bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced morphological heterogeneity of PCL in the presence of PVC with isothermal supercritical CO2 treatment
Authors: Shieh Yeong‐Tarng , Yang Huang‐Shung
Published: November 2005

This report presents a continuing study of the morphological changes of polycaprolactone (PCL) with isothermal supercritical CO2 treatments at 304 atm and 35 °C in the presence of poly(vinyl chloride) (PVC). DSC and small‐angle X‐ray scattering (SAXS) data find that the CO2‐assisted melting of PCL at 304 atm and 35 °C recrystallized in the presence of PVC during depressurization of CO2 can result in a decreased thickness of crystal lamellar layers. Heterogeneity, with a size (21.7 nm for pure PCL) larger than the crystal layer thickness (8.2 nm for pure PCL) and the amorphous layer thickness (4.4 nm for pure PCL), is formed after the supercritical CO2 treatment. The size of this heterogeneity is found to enhance from 21.7 nm for pure PCL to 29.8 and 34.9 nm for the PCL samples containing 10 and 25 wt % PVC, respectively. These big heterogeneities in the PCL/PVC blends formed during CO2 depressurization might arise from the segregated PVC‐rich amorphous domains that are located between bundles of the lamellar stacks, possibly as a result of the molecular dragging on PCL during depressurization of the PCL‐interacted CO2. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 85–93, 2006
Deposition of Hydrocarbon Films by Means of Helium‐Ethylene Fed Glow Dielectric Barrier Discharges
Authors: Fanelli Fiorenza , Fracassi Francesco , d'Agostino Riccardo
Published: November 2005

Summary: The present work provides a detailed study of helium‐ethylene dielectric barrier glow discharges. The effect of ethylene concentration, total gas flow rate, excitation frequency and applied voltage have been investigated in order to clarify both discharge operational mode, and coating composition. The discharge has been characterized by means of electrical measurements and optical emission spectroscopy, while the stable species contained in the gas effluent have been sampled and analyzed using gas chromatography with mass spectrometry detection to achieve indications on the reactive fragments generated inside the discharge. It has been observed that polyethylene‐like coatings can be obtained for a wide range of electrical conditions, and the deposition rates have been found to range between 20 and 80 nm · min−1.

FT‐IR spectrum of a film deposited by Glow Dielectric Barrier Discharge, GDBD, using a helium‐ethylene containing feed ([C2H4] = 0.4%).

magnified image

FT‐IR spectrum of a film deposited by Glow Dielectric Barrier Discharge, GDBD, using a helium‐ethylene containing feed ([C2H4] = 0.4%).
Protein Oxidation by Chronic Pulmonary Diseases in Children
Authors: Starosta V. , Griese M.
Published: November 2005

The oxidation of proteins may play an important role in the pathogenesis of chronic inflammatory lung diseases, and may contribute to lung damage. However, the extent of oxidation and the distribution among proteins are not known for most pediatric lung diseases. In this work, protein oxidation was assessed as protein carbonyls. Bronchoalveolar lavages (BAL) from children with chronic lung diseases were investigated by dot‐blot assay for content and for pattern of distribution of oxidized proteins by two‐dimensional (2D) electrophoresis and Western blotting. Significantly higher levels of protein oxidation than in healthy controls were determined in groups of patients with interstitial lung disease, gastro‐esophageal reflux disease, and pulmonary alveolar proteinosis. The proteins most sensitive to oxidation were serum albumin, surfactant protein A, and α1‐antitrypsin. Our data show increased oxidative stress in lungs of children with chronic pulmonary diseases, with significant interindividual variations. The extent of protein oxidation was proportional to the count of neutrophilic granulocytes in BAL fluid. These findings strongly support the concept that an abundance of reactive oxygen species produced during neutrophilic inflammation may be a deleterious factor, leading to pulmonary damage in these patients. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.
Tracheobronchopathia Osteochondroplastica in a 9‐year‐old Girl
Authors: Simsek Pelin Ozlem , Ozcelik Ugur , Demirkazik Figen , Unal Omer Faruk , Orhan Diclehan , Aslan Ayse Tana , Dogru Deniz
Published: November 2005

Tracheobroncopathia osteochondroplastica (TO) is a rare disease of adult males characterized by osteocartilagious submucosal nodules protruding into the airway lumen, causing variable degrees of airway obstruction. Here we describe a case of TO in a 9‐year‐old girl patient presenting with chronic cough, along with a brief review of this rare benign condition. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.
Prevalence of Asthma among Qatari Schoolchildren: International Study of Asthma and Allergies in Childhood, Qatar
Authors: Janahi Ibrahim A. , Bener Abdulbari , Bush Andrew
Published: November 2005

