bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fourth‐order compact finite volume scheme for fully nonlinear and weakly dispersive Boussinesq‐type equations. Part II: boundary conditions and validation
Authors: Cienfuegos R. , Barthélemy E. , Bonneton P. 
Published: October 2006

AbstractThis paper supplements the validation of the fourth‐order compact finite volume Boussinesq‐type model presented by Cienfuegos et al. (Int. J. Numer. Meth. Fluids 2006, in press). We discuss several issues related to the application of the model for realistic wave propagation problems where boundary conditions and uneven bathymetries must be considered. We implement a moving shoreline boundary condition following the lines given by Lynett et al. (Coastal Eng. 2002; 46:89–107), while an absorbing‐generating seaward boundary and an impermeable vertical wall boundary are approximated using a characteristic decomposition of the Serre equations. Using several benchmark tests, both numerical and experimental, we show that the new finite volume model is able to correctly describe nonlinear wave processes from shallow waters and up to wavelengths which correspond to the theoretical deep water limit. The results compare favourably with those reported using former fully nonlinear and weakly dispersive Boussinesq‐type solvers even when time integration is conducted with Courant numbers greater than 1.0. Furthermore, excellent nonlinear performance is observed when numerical computations are compared with several experimental tests on solitary waves shoaling over planar beaches up to breaking. A preliminary test including the wave‐breaking parameterization described by Cienfuegos (Fifth International Symposium on Ocean Wave Measurement Analysis, Madrid, Spain, 2005) shows that the Boussinesq model can be extended to deal with surf zone waves. Finally, practical aspects related to the application of a high‐order implicit filter as given by Gaitonde et al. (Int. J. Numer. Methods Engng 1999; 45:1849–1869) to damp out unphysical wavelengths, and the numerical robustness of the finite volume scheme are also discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Comparison of adjoint‐based and feature‐based grid adaptation for functional outputs
Authors: Balasubramanian R. , Newman J. C. 
Published: October 2006

AbstractAdjoint‐based and feature‐based grid adaptive strategies are compared for their robustness and effectiveness in improving the accuracy of functional outputs such as lift and drag coefficients. The output‐based adjoint approach strives to improve the adjoint error estimates that relate the local residual errors to the global error in an output function via adjoint variables as weight functions. A conservative adaptive indicator that takes into account the residual errors in both the primal (flow) and dual (adjoint) solutions is implemented for the adjoint approach. The physics‐based feature approach strives to identify and resolve significant features of the flow to improve functional accuracy. Adaptive indicators that represent expansions and compressions in the flow direction and gradients normal to the flow direction are implemented for the feature approach. The adaptive approaches are compared for functional outputs of three‐dimensional arbitrary Mach number flow simulations on mixed‐element unstructured meshes. Grid adaptation is performed with h‐refinement and results are presented for inviscid, laminar and turbulent flows. Copyright © 2006 John Wiley & Sons, Ltd.
A reduced‐order approach to four‐dimensional variational data assimilation using proper orthogonal decomposition
Authors: Cao Yanhua , Zhu Jiang , Navon I. M. , Luo Zhendong 
Published: October 2006

AbstractFour‐dimensional variational data assimilation (4DVAR) is a powerful tool for data assimilation in meteorology and oceanography. However, a major hurdle in use of 4DVAR for realistic general circulation models is the dimension of the control space (generally equal to the size of the model state variable and typically of order 107–108) and the high computational cost in computing the cost function and its gradient that require integration model and its adjoint model.In this paper, we propose a 4DVAR approach based on proper orthogonal decomposition (POD). POD is an efficient way to carry out reduced order modelling by identifying the few most energetic modes in a sequence of snapshots from a time‐dependent system, and providing a means of obtaining a low‐dimensional description of the system's dynamics. The POD‐based 4DVAR not only reduces the dimension of control space, but also reduces the size of dynamical model, both in dramatic ways. The novelty of our approach also consists in the inclusion of adaptability, applied when in the process of iterative control the new control variables depart significantly from the ones on which the POD model was based upon. In addition, these approaches also allow to conveniently constructing the adjoint model.The proposed POD‐based 4DVAR methods are tested and demonstrated using a reduced gravity wave ocean model in Pacific domain in the context of identical twin data assimilation experiments. A comparison with data assimilation experiments in the full model space shows that with an appropriate selection of the basis functions the optimization in the POD space is able to provide accurate results at a reduced computational cost. The POD‐based 4DVAR methods have the potential to approximate the performance of full order 4DVAR with less than 1/100 computer time of the full order 4DVAR. The HFTN (Hessian‐free truncated‐Newton)algorithm benefits most from the order reduction (see (Int. J. Numer. Meth. Fluids, in press)) since computational savings are achieved both in the outer and inner iterations of this method. Copyright © 2006 John Wiley & Sons, Ltd.
A numerical strategy for modelling rotating stall in core compressors
Authors: Vahdati M. 
Published: October 2006

