bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three‐dimensional finite element study of arching behavior in slope/drilled shafts system
Authors: Liang Robert Y. , Yamin Mohammad 
Published: October 2009

AbstractTwo‐dimensional slope stability analysis for a slope with a row of drilled shafts needs a mechanism to take into account the three‐dimensional effect of the soil arching due to the spaced drilled shafts on slope. To gain a better understanding of the arching mechanisms in a slope with evenly spaced drilled shafts socketed into a stable stratum (or a rock layer), the three‐dimensional finite element modelling technique was used for a comprehensive parametric study, where the nonlinear and plastic nature of the soil and the elastic behavior of the drilled shafts as well as the interface frictions were modelled. Various factors were varied in the parametric study to include (1) the rigidity of the drilled shafts as influenced by its diameter, modulus of elasticity, and total length; (2) shafts spacing and location on the slope; (3) the material properties of rock and the socket length of shaft; and (4) the soil movement and strength parameters. Evidences of soil arching and reduction in the stresses and displacements through the load transfer mechanisms due to the presence of the drilled shafts were elucidated through the finite element method (FEM) simulation results. Design charts based on regression analysis of FEM simulation results were created to obtain a numerical value of the load transfer factor for the arching mechanism provided by the drilled shafts on the slope. Observations of the arching behavior learned from the FEM simulations provide an insight into the behavior of drilled shafts stabilized slope. Copyright © 2009 John Wiley & Sons, Ltd.
Metabolic correlatives of brain activity in a FOS epilepsy patient
Authors: Peca Stefano , Carnì Marco , Di Bonaventura Carlo , Aprile Teresa , Hagberg Gisela E. , Giallonardo Anna Teresa , Manfredi Mario , Mangia Silvia , Garreffa Girolamo , Maraviglia Bruno , Giove Federico 
Published: October 2009

AbstractThe correlation and the interactions between neuronal activity and underlying metabolic dynamics are still a matter of debate, especially in pathological conditions. This study reports findings obtained on a subject suffering from fixation‐off sensitivity (FOS) epilepsy, exploited as a model system of triggerable anomalous electrical activity. Functional Magnetic Resonance Spectroscopy was used to investigate the metabolic response to visual spike‐inducing stimuli in a single voxel placed in the temporo‐occipital lobe of a FOS epilepsy patient. MRS measurements were additionally performed on a control group of five healthy volunteers. The FOS patient also underwent an EEG session with the same stimulus paradigm. Uniquely in the FOS patient, glutamate and glutamine concentration increased during the first 10 min of stimulation and then returned to baseline. On the other hand, FOS‐induced epileptic activity (spiking) endured throughout all the stimulation epoch. The observed metabolic dynamics may be likely linked to a complex interplay between alterations of the metabolic pathways of glutamate and modulation of the neuronal activity. Copyright © 2009 John Wiley & Sons, Ltd.
A two‐stage vehicle routing model for large‐scale bioterrorism emergencies
Authors: Shen Zhihong , Dessouky Maged M. , Ordóñez Fernando 
Published: October 2009

AbstractIn this article, we are interested in routing vehicles to service a large‐scale bioterrorism emergency. We describe the specifics of routing vehicles in such a large‐scale emergency and decompose the problem into two stages: a planning stage and an operational stage. In the planning stage, we generate the routes well in advance of any emergency. In the operational stage, we take into account the planned routes and the information revealed at the time of the emergency, to decide the delivery quantity and any adjustments to the routes. We propose mathematical formulations and solution approaches for both stages. Lastly, we demonstrate the effectiveness of our formulations and solution procedures in developing robust routes through numerical experiments. © 2009 Wiley Periodicals, Inc. NETWORKS, 2009
Recent results on Arc Routing Problems: An annotated bibliography
Authors: Corberán Angel , Prins Christian 
Published: October 2009