The aim of the present study is to determine the prevalence of asthma and allergic diseases among schoolchildren aged 6–14 years in the State of Qatar, based on a questionnaire designed by the International Study of Asthma and Allergy in Childhood (ISAAC). A cross‐sectional study of 3,283 school children living in both urban and rural areas (average age, 9.03 ± 1.99 years; 52.3% boys and 47.7% girls) was conducted between February 2003–February 2004. The population sample had a high prevalence of diagnosed asthma (19.8%), allergic rhinitis (30.5%), eczema (22.5%), and chest infection (11.9%). The frequency of asthma, allergic rhinitis, and eczema among parents reflected the same pattern as seen in their children. Overall, males had more asthma, allergic rhinitis, and chest infections than females. In general, the prevalence rate of asthma and allergic rhinitis decreased with age. The prevalence rate of asthma was significantly higher in mothers (11.8%) than in fathers (9.0%), but the frequency of allergic rhinitis symptoms was comparable (mothers, 18.5%; fathers, 17.5%). The prevalence rate of asthma (19.8%) in Qatari schoolchildren is very close to that in the neighboring Gulf country, Oman (20.7%), and higher than in some developing countries. Genetic factors related to the high rates of consanguinity may play an important role in the high prevalence rates noted in the Qatari population, but changes in lifestyle and environmental factors cannot be discounted as possible causes of the high prevalence noted in this study. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.
Adenotonsillectomy for Obstructive Sleep Apnea in Children with Prader‐Willi Syndrome
Authors: Pavone M. , Paglietti M.G. , Petrone A. , Crinò A. , De Vincentiis G.C. , Cutrera Renato
Published: November 2005

The aim of our study was to evaluate the efficacy of adenotonsillectomy for the treatment of obstructive sleep apnea syndrome (OSA) in pediatric patients with Prader‐Willi syndrome (PWS), and to describe the postoperative complications. Five patients (4 males; median age, 4.4 years; range, 1.6–14.2 years) were studied. All patients underwent an overnight cardiorespiratory sleep study. All patients had adenotonsillar hypertrophy (ATH), and two were also obese. The preoperative obstructive apnea/hypopnea index (AHI; median and range) was 12.2 (9.0–19.9) events/hr; the mean oxygen saturation was 95 (79–96)%; the nadir oxygen saturation was 71 (58–78)%; and the oxygen desaturation index (ODI) was 15.8 (11.4–35.9) events/hr. Preoperatively, patients were classified as having moderate to severe OSA. A second sleep study, performed 16 (3–43) months after adenotonsillectomy, showed a significant decrease in AHI (P = 0.009) and ODI (P = 0.009). Mean and nadir oxygen saturation did not differ significantly postsurgery (P = 0.188, P = 0.073, respectively). Four out of five children showed at least one postoperative complication. Difficult awakening from anesthesia, hemorrhages, and respiratory complications requiring reintubation and/or supplemental oxygen administration were observed. In conclusion, patients with PWS and OSA who underwent adenotonsillectomy showed a significant decrease in AHI and number of oxygen desaturations. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold
Authors: Qiu Yang , Tereshko Valentina , Kim Youngchang , Zhang Rongguang , Collart Frank , Yousef Mohammed , Kossiakoff Anthony , Joachimiak Andrzej
Published: November 2005

The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 Å by using multi‐wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone‐like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z‐score 8.1 and RMSD 3.6 Å over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross‐shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone‐like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Effect of linker segments on the stability of epithelial cadherin domain 2
Authors: Prasad Alka , Zhao Huaying , Rutherford John M. , Housley Nicole , Nichols Corey , Pedigo Susan
Published: November 2005

Epithelial cadherin is a transmembrane protein that is essential in calcium‐dependent cell–cell recognition and adhesion. It contains five independently folded globular domains in its extracellular region. Each domain has a seven‐strand β‐sheet immunoglobulin fold. Short seven‐residue peptide segments connect the globular domains and provide oxygens to chelate calcium ions at the interface between the domains (Nagar et al., Nature 1995;380:360–364). Recently, stability studies of ECAD2 (Prasad et al., Biochemistry 2004;43:8055–8066) were undertaken with the motivation that Domain 2 is a representative domain for this family of proteins. The definition of a domain boundary is somewhat arbitrary; hence, it was important to examine the effect of the adjoining linker regions that connect Domain 2 to the adjacent domains. Present studies employ temperature–denaturation and proteolytic susceptibility to provide insight into the impact of these linkers on Domain 2. The significant findings of our present study are threefold. First, the linker segments destabilize the core domain in the absence of calcium. Second, the destabilization due to addition of the linker segments can be partially reversed by the addition of calcium. Third, sodium chloride stabilizes all constructs. This result implies that electrostatic repulsion is a contributor to destabilization of the core domain by addition of the linkers. Thus, the context of Domain 2 within the whole molecule affects its thermodynamic characteristics. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions
Authors: Ruvinsky A. M. , Kozintsev A. V.
Published: November 2005

