bluuebunny/crossref_metadata_2025 huggingface dataset:
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
Authors: Wiehe Kevin , Pierce Brian , Mintseris Julian , Tong Wei Wei , Anderson Robert , Chen Rong , Weng Zhiping
Published: June 2005

We present an evaluation of the results of our ZDOCK and RDOCK algorithms in Rounds 3, 4, and 5 of the protein docking challenge CAPRI. ZDOCK is a Fast Fourier Transform (FFT)‐based, initial‐stage rigid‐body docking algorithm, and RDOCK is an energy minimization algorithm for refining and reranking ZDOCK results. Of the 9 targets for which we submitted predictions, we attained at least acceptable accuracy for 7, at least medium accuracy for 6, and high accuracy for 3. These results are evidence that ZDOCK in combination with RDOCK is capable of making accurate predictions on a diverse set of protein complexes. Proteins 2005;60:207–213. © 2005 Wiley‐Liss, Inc.
Protein–protein docking benchmark 2.0: An update
Authors: Mintseris Julian , Wiehe Kevin , Pierce Brian , Anderson Robert , Chen Rong , Janin Joël , Weng Zhiping
Published: June 2005

We present a new version of the Protein–Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound–unbound cases, with 52 rigid‐body cases, 13 medium‐difficulty cases, and 7 high‐difficulty cases with substantial conformational change. In addition, we retained 12 antibody–antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2. Proteins 2005;60:214–216. © 2005 Wiley‐Liss, Inc.
Approaching the CAPRI challenge with an efficient geometry‐based docking
Authors: Inbar Yuval , Schneidman‐Duhovny Dina , Halperin Inbal , Oron Assaf , Nussinov Ruth , Wolfson Haim J.
Published: June 2005

The last 3 rounds (3–5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large‐scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry‐based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side‐chain position refinement and the introduction of flexibility for both docking partners. Proteins 2005;60:217–223. © 2005 Wiley‐Liss, Inc.
Geometry‐based flexible and symmetric protein docking
Authors: Schneidman‐Duhovny Dina , Inbar Yuval , Nussinov Ruth , Wolfson Haim J.
Published: June 2005

We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3–5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run‐time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying Cn symmetry for any n in a matter of minutes on a desktop PC. Most of the algorithms presented here are available at the Tel Aviv University Structural Bioinformatics Web server (http://bioinfo3d.cs.tau.ac.il/). Proteins 2005;60:224–231. © 2005 Wiley‐Liss, Inc.
Performance of the first protein docking server ClusPro in CAPRI rounds 3–5
Authors: Comeau Stephen R. , Vajda Sandor , Camacho Carlos J.
Published: June 2005

To evaluate the current status of the protein–protein docking field, the CAPRI experiment came to life. Researchers are given the receptor and ligand 3‐dimensional (3D) coordinates before the cocrystallized complex is published. Human predictions of the complex structure are supposed to be submitted within 3 weeks, whereas the server ClusPro has only 24 h and does not make use of any biochemical information. From the 10 targets analyzed in the second evaluation meeting of CAPRI, ClusPro was able to predict meaningful models for 5 targets using only empirical free energy estimates. For two of the targets, the server predictions were assessed to be among the best in the field. Namely, for Targets 8 and 12, ClusPro predicted the model with the most accurate binding‐site interface and the model with the highest percentage of nativelike contacts, among 180 and 230 submissions, respectively. After CAPRI, the server has been further developed to predict oligomeric assemblies, and new tools now allow the user to restrict the search for the complex to specific regions on the protein surface, significantly enhancing the predictive capabilities of the server. The performance of ClusPro in CAPRI Rounds 3–5 suggests that clustering the low free energy (i.e., desolvation and electrostatic energy) conformations of a homogeneous conformational sampling of the binding interface is a fast and reliable procedure to detect protein–protein interactions and eliminate false positives. Not including targets that had a significant structural rearrangement upon binding, the success rate of ClusPro was found to be around 71%. Proteins 2005;60:239–244. © 2005 Wiley‐Liss, Inc.
Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets
Authors: Camacho Carlos J.
Published: June 2005

