bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA sequence selectivity of human topoisomerase I‐mediated DNA cleavage induced by camptothecin
Authors: Punchihewa Chandanamali , Carver Megan , Yang Danzhou
Published: April 2009

In probing the mechanism of inhibition of hypoxia inducible factor (HIF‐1) by campothecins, we investigated the ability of human topoisomerase I to bind and cleave HIF‐1 response element (HRE), which contains the known camptothecin‐mediated topoisomerase I cleavage site 5′‐TG. We observed that the selection of 5′‐TG by human topoisomerase I and topotecan depends to a large extent on the specific flanking sequences, and that the presence of a G at the −2 position (where cleavage occurs between −1 and +1) prevents the HRE site from being a preferred site for such cleavage. Furthermore, the presence of −2 T/A can induce the cleavage at a less preferred TC or TA site. However, in the absence of a more preferred site, the HRE site is shown to be cleaved by human topoisomerase I in the presence of topotecan. Thus, it is implied that the −2 base has a significant influence on the selection of the camptothecin‐mediated Topo I cleavage site, which can overcome the preference for +1G. While the cleavage site recognition has been known to be based on the concerted effect of several bases spanning the cleavage site, such a determining effect of an individual base has not been previously recognized. A possible base‐specific interaction between DNA and topoisomerase I may be responsible for this sequence selectivity.
Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 automethylation using top–down high resolution tandem mass spectrometry
Authors: Kuhn Peter , Xu Qingge , Cline Erika , Zhang Di , Ge Ying , Xu Wei
Published: April 2009

Coactivator‐associated arginine methyltransferase 1 (CARM1), originally defined as a coactivator for steroid receptors, is a member of the protein arginine methyltransferases. Here, we report the discovery and characterization of an automethylation event by AgCARM1, a CARM1 homologue in the mosquito Anopheles gambiae, using top–down high resolution tandem mass spectrometry, which allows fine mapping of modifications in the intact protein accurately and quantitatively without priori knowledge. Unexpectedly, we found that AgCARM1 has already been predominantly dimethylated during its expression in Escherichia coli. A single arginine methylation site, R485, was identified which is conserved among CARM1 in insects. No methylation was observed in the intact AgCARM1R485K mutant where R485 is mutated to lysine, which confirms that R485 is the only detectable methylation site. Using AgCARM1 methyltransferase defective mutants, we confirmed that this is an automethylation event and show the automethylation of AgCARM1 occurs intermolecularly. This study represents the first comprehensive characterization of an automethylation event by top–down mass spectrometry. The unexpected high percentage of automethylated recombinant AgCARM1 expressed in E. coli may shed light on other bacterially expressed post‐translational modifying enzymes, which could be modified but overlooked in biochemical and structural studies. Top–down high resolution tandem mass spectrometry thus provides unique opportunities for revealing unexpected protein modification, localizing specific modification to one amino acid, and delineating molecular mechanism of an enzyme.
Direct and indirect roles of His‐418 in metal binding and in the activity of β‐galactosidase (E. coli)
Authors: Juers Douglas H. , Rob Beatrice , Dugdale Megan L. , Rahimzadeh Nastaron , Giang Clarence , Lee Michelle , Matthews Brian W. , Huber Reuben E.
Published: April 2009

The active site of ß‐galactosidase (E. coli) contains a Mg2+ ion ligated by Glu‐416, His‐418 and Glu‐461 plus three water molecules. A Na+ ion binds nearby. To better understand the role of the active site Mg2+ and its ligands, His‐418 was substituted with Asn, Glu and Phe. The Asn‐418 and Glu‐418 variants could be crystallized and the structures were shown to be very similar to native enzyme. The Glu‐418 variant showed increased mobility of some residues in the active site, which explains why the substitutions at the Mg2+ site also reduce Na+ binding affinity. The Phe variant had reduced stability, bound Mg2+ weakly and could not be crystallized. All three variants have low catalytic activity due to large decreases in the degalactosylation rate. Large decreases in substrate binding affinity were also observed but transition state analogs bound as well or better than to native. The results indicate that His‐418, together with the Mg2+, modulate the central role of Glu‐461 in binding and as a general acid/base catalyst in the overall catalytic mechanism. Glucose binding as an acceptor was also dramatically decreased, indicating that His‐418 is very important for the formation of allolactose (the natural inducer of the lac operon).
Probing the conformation of the resting state of a bacterial multidrug ABC transporter, BmrA, by a site‐directed spin labeling approach
Authors: Do Cao Marie‐Ange , Crouzy Serge , Kim Miyeon , Becchi Michel , Cafiso David S. , Pietro Attilio Di , Jault Jean‐Michel
Published: April 2009