We present two novel methods to predict native protein‐ligand binding positions. Both methods identify the native binding position as the most probable position corresponding to a maximum of a probability distribution function (PDF) of possible binding positions in a protein active site. Possible binding positions are the origins of clusters composed, on the basis of root‐mean square deviations (RMSD), from the multiple ligand positions determined by a docking algorithm. The difference between the methods lies in the ways the PDF is derived. To validate the suggested methods, we compare the averaged RMSD of the predicted ligand docked positions relative to the experimentally determined positions for a set of 135 PDB protein‐ligand complexes. We demonstrate that the suggested methods improve docking accuracy by as much as 21–24% in comparison with a method that simply identifies the binding position as the energy top‐scored ligand position. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Molecular surface generation using a variable‐radius solvent probe
Authors: Bhat Sathesh , Purisima Enrico O.
Published: November 2005

Protein–ligand binding occurs through interactions at the molecular surface. Hence, a proper description of this surface is essential to our understanding of the process of molecular recognition. Recent studies have noted the inadequacy of using a fixed 1.4 Å solvent probe radius to generate the molecular surface. This assumes that water molecules approach all surface atoms at an equal distance irrespective of polarity, which is not the case. To adequately model the protein–water boundary requires that the solvent probe radius change according to the polarity of its contacting atoms, smaller near polar atoms and larger near apolar atoms. To our knowledge, no method currently exists to generate the molecular surface of a protein in this manner. Using a modification of the marching tetrahedra algorithm, we present a method to generate molecular surfaces using a variable radius solvent probe. The resulting surface lacks many of the unrealistic small crevices in nonpolar regions that are found when utilizing an invariant 1.4 Å solvent probe, while maintaining the fine detail of the surface at polar regions. On application of the method on a test set of 20 protein structures taken from the Protein Data Bank (PDB), we also find far fewer empty unsolvated cavities that are present when using only a 1.4 Å solvent probe, while the majority of solvated and polar cavities is retained. This suggests that the majority of empty cavities previously observed in protein structures might simply be artifacts of the surfacing method. We also find that the variable probe surface can have significant effects on electrostatic calculations by generating a better tuned description of the protein–water boundary. We also examined the binding interfaces of a diverse set of 55 protein–protein complexes. We find that using a variable probe results in an increase in perceived shape complementarity at these sites compared to using a 1.4 Å solvent probe. The molecular volume and surface area are geometric values that determine various important properties for macromolecules, and the altered description afforded by a variable solvent probe molecular surface can have significant implications in protein recognition, energetics, folding, and stability calculations. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Divalent ion‐binding properties of the two avian β‐parvalbumins
Authors: Henzl Michael T. , Agah Sayeh
Published: November 2005

Birds express three parvalbumins, one α isoform and two β isoforms. The latter are known as avian thymic hormone (ATH) and avian parvalbumin 3. Although both were discovered in thymus tissue, and presumably function in T‐cell maturation, they have been detected in other tissue settings. We have conducted detailed Ca2+‐ and Mg2+‐binding studies on recombinant ATH and the C72S variant of CPV3, employing global analysis of isothermal titration calorimetry data. In Hepes‐buffered saline, ATH binds Ca2+with apparent microscopic binding constants of 2.4 ± 0.2 × 108and 1.0 ± 0.1 × 108M−1. The corresponding values for CPV3‐C72S are substantially lower, 4.5 ± 0.5 × 107and 2.4 ± 0.2 × 107M−1, a 1.9‐kcal/mol difference in binding free energy. Thus, the β‐parvalbumin lineage displays a spectrum of Ca2+‐binding affinity, with ATH and the mammalian β isoform at the high‐ and low‐affinity extremes and CPV3 in the middle. Interestingly, despite its decreased Ca2+affinity, CPV3‐C72S exhibits increased affinity for Mg2+, relative to ATH. Whereas the latter displays Mg2+‐binding constants of 2.2 ± 0.2 × 104and 1.2 ± 0.1 × 104M−1, CPV3‐C72S yields values of 5.0 ± 0.8 × 104and 2.1 ± 0.3 × 104M−1. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 Å resolution reveals the presence of a new PLA2‐like protein with a novel cys 32–Cys 49 disulphide bridge with a bound sugar at the substrate‐binding site
Authors: Jabeen Talat , Singh Nagendra , Singh Rajendra K. , Jasti Jayasankar , Sharma Sujata , Kaur Punit , Srinivasan Alagiri , Singh Tej P.
Published: November 2005