AbstractThe paper will focus on one specific core‐compressor instability, rotating stall, because of the pressing industrial need to improve current design methods. The determination of the blade response during rotating stall is a difficult problem for which there is no reliable procedure. During rotating stall, the blades encounter the stall cells and the excitation depends on the number, size, exact shape and rotational speed of these cells. The long‐term aim is to minimize the forced response due to rotating stall excitation by avoiding potential matches between the vibration modes and the rotating stall pattern characteristics. Accurate numerical simulations of core‐compressor rotating stall phenomena require the modelling of a large number of bladerows using grids containing several tens of millions of points. The time‐accurate unsteady‐flow computations may need to be run for several engine revolutions for rotating stall to get initiated and many more before it is fully developed. The difficulty in rotating stall initiation arises from a lack of representation of the triggering disturbances which are inherently present in aeroengines. Since the numerical model represents a symmetric assembly, the only random mechanism for rotating stall initiation is provided by numerical round‐off errors. In this work, rotating stall is initiated by introducing a small amount of geometric mistuning to the rotor blades. Another major obstacle in modelling flows near stall is the specification of appropriate upstream and downstream boundary conditions. Obtaining reliable boundary conditions for such flows can be very difficult. In the present study, the low‐pressure compression (LPC) domain is placed upstream of the core compressor. With such an approach, only far field atmospheric boundary conditions are specified which are obtained from aircraft speed and altitude. A chocked variable‐area nozzle, placed after the last compressor bladerow in the model, is used to impose boundary conditions downstream. Such an approach is representative of modelling an engine.Using a 3D viscous time‐accurate flow representation, the front bladerows of a core compressor were modelled in a whole‐annulus fashion whereas the rest of bladerows are modelled in a single‐passage fashion. The rotating stall behaviour at two different compressor operating points was studied by considering two different variable‐vane scheduling conditions for which experimental data were available. Using a model with nine whole‐assembly models, the unsteady‐flow calculations were conducted on 32‐CPUs of a parallel cluster, typical run times being around 3–4 weeks for a grid with about 60 million points. The simulations were conducted over several engine rotations. As observed on the actual development engine, there was no rotating stall for the first scheduling condition while mal‐scheduling of the stator vanes created a 12‐band rotating stall which excited the 1st flap mode. Copyright © 2006 John Wiley & Sons, Ltd.
Hybrid lattice Boltzmann finite‐difference simulation of axisymmetric swirling and rotating flows
Authors: Huang Haibo , Lee T. S. , Shu C. 
Published: October 2006

AbstractThe axisymmetric flows with swirl or rotation were solved by a hybrid scheme with lattice Boltzmann method for the axial and radial velocities and finite‐difference method for the azimuthal (or swirl) velocity and the temperature. An incompressible axisymmetric lattice Boltzmann D2Q9 model was proposed to solve the axial and radial velocities through inserting source terms into the two‐dimensional lattice Boltzmann equation. Present hybrid scheme was firstly validated by simulations of Taylor–Couette flows between two concentric cylinders. Then the benchmark problems of melt flow in Czochralski crystal growth were studied and accurate results were obtained. Numerical experiment demonstrated that present axisymmetric D2Q9 model is more stable than the previous axisymmetric D2Q9 model (J. Comp. Phys. 2003; 186(1):295–307). Hence, compared with the previous model, present numerical method provides a significant advantage in simulation melt flow cases with high Reynolds number and high Grashof number. Copyright © 2006 John Wiley & Sons, Ltd.
Accelerating aging of zirconia femoral head implants: Change of surface structure and mechanical properties
Authors: Chowdhury S. , Vohra Yogesh K. , Lemons Jack E. , Ueno Masaru , Ikeda Junji 
Published: October 2006

