bluuebunny/crossref_metadata_2025_split huggingface dataset:
Umbrella spherical integration: a stable meshless method for non‐linear solids
Authors: Kucherov L. , Tadmor E. B. , Miller R. E. 
Published: September 2006

AbstractA stable meshless method for studying the finite deformation of non‐linear three‐dimensional (3D) solids is presented. The method is based on a variational framework with the necessary integrals evaluated through nodal integration. The method is truly meshless, requiring no 3D meshing or tessellation of any form. A local least‐squares approximation about each node is used to obtain necessary deformation gradients. The use of a local field approximation makes automatic grid refinement and the application of boundary conditions straightforward. Stabilization is achieved through the use of special ‘umbrella’ shape functions that have discontinuous derivatives at the nodes. Novel efficient algorithms for constructing the nodal stars and computing the nodal volumes are presented. The method is applied to four test problems: uniaxial tension, simple shear and bending of a bar, and cylindrical indentation. Convergence studies at infinitesimal strain show that the method is well‐behaved and converges with the number of nodes for both uniform and non‐uniform grids. Typical of meshless methods employing nodal integration, the total energy can be underestimated due to the approximate integration. At finite deformation the method reproduces known exact solutions. The bending example demonstrates an interesting example of torsional buckling resulting from the bending. Copyright © 2006 John Wiley & Sons, Ltd.
A numerical approach for limit analysis of orthotropic composite laminates
Authors: Pisano A. A. , Fuschi P. 
Published: September 2006

AbstractA numerical approach for limit analysis of structures whose constituent material exhibits orthotropic behaviour is presented and discussed. Attention is focused on orthotropic composite laminates under plane stress conditions. The proposed approach is an extension, in the context of orthotropic materials, of the linear matching method (LMM). The latter is based on a sequence of linear analyses performed on the analysed structure made of a fictitious linear viscous material with spatially varying moduli. Here the LMM is applied to structures made of materials obeying the Tsai–Wu criterion. An appropriate choice of the fictitious material, which in this case is assumed linear, viscous, orthotropic and suffering a distribution of assigned initial stresses, reduces the number of parameters to be spatially varied thus rendering the whole procedure applicable and reliable. The results obtained are highly promising as witnessed by a number of numerical examples which are carried out to verify the effectiveness of the proposed approach. Copyright © 2006 John Wiley & Sons, Ltd.
Weighted radial basis collocation method for boundary value problems
Authors: Hu H. Y. , Chen J. S. , Hu W. 
Published: September 2006

AbstractThis work introduces the weighted radial basis collocation method for boundary value problems. We first show that the employment of least‐squares functional with quadrature rules constitutes an approximation of the direct collocation method. Standard radial basis collocation method, however, yields a larger solution error near boundaries. The residuals in the least‐squares functional associated with domain and boundary can be better balanced if the boundary collocation equations are properly weighted. The error analysis shows unbalanced errors between domain, Neumann boundary, and Dirichlet boundary least‐squares terms. A weighted least‐squares functional and the corresponding weighted radial basis collocation method are then proposed for correction of unbalanced errors. It is shown that the proposed method with properly selected weights significantly enhances the numerical solution accuracy and convergence rates. Copyright © 2006 John Wiley & Sons, Ltd.
Fast frequency sweep computations using a multi‐point Padé‐based reconstruction method and an efficient iterative solver
Authors: Avery Philip , Farhat Charbel , Reese Garth 
Published: September 2006

AbstractProblems of the form Z(σ) u(σ)=f(σ), where Z is a given matrix, f is a given vector, and σ is a circular frequency or circular frequency‐related parameter arise in many applications including computational structural and fluid dynamics, and computational acoustics and electromagnetics. The straightforward solution of such problems for fine increments of σ is computationally prohibitive, particularly when Z is a large‐scale matrix. This paper discusses an alternative solution approach based on the efficient computation of u and its successive derivatives with respect to σ at a few sample values of this parameter, and the reconstruction of the solution u(σ) in the frequency band of interest using multi‐point Padé approximants. This computational methodology is illustrated with applications from structural dynamics and underwater acoustic scattering. In each case, it is shown to reduce the CPU time required by the straightforward approach to frequency sweep computations by two orders of magnitude. Copyright © 2006 John Wiley & Sons, Ltd.
Conductive polymer composites obtained from recycled poly(carbonate) and rubber blends for heating and sensing applications
Authors: Zribi K. , Feller J. F. , Elleuch K. , Bourmaud A. , Elleuch B. 
Published: September 2006