The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2‐like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2‐like protein (Cys–PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importantance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 Å and c = 68.4 Å corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2‐like monomer. A non‐protein high‐quality electron density was also observed at the substrate‐binding site in the PLA2‐like protein that has been interpreted as N‐acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2‐type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys–PLA2 with sixfold coordination. The conformations of the calcium‐binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N‐acetylglucosamine molecule is favorably placed in the substrate‐binding site of Cys–PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2‐like proteins. The formation of heterodimer seems to have been induced by zinc ion. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Folding pathway dependence on energetic frustration and interaction heterogeneity for a three‐dimensional hydrophobic protein model
Authors: Garcia Leandro G. , Pereira de Araújo Antônio F.
Published: November 2005

Monte Carlo simulations of a hydrophobic protein model of 40 monomers in the cubic lattice are used to explore the effect of energetic frustration and interaction heterogeneity on its folding pathway. The folding pathway is described by the dependence of relevant conformational averages on an appropriate reaction coordinate, pfold, defined as the probability for a given conformation to reach the native structure before unfolding. We compare the energetically frustrated and heterogeneous hydrophobic potential, according to which individual monomers have a higher or lower tendency to form contacts unspecifically depending on their hydrophobicities, to an unfrustrated homogeneous Go‐type potential with uniformly attractive native interactions and neutral non‐native interactions (called Go1 in this study), and to an unfrustrated heterogeneous potential with neutral non‐native interactions and native interactions having the same energy as the hydrophobic potential (called Go2 in this study). Folding kinetics are slowed down dramatically when energetic frustration increases, as expected and previously observed in a two‐dimensional model. Contrary to our previous results in two dimensions, however, it appears that the folding pathway and transition state ensemble can be significantly dependent on the energy function used to stabilize the native structure. The sequence of events along the reaction coordinate, or the order along this coordinate in which different regions of the native conformation become structured, turns out to be similar for the hydrophobic and Go2 potentials, but with analogous events tending to occur at lower pfold values in the first case. In particular, the transition state obtained from the ensemble around pfold = 0.5 is more structured for the hydrophobic potential. For Go1, not only the transition state ensemble but the order of events itself is modified, suggesting that interaction heterogeneity, in addition to energetic frustration, can have significant effects on the folding mechanism, most likely by modifying the probability of different contacts in the unfolded state, the starting point for the folding reaction. Although based on a simple model, these results provide interesting insight into how sequence‐dependent switching between folding pathways might occur in real proteins. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Computational characterization of the sequence landscape in simple protein alphabets
Authors: Shell M. Scott , Debenedetti Pablo G. , Panagiotopoulos Athanassios Z.
Published: November 2005

We characterize the “sequence landscapes” in several simple, heteropolymer models of proteins by examining their mutation properties. Using an efficient flat‐histogram Monte Carlo search method, our approach involves determining the distribution in energy of all sequences of a given length when threaded through a common backbone. These calculations are performed for a number of Protein Data Bank structures using two variants of the 20‐letter contact potential developed by Miyazawa and Jernigan [Miyazawa S, Jernigan WL. Macromolecules 1985;18:534], and the 2‐monomer HP model of Lau and Dill [Lau KF, Dill KA. Macromolecules 1989;22:3986]. Our results indicate significant differences among the energy functions in terms of the “smoothness” of their landscapes. In particular, one of the Miyazawa‐Jernigan contact potentials reveals unusual cooperative behavior among its species' interactions, resulting in what is essentially a set of phase transitions in sequence space. Our calculations suggest that model‐specific features can have a profound effect on protein design algorithms, and our methods offer a number of ways by which sequence landscapes can be quantified. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
Authors: Livesay Dennis R. , Jacobs Donald J.
Published: November 2005

Many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. Here we investigate an orthologous RNase H pair by using a minimal distance constraint model (DCM). The DCM is an all atom microscopic model [Jacobs and Dallakyan, Biophys J 2005;88(2):903–915] that accurately reproduces heat capacity measurements [Livesay et al., FEBS Lett 2004;576(3):468–476], and is unique in its ability to harmoniously calculate thermodynamic stability and flexibility in practical computing times. Consequently, quantified stability/flexibility relationships (QSFR) can be determined using the DCM. For the first time, a comparative QSFR analysis is performed, serving as a paradigm study to illustrate the utility of a QSFR analysis for elucidating evolutionarily conserved stability and flexibility profiles. Despite global conservation of QSFR profiles, distinct enthalpy‐entropy compensation mechanisms are identified between the RNase H pair. In both cases, local flexibility metrics parallel H/D exchange experiments by correctly identifying the folding core and several flexible regions. Remarkably, at appropriately shifted temperatures (e.g., melting temperature), these differences lead to a global conservation in Landau free energy landscapes, which directly relate thermodynamic stability to global flexibility. Using ensemble‐based sampling within free energy basins, rigidly, and flexibly correlated regions are quantified through cooperativity correlation plots. Five conserved flexible regions are identified within the structures of the orthologous pair. Evolutionary conservation of these flexibly correlated regions is strongly suggestive of their catalytic importance. Conclusions made herein are demonstrated to be robust with respect to the DCM parameterization. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Ensemble‐based signatures of energy propagation in proteins: A new view of an old phenomenon
Authors: Liu Tong , Whitten Steven T. , Hilser Vincent J.
Published: November 2005