AbstractArc routing problems are vehicle routing problems in which the tasks to be performed are located on some arcs or edges of a network, e.g., spreading salt on a road or collecting municipal refuse in a street. They have been much less studied than node routing problems but impressive developments have been achieved in the last decade. The objective of this article is to survey these recent results and to provide an annotated bibliography. Except for a few references, the period surveyed starts from the publication of the book “Arc routing: theory, solutions and applications”, edited by Dror in 2000. The article is made up of two main parts: one on uncapacitated (single vehicle) problems derived from the Chinese Postman Problem, the Rural Postman Problem, and the General Routing Problem; and one on multivehicle or capacitated problems such as the Capacitated Arc Routing Problem. © 2009 Wiley Periodicals, Inc. NETWORKS, 2010
New periodic wave solutions for nonlinear evolution equations with variable coefficients via mapping method
Authors: Abdou M.A. , Abd ElGawad S.S. 
Published: October 2009

AbstractAn extended mapping method with a computerized symbolic computation is used for constructing a new exact travelling wave solutions for nonlinear evolution equations arising in physics, namely, generalized Zakharov Kuznetsov equation with variable coefficients. As a result, many exact travelling wave solutions are obtained which include new periodic wave solution, trigonometric function solutions and rational solutions. The method is straightforward and concise, and it can also be applied to other nonlinear evolution equations with variable coefficients arising in mathematical physics. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Variational iteration method for solving three‐dimensional Navier–Stokes equations of flow between two stretchable disks
Authors: Rashidi M.M. , Shahmohamadi H. , Domairry G. 
Published: October 2009

AbstractThe similarity transform for the steady three‐dimensional Navier–Stokes equations of flow between two stretchable disks gives a system of nonlinear ordinary differential equations. In this article, the variational iteration method was used for solving these equations. The results have been compared with the numerical results. This article depicts that the VIM is an efficient and powerful method for solving nonlinear differential equations. This method is applicable to strongly and weakly nonlinear problems. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Stagnation slip flow and heat transfer over a nonlinear stretching sheet
Authors: Abbas Z. , Hayat T. 
Published: October 2009

AbstractStagnation slip flow and heat transfer characteristics of a viscous fluid over a nonlinear stretching surface has been investigated. The governing partial differential equations are transformed to nonlinear ordinary differential equations using similarity transformations. The analytical solution of the nonlinear system is obtained in series form using the very efficient homotopy analysis method (HAM). Convergence of the series solution is shown explicitly. Important features of flow and heat transfer characteristics are plotted and discussed. Comparison is made with existing numerical results when the stagnation‐point and slip effects are excluded. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Convergence of the interpolated coefficient finite element method for the two‐dimensional elliptic sine‐Gordon equations
Authors: Wang Cheng 
Published: October 2009

AbstractAn interpolated coefficient finite element method is presented and analyzed for the two‐dimensional elliptic sine‐Gordon equations with Dirichlet boundary conditions. It is proved that the discretization scheme admits at least one solution, and that a subsequence of the approximation solutions converges to an exact solution in L2‐norm as the mesh size tends to zero. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Finite element approximation of coupled seismic and electromagnetic waves in fluid‐saturated poroviscoelastic media
Authors: Santos Juan E. 
Published: October 2009

AbstractThis work presents a collection of global and iterative finite element procedures for the numerical approximation of coupled seismic and electromagnetic waves in 2D bounded fluid‐saturated porous media, with absorbing boundary conditions at the artificial boundaries. The equations being analyzed are the coupled Biot's equations of motion and Maxwell equations in the diffusive range. Both seismoelectric and electroseismic coupling are simultaneously included and analyzed in the model. The case of compressional and vertically polarized shear waves coupled with the transverse magnetic polarization (PSVTM‐mode) is analyzed in detail, including the derivation of a priori error estimates on the global finite element procedure and results on the convergence of a domain decomposition iterative algorithm. Later, the corresponding results for the case of horizontally polarized shear waves coupled with the transverse electric polarization (SHTE‐mode) are stated. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Integrated fast and high‐accuracy computation of convection diffusion equations using multiscale multigrid method
Authors: Wang Yin , Zhang Jun 
Published: October 2009

