bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localized failure of fibre‐reinforced elastic–plastic materials subjected to plane strain loading
Authors: Perić Dunja , Rasheed Hayder A. 
Published: December 2006

AbstractWe consider discontinuous bifurcations as the indicator of a localized failure for a class of composites that are characterized by elastic fibres reinforcing an elastic–plastic matrix. A macroscopic tangent stiffness tensor for the fibre‐reinforced composite is developed by consistently homogenizing the contribution of fibres in a spherical representative volume element. Analytical solutions are derived for the critical hardening modulus and corresponding bifurcation directions for the case of plane strain loading. Properties of the solutions are further illustrated on the example of the non‐associated Drucker–Prager model at onset of yielding. Results show that presence of fibres decreases the critical hardening modulus, thus inhibiting the onset of strain localization. The rate of decrease in the critical hardening modulus is the highest for pure shear, followed by uniaxial tension, uniaxial compression, biaxial tension and biaxial compression. The main fibre parameters that control the onset of strain localization are their volumetric content and their stiffness modulus whereby very stiff fibres can produce the most significant decrease in the critical hardening modulus, especially for the state of biaxial tension. The critical hardening modulus for the non‐associated Drucker–Prager model exhibits a full range of localization modes including compaction bands, dilation bands, and transition in the form of shear bands regardless of the presence of fibres. Presence of fibres affects bifurcation directions, except in the case when Poisson's ratio of the matrix is equal to 0.25. The results demonstrate stabilizing effects of fibres by which they provide the control against the onset of strain localization. Copyright © 2006 John Wiley & Sons, Ltd.
Accelerating strategies to the numerical simulation of large‐scale models for sequential excavation
Authors: Noronha M. , Duenser Ch. , Beer G. 
Published: December 2006

AbstractIn this paper, a novel combination of well‐established numerical procedures is explored in order to accelerate the simulation of sequential excavation. Usually, large‐scale models are used to represent these problems. Due to the high number of equations involved, the solver algorithm represents the critical aspect which makes the simulation very time consuming. The mutable nature of the excavation models makes this problem even more pronounced. To accomplish the representation of geometrical and mechanical aspects in an efficient and simple manner, the proposed solution employs the boundary element method with a multiple‐region strategy. Together with this representational system, a segmented storage scheme and a time‐ordered tracking of the changes form an adequate basis for the usage of fast updating methods instead of frontal solvers. The present development employs the Sherman–Morrison–Woodbury method to speed up the calculation due to sequential changes. The efficiency of the proposed framework is illustrated through the simulation of test examples of 2D and 3D models. Copyright © 2006 John Wiley & Sons, Ltd.
Element‐based preconditioners for elasto‐plastic problems in geotechnical engineering
Authors: Augarde C. E. , Ramage A. , Staudacher J. 
Published: December 2006

AbstractIterative solvers are widely regarded as the most efficient way to solve the very large linear systems arising from finite element models. Their memory requirements are small compared to those for direct solvers. Consequently, there is a major interest in iterative methods and particularly the preconditioning necessary to achieve rapid convergence. In this paper we present new element‐based preconditioners specifically designed for linear elasticity and elasto‐plastic problems. The study presented here is restricted to simple associated plasticity but should find wide application in other plasticity models used in geotechnics. Copyright © 2006 John Wiley & Sons, Ltd.
BXL‐628, a vitamin D receptor agonist effective in benign prostatic hyperplasia treatment, prevents RhoA activation and inhibits RhoA/Rho kinase signaling in rat and human bladder
Authors: Morelli Annamaria , Vignozzi Linda , Filippi Sandra , Vannelli Gabriella Barbara , Ambrosini Stefano , Mancina Rosa , Crescioli Clara , Donati Silvia , Fibbi Benedetta , Colli Enrico , Adorini Luciano , Maggi Mario 
Published: December 2006