The ability of a protein to transmit the energetic effects of binding from one site to another constitutes the underlying basis for allosterism and signal transduction. Despite clear experimental evidence indicating the ability of proteins to transmit the effects of binding, the means by which this propagation is facilitated is not well understood. Using our previously developed ensemble‐based description of the equilibrium, we investigated the physical basis of energy propagation and identified several fundamental and general aspects of energetic coupling between residues in a protein. First, partitioning of a conformational ensemble into four distinct sub‐ensembles allows for explanation of the range of experimentally observed coupling behaviors (i.e., positive, neutral, and negative coupling between various regions of the protein structure). Second, the relative thermodynamic properties of these four sub‐ensembles define the energetic coupling between residues as either positive, neutral, or negative. Third, analysis of the structural and thermodynamic features of the states within each sub‐ensemble reveals significant variability. This third result suggests that a quantitative description of energy propagation in proteins requires an understanding of the structural and energetic features of more than just one or a few low‐energy states, but also of many high‐energy states. Such findings illuminate the difficulty in interpreting energy propagation in proteins in terms of a structural pathway that physically links coupled sites. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Assessing protein disorder and induced folding
Authors: Receveur‐Bréchot Véronique , Bourhis Jean‐Marie , Uversky Vladimir N. , Canard Bruno , Longhi Sonia
Published: November 2005

Intrinsically disordered proteins (IDPs) defy the structure–function paradigm as they fulfill essential biological functions while lacking well‐defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the use of multiples techniques. Proteins 2006. © 2005 Wiley‐Liss, Inc.
A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants
Authors: Barone Vincenzo , De Rienzo Francesca , Langella Emma , Menziani M. Cristina , Rega Nadia , Sola Marco
Published: November 2005

Semiquantitative relationships between thermodynamic parameters of Cu2+ reduction experimentally measured for a series of azurin mutants and the solvation free energy of the oxidized state of the proteins were derived. Solvation free energy calculations were carried out within an ONIOM/PCM scheme specifically adapted to this protein series. The method proved to be able to capture the main determinants of the measured reduction parameters, providing satisfactory predictions of the E°′. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Incident investigation: Process to identify root causes of mechanical failures
Authors: Dowell A. M. (Art)
Published: November 2005

This paper describes an actual incident investigation into unexpected premature failure of sealed diaphragm pressure transmitters in a chemical process. Some nontypical investigation tools from the CCPS Guidelines for Investigating Chemical Process Incidents (2nd edition) were used.

A typical failure allowed a release of a corrosive process fluid with potential injury to personnel. The failures also required a shutdown of the process with loss of production. The cause of the problem was elusive; pressure transmitters from the same manufacturer had no problems in a similar process unit, although component designs differed between the two units.

The investigation included confirmation of materials of construction, photographic and visual analyses of failed components, simulation of assembly of the pressure transmitter in the process and measurement of torque values, and brainstorming of possible failure mechanisms. Several hypotheses were tested using a fact–hypothesis matrix to determine most likely cause scenarios. Similarly, a matrix was used to illustrate which scenarios could be prevented by which corrective actions. The investigation included a root cause analysis tree to confirm cause scenarios.

The paper discusses the incident investigation process, including diversity of skills on the investigation team, and how each of the tools was used. The paper also discusses the communication of the findings to operations. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2006
Optical properties of Ge nanowires grown on Si(100) and (111) substrates: Nanowire–substrate heterointerfaces
Authors: Kamenev B. V. , Sharma V. , Tsybeskov L. , Kamins T. I.
Published: November 2005

We report photoluminescence (PL) and Raman scattering (RS) measurements of (111) oriented Ge nanowires (NWs) grown by chemical vapor deposition on (100) and (111) silicon substrates. Our PL measurements strongly suggest that the observed emission originates at low‐defect density Ge NW – Si substrate interfaces. Both, PL and RS data indicate that Si–Ge intermixing and strain are more pronounced for the Ge NW – (111) Si interface, while NWs grown on (100) Si substrates are relaxed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The influence of Sn4+ and/or Mo6+ ions on the structure, electrical and gas sensing properties of Mg‐ferrite
Authors: Rezlescu N. , Doroftei C. , Rezlescu E. , Popa P. D.
Published: November 2005