The CAPRI‐II experiment added an extra level of complexity to the problem of predicting protein–protein interactions by including 5 targets for which participants had to build or complete the 3‐dimensional (3D) structure of either the receptor or ligand based on the structure of a close homolog. In this article, we describe how modeling key side‐chains using molecular dynamics (MD) in explicit solvent improved the recognition of the binding region of a free energy– based computational docking method. In particular, we show that MD is able to predict with relatively high accuracy the rotamer conformation of the anchor side‐chains important for molecular recognition as suggested by Rajamani et al. (Proc Natl Acad Sci USA 2004;101:11287–11292). As expected, the conformations are some of the most common rotamers for the given residue, while latch side‐chains that undergo induced fit upon binding are forced into less common conformations. Using these models as starting conformations in conjunction with the rigid‐body docking server ClusPro and the flexible docking algorithm SmoothDock, we produced valuable predictions for 6 of the 9 targets in CAPRI‐II, missing only the 3 targets that underwent significant structural rearrangements upon binding. We also show that our free energy– based scoring function, consisting of the sum of van der Waals, Coulombic electrostatic with a distance‐dependent dielectric, and desolvation free energy successfully discriminates the nativelike conformation of our submitted predictions. The latter emphasizes the critical role that thermodynamics plays on our methodology, and validates the generality of the algorithm to predict protein interactions. Proteins 2005;60:245–251. © 2005 Wiley‐Liss, Inc.
ATTRACT: Protein–protein docking in CAPRI using a reduced protein model
Authors: Zacharias Martin
Published: June 2005

Protein–protein complex structures have been predicted for CAPRI Rounds 3 and 5 using a reduced protein model. Proteins are represented by up to 3 pseudoatoms per amino acid. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to another protein. The reduced protein model allows one to perform systematic docking minimization of many thousand start structures in reasonable computer time. Flexibility of critical surface side‐chains can be accounted for by a multiple conformational copy approach. The multicopy approach allows simultaneous adjustment of side‐chain conformations and optimization of translational and rotational degrees of freedom of one protein with respect to the partner during docking. For 3 (Targets 8, 14, and 19) out of 5 CAPRI targets, the approach resulted in predictions in close agreement with experiment [root‐mean‐square deviation (RMSD) of backbone atoms within 10 Å of the protein–protein interface < 1.8 Å]. The comparison of predicted and experimental structures of the CAPRI targets indicates that besides local conformational changes (e.g., changes in side‐chain conformations), global conformational changes of the protein backbone can be critical for complex formation. These conformational changes not accounted for during docking are a likely reason for the unrealistic predictions in 2 cases (Targets 9 and 18). Proteins 2005;60:252–256. © 2005 Wiley‐Liss, Inc.
Study of protein–protein interaction using conformational space annealing
Authors: Lee Kyoungrim , Sim Jaehyun , Lee Jooyoung
Published: June 2005

We apply conformational space annealing (CSA), an efficient global optimization method, to the study of protein–protein interaction. The CSA is incorporated into the Tinker molecular modeling package along with a B‐spline method for CAPRI Round 5 experiments. We have used an energy function for the protein–protein interaction that consists of electrostatic interaction, van der Waals interaction, and solvation energy terms represented by the occupancy desolvation method. The parameters of the AMBER94 all‐atom empirical force field are used. Each energy term is calculated by precalculated grid potentials and B‐spline method approximation. The ligand protein is placed inside a sphere of 50 Å radius centered at an appropriate location, and the CSA rigid docking studies are carried out to find stable complexes. Up to 10 complexes are selected using the K‐mean clustering method and biological information when available. These complexes are energy‐minimized for further refinement by considering the flexibility of interacting proteins. The results show that the CSA method has a potential for the study of protein–protein interaction. Proteins 2005;60:257–262. © 2005 Wiley‐Liss, Inc.
Incorporation of flexibility into rigid‐body docking: Applications in rounds 3–5 of CAPRI
Authors: Smith Graham R. , Fitzjohn Paul W. , Page Christopher S. , Bates Paul A.
Published: June 2005

We have submitted models for all 9 targets in Rounds 3–5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid‐body docking with a variety of initial conformations generated by molecular dynamics. Proteins 2005;60:263–268. © 2005 Wiley‐Liss, Inc.
Docking essential dynamics eigenstructures
Authors: Mustard Diana , Ritchie David W.
Published: June 2005

This article describes our attempts to dock the targets in CAPRI Rounds 3–5 using Hex 4.2, and it introduces a novel essential dynamics approach to generate multiple feasible conformations for docking. In the blind trial, the basic Hex algorithm found 1 high‐accuracy solution for CAPRI Target 12, and several further medium‐ and low‐accuracy solutions for Targets 11, 12, 13, and 14. Subsequent a posteriori docking of the targets using essential dynamics “eigenstructures” was found to give consistently better predictions than rigidly docking only the unbound or model‐built starting structures. Some suggestions to improve this promising new approach are presented. Proteins 2005;60:269–274. © 2005 Wiley‐Liss, Inc.
Scoring docking models with evolutionary information
Authors: Tress Michael , de Juan David , Graña Osvaldo , Gómez Manuel J. , Gómez‐Puertas Paulino , González Jose M. , López Gonzalo , Valencia Alfonso
Published: June 2005

We have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases. Proteins 2005;60:275–280. © 2005 Wiley‐Liss, Inc.
Protein–protein docking using 3D‐Dock in rounds 3, 4, and 5 of CAPRI
Authors: Carter Phil , Lesk Victor I. , Islam Suhail A. , Sternberg Michael J.E.
Published: June 2005