AbstractBACKGROUNDBXL‐628 is a calcitriol analog shown to decrease prostate growth in preclinical and clinical studies. BPH symptoms are generated not only by prostate overgrowth but also by bladder overactivity, resulting from an increased RhoA/Rho‐kinase signaling. Because bladder smooth muscle cells express VDR, we studied effects of BXL‐628 on this pathway.METHODSRhoA and Rho‐kinase gene expression and functional activity were studied in rat and human bladder smooth muscle by real‐time RT‐PCR, immuno‐kinase assays, western blot analysis, confocal microscopy, in vitro contractility, and cell migration.RESULTSIn bladder smooth muscle, carbachol responsiveness was delayed and Rho‐kinase activity reduced by BXL‐628 treatment because of impaired RhoA membrane translocation and activation. Accordingly, RhoA‐mediated biological functions, such as cell migration and cytoskeleton remodeling were also inhibited by BXL‐628.CONCLUSIONSBXL‐628 inhibits RhoA/Rho‐kinase signaling, a calcium sensitizing pathway, suggesting its possible clinical use in the treatment of altered bladder contractility often associated with BPH‐induced lower urinary tract symptoms. Prostate 67:234–247, 2007. © 2006 Wiley‐Liss, Inc.
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
Authors: Li Xin , Jacobson Matthew P. , Zhu Kai , Zhao Suwen , Friesner Richard A. 
Published: December 2006

AbstractWe have developed a new method (Independent Cluster Decomposition Algorithm, ICDA) for creating all‐atom models of proteins given the heavy‐atom coordinates, provided by X‐ray crystallography, and the pH. In our method the ionization states of titratable residues, the crystallographic mis‐assignment of amide orientations in Asn/Gln, and the orientations of OH/SH groups are addressed under the unified framework of polar states assignment. To address the large number of combinatorial possibilities for the polar hydrogen states of the protein, we have devised a novel algorithm to decompose the system into independent interacting clusters, based on the observation of the crucial interdependence between the short range hydrogen bonding network and polar residue states, thus significantly reducing the computational complexity of the problem and making our algorithm tractable using relatively modest computational resources. We utilize an all atom protein force field (OPLS) and a Generalized Born continuum solvation model, in contrast to the various empirical force fields adopted in most previous studies. We have compared our prediction results with a few well‐documented methods in the literature (WHATIF, REDUCE). In addition, as a preliminary attempt to couple our polar state assignment method with real structure predictions, we further validate our method using single side chain prediction, which has been demonstrated to be an effective way of validating structure prediction methods without incurring sampling problems. Comparisons of single side chain prediction results after the application of our polar state prediction method with previous results with default polar state assignments indicate a significant improvement in the single side chain predictions for polar residues. Proteins 2007. © 2006 Wiley‐Liss, Inc.
A topologically related singularity suggests a maximum preferred size for protein domains
Authors: Zbilut Joseph P. , Chua Gek Huey , Krishnan Arun , Bossa Cecilia , Rother Kristian , Webber Charles L. , Giuliani Alessandro 
Published: December 2006

AbstractA variety of protein physicochemical as well as topological properties, demonstrate a scaling behavior relative to chain length. Many of the scalings can be modeled as a power law which is qualitatively similar across the examples. In this article, we suggest a rational explanation to these observations on the basis of both protein connectivity and hydrophobic constraints of residues compactness relative to surface volume. Unexpectedly, in an examination of these relationships, a singularity was shown to exist near 255–270 residues length, and may be associated with an upper limit for domain size. Evaluation of related G‐factor data points to a wide range of conformational plasticity near this point. In addition to its theoretical importance, we show by an application of CASP experimental and predicted structures, that the scaling is a practical filter for protein structure prediction. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Strategies for high‐throughput comparative modeling: Applications to leverage analysis in structural genomics and protein family organization
Authors: Mirkovic Nebojsa , Li Zhaohui , Parnassa Andrew , Murray Diana 
Published: December 2006