AbstractConductive polymer composites (CPCs) can be obtained by blending an insulating polymer matrix with conductive fillers. When the percolation of the dispersed particles is achieved, it is possible to obtain a sensible material for self‐regulated heating by the Joule effect. To fit the durable development concept only recycled materials have been used to design CPCs, i.e. poly(carbonate) (PC) pellets cut out from signal panels and crushed rubber particles from car tires. The conductive properties of the CPCs have been investigated to determine the percolation conditions and the conductivity level with regard to heating and sensing applications. High amplitude positive temperature coefficient (PTC) effects are obtained with [poly(carbonate)‐carbon black]80%/crushed rubber 20% CPC, i.e. (PC‐CB)80/CR20 m/m, over 120°C allowing self‐regulated heating. This result is noteworthy as there are no other results reported in the literature for amorphous thermoplastic matrices like PC. A positive synergy is found between carbon black (CB) and crushed rubber (CR) particles, which act as a PTC booster. Nevertheless, rubber particles already conductive must be doped by the addition of at least 5% v/v CB to achieve higher conductivities. The response amplitudes obtained with (PC‐CB)/CR CPC are large enough to allow sensing and have a good selectivity towards the studied vapors (toluene and dichloromethane); large CR particles are found to be more suitable for this application. Copyright © 2006 John Wiley & Sons, Ltd.
Chemokine receptor expression profiles in nasopharyngeal carcinoma and their association with metastasis and radiotherapy
Authors: Ou D‐L , Chen C‐L , Lin S‐B , Hsu C‐H , Lin L‐I 
Published: September 2006

AbstractNasopharyngeal carcinoma (NPC) is an epithelial cancer that metastasizes predictably to cervical lymph nodes or distant organs. To assess whether the chemokine receptors of NPC cells play important roles in metastasis and are associated with radiotherapy history, the significance of various chemokine receptors (CCR1–10, CXCR1–6, XCR1, and CX3CR1) in NPC cell lines (TW01, TW04, HONE1, BM1, and AS1) and 52 NPC tumour biopsies from 48 patients with NPC was evaluated by mRNA and cytometric analyses, chemotaxis and actin polymerization assays, and immunohistochemical staining. Quantitative real‐time reverse transcription‐polymerase chain reaction revealed substantial expression of CCR7, CCR9, CXCR4, and CXCR6 mRNA in all the NPC cell lines. Of these, however, only CCR7, CXCR4, and CXCR6 were functional in NPC cells. Negative immunoreactivity for CCR7, CXCR4, and CXCR6 was demonstrated in almost all nasopharyngeal (NP) specimens from patients with primary NPC (n = 12) and in those with regional metastatic NPC (n = 15). However, expression of two or three of these chemokine receptors was demonstrated in NP specimens from patients with liver metastasis. Strong positivity was demonstrated for all three of these chemokine receptors in almost all of the regional and distant metastasis specimens. Significant differences in the expression of CCR7, CXCR4, and CXCR6 were found between primary tumours and metastases (p < 0.001, p < 0.001, and p < 0.002, respectively). This observation was further confirmed by laser capture microdissection of freshly frozen tumours from primary (n = 5) and metastatic (n = 8) NPC sites (p = 0.04, 0.03, and 0.03 for CCR7, CXCR4, and CXCR6, respectively). Finally, significant differences in CXCR4 expression were demonstrated between de novo and post‐radiotherapy groups (1/22 vs. 5/8; p < 0.003). It appears reasonable to conclude, therefore, that CCR7, CXCR4, and CXCR6 are expressed and active in human NPC metastases, while CXCR4 expression is associated with radiotherapy history. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Risk minimization practices for pregnancy prevention: understanding risk, selecting tools
Authors: Uhl Kathleen , Trontell Anne , Kennedy Dianne 
Published: September 2006

AbstractAccording to the March of Dimes, approximately 4% (1/28) of babies are born in the US each year with a birth defect. For the majority of birth defects the etiology is unknown, although chemicals, including drug exposures, probably account for less than 1% of all birth defects. The identification of potential human teratogenicity during drug development is important because drug‐induced adverse fetal effects are potentially preventable with the application of risk assessment strategies and risk minimization tools and programs to minimize risk of pregnancy exposure while preserving access to drug benefits; risk assessment and risk minimization together comprise risk management. It is important that risk minimization programs intended to limit fetal exposure use a consistent approach and are tailored to the product‐specific risk concerns in order to optimize the benefit–risk balance for a particular drug. This paper highlights general considerations in developing specific risk minimization programs to prevent fetal drug exposure including the relative advantages and disadvantages of each strategy. Published in 2006 by John Wiley and Sons Ltd.
Differential AC‐chip calorimeter for glass transition measurements in ultrathin films
Authors: Huth H. , Minakov A. A. , Schick C. 
Published: September 2006