AbstractRecently, alternations of zirconia ceramic femoral heads of total hip prostheses during in vivo conditions have caused concern in the medical disciplines regarding phase transformation of zirconia prosthetic components. In this paper, we have investigated the mechanical and structural properties of different laboratory aged zirconia femoral heads and correlated changes in mechanical properties with the phase compositions of the sample. From laser microscope observation, cross‐sectional Scanning electron microscopy imaging, and X‐ray diffraction analysis on the surface of the zirconia femoral heads, we found monoclinic to tetragonal phase transformation in zirconia prostheses over time during the aging process in the laboratory. Mechanical properties, mainly hardness (H) and Young's modulus (E) values, were measured by nanoindentation technique on the surface of these implants. The results showed that both H and E values decreased with increased monoclinic phase in zirconia, thus confirming a phase transformation over time during aging. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Evaluation of bone regeneration at critical‐sized calvarial defect by DBM/AM composite
Authors: Qiu Qing‐Qing , Mendenhall H. Vince , Garlick David S. , Connor Jerome 
Published: October 2006

AbstractThis study investigated the bone‐regenerative potential of a demineralized bone and acellular matrix (DBM/AM) composite (AlloCraft™ DBM) in comparison with autologous bone using an in vivo model. Critical‐sized calvarial defects (5 mm) were created in athymic rats. The defects were grafted with either the DBM/AM composite or the acellular human dermal matrix (AM), and compared with the defects filled with autologous bone (positive control) and the empty defect (negative control). Histological and radiographic assessments were carried out at 4 and 8 weeks after surgery to determine the biological healing, the amount and type of new bone formation and the percentage of new bone filled in the critical defects. At 4 weeks, DBM/AM composite group had the highest percentage of the defect filled with new bone (84%), which was significantly greater than autologous bone (62%), AM (41%), and untreated control (32%) groups. At 8 weeks, the DBM/AM continued to have the highest percentage of the defect filled with new bone (91%). The autologous bone group increased the percentage of bone fill to 83%. The defects either filled with AM or left untreated still had less of the defect filled with new bone, 57% and 33%, respectively. The total healing of defects grafted with DBM/AM was comparable with autologous bone group at 8 weeks. The results demonstrated that the DBM/AM composite promoted new bone formation more rapidly than autologous bone at calvarial defect in athymic rats. The study supports that DBM/AM is a potential substitute of autologous bone for bone repair. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Influence of changes in the composition of an acrylic bone cement on its polymerization kinetics
Authors: Lewis Gladius , Mishra Sanjay R. 
Published: October 2006

AbstractIt has been suggested in the literature that a lower polymerization rate of an acrylic bone cement is favorable for the in vivo longevity of a cemented arthroplasty. The present work was a study of the influence of three changes in the composition of an acrylic bone cement (when taken separately) on the cement polymerization rate at 37°C (assumed to be the temperature in the bone bed during a cemented arthroplasty) [k′]. The changes were the amount of copolymer as a proportion of the total powder weight (in cements in which there is a copolymer in the powder), the amount of DMPT as a proportion of the total volume of the liquid monomer, and the accelerator. k′ was calculated using values of the activation energy and the frequency factor (assuming the polymerization reaction is Arrhenius in nature) that were computed from measurements made using the nonisothermal mode of differential scanning calorimetry. Statistical analysis (one‐way ANOVA, with Bonferroni correction, and factorial ANOVA) of the k′ values showed that the change in accelerator had a significant influence on k′. The importance of this finding, together with results from two relevant literature reports, is discussed within the context of the use of modified bone cements in cemented arthroplasties. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Diatropicity of tetraazanaphthalenes
Authors: Cuesta I. García , de Merás A. Sánchez , Lazzeretti P. 
Published: October 2006