In rounds 3–5 of CAPRI, the community‐wide experiment on the comparative evaluation of protein–protein docking for structure prediction, we applied the 3D‐Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid‐based shape complementarity search. The product of this is a large number of potential interacting conformations that are subsequently ranked by interface residue propensities and interaction energies. Refinement through detailed energetics and optimization of side‐chain positions using a rotamer library is also performed. For rounds 3, 4, and 5 of the CAPRI evaluation, where possible, we clustered functional residues on the surfaces of the monomers as an indication of binding sites, using sequence based evolutionary conservations. In certain targets this provided a very useful tool for identifying the areas of interaction. During round 5, we also applied the techniques of side‐chain trimming and geometrical clustering described in the literature. Of the nine target complexes in rounds 3–5, we predicted conformations that contained at least some correct contact residues for seven of these systems. For two of the targets, we submitted predictions that were considered as medium‐quality. These were a nidogen–laminin complex for target 8 (T08) and a serine‐threonine phosphatase bound to a targeting subunit (T14). For a further three target systems, we produced models that were rated as acceptable predictions. Proteins 2005;60:281–288. © 2005 Wiley‐Liss, Inc.
Development and testing of an automated approach to protein docking
Authors: Tovchigrechko Andrei , Vakser Ilya A.
Published: June 2005

A new version of GRAMM was applied to Targets 14, 18, and 19 in CAPRI Round 5. The predictions were generated without manual intervention. Ten top‐ranked matches for each target were submitted. The docking was performed by a rigid‐body procedure with a smoothed potential function to accommodate conformational changes. The first stage was a global search on a fine grid with a projection of a smoothed Lennard–Jones potential. The top predictions from the first stage were subjected to the conjugate gradient minimization with the same smoothed potential. The resulting local minima were reranked according to the weighted sum of Lennard–Jones potential, pairwise residue–residue statistical preferences, cluster occupancy, and the degree of the evolutionary conservation of the predicted interface. For Targets 14 and 18, the conformation of the complex was predicted with root‐mean‐square deviation (RMSD) of the ligand interface atoms 0.68 Å and 1.88 Å correspondingly. For Target 19, the interface areas on both proteins were correctly predicted. The performance of the procedure was also analyzed on the benchmark of bound–unbound protein complexes. The results show that, on average, conformations of only 3 side‐chains need to be optimized during docking of unbound structures before the backbone changes become a limiting factor. The GRAMM‐X docking server is available for public use at http://www.bioinformatics.ku.edu. Proteins 2005;60:296–301. © 2005 Wiley‐Liss, Inc.
Progress in computation and amide hydrogen exchange for prediction of protein–protein complexes
Authors: Law Dennis , Hotchko Matthew , Ten Eyck Lynn
Published: June 2005

The macromolecular docking problem that must be solved for experimental biologists is prediction of the structures of complexes for which the components are known or reliably modeled in the unbound state, but the structure of the complex is unknown. The current state of the art in macromolecular docking is such that solving this problem usually requires supplementary experimental chemical and/or biological information to evaluate computational predictions. Amide 1H/2H exchange measured by mass spectroscopy is a promising approach for obtaining such information, because it can reveal interfacial regions of each member of the complex and identify regions of conformational flexibility in the structure. In a previous article (Anand et al., Proc Natl Acad Sci USA 2003;100:13264–13269), we used 1H/2H exchange data to predict the structure of a complex between regulatory and catalytic subunits of protein kinase A. Comparison of the prediction with a recent crystal structure determination (Kim et al., Science 2005;307:690–696) showed large conformational change in the regulatory subunit on formation of the complex. Analysis of the prediction, previous CAPRI results, novel data processing methods for the 1H/2H exchange data, and new fragment docking computations give grounds for cautious optimism that this method can be useful even in cases of substantial conformational change. Proteins 2005;60:302–307. © 2005 Wiley‐Liss, Inc.
Improving CAPRI predictions: Optimized desolvation for rigid‐body docking
Authors: Fernández‐Recio Juan , Abagyan Ruben , Totrov Maxim
Published: June 2005

The ICM Docking and Interface Side‐Chain Optimization (ICM‐DISCO) showed promising predictive results during the first CAPRI experiment by successfully finding medium‐ or high‐accuracy models in 3 of the 7 targets. A key factor was the ability to recognize near‐native rigid‐body geometries in a relatively low number of alternative docking poses, together with the successful refinement of the rigid‐body docking interfaces. Since then, we have focused on improving the scoring function to optimally discriminate the near‐native rigid‐body conformations. For that, we have defined a new desolvation descriptor for rigid‐body docking, based on atomic solvation parameters (ASPs) derived from octanol–water transfer experiments. This and other new approaches have been gradually incorporated into our docking procedure during our participation on the second CAPRI experiment. Overall, we produced reasonable models for 8 of the 9 official targets. Especially encouraging were those cases in which a homology model of 1 of the subunits had to be used during the docking simulations. And not less gratifying has been the successful prediction of antibody–antigen targets in a completely automatic, unrestrained fashion. In summary, our success rate (89%) shows a consistent improvement over the previous CAPRI rounds, and suggests that a correct desolvation description is key for improved protein–protein docking predictions. Proteins 2005;60:308–313. © 2005 Wiley‐Liss, Inc.
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
Authors: Zhang Chi , Liu Song , Zhou Yaoqi
Published: June 2005

We entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid‐body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE‐based statistical energy function, (4) clustering based on pairwise root‐mean‐square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side‐chain conformations of the top‐ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. Proteins 2005;60:314–318. © 2005 Wiley‐Liss, Inc.
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
Authors: Ma Xiao Hui , Li Chun Hua , Shen Long Zhu , Gong Xin Qi , Chen Wei Zu , Wang Cun Xin
Published: June 2005

An efficient biologically enhanced sampling geometric docking method is presented based on the FTDock algorithm to predict the protein–protein binding modes. The active site data from different sources, such as biochemical and biophysical experiments or theoretical analyses of sequence data, can be incorporated in the rotation–translation scan. When discretizing a protein onto a 3‐dimensional (3D) grid, a zero value is given to grid points outside a sphere centered on the geometric center of specified residues. In this way, docking solutions are biased toward modes where the interface region is inside the sphere. We also adopt a multiconformational superposition scheme to represent backbone flexibility in the proteins. When these procedures were applied to the targets of CAPRI, a larger number of hits and smaller ligand root‐mean‐square deviations (RMSDs) were obtained at the conformational search stage in all cases, and especially Target 19. With Target 18, only 1 near‐native structure was retained by the biologically enhanced sampling geometric docking method, but this number increased to 53 and the least ligand RMSD decreased from 8.1 Å to 2.9 Å after performing multiconformational superposition. These results were obtained after the CAPRI prediction deadlines. Proteins 2005;60:319–323. © 2005 Wiley‐Liss, Inc.
Simazine dynamics in a vineyard soil at Casablanca valley, Chile
Authors: Alister Claudio , Lopez Ramiro , Kogan Marcelo
Published: June 2005

Field dissipation, soil movement and laboratory leaching studies were performed to elucidate the effect of two rainfall amounts in the behaviour and environmental fate of simazine under climatic conditions at Casablanca Valley, Chile. Dissipation and soil movement were studied in a field vineyard with a sandy loam soil (Inceptisol; 74.08% sand; 14.87% silt and 11.04% clay). Simazine was applied to bare soil at 2.0 kg AI ha−1, and its concentration was measured using immunoassay (ELISA) at 0, 10, 20, 40 and 90 days after application under two rainfall amounts, natural field conditions (39 mm) and modified conditions (39 + 180 mm). Simazine leaching was studied using soil core PVC lysimeters (0.9 m height; 0.22 m diameter). Field dissipation data were adjusted with a bi‐exponential model. Half‐life (DT50) values varied between 31.3 (±2.5) and 19.0 (±4.2) days under natural and modified conditions, respectively. Simazine Kd varied from 0.42 to 2.15 (Koc 32.6–216.2) in the soil profile. Simazine was detected at a 90‐cm soil depth in concentrations of 0.0085 (±0.0043) mg kg−1 and 0.0321 (±0.001) mg kg−1 under field and modified conditions, respectively. The maximum simazine leachate concentrations were 0.013 (±0.00084) mg litre−1 (0.012% of total applied simazine) and 0.0084 (±0.00082) mg litre−1 (0.11% of total applied simazine) for field and modified conditions respectively. These data indicate that water quantity has a significant effect on the DT50 and the amount of simazine that moved through the soil profile, but not on the soil depth reached by this herbicide. Copyright © 2005 Society of Chemical Industry
AC‐Stark effect in a semi‐spherical quantum dot
Authors: Rodríguez Arezky H. , Meza‐Montes L. , Trallero‐Giner C. , Ulloa S. E.
Published: June 2005

We present a theoretical approach to study the effects of an ac‐field applied to quantum dots with semi‐spherical symmetry. Using the Floquet formalism for this periodically driven system, the time‐dependent Hamiltonian in the effective mass approximation is solved. We show that the Hilbert space of solutions is separated into orthogonal subspaces with different z‐component of the angular momentum. We give an explicit analytical representation for electronic states as a function of the intensity and frequency of the electric field. Under the two level approximation, two particular cases are studied: the low‐ and high‐frequency regimes, which result of comparing the ac‐field frequency to the characteristic level splitting at zero field. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chirality assignments in carbon nanotubes based on resonant Raman scattering
Authors: Thomsen C. , Telg H. , Maultzsch J. , Reich S.
Published: June 2005