AbstractThe technological breakthroughs in structural genomics were designed to facilitate the solution of a sufficient number of structures, so that as many protein sequences as possible can be structurally characterized with the aid of comparative modeling. The leverage of a solved structure is the number and quality of the models that can be produced using the structure as a template for modeling and may be viewed as the “currency” with which the success of a structural genomics endeavor can be measured. Moreover, the models obtained in this way should be valuable to all biologists. To this end, at the Northeast Structural Genomics Consortium (NESG), a modular computational pipeline for automated high‐throughput leverage analysis was devised and used to assess the leverage of the 186 unique NESG structures solved during the first phase of the Protein Structure Initiative (January 2000 to July 2005). Here, the results of this analysis are presented. The number of sequences in the nonredundant protein sequence database covered by quality models produced by the pipeline is ∼39,000, so that the average leverage is ∼210 models per structure. Interestingly, only 7900 of these models fulfill the stringent modeling criterion of being at least 30% sequence‐identical to the corresponding NESG structures. This study shows how high‐throughput modeling increases the efficiency of structure determination efforts by providing enhanced coverage of protein structure space. In addition, the approach is useful in refining the boundaries of structural domains within larger protein sequences, subclassifying sequence diverse protein families, and defining structure‐based strategies specific to a particular family. Proteins 2007. © 2006 Wiley‐Liss, Inc.
The role of phosphorylation on the structure and dynamics of phospholamban: A model from molecular simulations
Authors: Pantano Sergio , Carafoli Ernesto 
Published: December 2006

AbstractPhospholamban (PLB) is a small membrane protein that regulates the activity of the calcium ATP‐ase in the cardiac, slow‐twitch, and smooth muscle sarcoplasmic reticulum through the reversible phosphorylation of Ser16. We present here a comparative molecular dynamics study of unmodified and phosphorylated PLB immersed in a phospholipid membrane. The study has been performed under different ionic strength conditions, using the NMR structures of two PLB variants determined in mixed organic solvent and dodecylphosphocholine micelles. The simulations indicate that all PLB forms studied display a highly dynamic behavior of the N‐terminal cytoplasmic moiety, with a decrease of its helical content in the phosphorylated forms. The cytoplasmic domain undergoes large collective motions sampling conformations parallel as well as perpendicular to the membrane surface in all the simulations. The transmembrane domain retains a tightly folded helical conformation with a small tilt with respect to the membrane plane probably induced by the presence of Asn30 and Asn34 within the hydrophobic environment. Furthermore, the phosphoric group on Ser16 establishes transient electrostatic interactions with the phospholipid heads. We propose a model in which phosphorylation diminishes the probability of interactions of PLB with residues near Lys400 in the SERCA pump, thus relieving itsinhibition. Proteins 2007 © 2006 Wiley‐Liss, Inc.
Ancestral sequence evolutionary trace and crystal structure analyses of alkaline α‐amylase from Bacillus sp. KSM‐1378 to clarify the alkaline adaptation process of proteins
Authors: Shirai Tsuyoshi , Igarashi Kazuaki , Ozawa Tadahiro , Hagihara Hiroshi , Kobayashi Tohru , Ozaki Katsuya , Ito Susumu 
Published: December 2006

AbstractThe crystal structure of alkaline liquefying α‐amylase (AmyK) from the alkaliphilic Bacillus sp. KSM‐1378 was determined at 2.1 Å resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys–Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg–Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Role of intrinsic disorder in transient interactions of hub proteins
Authors: Singh Gajinder Pal , Ganapathi Mythily , Dash Debasis 
Published: December 2006

AbstractHubs in the protein–protein interaction network have been classified as “party” hubs, which are highly correlated in their mRNA expression with their partners while “date” hubs show lesser correlation. In this study, we explored the role of intrinsic disorder in date and party hub interactions. The data reveals that intrinsic disorder is significantly enriched in date hub proteins when compared with party hub proteins. Intrinsic disorder has been largely implicated in transient binding interactions. The disorder to order transition, which occurs during binding interactions in disordered regions, renders the interaction highly reversible while maintaining the high specificity. The enrichment of intrinsic disorder in date hubs may facilitate transient interactions, which might be required for date hubs to interact with different partners at different times. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Temperature and pressure dependence of carrier recombination processes in GaAsSb/GaAs quantum well lasers
Authors: Hild Konstanze , Sweeney Stephen J. , Marko Igor P. , Jin Shirong R. , Johnson Shane R. , Chaparro Sergio A. , Yu Shuiqing , Zhang Yong‐Hang 
Published: December 2006