The influence of partial replacing of Mg and Fe ions by Sn and Mo ions, respectively, on the structural and conductivity properties of MgFe2O4 ferrite is studied by means XRD, SEM and resistivity measurements. Four compositions of ferrites, Mg1–xSnxMoyFe2–yO4 (x = 0, 0.1 and y = 0, 0.02) were prepared by autocombustion, starting from metal nitrates. The presence of foreign phase was evidenced in the Sn containing ferrite. Also, Sn and Mo ions induced structural changes regarding grain size and porosity. The finest granulation, of about 100 nm, was observed in the Sn containing sample, Mg0.9Sn0.1Fe2O4 having the highest porosity. The electrical resistivity increased with about two orders in magnitude when Sn4+ ions partially substituted Mg in MgFe2O4 ferrite. All samples were tested for sensing properties to reducing gases: ethanol and acetone. The gas sensitivity considerably depends on the kind of substituent ion and the type of gas to be detected. All the ferrites were more sensitive to acetone than to ethanol. It was revealed that among all ferrites tested, Mg0.9Sn0.1Fe2O4 is the most sensitive to acetone. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of a new transparent‐conducting material of ZnO doped ITO thin films
Authors: Ali H. M.
Published: November 2005

Thin films of indium tin oxide (ITO) doped with zinc oxide have the remarkable properties of being conductive yet still highly transparent in the visible and near‐IR spectral ranges. The Electron beam deposi‐ tion technique is one of the simplest and least expensive ways of preparing. High‐quality ITO thin films have been deposited on glass substrates by Electron beam evaporation technique. The effect of doping and substrate deposition temperature was found to have a significant effect on the structure, electrical and optical properties of ZnO doped ITO films. The average optical transmittance has been increased with in‐ creasing the substrate temperature. The maximum value of transmittance is greater than 84% in the visible region and 85% in the NIR region obtained for film with Zn/ITO = 0.13 at substrate temperature 200 °C. The dielectric constant, average excitation energy for electronic transitions (E o), the dispersion energy (E d), the long wavelength refractive index (n ∞), average oscillator wave length (λ o) and oscillator strength S o for the thin films were determined and presented in this work. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interstitial to antisite defect conversion during the molecular beam epitaxial deposition on c(4 3 4) GaAs(001) surfaces
Authors: Kunsági‐Máté S. , Schür C. , Marek T.
Published: November 2005

In the model describing the origin of excess arsenic content in low‐temperature grown GaAs layers developed by the research group of professor Strunk during the last ten years, formation of an interstitial As atom was identified as precursor to excess arsenic formation. After an As2 molecule interacts with the GaAs surface, a metastable conformation can form, where one of the As atoms of the As2 molecule is located in an interstitial position. Starting from this geometry, during growth stable conformations can easily arise by the assistance of one or two arriving Ga atoms which stabilize the interstitial As atom in its position by forming a half or full cage‐like structure. Another model describes how the antisite excess As atoms form in GaAs layers by an incomplete exchange of As atoms in the surface reconstruction layer with arriving Ga atoms. The present article connects these two aspects of the excess As formation by analyzing the stability of the interstitial excess As atom, calculated in four different atomic arrangements according to experimentally observed surface structures. Energies of initial, final and transition states of interstitial to antisite reaction path were calculated by DFT/B3LYP/6‐31++G method. Results show that interstitial to antisite conversion happens preferably after a half‐cage formation, while after a full cage has been formed, the interstitial As atom remains fixed in its position. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Radiation‐induced effects in GaN by photoconductivity analysis
Authors: Castaldini A. , Cavallini A. , Polenta L.
Published: November 2005

Spectral photoconductivity is a very efficient tool to explore the forbidden gap of wide gap semiconductors, detecting band‐to‐band or deep level‐to‐band transitions of the charge carriers.

In this paper we present some results obtained by spectral photoconductivity concerning HVPE (hydride vapour phase epitaxy) grown gallium nitride submitted to high energy proton irradiation. The behaviour of the material before and after irradiation may give information on the characteristics of the deep bands and their association to surface or bulk defects. In particular we observed how irradiation quenches the yellow band and correspondingly inhibits persistent photocurrent effects. Persistent photocurrent measurements carried out at different temperatures give further insights on the radiation‐induced effects.