Resonant Raman scattering is a well‐known method for investigating the optical transitions in solids [1]. Here we show that the fully symmetric radial breathing mode (RBM) of carbon nanotubes can be used to derive an assignment of their chiral indices. Our assignment is based on a plot of the resonance maxima for the radial breathing modes as a function of laser excitation energy versus inverse ωRBM, a so‐called Kataura plot. Different from recent luminescence measurements [2], the chirality of both semiconducting and metallic nanotubes can be investigated. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
XPS, SEM and XRD investigations of CdSe films prepared by chemical bath deposition
Authors: Vargas‐Hernández C. , Lara V. C. , Vallejo J. E. , Jurado J. F. , Giraldo O.
Published: June 2005

Chemical bath deposition (CBD), a direct low cost technique that involves a cadmium salt solution, a complexing agent and a chalcogen source, was used to prepare CdSe semiconductor films. The most favourable conditions for acceptable quality CdSe films grown on glass were obtained. Commercially available microscope glass slides (with a size of 1 cm × 1 cm × 1 mm) were used as substrates to deposit CdSe films. CdSe films were deposited in a freshly prepared aqueous solution containing CdSO4 (0.2–0.4 M), NH4OH (3.8–14 M) as a complexing agent for slow release of Cd2+ ions, and Na2SeSO3 (0.118 and 0.16) as a source of Se2– ions. The solutions were prepared in deionized water. The glass slides were immersed in a mixture of CdSO4–NH4OH for 5 min before the solution of Na2SeSO3 was added. The bath temperature varied from 20 to 60 °C. Structural and morphological quality of the films was analyzed by XRD, SEM, EDS, and XPS. The results show that the crystallinity of the CdSe films as‐deposited is improved by increasing temperature. The initial growth stages of CdSe films at 20 and 60 °C start on CdOx and Cd(OH)2 buffer layers respectively. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tunneling and ferroelectric properties of SRO/PZT/Pt capacitor structures
Authors: Delgado E. , Cortes A. , Lopera W. , Osorio J. , Prieto P.
Published: June 2005

Tunneling measurements at different temperatures were carried out in SrRuO3/Pb(Zr0.52Ti0.48)O3/Pt capacitor structures grown on (100) SrTiO3 single‐crystal substrates using a high‐oxygen pressure on axis sputtering technique. Crystalline quality and structure were measured by X‐ray diffractometry (XRD). The surface roughness and morphology were studied by atomic force microscopy (AFM). Electrical characterization was carried out by P–E hysteresis loops and fatigue measurements on different capacitors. Capacitor structures with electrode areas of 5.0 × 10–4 and 6.5 × 10–3 cm2 revealed remanent polarizations around of 30 µC/cm2 at room temperature. Current–voltage characteristics (I–V curves) demonstrated slight hysteretic behavior while the bias voltage dependence of the dynamic conductance measurements presented a parabolic characteristic, indicating electron tunneling. A Brinkman fit of the normalized conductance curves as a function of temperature gives barrier thicknesses below 2 nm. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cd desorption induced by Zn exposure during atomic layer epitaxy of CdxZn1–xTe
Authors: Larramendi E. M. , de Melo O. , Hernández‐Calderón I.
Published: June 2005

The substitution of surface Cd atoms by Zn atoms during the growth of CdxZn1–xTe by atomic layer epitaxy has been studied as a function of substrate temperature and Zn exposure time by means of the analysis of the photoluminescence spectra of CdxZn1–xTe/ZnTe quantum wells. For substitution and desorption of Cd induced by Zn exposure an activation energy of 1.5 eV was found. The complexity of this desorption process was denoted by the fourth order of the kinetic reaction in the 250–280 °C temperature range. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum islands formation and optical properties of CdZnTe/ZnTe quantum wells grown by atomic layer epitaxy
Authors: Larramendi E. M. , de Melo O. , Hernández‐Calderón I.
Published: June 2005

In this work we report on optical properties of CdZnTe/ZnTe quantum wells (QWs) grown by atomic layer epitaxy (ALE) and the formation of quantum island during the QWs growth. The photoluminescence (PL) emission of QWs at lower temperature (250 °C) consists of two peaks. From studying the dependence of the PL integrated emission with the excitation intensity, it is found that theses both PL features have different nature. The high‐energy sharp peak is associated to the excitonic recombination in the CdZnTe/ZnTe alloy quantum well while the low‐energy contributions (wide peak) are assigned to the recombination in the quantum islands (compositional fluctuations with high Cd molar fraction embedded inside the active zone of the QW). The temperature dependence of the PL FWHM, energy, and intensity confirm the enhancement of the quantum efficiency of optical recombination in quantum islands. The formation of quantum islands is more likely at lower growth temperature as evidenced by the optical properties of the QWs grown at different temperatures. Since the QWs growth is following an ALE procedure (Cd–Te–Zn–Te cycles), the existence of a Cd desorption induced by Zn exposure (Cd atoms are replaced by Zn atoms) leads to the formation of the compositional fluctuations (islands) on the growing surface at lower temperatures. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of applied magnetic fields on direct and indirect excitons in coupled semiconductor quantum wells
Authors: Reyes‐Gómez E. , Oliveira L. E. , de Dios‐Leyva M.
Published: June 2005