AbstractWe investigated the temperature and pressure dependence of carrier recombination processes occurring in GaAsSb edge‐emitting lasers operating near 1.3 μm. Below ∼100 K, the threshold current, I th, is dominated by the radiative current, I rad, and is proportional to temperature, T. However, above 100 K, non‐radiative recombination increases abruptly such that by 125 K it accounts for 40% of I th. From high pressure measurements at this temperature, we find that the non‐radiative current decreases with increasing pressure, consistent with the presence of Auger recombination. At room temperature, non‐radiative recombination accounts for ∼90% I th and gives rise to a super‐linear temperature dependence of I th, in spite of the fact that I rad ∝ T. At room temperature the non‐radiative current increases with increasing pressure, indicating that under ambient operating conditions, the devices are also limited by carrier leakage into the Γ‐minimum of the GaAs barriers and possibly also into the X‐minima of the GaAsP confining layers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carrier recombination mechanisms in mid‐infrared GaInAsSb quantum well lasers
Authors: O'Brien K. , Sweeney S. J. , Adams A. R. , Jin S. R. , Ahmad C. N. , Murdin B. N. , Salhi A. , Rouillard Y. , Joullié A. 
Published: December 2006

AbstractHydrostatic pressure and spontaneous emission techniques have been used to examine the important recombination mechanisms in type‐I GaInAsSb/GaSb quantum well lasers. High pressure results indicate that Auger recombination dominates the threshold current of 2.11 μm and 2.37 μm devices and is the origin of their temperature sensitivity around room temperature. While the characteristics of the 2.37 μm devices are much improved by the suppression of the CHSH Auger process, since its spin–orbit splitting energy is greater than its band gap, other important Auger processes such as CHHL and CHCC persist. In the larger band gap 2.11 μm devices, an increase in threshold current with pressure is observed suggesting that CHSH Auger is present in these devices at atmospheric pressure and contributes to performance degradation at these shorter wavelengths. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tuning of the high‐brightness tapered laser and its applications
Authors: Bohdan R. , Bercha A. , Mariani O. , Wojdak M. , Dybala F. , Adamiec P. , Trzeciakowski W. , Weber J. , Kelemen M. T. 
Published: December 2006

AbstractTapered lasers offer high beam quality together with high power. Wavelength tunability is therefore a valuable feature for such laser, making it a compact alternative for e.g. Titanium‐Sapphire laser. We demonstrate the combination of fine tuning by grating (in the 30 nm range) with the coarse tuning by pressure (up to 12 kbar) for a high power tapered laser emitting around 960 nm at ambient pressure. At the fixed current of 1.5 A the laser was tuned in a 100 nm range (from 980 nm to 880 nm) emitting between 200 mW and 300 mW with high quality of the beam.We examined the possibility of using pressure‐tuned tapered laser diodes in spectroscopy and we demonstrated high spatial resolution for photocurrent and photoreflectance measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Artificial neural network‐based hysteresis estimation of capacitive pressure sensor
Authors: Dibi Zohir , Lamine Hafiane M. 
Published: December 2006

AbstractThe output of the Capacitive Pressure Sensor (CPS) depends both on the input pressure and on its recent history, an effect called hysteresis. A Switched Capacitor Interface (SCI) converts and amplifies either the change in capacitance of pressure‐sensor into an equivalent voltage and the difference between the input pressure due to the hysteresis effect. A new approach to CPS modeling based on artificial neural network (ANN) is proposed taken into account the dynamic environment in which the temperature variation is quite large and the response characteristics of a CPS are highly nonlinear and temperature dependent. The first model is used to simulate the behaviour of the CPS. The second model is based on inverse modeling, which can be used to compensate the hysteresis effect the temperature drift and the nonlinearity. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Pressure dependence of Raman modes in DWCNT filled with PbI2 semiconductor
Authors: González J. , Power Ch. , Belandria E. , Broto J. M. , Puech P. , Sloan J. , Flahaut E. 
Published: December 2006