AbstractWe present an explicit sixth‐order compact finite difference scheme for fast high‐accuracy numerical solutions of the two‐dimensional convection diffusion equation with variable coefficients. The sixth‐order scheme is based on the well‐known fourth‐order compact (FOC) scheme, the Richardson extrapolation technique, and an operator interpolation scheme. For a particular implementation, we use multiscale multigrid method to compute the fourth‐order solutions on both the coarse grid and the fine grid. Then, an operator interpolation scheme combined with the Richardson extrapolation technique is used to compute a sixth‐order accurate fine grid solution. We compare the computed accuracy and the implementation cost of the new scheme with the standard nine‐point FOC scheme and Sun–Zhang's sixth‐order method. Two convection diffusion problems are solved numerically to validate our proposed sixth‐order scheme. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
An improved compact finite difference scheme for solving an N‐carrier system with Neumann boundary conditions
Authors: Dai Weizhong 
Published: October 2009

AbstractRecently, we have developed a higher‐order and unconditionally stable compact finite difference scheme for solving a model of energy exchanges in an N‐carrier system with Neumann boundary conditions, which extends the concept of the well‐known parabolic two‐step model for microheat transfer. However, the combined compact finite difference scheme for the boundary is second‐order accurate. Unfortunately, our statement in (Dai and Tzou, Numer Methods Partial Differential Equation, Zhao et al., Numer Methods Partial Differential Equations 23 (2007), 949–959.), that it is a fourth‐order scheme is inaccurate, because the scheme was multiplied by Δx2 in the derivation. In this article, we develop a new combined compact finite difference scheme for the boundary, which is third‐order accurate. Using the exact same proof for stability analysis as in (Dai and Tzou, Numer Methods Partial Differential Equations), the new scheme is unconditionally stable with respect to the initial conditions and source terms. The improved compact scheme is then tested by a numerical example. Results show that the convergence rate with respect to the spatial variable from the new scheme is higher and the solution is much more accurate, when compared with those obtained using our previous compact scheme in (Dai and Tzou, Numer Methods Partial Differential Equations). © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Ultraviolet‐induced crosslinking of poly(butylene succinate) and its thermal property, dynamic mechanical property, and biodegradability
Authors: Huang Xi , Li Chuncheng , Zhu Wenxiang , Zhang Dong , Guan Guohu , Xiao Yaonan 
Published: October 2009

AbstractCrosslinking is an effective way to improve polymer properties. This paper focuses on ultraviolet‐induced crosslinking of poly(butylene succinate) (PBS) in the presence of a photoinitiator and a crosslinking agent at ambient temperature. The effects of the concentration of photoinitiator, the crosslinking agent content, and the irradiation time on the crosslink behavior were investigated. To obtain an appropriate gel fraction in different irradiation times, 3.0 wt% of photoinitiator and 10.0 wt% of crosslinking agent were proved to be the optimum choice. Furthermore, properties such as thermal properties, dynamic mechanical property, and enzymatic degradation of PBS before and after crosslinking were examined. Differential scanning calorimetry (DSC) analysis revealed that glass transition temperature (Tg) increased with increase in gel fraction, while melting temperature (Tm) and the degree of crystallinity decreased. This may be caused by the reduced molecular chain mobility and inhibited molecular motion for crystallization in crosslinked samples. The crosslinked polymer also showed improved thermal stability and dynamic mechanical property. In addition, the introduction of crosslinking retarded the enzymatic degradation rate of PBS, but it was still biodegradable. The improved properties of crosslinked PBS will extend the application of PBS. Copyright © 2009 John Wiley & Sons, Ltd.
Preparation of biocompatible multi‐walled carbon nanotubes as potential tracers for sentinel lymph nodes
Authors: Li Junjun , Yang Feng , Guo Guiquan , Yang Dong , Long Jiang , Fu Deliang , Lu Jennifer , Wang Changchun 
Published: October 2009