We have investigated magnetic‐field effects on the direct‐ and indirect‐exciton dispersions and on the exciton effective mass in the plane perpendicular to the applied field, within the variational framework and effective‐mass approximation, for coupled GaAs–(Ga,Al)As quantum wells. The simple hydrogen‐like envelope wave function we have used provides the expected behavior for the exciton dispersion law in a wide range of the center‐of‐mass momenta, and leads to an analytical expression for the exciton effective mass. Theoretical results for the magnetic‐field dependent exciton dispersion and effective mass are in quite good agreement with available experimental measurements. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the phase diagram of a two‐dimensional electron gas near integer fillings and fractions such as 1/5 and 1/7
Authors: Claro Francisco , Cabo Alejandro , March Norman H.
Published: June 2005

The phase diagram of the 2DEG at high magnetic fields is discussed in the light of recent experiments showing the presence of crystalline phases around integer as well as certain fractional fillings. We suggest that a Hall crystal is a proper competing phase compatible with the odd denominator rule that characterizes the fractional quantum Hall effect, and that near integer filling a pinned crystal coexists with an incompressible fluid with no longitudinal resistance. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Organic thin films grown by hot wall epitaxy on inorganic substrates
Authors: Sitter H. , Andreev A. , Teichert Ch. , Hlawacek G. , Haber T. , Smilgies D.‐M. , Resel R. , Ramil Alberto M. , Sariciftci N. S.
Published: June 2005

In this work we use Atomic Force Microscopy and X‐ray diffraction to study the morphology and thegrowth kinetics of para‐sexiphenyl layers deposited by hot wall epitaxy on crystalline mica (001) and KCl(001) substrates. It is shown that para‐sexiphenyl forms on mica very long parallel oriented crystalline needles with one preferential direction. In contrast, on KCl (001) the growth is characterized by a co‐existence of long needles (“laying” molecules) and terrace structured islands (“standing” molecules). The former belong to the initial growth stage of the films, generating a rectangular network in accordance with the surface symmetry of the substrate. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effective index model and guided modes in a photonic crystal fiber
Authors: Arriaga J.
Published: June 2005

We analyze the guided modes of photonic crystal fibers. We compare the values of the V‐parameter obtained using the effective index for the fundamental space‐filling mode with those values obtained by using the effective index of the modes propagating in the photonic crystal fiber. We obtain the condition for single‐mode operation. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanoscopic characterization of Pr2Zr2O7 at Zr sites
Authors: Martínez J. A. , Caracoche M. C. , Rivas P. C. , Rodríguez A. M. , Bondioli F. , Manfredini T. , Ferrari A. M.
Published: June 2005

By using Perturbed Angular Correlation Spectroscopy, a suitable technique to explore internal fields at nanoscopic scale, the electric field gradients at Zr4+ sites in the Pr2Zr2O7 compound have been determined as a function of temperature. Three nonequivalent nanoconfigurations are present, which have been interpreted with the aid of point charge model calculations. Two of them correspond to pyrochlore – oxygen defective and perfect structures –, and the third one to the pyrochlore‐related defect fluorite structure. The most abundant interaction is a disordered and fluctuating electric field gradient, which describes the oxygen defective pyrochlore. As temperature increases, its gradual and reversible transformation towards the perfect form is observed. Below 750 °C the oxygen vacancies movement, which exhibits an activation energy of 0.14 eV, is assumed to be due to vacancies jumping among 48f equivalent sites. At higher temperatures the movement is interpreted as the fast diffusion of oxygen vacancies involving 48f and 8b sites, thus giving place to anionic disorder. The activation energy for this movement has been determined to be of 0.85 eV. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantum and conversion efficiency calculation of AlGaAs/GaAs multiple quantum well solar cells
Authors: Rimada J. C. , Hernandez L. , Connolly J. P. , Barnham K. W. J.
Published: June 2005

