen (N2) fixation plays a critical role in sustainable nitrogen management in agriculture and in the Earth's nitrogen cycle. Signaling between rhizobia and legumes initiates development of a unique plant organ, the root nodule, where bacteria undergo endocytosis and become surrounded by a plant membrane to form a symbiosome. Between this membrane and the encased bacteria exists a matrix-filled space (the symbiosome space) that is thought to contain a mixture of plant- and bacteria-derived proteins. Maintenance of the symbiosis state requires continuous communication between the plant and bacterial partners. Here, we show in the model legume Medicago truncatula that a novel family of six calmodulin-like proteins (CaMLs), expressed specifically in root nodules, are localized within the symbiosome space. All six nodule-specific CaML genes are clustered in the M. truncatula genome, along with two other nodule-specific genes, nodulin-22 and nodulin-25. Sequence comparisons and phylogenetic analysis suggest that an unequal recombination event occurred between nodulin-25 and a nearby calmodulin, which gave rise to the first CaML, and the gene family evolved by tandem duplication and divergence. The data provide striking evidence for the recruitment of a ubiquitous Ca2+-binding gene for symbiotic purposes.
Carbonic Anhydrase and Its Influence on Carbon Isotope Discrimination during C4 Photosynthesis. Insights from Antisense RNA in Flaveria bidentis
Authors: Cousins Asaph B. , Badger Murray R. , von Caemmerer Susanne
Published: March 2006

In C4 plants, carbonic anhydrase (CA) facilitates both the chemical and isotopic equilibration of atmospheric CO2 and bicarbonate (HCO3−) in the mesophyll cytoplasm. The CA-catalyzed reaction is essential for C4 photosynthesis, and the model of carbon isotope discrimination (Δ13C) in C4 plants predicts that changes in CA activity will influence Δ13C. However, experimentally, the influence of CA on Δ13C has not been demonstrated in C4 plants. Here, we compared measurements of Δ13C during C4 photosynthesis in Flaveria bidentis wild-type plants with F. bidentis plants with reduced levels of CA due to the expression of antisense constructs targeted to a putative mesophyll cytosolic CA. Plants with reduced CA activity had greater Δ13C, which was also evident in the leaf dry matter carbon isotope composition (δ13C). Contrary to the isotope measurements, photosynthetic rates were not affected until CA activity was less than 20% of wild type. Measurements of Δ13C, δ13C of leaf dry matter, and rates of net CO2 assimilation were all dramatically altered when CA activity was less than 5% of wild type. CA activity in wild-type F. bidentis is sufficient to maintain net CO2 assimilation; however, reducing leaf CA activity has a relatively large influence on Δ13C, often without changes in net CO2 assimilation. Our data indicate that the extent of CA activity in C4 leaves needs to be taken into account when using Δ13C and/or δ13C to model the response of C4 photosynthesis to changing environmental conditions.
CYP707A1 and CYP707A2, Which Encode Abscisic Acid 8′-Hydroxylases, Are Indispensable for Proper Control of Seed Dormancy and Germination in Arabidopsis
Authors: Okamoto Masanori , Kuwahara Ayuko , Seo Mistunori , Kushiro Tetsuo , Asami Tadao , Hirai Nobuhiro , Kamiya Yuji , Koshiba Tomokazu , Nambara Eiji
Published: March 2006

Endogenous abscisic acid (ABA) levels are regulated by both biosynthesis and catabolism of the hormone. ABA 8′-hydroxylase is considered to be the key catabolic enzyme in many physiological processes. We have previously identified that four members of the Arabidopsis (Arabidopsis thaliana) CYP707A gene family (CYP707A1 to CYP707A4) encode ABA 8′-hydroxylases, and that the cyp707a2 mutants showed an increase in ABA levels in dry and imbibed seeds. In this study, we showed that the cyp707a1 mutant accumulated ABA to higher levels in dry seeds than the cyp707a2 mutant. Expression analysis showed that the CYP707A1 was expressed predominantly during mid-maturation and was down-regulated during late-maturation. Concomitantly, the CYP707A2 transcript levels increased from late-maturation to mature dry seed. Phenotypic analysis of single and double cyp707a mutants indicates that the CYP707A1 is important for reducing ABA levels during mid-maturation. On the other hand, CYP707A2 is responsible for the regulation of ABA levels from late-maturation to germination. Moreover, CYP707A1 and CYP707A3 were also shown to be involved in postgermination growth. Spatial expression analysis suggests that CYP707A1 was expressed predominantly in embryo during mid-maturation, whereas CYP707A2 expression was detected in both embryo and endosperm from late-maturation to germination. Our results demonstrate that each CYP707A gene plays a distinct role during seed development and postgermination growth.
Microradian X-ray diffraction in colloidal photonic crystals
Authors: Petukhov A. V. , Thijssen J. H. J. , 't Hart D. C. , Imhof A. , van Blaaderen A. , Dolbnya I. P. , Snigirev A. , Moussaïd A. , Snigireva I.
Published: March 2006