AbstractUnpolarized Raman spectra of tangential modes on DWNTs filled with 1D nanocrystalline PbI2 semiconductor excited with 647 nm were studied at room temperature and elevated pressure up to 30 GPa. The tangential optical phonon modes of the carbon nanotubes are sensitive to the in plane stress and split into a contribution associated with the external and internal tube. Up to 11 GPa we find a pressure coefficient for the internal tube of 3.7 cm–1 GPa–1 and for the external tube of 6.3 cm–1 GPa–1. In addition, the tangential band of the external tubes broadens and decreases in amplitude. The corresponding Raman features of the internal tubes appear to be considerably less sensitive to pressure. In the range 11 to 15 GPa we observed a discontinuity in the slope (red shift) of the pressure dependence of the frequency of the tangential modes. This phase transition is associated to a possible structural distortion of the nanotube cross‐section. When increasing the pressure furthermore up to 30 GPa the pressure coefficients for the tangential modes associated to the internal and external tubes are the same (10.6 cm–1 GPa–1). All findings lead to the conclusion that the outer tubes act as a protection shield fore the inner tubes (at least up to 11 GPa). (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ab initio study of double‐wall carbon nanotubes under uniaxial pressure
Authors: Fagan Solange B. , Lemos V. 
Published: December 2006

AbstractAb initio calculations were performed in (5,5)@(10,10) double‐wall carbon nanotubes subjected to external forces applied in the radial direction. The inner tubes were found to be less sensitive to pressure than the outer tubes. The electronic band structure was preserved practically unchanged for uniaxial pressures up to 1 GPa. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Raman spectroscopy of single‐walled carbon nanotubes at high pressure: Effect of interactions between the nanotubes and pressure transmitting media
Authors: Proctor J. E. , Halsall M. P. , Ghandour A. , Dunstan D. J. 
Published: December 2006

AbstractWe have studied single‐walled carbon nanotubes (SWNT) at high pressure using Raman spectroscopy, in a variety of common solvents as hydrostatic pressure‐transmitting media. We find that the response of the Raman G‐band to high pressure varies significantly with choice of solvent. In particular, with hexane we observe a new irreversible effect – a flat Raman response to 0.7 GPa. We draw tentative conclusions from this work – that the solvents used can penetrate the interstitial spaces between nanotubes in a bundle and, following the approach of Amer et al. [1], that absorption of the pressure‐transmitting media plays a role in the response of the SWNTs to high pressure. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction of a methanol molecule with C60 under pressure
Authors: Lemos V. , Guerini S. , Abreu R. F. , Mendes Filho J. , Fagan Solange B. 
Published: December 2006

AbstractThe interaction between a C60 molecule with methanol, the main composition of the currently employed pressure transmitting fluid was studied. The simulations include C60 under hydrostatic or uniaxial pressure interacting with methanol. The relaxed structure as well as the binding energies and the electronic density of states were obtained. The analysis of binding energy indicates that the methanol molecule is attracted to C60 under hydrostatic pressure, while repulsed if the pressure is uniaxial. The results establish that the mechanisms of interaction between this nanometer scale system and the medium may change during the compression. Density of states results indicate severe changes in the Raman spectrum of the system under compression. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
12th International Conference on High Pressure Semiconductor Physics (HPSP‐12): Concluding remarks
Authors: Cardona M. 
Published: December 2006

AbstractThese concluding remarks discuss the attractiveness of Barcelona as a venue for conferences like the HPSP and the highlights of the work presented at the HPSP‐12. The discussion is complemented by information concerning the previous eleven HPSP and a historical review of the field. These concluding remarks end with a few bibliometric data which include the development of the field in Spain, and in particular in Barcelona, since 1975. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)