The quantum well solar cell (QWSC) is a novel device that has been proposed by Barnham and co‐workers at Imperial College London. In this work, the quantum efficiency for AlGaAs/GaAs QWSC has been calculated and compared with available data from the group at Imperial College London. Quantum efficiency calculations will be presented and compared with experimental data for several AlGaAs/GaAs QWSC, obtaining good agreement. The photocurrent then is calculated from the quantum efficiency calculations and included in the J(V) relation to optimize the efficiency of AlGaAs/GaAs QWSC. It also shows that for a range of quantum well widths and barrier bandgaps the conversion efficiencies of the quantum well solar cell are higher than the corresponding homogeneous p–i–n solar cell. Our results give a broad representation of quantum well solar cell operation, and provide a profitable guide for designing and interpreting the performance characteristics of AlGaAs/GaAs QWSCs. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Confinement factor, near and far field patterns in InGaN MQW laser diodes
Authors: Martín J. , Sánchez M.
Published: June 2005

In this work the influence of the QW number in the active region on spectral characteristics in InGaN multi quamtun well lasers is analyzed. A comparison between the abrupt index step structure (Step) and a graded‐index structure (GRIN) is done. The effect of the introduction of a p‐AlxGa1–xN electron blocking layer, placed above the last InGaN barrier in the Step structure is also analyzed. Calculations of the confinement factor, near and far field patterns were carried out. We found that with the adequate aluminum content in this layer, the confinement factor, near and far field patterns are improved, and values similar to those obtained with GRIN structure can be reached. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cubic and hexagonal boron‐nitride (c‐BN/h‐BN) thin films deposited in situ by r.f. magnetron sputtering
Authors: Caicedo J. M. , Bejarano G. , Zambrano G. , Baca E. , Morán O. , Prieto P.
Published: June 2005

Cubic boron‐nitride (c‐BN)/hexagonal boron nitride (h‐BN) thin films were grown in situ on (100) oriented silicon substrates by r.f. (13.56 MHz) magnetron sputtering technique. In order to obtain the highest fraction of the c‐BN phase, a negative d.c bias voltage, varying from 0 to –200 V was applied to the substrate during deposition. Another set of boron nitride thin films was deposited in situ on (100) oriented silicon substrates under r.f. bias voltage. The substrate holder was biased from 0 to –350 V by connecting such to an auxiliary r.f. generator (operated at 13.56 MHz). Films were characterized by Fourier Transformed Infrared Spectroscopy (FTIR) and Atomic Force Microscope (AFM). Well‐defined peaks at 787 cm–1, 1100 cm–1 and 1387 cm–1, corresponding to the 2Au (out‐plane bending of B–N–B bond) h‐BN vibration mode, the F2 (stretching) c‐BN Transversal Optical (TO) mode and the E1u (in‐plane stretching of B–N bond) vibration mode of the h‐BN, respectively, were observed in the FTIR spectra. A maximal fraction of the c‐BN phase close to 85% was obtained under a bias voltage of –150 V at substrate temperature of 300 °C and a total pressure of 4 × 10–2 mbar. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamics of structural relaxation upon Rydberg excitation of an NO impurity in rare gas solid matrices
Authors: Rubayo‐Soneira J. , Castro‐Palacios J. C. , Rojas‐Lorenzo G.
Published: June 2005

We study the dynamics of structural relaxation, induced by excitation of an NO molecule, to its A2Σ+ Rydberg state in rare gas (RG) solids. Classical molecular dynamics simulations were carried out to describe the dynamics of the cage, formed by RG atoms surrounding the NO molecule. The results show a behaviour characterized by an impulsive expansion of the cage radius at short times, followed by a complex oscillatory pattern around the average NO–RG distance of ∼3.9 Å for NO(A2Σ+)–Ne, ∼4 Å for NO(A2Σ+)–Ar, ∼4.24 Å for NO(A2Σ+)–Kr, and ∼4.55 Å for NO(A2Σ+)–Xe. The size of the cage radius in the Rydberg state increases from ∼5% (Xe) to ∼25% (Ne) when compared with the initial cage radius. The experimental work showed a recurrence time of ∼1.4 ps (Ne) and ∼0.8 ps (Ar), while in our theoretical results we obtained ∼2 ps (Ne) and 0.8 ps (Ar), which is in good agreement with experimental results. The molecular dynamics simulations of the higher shells reveal a high degree of directionality of the propagation of the deformation in the solids, except in the NO–Ne solid system. We explained the dependences of the different behaviour in each system. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electric‐field gradient characterization at 181Ta impurities in sapphire single crystals
Authors: Rentería M. , Darriba G. N. , Errico L. A. , Muñoz E. L. , Eversheim P. D.
Published: June 2005

We report Perturbed‐Angular‐Correlation (PAC) experiments on corundum Al2O3 single crystals implanted with 181Hf/181Ta ions at the ISKP at Bonn and measured at La Plata with high efficiency and time‐resolution. The magnitude, asymmetry, and orientation (with respect to the crystalline axes) of the electric‐field gradient (EFG) tensor were determined measuring the spin‐rotation curves as a function of different orientations of the single crystals relative to the detector system. These results are analyzed in the framework of point‐charge model and ab initio Full‐Potential Linearized‐Augmented Plane Wave calculations, and compared with EFG results coming from PAC experiments with 111In/111Cd impurities. This combined study enables the determination of lattice relaxations induced by the presence of the impurity and the state of charge of a deep impurity donor level in the band gap of the semiconductor. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chemical bath deposited CdS films using magnetic treated solutions
Authors: Calzadilla O. , Hernández E. , Larramendi E. M. , Caballero‐Briones F. , Zapata‐Torres M. , Meléndez‐Lira M. , Zapata‐Navarro A.
Published: June 2005