Previously published 3‐D structures of a prototypic ATP‐binding cassette (ABC) transporter, MsbA, have been recently corrected revealing large rigid‐body motions possibly linked to its catalytic cycle. Here, a closely related multidrug bacterial ABC transporter, BmrA, was studied using site‐directed spin labeling by focusing on a region connecting the transmembrane domain and the nucleotide‐binding domain (NBD). Electron paramagnetic resonance (EPR) spectra of single spin‐labeled cysteine mutants suggests that, in the resting state, this sub‐domain essentially adopts a partially extended conformation, which is consistent with the crystal structures of MsbA and Sav1866. Interestingly, one of the single point mutants (Q333C) yielded an immobilized EPR spectrum that could arise from a direct interaction with a vicinal tyrosine residue. Inspection of different BmrA models pointed to Y408, within the NBD, as the putative interacting partner, and its mutation to a Phe residue indeed dramatically modified the EPR spectra of the spin labeled Q333C. Moreover, unlike the Y408F mutation, the Y408A mutation abolished both ATPase activity and drug transport of BmrA, suggesting that a nonpolar bulky residue is required at this position. The spatial proximity of Q333 and Y408 was also confirmed by formation of a disulfide bond when both Q333 and T407 (or S409) were replaced jointly by a cysteine residue. Overall, these results indicate that the two regions surrounding Q333 and Y408 are close together in the 3‐D structure of BmrA and that residues within these two sub‐domains are essential for proper functioning of this transporter.
Motif‐directed flexible backbone design of functional interactions
Authors: Havranek James J. , Baker David
Published: April 2009

Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse‐grained sampling of possible side‐chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side‐chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side‐chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movements that can give rise to any specified set of desired side‐chain atomic placements and interactions, using protein–DNA interfaces as a model system. We use a library of previously observed protein–DNA interactions (motifs) and a rotamer‐based description of side‐chain conformation freedom to identify placements for the protein backbone that can give rise to a favorable side‐chain interaction with DNA. We describe a tree‐search algorithm for identifying those combinations of interactions from the library that can be realized with minimal perturbation of the protein backbone. We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations.
Evolutionary constraints on structural similarity in orthologs and paralogs
Authors: Peterson Mark E. , Chen Feng , Saven Jeffery G. , Roos David S. , Babbitt Patricia C. , Sali Andrej
Published: April 2009

Although a quantitative relationship between sequence similarity and structural similarity has long been established, little is known about the impact of orthology on the relationship between protein sequence and structure. Among homologs, orthologs (derived by speciation) more frequently have similar functions than paralogs (derived by duplication). Here, we hypothesize that an orthologous pair will tend to exhibit greater structural similarity than a paralogous pair at the same level of sequence similarity. To test this hypothesis, we used 284,459 pairwise structure‐based alignments of 12,634 unique domains from SCOP as well as orthology and paralogy assignments from OrthoMCL DB. We divided the comparisons by sequence identity and determined whether the sequence‐structure relationship differed between the orthologs and paralogs. We found that at levels of sequence identity between 30 and 70%, orthologous domain pairs indeed tend to be significantly more structurally similar than paralogous pairs at the same level of sequence identity. An even larger difference is found when comparing ligand binding residues instead of whole domains. These differences between orthologs and paralogs are expected to be useful for selecting template structures in comparative modeling and target proteins in structural genomics.
Real‐time response in AdS/CFT with application to spinors
Authors: Iqbal N. , Liu H.
Published: April 2009

We discuss a simple derivation of the real‐time AdS/CFT prescription as an analytic continuation of the corresponding problem in Euclidean signature. We then extend the formalism to spinor operators and apply it to the examples of real‐time fermionic correlators in CFTs dual to pure AdS and the BTZ black hole.
Is N = 8 supergravity a finite field theory?
Authors: Stelle K.S.
Published: April 2009

Advances in calculational technique permit the study of ultraviolet structure in maximal super Yang‐Mills and maximal supergravity theories at heretofore unattainable loop orders. Hints from string theory suggest that maximal supergravity might have a similar ultraviolet behavior in D = 4 spacetime dimensions as maximal super Yang‐Mills theory and so be ultraviolet convergent. Yet what is known of field theoretic nonrenormalization theorems suggests only that ${1 \over 2}$‐BPS counterterms are excluded. A key test of the relative finiteness properties of the two theories will be the ultraviolet divergences in D = 5 maximal supergravity at the four‐loop level.
A century of process safety—And more
Authors: Crowl Daniel A.
Published: April 2009

In November of 2008 the American Institute of Chemical Engineers convened in Philadelphia to celebrate their 100th anniversary. During that celebration a special session was offered entitled “A Century of Process Safety.” The session was co‐chaired by Dan Crowl of Michigan Tech University and Bruce Vaughen of Cabot Corporation. The session was sponsored by the AIChE Education Division, the AIChE Center for Chemical Process Safety, and the AIChE Safety and Health Division.

This session brought together noted AIChE process safety professionals to review the history of process safety at AIChE and to highlight the technical and educational accomplishments achieved. This included a history of (a) safety in industry, (b) the U.S. Occupational Safety and Health Administration, (c) the Safety and Health Division, (d) the Center for Chemical Process Safety, and (e) the Safety and Chemical Engineering Education (SACHE) Program. Two chemical companies, Dupont and Air Products, presented historical perspectives on their safety programs and provided perspectives on recent industrial progress.