Ultra-high-resolution small-angle X-ray scattering in various colloidal photonic crystals is reported. It is demonstrated that an angular resolution of about two microradians is readily achievable at a third-generation synchrotron source using compound refractive optics. The scheme allows fast acquisition of two-dimensional X-ray diffraction data and can be realised at sample–detector separations of only a few metres. As a result, diffraction measurements in colloidal crystals with interplanar spacings larger than a micrometre, as well as determination of the range of various order parameters from the width of the Bragg peaks, are made possible.
The combined use of Patterson and Monte Carlo methods for the decomposition of a powder diffraction pattern
Authors: Altomare Angela , Cuocci Corrado , Giacovazzo Carmelo , Moliterni Anna Grazia Giuseppina , Rizzi Rosanna
Published: March 2006

The success ofab initiocrystal structure solution by powder diffraction data is strictly related to the quality of the integrated intensity estimates. A new method that is able to improve the pattern decomposition step has been developed. It combines the inversion of a suitably modified Patterson map with the use of the Hamming codes [13,10] and [40,36] in order to explore more decomposition trials. The new approach has been introduced inEXPO2005, an updated version ofEXPO2004, and successfully applied to a set of known organic and inorganic structures.
Angle calculations for a three-circle goniostat
Authors: Thorkildsen Gunnar , Larsen Helge B. , Beukes Jon Are
Published: March 2006

A general procedure for angle calculations for a three-circle goniostat has been developed. This new approach is based on a vector description of the transformation of a reciprocal-lattice vector under the action of a rotation shaft. It does not invoke the use of rotation matrices and applies equally well to cases where the directions of the rotation axes do not conform with coordinate axes of the laboratory system adopted for the analysis.
High-pressure X-ray investigation of zincite ZnO single crystals using diamond anvils with an improved shape
Authors: Sowa Heidrun , Ahsbahs Hans
Published: March 2006

A high-pressure cell for single-crystal investigations requires large opening angles. If it does not contain any beryllium but only two diamonds mounted on steel backing plates, normally only lower pressures can be attained without risk of disruption of the diamond anvils [Ahsbahs (2004).Z. Kristallogr.219, 305–308]. In order to enable pressures up to at least 10 GPa, specially shaped anvils were designed. In a first study with such anvils, the high-pressure behaviour of zincite ZnO was investigated up to the transition pressure of about 9.5 GPa. A slight decrease of the axial ratioc/awith increasing pressure was observed. The fit of the Birch–Murnaghan equation of state gave a bulk modulusK= 146.5 (8) GPa with a fixed pressure derivativeK′ = 4. During the phase transformation, the single crystals were destroyed. The pronounced preferred orientation of the obtained material, however, enabled the determination of the orientation relations between the low-pressure wurtzite-type and the high-pressure NaCl-type phase. The orientation relations are similar to those in CdS and CdSe.
Glancing-incidence X-ray diffraction for depth profiling of polycrystalline layers
Authors: Colombi Paolo , Zanola Paolo , Bontempi Elza , Roberti Roberto , Gelfi Marcello , Depero Laura E.
Published: March 2006

On the basis of glancing-incidence X-ray diffraction (GIXRD) spectra collected at different incidence angles, it is possible to obtain structural information at different depths. In the case of an ideal crystalline material, the integrated intensity of each crystalline-phase reflection is correlated to the irradiated volume of the phase. In this work, it is shown that quantitative information on the thickness of thin polycrystalline layers can be obtained by means of GIXRD. Experiments have been performed on thin films of gold with different thicknesses, sputtered on glass slides. The film thickness has been carefully evaluated by X-ray reflectivity (XRR) experiments. XRR and GIXRD data are compared, and the consistency of the thickness values of the crystalline gold layer is shown.
Growth and structure of α-lactalbumin nanotubes
Authors: Graveland-Bikker J. F. , Fritz G. , Glatter O. , de Kruif C. G.
Published: March 2006

Partial hydrolysis of α-lactalbumin by a protease fromBacillus licheniformisunder appropriate conditions leads to the formation of nanotubular structures. The growth of α-lactalbumin nanotubes and their dimensions were analysed using transmission electron microscopy, static light scattering and small-angle X-ray scattering. The scattering data were fitted using a model describing the growth of the tubes and using the form factor of a hollow tube. The cylinder diameter was calculated to be 19.9 (2) nm and the cavity diameter 8.7 (7) nm. The elongation rate of the nanotubes was about 10 nm min−1under the experimental conditions.