The possible correlation among the deep‐related transitions and the persistent photo‐effects is here proposed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Statistical analysis of vanadium in gallium arsenide
Authors: Rebey A. , Bchetnia A. , Jani B. El
Published: November 2005

The electrical properties of vanadium‐doped GaAs grown by metalorganic vapor phase epitaxy were studied between 77 and 300 K. The temperature‐dependent electron concentration, for different partial pressures of VCl4, was simulated using the charge balance equation. A calculation model was used with parameters (energy levels and V concentration) derived from photoluminescence, deep‐level transient spectroscopy and secondary ion mass spectroscopy measurements. The magnitude and the temperature dependence of neutral and ionized V concentrations were determined. It is shown that most of the V concentration is inactive. This is in good agreement with some previous reports in the literature. The detailed analysis including the probability of V donor incorporation in GaAs was then extended to explain the evolution of electron concentration as a function of partial pressure of VCl4. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Mixed mode electrical transport behavior in nanocrystalline La–Ca‐Manganite synthesized by microwave refluxing
Authors: Nayak Bibhuti B. , Vitta Satish , Bahadur D.
Published: November 2005

Nanocrystalline La0.67Ca0.33MnO3 powders were prepared from organic precursors using a microwave synthesis technique. A variation of the precursor solution pH and annealing temperature was found to change the effective Mn4+ concentration which leads to variations in electronic behavior. In all the cases however, a single phase microstructure was observed showing the stability of orthorhombic manganite. The nanocrystalline manganite prepared from a solution with a pH of 10.5 has the lowest Mn4+ and accordingly low electrical and magnetic transition temperatures. The electrical transport behavior of powders prepared from precursor solutions with pH of 11.5 and 12.5 could be modeled using an effective medium approach across the whole temperature range, 30 K to 300 K. The magnetoresistance in these nanocrystalline manganites increases with decreasing temperature, an effect of increased grain boundaries. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of InN related to surface plasmons
Authors: Shubina T. V. , Leymarie J. , Jmerik V. N. , Toropov A. A. , Vasson A. , Amano H. , Schaff W. J. , Monemar B. , Ivanov S. V.
Published: November 2005

We report on the complex nature of infrared luminescence and absorption in InN films, which cannot be entirely explained by the concept of a conventional narrow‐gap semiconductor. In particular, it concerns the detection of peaks near absorption edges by both thermally detected optical absorption and photoluminescence excitation spectroscopy and the observation of extraordinarily strong resonant enhancement of emission. To describe the experimental data a model is proposed, which takes into account surface plasmons in metal‐like inclusions, modifying the optical properties of InN. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron–hole complexes in individual semimagnetic quantum dots
Authors: Dorozhkin P. S. , Brichkin A. S. , Kulakovskii V. D. , Chernenko A. V. , Zaitsev S. V. , Ivanov S. V. , Toropov A. A.
Published: November 2005

We compare magneto‐photoluminescence spectra of individual semimagnetic quantum dots (QDs) with different strengths of exchange interaction between a localized exciton and surrounding magnetic ions. The spectra of individual QDs with strong magnetic exchange interaction show a single line corresponding to a ground‐state exciton. In QDs with weak interaction, exciton and biexciton spectra are identified, both showing a fine structure due to electron–hole exchange interaction. The anticrossing of dark and bright exciton states in low‐symmetry QDs is demonstrated in magnetic fields in the Faraday geometry. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photon losses in porous silicon microcavities
Authors: Rubo Yuri G. , Solano M. Toledo , del Río J. A.
Published: November 2005

We study theoretically the optical losses in a microcavity made of porous silicon. A quantum derivation of the shape of the resonant transmittance peak for the general case is presented and then we analyze the effect of Rayleigh scattering of light on the disordered structure of porous silicon in details. We introduce a simple model of porous silicon disorder, which allows to estimate the total rate of the Rayleigh scattering from the fundamental microcavity mode. We also investigate the angular distribution of scattered photons. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Roles for aluminium indium nitride insertion layers in fabrication of GaN‐based microcavities
Authors: Bejtka K. , Rizzi F. , Edwards P. R. , Martin R. W. , Gu E. , Dawson M. D. , Watson I. M. , Sellers I. R. , Semond F.
Published: November 2005

AlInN alloys achieve an in‐plane lattice match to hexagonal GaN at an indium nitride mole fraction of ∼18%. Meanwhile Al0.82In0.18N displays a refractive index contrast of ∼7% with GaN at visible wavelengths. We illustrate the use of Al0.82In0.18N insertion layers to control layer thicknesses during homoepitaxial growth of GaN‐based microcavities, using in situ optical reflectometry. The structures discussed are 3λ /2 microcavities incorporating distributed InGaN quantum wells tailored for emission at ∼400 nm. As‐grown samples have been characterised by techniques including cathodoluminescence spectroscopy. In addition to their role in growth monitoring, there are several post‐growth processing steps in which Al0.82In0.18N insertion layers can assist microcavity fabrication. We focus here on a demonstration of the ∼1:5 etch rate selectivity obtainable between Al0.82In0.18N and GaN in reactive ion etching. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resonant acousto‐optic response of microcavity polaritons
Authors: Ivanov A. L.
Published: November 2005