This article provides an introduction to this unique series of papers and also presents additional historical detail. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
A history of process safety and loss prevention in the American Institute of Chemical Engineers
Authors: Hendershot Dennis C.
Published: April 2009

Process safety has always been an important consideration in chemical engineering, and the activities of the American Institute of Chemical Engineers (AIChE) have expanded over the years to more formally focus on this critical aspect of chemical engineering practice. Early initiatives included the annual symposia on Safety in Ammonia and Related Plants, dating back to the early 1950s, and the Loss Prevention Symposium, first held in 1967. These activities led to the formation of the AIChE's Safety and Health Division in 1979, and the division assumed responsibility for these existing programming activities. Following the Bhopal tragedy in India, AIChE formed the Center for Chemical Process Safety (CCPS) in 1985 as an industry alliance to share and enhance process safety expertise in the industry. One of the early CCPS activities was the creation of the Safety and Chemical Engineering Education (SACHE) program to enhance teaching of process safety in the university chemical engineering curriculum. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
Risk analysis for operation of aluminum heat exchangers contaminated by mercury
Authors: Wilhelm S. Mark
Published: April 2009

Brazed aluminum plate‐fin heat exchangers are extensively used in gas separation processes including LNG, LPG, NGL, nitrogen rejection and olefins manufacture. In situations where mercury is a trace component of feed gas or liquid feeds to crackers, condensation of liquid or precipitation of solid mercury can occur in heat exchanger passes, even with functional mercury removal systems in place. Mercury in liquid phase causes, under certain well‐defined conditions, liquid metal embrittlement of susceptible metallurgy or amalgam corrosion of core fins, both of which can lead to sudden loss of pressure containment. Mercury‐contaminated aluminum heat exchangers require close scrutiny and quantitative risk assessment to allow safe operation, remediation or to justify replacement. The risk analysis procedure involves computational prediction of mercury deposition, inspection of critical areas, detailed assessment of metallurgy and fabrication, strain analysis of temperature changes during trips and shutdowns and oxide fatigue analysis. Assigning probability of equipment failure requires a complete understanding of the mechanisms of liquid metal embrittlement and amalgam corrosion that operate on aluminum plate‐fin heat exchangers. Statistical correlations to known failures are essential to assignment of probability‐based risk factors. Probabilities of leak and rupture failure modes can be estimated using amounts and locations of mercury deposits determined from focused inspection or calculated thermodynamically. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
Integration of safety management effectiveness into QRA calculations
Authors: Acikalin Aydan
Published: April 2009

Quantitative Risk Analysis (QRA) has become an often used method in the process industry for improving safety and for land‐use planning. In computing the risk by this methodology the frequency of an accident is often assessed by using generic failure frequencies which are based on historical data of incidents from databases. Little or no adjustment is made for the effectiveness of the safety management of the industrial site. Since most incidents are caused by management problems, QRA has to take into account the local safety management system. Otherwise, the results of QRA will not provide reliable information of the hazards and the corresponding risk from installations. Therefore, today's understanding of safe industrial operations requires an integrated risk assessment under the consideration of technical, organizational, and managerial aspects.

This article describes a method which allows assessing the effectiveness of the local safety management system and its integration into the QRA using a single management factor. This method was developed with the aim of providing a tool which would allocate a quantitative measure for the effectiveness of the local Safety Management System for the purpose of using it directly in the QRA. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
Reactive chemicals emergency response and post‐event calorimetric testing
Authors: Frurip David , Bakkum Koos , Johnstone Harold , Tesolin‐Gee Amy , Vallieu Brian , Van Gelder Klaas
Published: April 2009

A serious upset in process conditions may result in a Reactive Chemicals incident. In such an emergency, procedures must be implemented to prevent injuries, mitigate the event and minimize property loss and/or environmental release as dictated by the required facility Emergency Plan. This article describes the process the Dow Chemical Company uses for engaging Reactive Chemicals experts in an emergency situation. In order to be effective, the Reactive Chemicals expert must have or be provided with in‐depth knowledge of the process streams and raw materials involved. The information is crucial for understanding what is happening, what might happen in the immediate future, and what can be done to successfully mitigate the Reactive Chemicals incident. Following the incident, calorimetric experiments are typically performed to confirm or refute the hypotheses of what caused the event; additionally, the experiments provide information as to reactive chemicals hazards that may potentially still exist in the process streams. The aforementioned process will be illustrated by describing an actual event.

Useful methods are described and recommended for (a) characterizing and storing reactive chemicals, and (b) responding and mitigating safety incidents with reactive chemicals. The role of a reactive chemicals “expert” during and after a plant emergency is important and potentially critical to the safe handling of an ongoing event and also in determining the root cause of the incident. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2010
Improving process safety by addressing the human element
Authors: Haesle John , Devlin Chris , Mccavit Jack L.
Published: April 2009

Celanese had several process safety incidents and near misses in 1996. Although there were several root causes, this article will address only one of them; human error. The system which was developed by Celanese to improve this human element is the conduct of operations system. The conduct of operations system has improved process safety performance of the human element by focusing on three operational areas: training, procedures, and general operations.