AbstractA differential AC‐chip calorimeter capable of measuring the step in heat capacity at the glass transition in nanometer‐thin films is described. Because of the differential setup, pJ/K sensitivity is achieved. Heat capacity can be measured for sample masses below 1 ng in broad temperature range as needed for the study of the glass transition in nanometer‐thin polymeric films. Relative accuracy is sufficient to investigate the changes in heat capacity as the step at the glass transition of polystyrene. The step is about 25% of the total heat capacity of polystyrene. The calorimeter allows for the frequency dependent measurement of complex heat capacity in the frequency range from 1 Hz to 1 kHz. The glass transition in thin polystyrene films (50–4 nm) was determined at well‐defined experimental time scales. No thickness dependency of the glass transition temperature was observed within the error limits (±3 K)—neither at constant frequency (40 Hz) nor for the trace in the activation diagram (1 Hz–1 kHz). © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2996–3005, 2006
Interpreting the dynamics of nano‐confined glass‐formers and thin polymer films: Importance of starting from a viable theory for the bulk
Authors: Ngai K.L. 
Published: September 2006

AbstractThe changes of the dynamic properties of the nanoconfined materials vary greatly depending on the nature of the interfaces, the chemical structure of the nanoconfined glass‐former, the experimental methods used, and, in the case of polymers, the length‐scale of the dynamics probed. Just for the glass transition temperature (Tg) alone, it can decrease, increase, or remain the same depending upon the experimental or simulation conditions. The conventional theories of Tg are unable to explain the range of behaviors seen at the nanometer size scale, and some of the theories give even conflicting predictions on the effect of small size or nanoconfinement on Tg. These problems of conventional theories orginate from the neglect or inadaquate treatment of the many‐molecule relaxation, showing up already when applied to the bulk for not being able to explain some general properties of glass transition. Thus, it is not surprising to find the conventional theories fail to explain the range of behaviors of the more complicated case of materials in nanoconfinement. On the other hand, based on concepts and parameters that capture the essentials of many‐molecule relaxation, the Coupling Model is not only consistent with the general properties of bulk glass‐formers but can also explain the range of behaviors found in materials subjected to nanoconfinement. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2980–2995, 2006
Physicochemical descriptors to discriminate protein–protein interactions in permanent and transient complexes selected by means of machine learning algorithms
Authors: Block Peter , Paern Juri , Hüllermeier Eyke , Sanschagrin Paul , Sotriffer Christoph A. , Klebe Gerhard 
Published: September 2006

AbstractAnalyzing protein–protein interactions at the atomic level is critical for our understanding of the principles governing the interactions involved in protein–protein recognition. For this purpose, descriptors explaining the nature of different protein–protein complexes are desirable. In this work, the authors introduced Epic Protein Interface Classification as a framework handling the preparation, processing, and analysis of protein–protein complexes for classification with machine learning algorithms. We applied four different machine learning algorithms: Support Vector Machines, C4.5 Decision Trees, K Nearest Neighbors, and Naïve Bayes algorithm in combination with three feature selection methods, Filter (Relief F), Wrapper, and Genetic Algorithms, to extract discriminating features from the protein–protein complexes. To compare protein–protein complexes to each other, the authors represented the physicochemical characteristics of their interfaces in four different ways, using two different atomic contact vectors, DrugScore pair potential vectors and SFCscore descriptor vectors. We classified two different datasets: (A) 172 protein–protein complexes comprising 96 monomers, forming contacts enforced by the crystallographic packing environment (crystal contacts), and 76 biologically functional homodimer complexes; (B) 345 protein–protein complexes containing 147 permanent complexes and 198 transient complexes. We were able to classify up to 94.8% of the packing enforced/functional and up to 93.6% of the permanent/transient complexes correctly. Furthermore, we were able to extract relevant features from the different protein–protein complexes and introduce an approach for scoring the importance of the extracted features. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Thermal versus mechanical unfolding of ubiquitin
Authors: Irbäck Anders , Mitternacht Simon 
Published: September 2006

AbstractThe authors studied the temperature‐induced unfolding of ubiquitin by all‐atom Monte Carlo simulations. The unfolding behavior is compared with that seen in previous simulations of the mechanical unfolding of this protein, based on the same model. In mechanical unfolding, secondary‐structure elements were found to break in a quite well‐defined order. In thermal unfolding, the authors saw somewhat larger event‐to‐event fluctuations, but the unfolding pathway was still far from random. Two long‐lived secondary‐structure elements could be identified in the simulations. These two elements have been found experimentally to be the thermally most stable ones. Interestingly, one of these long‐lived elements, the first β‐hairpin, was found to break early in the mechanical unfolding simulations. Their combined simulation results thus enable the authors to predict in detail important differences between the thermal and mechanical unfolding behaviors of ubiquitin. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Theoretical study of the reaction of alkynes with furan catalyzed by AuCl3 and AuCl
Authors: Rabaâ Hassan , Engels Bernd , Hupp Thomas , Hashmi A. Stephen K. 
Published: September 2006