We review the optical properties of microcavity polaritons parametrically driven by a surface acoustic wave (SAW). In this case the acoustically‐induced quasi‐energy (Brillouin) spectrum of microcavity polaritons is well‐developed even for modest acoustic intensities. As a result, in sharp contrast with conventional acousto‐optics, the resonantly enhanced Bragg spectra reveal a robust structure with multiple orders of diffracted light, i.e. a Brillouin band structure of SAW‐driven polaritons can be directly visualized. In particular, for a GaAs‐based microcavity pumped by the SAW of ν saw = 1 GHz and I ac ≃ 100 W/cm2, the main acoustically‐induced band gap in the polariton spectrum can be as large as Δ acMC ≃ 0.6 meV, and the Bragg replicas up to n = 3 can be observed. Finally, we discuss the resonant acousto‐optic effect in (GaAs) microcavities for device applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Conductance of Aharonov–Bohm interferometers embedded with an interacting dot: slave‐boson mean‐field calculation
Authors: Takagaki Y. , Ploog K. H.
Published: November 2005

We numerically calculate the conductance of a one‐dimensional Aharonov–Bohm loop containing a weakly coupled dot. The Coulomb repulsion is taken into account in the dot within the slave‐boson mean‐field approximation. We avoid the so‐called phase locking by attaching an additional lead to the loop. The phase of the electron wavefunction deduced from the Aharonov–Bohm oscillation changes gradually by π when the Fermi energy sweeps across a transmission resonance in the dot. The asymmetric lineshape of Fano‐type resonances is also examined. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Impurity levels in the layered semiconductor p‐GaSe doped with group V elements As, Bi and Sb
Authors: Shigetomi S. , Ikari T.
Published: November 2005

The radiative and non radiative recombination mechanisms in the As, Sb and Bi‐doped GaSe have been investigated on the basis of photoluminescence (PL) and Hall effect measurements. The PL features (at 77 K) related to the impurity levels coming from the As, Sb and Bi atoms are dominated by a broad emission band at about 1.7 eV. From the temperature dependences of the peak energy and PL intensity and the dependence of excitation intensity of peak energy, it was found that the 1.7 eV emission band is due to the transition from the shallow donor level at about 0.08 eV below the conduction band to the deep acceptor. In addition it was found, from the temperature dependence of hole concentration, that a deep acceptor level at about 0.6 eV above the valence band is formed by the doping atoms. It is associated with defects or defect complexes. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Incorporation of nitrogen acceptors in ZnO powder
Authors: Pfisterer D. , Sann J. , Hofmann D. M. , Plana M. , Neumann A. , Lerch M. , Meyer B. K.
Published: November 2005

We report on the preparation and characterization of N‐doped ZnO powders. EPR measurements revealed the presence of N‐acceptors similar to those found in single crystals (Aiso = 1.225 mT, Aaniso = 0.864 mT, g‖ = 1.9953, g⊥ = 1.9633). The photoluminescence of the samples shows donor to shallow acceptor recombinations. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bound states of helium atom in dense plasmas
Authors: Kar Sabyasachi , Ho Y. K.
Published: November 2005

We have obtained the bound 1s2 1S, 1s2s 1,3S, and 1s2p 1,3P states energies of helium atom in dense plasma environments in accurate variation calculations. A screened Coulomb potential to represent the Debye model is used for the interaction between the charged particles. A correlated wave function consisting of a generalized exponential expansion has been used to take care of the correlation effect. The 1s2 1S, 1s2s 1,3S, and 1s2p 1,3P states energies along with the ionization potential, the energy splitting between the 1s2s 3S, and 1s2s 1S states, transition energies between the ground state and low‐excited states of He estimated for various Debye lengths, are reported. The results show high degree of accuracy even under strong plasma conditions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Analyzing the contribution of individual resonance poles of the S‐matrix to two‐channel scattering
Authors: Rakityansky S. A. , Elander N.
Published: November 2005

A two‐channel problem is considered within a method based on first‐order differential equations that are equivalent to the corresponding Schrödinger equation but more convenient for dealing with resonant phenomena. Using these equations, it is possible to calculate directly the Jost matrix for practically any complex value of the energy. The spectral points (bound and resonant states) can therefore be located in a rigorous way, namely, as zeros of the Jost matrix determinant. When calculating the Jost matrix, the differential equations are solved and thus, at the same time, the wave function is obtained with the correct asymptotic behavior analytically embedded in the solution. The method offers a very accurate way of calculating not only total widths of resonances but their partial widths as well. For each pole of the S‐matrix, its residue can be calculated rather accurately, which makes it possible to obtain the Mittag–Leffler‐type expansion of the S‐matrix as a sum of the singular terms (representing the resonances) and the background term (contour integral). As an example, the two‐channel model by Noro and Taylor is considered. It is demonstrated how the contributions of individual resonance poles to the scattering cross section can be analyzed using the Mittag–Leffler expansion and the Argand plot technique. This example shows that even poles situated far away from the physical real axis may make significant contributions to the cross section. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006