Conduct of operations is a proactive approach to improve the current practices, improve the support systems and the behavior of the operator. The benefits include the following:

Consistent application of training and procedures

Reduction in human error, and

Less process safety incidents

This article will describe the need for and the content of conduct of operations system as implemented by Celanese. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
Effects of pyrrolizidine alkaloids on the performance of plant‐parasitic and free‐living nematodes
Authors: Thoden Tim C , Boppré Michael , Hallmann Johannes
Published: April 2009

BACKGROUND: Chemical nematicides such as methyl bromide have for decades played a significant role in the management of plant‐parasitic nematodes. Their application is problematic because of negative environmental impacts, and therefore methyl bromide was phased out in Europe in 2005. A possible alternative to synthetically derived nematicides is seen in the use of plants and/or their secondary metabolites. These plants could either be used as nematicidal green manure or as a source for nematicidal extracts. This study aimed to evaluate the effects of 1,2‐dehydropyrrolizidine alkaloids (PAs), a group of secondary plant metabolites found in hundreds of plant species throughout the world, on the performance of plant‐parasitic and free‐living nematodes.

RESULTS: PAs induced nematicidal, ovicidal and repellent effects on different plant‐parasitic and free‐living nematodes. There was no conclusive ranking in toxicity for the different structural types of PAs tested. However, the effects were often more pronounced for the tertiary than for the oxidised form of PAs. Further, large differences were observed in the susceptibility of different nematode species to PAs.

CONCLUSIONS: PAs do affect several performance parameters and developmental stages of nematodes. Therefore, PA‐producing plants such as species of Crotalaria, Ageratum or Senecio might be promising candidates for nematode management strategies. [Correction made here after initial online publication] Copyright © 2009 Society of Chemical Industry
Folding transitions in calpain activator peptides studied by solution NMR spectroscopy
Authors: Toke Orsolya , Bánóczi Zoltán , Tárkányi Gábor , Friedrich Péter , Hudecz Ferenc
Published: April 2009

Calpastatin, the endogenous inhibitor of calpain, a cysteine protease in eukaryotic cells, is an intrinsically unstructured protein, which upon binding to the enzyme goes through a conformational change. Peptides calpA (SGKSGMDAALDDLIDTLGG) and calpC (SKPIGPDDAIDALSSDFTS), corresponding to the two conserved subdomains of calpastatin, are known to activate calpain and increase the Ca2+ sensitivity of the enzyme. Using solution NMR spectroscopy, here we show that calpA and calpC are disordered in water but assume an α‐helical conformation in 50% CD3OH. The position and length of the helices are in agreement with those described in the literature for the bound state of the corresponding segments of calpastatin suggesting that the latter might be structurally primed for the interaction with its target. According to our data, the presence of Ca2+ induces a backbone rearrangement in the peptides, an effect that may contribute to setting the fine conformational balance required for the interaction of the peptides with calpain. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Spectroscopic ellipsometry studies of Mg‐doped ZnO thin films prepared by the sol–gel method
Authors: Yang Shenghong , Liu Ying , Zhang Yueli , Mo Dang
Published: April 2009

Zn1–x Mgx O (ZMO) thin films with x = 0, 0.1, 0.2, and 0.3 were prepared on Si(100) substrates by the sol–gel method. The influence of Mg content on the structural and the optical properties was studied by X‐ray diffraction and spectroscopic ellipsometry (SE) in the UV–visible region. The measured SE spectra were analyzed with an appropriate procedure to accurately determine the thickness and the optical constants of the thin films. It was found that the optical constants of the ZMO films are functions of the film composition. The refractive indices of the ZMO films decrease with increasing Mg content, and the optical bandgap energy exhibits nonlinear behavior or a bowing effect with the change of Mg mole fraction. A maximum band gap of ∼3.91 eV was achieved at x = 0.3. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strong modes discrimination and low threshold in cw regime of 1300 nm AlInGaAs/InP VCSEL induced by photonic crystal
Authors: Czyszanowski Tomasz , Sarzała Robert P. , Dems Maciej , Thienpont Hugo , Nakwaski Włodzimierz , Panajotov Krassimir
Published: April 2009

A self‐consistent electrical‐thermal‐optical‐gain modeling of threshold characteristics of an InP‐based 1300 nm AlInGaAs photonic‐crystal vertical‐cavity surface‐emitting diode laser is presented. It is shown that low threshold characteristics and strong transverse‐mode discrimination can be simultaneously achieved for optimized photonic crystal structure and current aperture. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High performance and high reliability AlGaN/GaN HEMTs
Authors: Kikkawa Toshihide , Makiyama Kozo , Ohki Toshihiro , Kanamura Masahito , Imanishi Kenji , Hara Naoki , Joshin Kazukiyo
Published: April 2009