AbstractCarbon nanotubes (CNTs) are capable of traversing cellular membranes by endocytosis and are therefore promising materials for use in imaging and drug delivery. Unfortunately, pristine CNTs are practically insoluble and tend to accumulate inside cells, organs and tissues. To overcome the poor dispersibility and toxicity of pristine CNTs, hydrophilic functionalization of CNTs has been intensively investigated. Water‐soluble multi‐walled carbon nanotubes (MWCNTs) were prepared by in situ polymerization of acrylic acid in a poor solvent for poly(acrylic acid) (PAA). The solvent type influenced the grafted density and chain length of PAA. MWCNTs with a high grafted density of PAA (22 wt%) could be well dispersed in water, NaCl aqueous solution (0.9 wt%) and cell culture media. The in vitro cytotoxicity of these MWCNTs for endothelial cells is reasonably low even at high concentration of PAA‐g‐MWCNT (70 µg mL−1). The experimental results show that the biocompatibility of these MWCNTs is sufficient for biological applications. PAA‐g‐MWCNTs were successfully utilized for lymph node tracing. Experimental results suggest that PAA‐g‐MWCNTs have potential to be used as a vital staining dye, which may simplify the identification of lymph nodes during surgery. Copyright © 2009 Society of Chemical Industry
Thermal and morphological properties of high‐density polyethylene/ethylene–vinyl acetate copolymer composites with polyhedral oligomeric silsesquioxane nanostructure
Authors: Scapini Patrícia , Figueroa Carlos A , Amorim Cíntia LG , Machado Giovanna , Mauler Raquel S , Crespo Janaina S , Oliveira Ricardo VB 
Published: October 2009

AbstractThe demand for improved properties of common polymers keeps increasing, and several new approaches have been investigated. In the study reported here, composites with a polymer matrix comprising a blend of high‐density polyethylene with ethylene–vinyl acetate copolymer (EVA), and with polyhedral oligomeric silsesquioxane (POSS) as a nanostructure, were processed and characterized in terms of their thermal and morphological properties. For the preparation of the composites, the concentrations of the blend components (0, 50 and 100 wt%) and of the POSS (0, 1 and 5 wt%) were varied. X‐ray diffraction results indicated that the presence of EVA in the composites led to the appearance of crystalline domains at lower POSS concentrations. Transmission and scanning electron microscopy showed that samples with 1 wt% of POSS had a homogeneous distribution in the polymer matrix with average dimensions of ca 150 nm. However, the formation of aggregates occurred in samples with 5 wt% of POSS. Differential scanning calorimetry and thermogravimetic analyses indicated that the POSS did not affect the melt and degradation temperatures of the polymer matrix. POSS underwent aggregation at higher concentrations during the composite processing, indicating a solubility limit of around 1 wt%. The presence of EVA in the composite favors POSS aggregation due to an increase in the polarity of the polymer matrix. Copyright © 2009 Society of Chemical Industry
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
Authors: Antes Iris 
Published: October 2009

AbstractMolecular docking programs play an important role in drug development and many well‐established methods exist. However, there are two situations for which the performance of most approaches is still not satisfactory, namely inclusion of receptor flexibility and docking of large, flexible ligands like peptides. In this publication a new approach is presented for docking peptides into flexible receptors. For this purpose a two step procedure was developed: first, the protein–peptide conformational space is scanned and approximate ligand poses are identified and second, the identified ligand poses are refined by a new molecular dynamics‐based method, optimized potential molecular dynamics (OPMD). The OPMD approach uses soft‐core potentials for the protein–peptide interactions and applies a new optimization scheme to the soft‐core potential. Comparison with refinement results obtained by conventional molecular dynamics and a soft‐core scaling approach shows significant improvements in the sampling capability for the OPMD method. Thus, the number of starting poses needed for successful refinement is much lower than for the other methods. The algorithm was evaluated on 15 protein–peptide complexes with 2–16mer peptides. Docking poses with peptide RMSD values <2.10 Å from the equilibrated experimental structures were obtained in all cases. For four systems docking into the unbound receptor structures was performed, leading to peptide RMSD values <2.12 Å. Using a specifically fitted scoring function in 11 of 15 cases the best scoring poses featured a peptide RMSD ≤2.10 Å. Proteins 2010. © 2009 Wiley‐Liss, Inc.
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
Authors: Kahraman Abdullah , Morris Richard J. , Laskowski Roman A. , Favia Angelo D. , Thornton Janet M. 
Published: October 2009