AbstractA general scheme for the endo‐ and exo‐cyclization of furan reactivity with [L‐AuIII, IClx] with (x = 3, 1 and L‐acetylene and vinylidene) complexes is investigated using density functional theory (DFT) code. Two conceivable mechanisms via a [4 + 2] Diels–Alder process or carbene complex are analyzed. According to the activation energy values of the gold (III and I) catalyst, the first mechanism, which implies the Diels–Alder reaction of AuIII, is thermodynamically favored and gives more evidence of the intramolecular addition of the furan with the alkynes. The second mechanism, presumably assisted by the spontaneous formation of the exo‐vinylidene complexes and intermediates of gold (III, I) by forming the carbene complex, is kinetically favored. Additionally, we compare our results with other structures with intramolecular additions that exhibit the quasi‐similarity of gold analogue structures. Differences in activation energies are observed, according to the functional used. Finally, we probe the solvent effects, which decrease the energy barrier in the path. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Resistance distance and Kirchhoff index in circulant graphs
Authors: Zhang Heping , Yang Yujun 
Published: September 2006

AbstractThe resistance distance rij between vertices i and j of a connected (molecular) graph G is computed as the effective resistance between nodes i and j in the corresponding network constructed from G by replacing each edge of G with a unit resistor. The Kirchhoff index Kf(G) is the sum of resistance distances between all pairs of vertices. In this work, closed‐form formulae for Kirchhoff index and resistance distances of circulant graphs are derived in terms of Laplacian spectrum and eigenvectors. Special formulae are also given for four classes of circulant graphs (complete graphs, complete graphs minus a perfect matching, cycles, Möbius ladders Mp). In particular, the asymptotic behavior of Kf(Mp) as p → ∞ is obtained, that is, Kf(Mp) grows as ⅙p3 as p → ∞. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study of molecular interaction between tirapazamine enzymatic catalysis metabolites and water
Authors: Li Lai‐Cai , Zha Dong , Zheng Yan , Wang Xin , Tian An‐Min , Wong Ning‐Bew 
Published: September 2006

AbstractThe weakly hydrogen‐bonded complexes, between tirapazamine enzymatic catalysis metabolites and water, have been investigated by density functional theory (DFT), using the B3LYP hybrid functional. The geometries of these complexes have been fully optimized at the B3LYP/6‐31G(d) and B3LYP/6‐311+G(d) levels. The stabilization energies and charge changes of some atoms have been calculated and analyzed. The results indicate that the catalysis metabolites and water can form stable hydrogen‐bonded complexes. Nine complexes are identified. It is important and necessary to add zero‐point vibrational energy (ZPVE) and basis set superposition error (BSSE) corrections for calculating stabilization energy. The results also reveal an important relationship between the relative stabilities of hydrogen‐bonded complexes and the final products of tirapazamine medication. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Finite element investigation of the ground states of the helium trimers 4He3 and 4He2–3He
Authors: Salci Moses , Yarevsky Evgeny , Levin Sergey B. , Elander Nils 
Published: September 2006

AbstractA three‐dimensional finite element method is applied to the ground states of the symmetric and asymmetric atomic helium trimers 4He3 and 4He2–3He. Three different He–He interaction potentials of hard‐core nature were studied. Two extrapolation procedures based on the convergence properties of the finite element method are investigated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone
Authors: Lu Xiu Hui , Yu Hai Bin , Wu Wei Rong , Xu Yue Hua 
Published: September 2006

AbstractMechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Single‐electron halogen bond: Ab initio study
Authors: Wang Yan‐Hua , Zou Jian‐Wei , Lu Yun‐Xiang , Yu Qing‐Sen , Xu Hui‐Ying 
Published: September 2006

AbstractAb initio calculations have been performed on single‐electron halogen bonds between methyl radical and bromine‐containing molecules to gain a deeper insight into the nature of such noncovalent interactions. Bader's atoms in molecules (AIM) theory have also been applied to the analysis of the linking of the single‐electron halogen bond. Various characteristics of the RBr…CH3 interaction, i.e., binding energies, geometrical parameters and topological properties of the electron density have been determined. The presence of the bond critical points (BCPs) between the bromine atom and methyl radical and the values of electron density and Laplacian of electron density at these BCPs indicate the closed‐shell interactions in the complexes. The single‐electron halogen bonds, which are significantly weaker than the normal halogen bonds, exhibit equally bond strength as compared to the single‐electron hydrogen bond. It has been also found that plotting of the binding energies versus topological properties of the electron density at the BCPs gives two straight lines. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007