In this paper, a current status and future technologies of high‐power GaN HEMTs was described. First, commercialization roadmap was shown with output power and efficiency status. Power electronics benchmark was also introduced. Reliability improvement technologies were addressed with recent issues such as drift phenomena. Then, future requirements for expanding GaN electronics market were shown with some recent device developments. Novel E‐mode recessed GaN‐HEMT has been developed using the triple cap layer structure. High‐k insulated gate HEMTs using Ta2O5 were also developed. Finally, we described the next generation GaN HEMTs for millimeter‐wave applications. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
CIGS solar cell with CdS buffer layer deposited by ammonia‐free process
Authors: Komaki H. , Yamada A. , Sakurai K. , Ishizuka S. , Kamikawa‐Shimizu Y. , Matsubara K. , Shibata H. , Niki S.
Published: April 2009

We have successfully fabricated high‐efficiency CuInGaSe2 (CIGS) solar cells with CdS film deposited by ammonia‐free process. The CdS films were formed on CIGS films by chemical bath deposition from an aqueous solution containing cadmium acetate and thioacetamide. The properties of CdS films deposited on soda lime glass were investigated by atomic force microscopy and optical transmission measurement. By optimizing the concentration of the solution used for the formation of CdS films and the thickness of i‐ZnO films used for solar cell production, high‐efficiency ammonia‐free cells were fabricated. The properties of the ammonia‐free cell fabricated by the optimized process were VOC = 0.695 V, JSC = 32.812 mA/cm2, FF = 0.755 and η = 17.22%. These values are comparable to those of the cells produced by the conventional process using ammonia. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Whispering gallery modes in silicon nanocrystal coated microcavities
Authors: Bianucci P. , Rodríguez J. R. , Clements C. , Hessel C. M. , Veinot J. G. C. , Meldrum A.
Published: April 2009

We present photoluminescence studies of silicon‐nanocrystal (Si‐NC) coated microcavities. The particular geometries studied are hollow fibers where there is a Si‐NC coating in the inner surface and regular optical fibers and glass microspheres where the coating is on the outside surface. The coatings were prepared using an inexpensive and straightforward solution‐based process that yields a high‐quality film. The measured photoluminescence spectra from the resonators show high Q ‐factor (between 1200 and 2800) resonant modes that correspond with the whispering gallery modes expected from the confinement geometries. The presence of these modes is also an indication that the emission of the Si‐NCs is coupled to the cavity. The combination of Si‐NCs and optical microcavities with strong confinement has promising potential for applications like sensing, optical communications and may be a possible route toward a Si‐NC laser. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The fabrication and optical characterisation of SnO2 cluster films
Authors: Boyd Euan , Henseler Martin J. H. , Mackenzie David M. A. , Brown Simon A.
Published: April 2009

SnO2 nano‐clusters have been produced using a low temperature oxidation process. Tin clusters with a diameter of 7 nm were oxidised by heating in air at 250 °C for 24 hours. The oxidised clusters were studied using transmission electron microscopy (TEM), showing that the clusters do not coalescence or change their size significantly. The optical transmission of 50 nm thick SnO2 cluster films is greater than 90% from 800 nm to 380 nm and shows strong absorption for λ < 380 nm. The photoconductivity was characterised by a large peak at 3.9 eV with a smaller peak at 3.5 eV. Persistent photoconductivity is observed with long characteristic times and a strong dependence on the ambient atmosphere during the measurement. This was attributed to carrier production due to photo‐induced desorption of oxygen from the surface. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Time‐resolved THz spectroscopy in a parallel plate waveguide
Authors: Cooke David G. , Jepsen Peter Uhd
Published: April 2009

We demonstrate time‐resolved terahertz spectroscopy inside a novel parallel plate waveguide where one of the metallic plates is replaced by a transparent conducting oxide. Considerable improvements to the waveguide loss coefficient are shown, with a power absorption coefficient of 4 cm–1 at 0.5 THz. The time resolution of the technique is shown to be limited by the spatial excitation profile, which for sharply focused beams can approach ∼1 ps time scales. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic structure of the amorphous oxide semiconductor a‐InGaZnO4–x: Tauc–Lorentz optical model and origins of subgap states
Authors: Kamiya Toshio , Nomura Kenji , Hosono Hideo
Published: April 2009

This paper discusses an optical model and subgap electronic states for a representative amorphous oxide semiconductor, InGaZnO4 (a‐IGZO). Parameterized optical models were developed based on the Tauc–Lorentz model combined with a Lorentz‐type oscillator. The measured optical absorption spectra exhibit nearly linear dependences on photon energy (E) between 3 eV < E < 5 eV, which requires the transition energies in the Tauc–Lorentz model (E0,TL) being around 4 eV. The optimized parameters for the fixed E0,TL of 3.7 eV are provided for four different a‐IGZO films with root‐mean‐square errors less than 1%. Formation energies of crystalline IGZO, stoichiometric a‐IGZO, oxygen deficient a‐IGZO and their constituent oxides were calculated by the density functional theory using the local density approximation (LDA) and generalized gradient approximation with PBE96 functionals (PBE). PBE gives larger unit cell volumes at the ground states and better agreement in the formation energies than LDA does. The formation energies of an oxygen deficiency in a‐IGZO were calculated to be 3.2–3.5 eV. The calculated electronic structures of stoichiometric a‐IGZO models exhibit somewhat large dispersions for conduction bands (CB), which are not largely affected by the disordered structure in a‐IGZO, while the dispersions of the valence bands (VBs) are very small, unlike the crystalline IGZO, showing that a‐IGZO have strongly localized states at the VB maximums (VBMs). Oxygen‐deficient a‐IGZO models showed that oxygen deficiencies form both a deep localized state at 0.4–1 eV above VBM and a shallow donor state depending on local atomic configurations. An oxygen deficiency that forms a deep state breaks the dispersion of the CB, which could be an origin of the subgap states observed near CB. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Light emission from dark excitons in light emitting devices
Authors: Singh Jai , Kugler S.
Published: April 2009