AbstractMost function prediction methods that identify cognate ligands from binding site analyses work on the assumption of molecular complementarity. These approaches build on the conjectured complementarity of geometrical and physicochemical properties between ligands and binding sites so that similar binding sites will bind similar ligands. We found that this assumption does not generally hold for protein–ligand interactions and observed that it is not the chemical composition of ligand molecules that dictates the complementarity between protein and ligand molecules, but that the ligand's share within the functional mechanism of a protein determines the degree of complementarity. Here, we present for a set of cognate ligands a descriptive analysis and comparison of the physicochemical properties that each ligand experiences in various nonhomologous binding pockets. The comparisons in each ligand set reveal large variations in their experienced physicochemical properties, suggesting that the same ligand can bind to distinct physicochemical environments. In some protein ligand complexes, the variation was found to correlate with the electrochemical characteristic of ligand molecules, whereas in others it was disclosed as a prerequisite for the biochemical function of the protein. To achieve binding, proteins were observed to engage in subtle balancing acts between electrostatic and hydrophobic interactions to generate stabilizing free energies of binding. For the presented analysis, a new method for scoring hydrophobicity from molecular environments was developed showing high correlations with experimental determined desolvation energies. The presented results highlight the complexities of molecular recognition and underline the challenges of computational structural biology in developing methods to detect these important subtleties. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation
Authors: Poger David , Mark Alan E. 
Published: October 2009

AbstractAtomistic molecular dynamics simulations have been used to investigate the conformational changes associated with the binding of human growth hormone (hGH) to the extracellular domains (ECD) of the human growth hormone receptor (hGHR), thereby shedding light on the mechanism of activation. It is shown that the removal of hGH from the hormone‐bound receptor complex results in a counter‐clockwise rotation of the twosubunits relative to each other by 30°–64° (average 45° ± 14°), in close agreement in terms of both the magnitude and direction of the rotation with that proposed based on mutagenesis experiments. In addition to providing evidence to support a rotational activation mechanism, the simulations have enabled the nature of the interaction interfaces in both the cytokine‐bound and unliganded hGHR states to be analyzed in detail. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Pressure perturbation calorimetry of apolipoproteins in solution and in model lipoproteins
Authors: Benjwal Sangeeta , Gursky Olga 
Published: October 2009

AbstractHigh‐density lipoproteins (HDLs) are complexes of lipids and proteins (termed apolipoproteins) that remove cell cholesterol and protect from atherosclerosis. Apolipoproteins contain amphipathic α‐helices that have high content (≥1/3) and distinct distribution of charged and apolar residues, adopt molten globule‐like conformations in solution, and bind to lipid surfaces. We report the first pressure perturbation calorimetry (PPC) study of apolipoproteins. In solution, the main HDL protein, apoA‐I, shows relatively large volume contraction, ΔVunf = −0.33%, and an apparent reduction in thermal expansivity upon unfolding, Δαunf ≤ 0, which has not been observed in other proteins. We propose that these values are dominated by increased charged residue hydration upon α‐helical unfolding, which may result from disruption of multiple salt bridges. At 5°C, apoA‐I shows large thermal expansion coefficient, α(5°) = 15·10−4 K−1, that rapidly declines upon heating from 5 to 40°C, α(40°) − α(5°) = −4·10−4 K−1; apolipoprotein C‐I shows similar values of α(5°) and α(40°). These values are larger than in globular proteins. They indicate dominant effect of charged residue hydration, which may modulate functional apolipoprotein interactions with a broad range of their protein and lipid ligands. The first PPC analysis of a protein–lipid complex is reported, which focuses on the chain melting transition in model HDL containing apoA‐I or apoC‐I, dimyristoyl phosphatidylcholine, and 0–20% cholesterol. The results may provide new insights into volumetric properties of HDL that modulate metabolic lipoprotein remodeling during cholesterol transport. Proteins 2010. © 2009 Wiley‐Liss, Inc.