CdS thin films were obtained by chemical bath deposition onto corning glass slides using precursor solutions previously treated in a steady magnetic field. The kinetic growth was affected in dependence of the magnetic field intensity used in the solution treatments. The growth rate is slower when magnetized solutions are used; however, the reaction exhaustion is more delayed. The magnetic treatments improve the conversion of starting materials in thin films. Thus, the bath is more efficient and thicker films can be obtained. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Femtosecond dynamics of the transmission of gold arrays of sub‐wavelength holes
Authors: Halté V. , Benabbas A. , Guidoni L. , Bigot J.‐Y.
Published: June 2005

We have studied the dynamics of arrays of sub‐wavelength holes in a gold film using femtosecond pump‐probe optical spectroscopy. The real and imaginary parts of the complex non linear dielectric function ϵ of the nanostructures strongly depend on the time‐dependent redistribution of the electrons excited by the pump pulses. The dynamical behavior of ϵ allows us to explain the spectral broadening and the shift of the two resonances present in the linear transmission of the arrays. In addition, we present new experimental results allowing to compare the spectral behavior of the two transmission resonances as well as the transmission window of thick films near the interband transitions of gold. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Functional form and risk adjustment of hospital costs: Bayesian analysis of a Box–Cox random coefficients model
Authors: Hollenbeak Christopher S.
Published: June 2005

While risk‐adjusted outcomes are often used to compare the performance of hospitals and physicians, the most appropriate functional form for the risk adjustment process is not always obvious for continuous outcomes such as costs. Semi‐log models are used most often to correct skewness in cost data, but there has been limited research to determine whether the log transformation is sufficient or whether another transformation is more appropriate. This study explores the most appropriate functional form for risk‐adjusting the cost of coronary artery bypass graft (CABG) surgery. Data included patients undergoing CABG surgery at four hospitals in the midwest and were fit to a Box–Cox model with random coefficients (BCRC) using Markov chain Monte Carlo methods. Marginal likelihoods and Bayes factors were computed to perform model comparison of alternative model specifications. Rankings of hospital performance were created from the simulation output and the rankings produced by Bayesian estimates were compared to rankings produced by standard models fit using classical methods. Results suggest that, for these data, the most appropriate functional form is not logarithmic, but corresponds to a Box–Cox transformation of −1. Furthermore, Bayes factors overwhelmingly rejected the natural log transformation. However, the hospital ranking induced by the BCRC model was not different from the ranking produced by maximum likelihood estimates of either the linear or semi‐log model. Copyright © 2005 John Wiley & Sons, Ltd.
Estimation of age‐specific sensitivity and sojourn time in breast cancer screening studies
Authors: Cong Xiuyu J. , Shen Yu , Miller Anthony B.
Published: June 2005

This study investigates statistical approaches to quantitatively describing the age effect on screening sensitivity and sojourn time distribution in breast cancer screening studies. Such an investigation is directly motivated by the need to understand the inherent relationships between age and these important quantities. We incorporate the age effect through generalized linear models under a progressive disease modelling framework and obtain the corresponding parameter estimators using the maximum likelihood method. Among a set of potential models, we use Akeike's information criterion and likelihood ratio test in model selection and inferences. Extensive simulation studies show that the estimators have reasonable accuracy and the model selection criterion works well. The proposed methods are illustrated using data from two large breast cancer screening trials. The results show that the screening sensitivity increases with age at screening examinations based on these two trials. Copyright © 2005 John Wiley & Sons, Ltd.
Multiple comparisons between two groups on multiple Bernoulli outcomes while accounting for covariates
Authors: Troendle James F.
Published: June 2005

The problem of adjusting for multiplicity when one has multiple outcome variables can be handled quite nicely by step‐down permutation tests. More difficult is the problem when one wants an analysis of each outcome variable to be adjusted for some covariates and the outcome variables are Bernoulli. Special permutations can be used where the outcome vectors are permuted within each strata of the data defined by the levels of the (made discrete) covariates. This method is described and shown to control the familywise error rate at any prespecified level. The method is compared through simulation to a vector bootstrap approach, also using a step‐down testing procedure. It is seen that the method using permutations within strata is superior to the vector bootstrap in terms of error control and power. The method is illustrated on a data set of 55 minor malformations of babies of diabetic and non‐diabetic mothers. Published in 2005 by John Wiley & Sons, Ltd.