Applying the first order perturbation theory and a new time‐dependent spin–orbit–photon interaction operator the rate of spontaneous emission from triplet (dark) excitons calculated in organic molecular solids, conjugated polymers and quantum dots is reviewed. The rates are found to be in good agreement with the experimental results in materials where the concept of Wannier–Mott type excitons is applicable, for example, in inorganic amorphous solids, conjugated polymers and quantum dots. In organic molecular solids or molecules, where Frenkel type excitons are formed, the calculated rates do not compare well with experiments. Application of the current theory is critically examined and discussed in light of the traditional approach of the second‐order perturbation theory used for the triplet radiative recombination. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Visible anisotropic deformation of chalcogenide glass by optical force
Authors: Tanaka Keiji , Terakado Nobuaki , Saitoh Akira
Published: April 2009

Semi‐free As2S3 glass flakes undergo sub‐mm scale anisotropic deformation upon illumination of linearly‐polarized cw bandgap light. The mechanism has been ascribed to photo‐induced birefringence, optical torque, and photo‐induced fluidity. Quantitative measurements demonstrate that generated optical torque is ∼10–20 Nm under a light intensity of 1 mW. This value combined with measured deformation rates for As2S3 cantilevers suggests a related photo‐induced fluidity of 10–1 P–1, which is much more fluidal (∼ten orders) than that reported in the conventional photo‐induced fluidity. Reasons for this discrepancy are discussed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coherent phases and magnetoexcitons in graphene
Authors: Lozovik Yu. E. , Sokolik A. A. , Willander M.
Published: April 2009

Unique band structure peculiarities of graphene imply that near Fermi level electrons are described by two‐dimensional Dirac equation for massless particles. We investigate how these peculiarities manifest in electron–hole pairing and properties of indirect magnetoexcitons in two spatially separated, independently gated graphene layers. For electron–hole pairing, we derive asymptotical expressions for the gap in energy spectrum and discuss system behavior at various controlling parameters. We derive dispersion relations for magnetoexcitons and their effective‐mass decompositions, and also discuss a possibility of magnetoexcitonic superfluidity. The systems under consideration can reveal coherent properties, dissipationless currents and Josephson phenomena at room temperature. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electroreflectance spectroscopy on III‐N quantum wells
Authors: Drabinska Aneta , Baranowski Jacek M. , Pakula Krzysztof , Caban Piotr , Strupinski Wlodzimierz
Published: April 2009

In this paper we present electro‐reflectance measurements on 10 nm GaN and 3 nm In0.1Ga0.9N quantum wells. In electro‐reflectance spectrum line from QW, and its evolution with bias is observed. It was possible to reduce to zero internal electric field in quantum well and Stark shift of about 25 meV for 220 kV/cm electric field was measured. The inversion of phase and vanishing to zero of the amplitude of electro‐reflectance signal was observed during the change of direction of electric field in the quantum well. The analysis of Franz–Keldysh oscillations from barriers allowed to discuss the influence of the electric field to the properties of the quantum well. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carrier transport in nanodevices: revisiting the Boltzmann and Wigner distribution functions
Authors: Brosens Fons , Magnus Wim
Published: April 2009

In principle, transport of charged carriers in nanometer sized solid‐state devices can be fully characterized once the non‐equilibrium distribution function describing the carrier ensemble is known. In this light, we have revisited the Boltzmann and the Wigner distribution functions and the framework in which they emerge from the classical respectively quantum mechanical Liouville equation. We have assessed the method of the characteristic curves as a potential workhorse to solve the time dependent Boltzmann equation for carriers propagating through spatially non‐uniform systems, such as nanodevices. In order to validate the proposed solution strategy, we numerically solve the Boltzmann equation for a one‐dimensional conductor mimicking the basic features of a biased low‐dimensional transistor operating in the on‐state. Finally, we propose a computational scheme capable of extending the benefits of the above mentioned solution strategy when it comes to solve the Wigner–Liouville equation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effects of surface transition layers on the phase diagrams and the pyroelectric properties of ferroelectric thin films
Authors: Oubelkacem A. , Esssaoudi I. , Ainane A. , Saber M. , Dujardin F. , Gonzalez J.
Published: April 2009

By taking into account surface transition layers STLs and single surface transition layer SSLs (introduced for comparison), the phase‐transition and pyroelectric properties of ferroelectric thin films described by the transverse Ising model (TIM) are discussed in the framework of the effective‐field theory, based on the probability distribution technique. We discuss an N ‐layer film of simple cubic symmetry with nearest‐neighbor exchange interaction in which the exchange‐interaction strength is assumed to be different from the bulk values in surface layers. We derive and illustrate expressions for the phase‐transition and pyroelectric profiles. We demonstrate that the phase transition depends more strongly on intra‐layer interaction than inter‐layer interaction and the ferroelectricity of a film will disappear at a critical STL thickness if the intra‐layer and inter‐layer interactions are weak. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Release of potassium sorbate from active films of sodium alginate crosslinked with calcium chloride
Authors: Zactiti E. M. , Kieckbusch T. G.
Published: April 2009

The release of potassium sorbate from alginate films was evaluated considering different active agent concentrations in the film and three levels of alginate crosslinking. The mechanism involved in the diffusional process was investigated using the Power Law Model. The results indicated that potassium sorbate diffusion in alginate films has characteristics of Fickian and non‐Fickian behaviour. Effective diffusion coefficients obtained using the solution in series derived from Fick's Second Law are close to values obtained by the short‐time solution, indicating that the influence of swelling on effective diffusivity, although perceptible, is small, allowing the use of an average effective diffusivity. The values of effective diffusivity found indicate that alginate films have a potential use as systems for release of active substances. Copyright © 2009 John Wiley & Sons, Ltd.
Ensemble estimation of background‐error variances in a three‐dimensional variational data assimilation system for the global ocean
Authors: Daget N. , Weaver A. T. , Balmaseda M. A.
Published: April 2009

This paper studies the sensitivity of global ocean analyses to two flow‐dependent formulations of the background‐error standard deviations (σb) for temperature and salinity in a three‐dimensional variational data assimilation (3D‐Var) system. The first formulation is based on an empirical parameterization of σb in terms of the vertical gradients of the background temperature and salinity fields, while the second formulation involves a more sophisticated approach that derives σb from the spread of an ensemble of background states. The ensembles are created by explicitly perturbing both the surface fluxes (wind stress, fresh water and heat) used to force the model and the observations (temperature and salinity profiles) used in the assimilation process. The two formulations are compared in two cycled 3D‐Var experiments for the period 1993‐‐2000. In both experiments, the observation‐error standard deviations (σo) are geographically dependent and estimated from a model‐data comparison prior to assimilation. An additional 3D‐Var experiment that employs the parametrized σb but a simpler σo formulation, and a control experiment involving no data assimilation, were also conducted and used for comparison.

All 3D‐Var experiments produce a significant reduction in the mean and standard deviation of the temperature and salinity innovations compared to those of the control experiment. The largest differences between the two σb formulations occur in the upper 150 m, where the parametrized σb are notably larger than the ensemble σb. In this region, the innovation statistics are slightly better for the parametrized σb. Statistical consistency checks indicate that both schemes underestimate σb, the underestimation being stronger with the ensemble formulation. The error growth between cycles, however, is much reduced with the ensemble σb, suggesting that the analyses produced with the ensemble σb are in better balance than those produced with the parametrized σb. This claim is supported by independent data comparisons involving model fields not directly constrained by the assimilated temperature and salinity profiles. In particular, sea‐surface height (SSH) anomalies in the northwest Atlantic and zonal velocities in the equatorial Pacific are clearly better with the ensemble σb than with the parametrized σb. Results also show that while some aspects of those variables are improved with data assimilation (SSH anomalies and currents in the central and eastern Pacific), other aspects are degraded (SSH anomalies in the northwest Atlantic, currents in the western Pacific). Areas for improving the ensemble method and for making better use of the ensemble information are discussed. Copyright © 2009 Royal Meteorological Society
Achieving super‐resolution X‐ray imaging with mobile C‐arm devices
Authors: Bodensteiner C. , Darolti C. , Schweikard A.
Published: April 2009

Background

The term super‐resolution refers to the process of combining a set of low‐resolution images into a high‐resolution image using image processing methods. This work is concerned with the reconstruction of high‐resolution X‐ray images. Specifically, we address the problem of acquiring X‐ray images from multiple, very close view points.

Methods

We propose to use a novel experimental robotic C‐arm device to create high‐resolution X‐ray images. For this purpose, we suggest different strategies for acquiring multiple low‐resolution images, and we provide the steps to achieve acquisition‐error compensation. Compared to visible light images, X‐ray images have the particularity that parallax effects render super‐resolution very difficult. Using the acquired multi‐frame data, we evaluate recent well‐known super‐resolution reconstruction algorithms. The same algorithms are evaluated based on synthetic 3D phantom data and real X‐ray images.

Results

In experiments with both synthetic and real projection data, we successfully reconstruct up to four times higher‐resolution images. These images reveal structures and details which are not perceivable in the low‐resolution images.

Conclusions

The advantage of super‐resolution techniques for X‐ray is the potential reduction of radiation dose for patients and medical personnel. Potential medical applications include the diagnosis of early‐stage osteoporosis and the detection of very small calcifications. Copyright © 2009 John Wiley & Sons, Ltd.
Analytical formulation to compute QFT bounds: The envelope method
Authors: Martín‐Romero Juan José , Gil‐Martínez Montserrat , García‐Sanz Mario
Published: April 2009

This paper describes an analytical formulation to compute quantitative feedback theory (QFT) bounds in one‐degree‐of‐freedom feedback control problems. The new approach is based on envelope curves and shows that a QFT control specification can be expressed as a family of circumferences. Then, the controller bound is defined by the envelope curve of this family and can be obtained as an analytical function. This offers the possibility of studying the QFT bounds in an analytical way with several useful properties. Gridding methods are avoided, resulting in a lower computational effort procedure. The new formulation improves the accuracy of previous methods and allows the designer to calculate multivalued bounds. Copyright © 2009 John Wiley & Sons, Ltd.
Examination of the interface of a model adhesive joint by surface analysis: a study by XPS and ToF‐SIMS
Authors: Abel Marie‐Laure , Watts John F
Published: April 2009

Model samples of the interface of an adhesive joint containing small levels of aminopropyl triethoxysilane (APS) have been prepared in order to examine the interface formed with an aluminium substrate. X‐ray photoelectron spectroscopy (XPS) and time of flight secondary ion mass spectrometry (ToF‐SIMS) have been used to analyse and image the interface region in between the aluminium and an epoxy adhesive in order to ascertain the reactions by the organosilane which is present as a minor component within the system.

It was found that APS was present at the interface between the adhesive and the substrate and that it had reacted with the substrate forming a covalent bond and was also crosslinked within the adhesive. Evidence of near to full hydrolysis of APS is also present within the spectra. Copyright © 2009 John Wiley & Sons, Ltd.
Film characteristics of anodic oxidized AZ91D magnesium alloy by applied power
Authors: Jang Yong Seok , Kim Yu Kyoung , Park IL Song , Lee Sook Jeong , Lee Min Ho , Yoon Jeong Mo , Bae Tae Sung
Published: April 2009

This study examined the film characteristics of an anodized AZ91D magnesium alloy by varying the direct current and pulse frequency conditions. In order to evaluate the effect of the pulse frequency on film formation, anodic oxidation was carried out by applying direct current and pulse current at a current density of 300 mA/cm2. Compared with the sample groups treated with the direct current, a large number of small arcs were generated continuously on the film treated with the pulse current and the film formation rate was found to increase. Homogeneous and compact pores were formed with increasing frequency, and the rate of formation was increased rapidly to the arrival voltage. The film thickness increased and the surface roughness decreased with increasing anodic oxidation time at a fixed frequency of 125 Hz. However, treatment for more than 3 min led to decomposition of the oxidized film onto the previously formed film, which caused an increase in the number of cracks and pores within the film. The most uniform and smallest pores were acquired when the surface was anodized for 3 min at a current density and frequency of 300 mA/cm2 and 125 Hz, respectively. X‐ray diffraction revealed the formation of MgO and Mg2SiO4 peaks, with a relative decrease in peak intensity for the MgO and Mg substrate. The Vickers hardness value was higher on the treated groups than on the untreated group, and the potentiodynamic polarization test revealed satisfactory corrosion resistance through a decrease in corrosion density and a large improvement in the corrosion potential. Copyright © 2009 John Wiley & Sons, Ltd.
Post‐oxidizing effects on surface characteristics of salt bath nitrocarburized AISI 02 tool steel type
Authors: Fares M. L. , Chaoui K. , Le Coze J.
Published: April 2009

The effect of post‐oxidizing treatment on the characteristics of modified surface layers produced by salt bath nitrocarburizing on the industrial American Iron and Steel Institute (AISI) 02 tool steel types is investigated. Nitrocarburizing treatment is performed for 6 h and 8 h at 570 °C and post‐oxidizing treatment for 30, 60 and 90 min at 520 °C, using argon–steam mixture. Formed layers are characterized by their basic properties such as thickness layer, depth, surface hardness and wear resistance. Detailed estimation of the modified metal surface quality, in terms of chemical composition, formed phases, microstructures and diffusion mechanisms are performed by metallographic techniques, EDX, X‐ray diffraction, scanning electron microscopy (SEM) and glow discharge optical electron spectroscopy (GDOES). The corrosion resistance was investigated in 0.4 M H2SO4 solutions, using steady‐state electrochemical polarization methods. The obtained results revealed the existence of a superficial oxide layer which consists of magnetite (Fe3O4) and hematite (Fe2O3) and the presence of an ε‐phase associated with a small amount of γ′‐phase. Important improvements in wear, microhardness and corrosion resistance occur after these treatments and it is specifically concluded that the sole application of a nitrocarburizing treatment does not significantly ameliorate the corrosion resistance of the as‐received steel. In fact, post‐oxidation treatment contributes to increase corrosion resistance by forming a dense magnetite layer and at the same time, it partially covers the compound layer pores. Copyright © 2009 John Wiley & Sons, Ltd.