AbstractTetraazanaphthalenes are diatropic molecules, whose magnetic response to a magnetic field perpendicular to the molecular plane closely resembles that of naphthalene. The out‐of‐plane component of the magnetic susceptibility tensor and its strong anisotropy can be used as quantifiers of magnetic aromaticity. Maps showing streamlines and modulus of the current density field provide clear evidence for diatropicity of these systems. They also explain the strong anisotropy of carbon and nitrogen magnetic shielding, which is determined by the big out‐of‐plane component of the nuclear shielding tensor. The electronic ring currents observed in the map deshield the nuclei of ring hydrogens by enforcing the local magnetic field and diminishing the out‐of‐plane component of proton shielding. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Indian summer monsoon rainfall and its link with ENSO and Indian Ocean climate indices
Authors: Ihara Chie , Kushnir Yochanan , Cane Mark A. , De La Peña Victor H. 
Published: October 2006

AbstractWe examine the relationship between the state of the equatorial Indian Ocean, ENSO, and the Indian summer monsoon rainfall using data from 1881 to 1998. The zonal wind anomalies and SST anomaly gradient over the equatorial Indian Ocean are used as indices that represent the condition of the Indian Ocean. Although the index defined by the zonal wind anomalies correlates poorly with Indian summer monsoon rainfall, the linear reconstruction of Indian summer monsoon rainfall on the basis of a multiple regression from the NINO3 and this wind index better specifies the Indian summer monsoon rainfall than the regression with only NINO3. Using contingency tables, we find that the negative association between the categories of Indian summer monsoon rainfall and the wind index is significant during warm years (El Niño) but not during cold years (La Niña). Composite maps of land precipitation also indicate that this relationship is significant during El Niño events. We conclude that there is a significant negative association between Indian summer monsoon rainfall and the zonal wind anomalies over the equatorial Indian Ocean during El Niño events. A similar investigation of the relationship between the SST index and Indian summer monsoon rainfall does not reveal a significant association. Copyright © 2006 Royal Meteorological Society.
Electrical stimulation based on chronaxie reduces atrogin‐1 and myoD gene expressions in denervated rat muscle
Authors: Russo Thiago Luiz , Peviani Sabrina Messa , Freria Camila Marques , Gigo‐Benato Davilene , Geuna Stefano , Salvini Tania Fátima 
Published: October 2006

AbstractDenervation induces muscle fiber atrophy and changes in the gene expression rates of skeletal muscle. Electrical stimulation (ES) is a procedure generally used to treat denervated muscles in humans. This study evaluated the effect of ES based on chronaxie and rheobase on the expression of the myoD and atrogin‐1 genes in denervated tibialis anterior (TA) muscle of Wistar rats. Five groups were examined: (1) denervated (D); (2) D+ES; (3) sham denervation; (4) normal (N); and (5) N+ES. Twenty muscle contractions were stimulated every 48 h using surface electrodes. After 28 days, ES significantly decreased the expression of myoD and atrogin‐1 in D+ES compared to the D group. However, ES did not prevent muscle‐fiber atrophy after denervation. Thus, ES based on chronaxie values and applied to denervated muscles using surface electrodes, as normally used in human rehabilitation, was able to reduce the myoD and atrogin‐1 gene expressions, which are related to muscular growth and atrophy, respectively. The results of this study provide new information for the treatment of denervated skeletal muscle using surface ES. Muscle Nerve, 2006
Stress urinary incontinence as the presenting symptom of primary male urethral diverticulum—A case report and literature review
Authors: Wang Shao‐Chuan , Lin Alex T.L. , Chen Kuang‐Kuo 
Published: October 2006

AbstractPrimary male urethral diverticulum is quite uncommon. It is even more unusual for urinary incontinence to be a presenting symptom of primary male urethral diverticulum. Herein, we report on a 32‐year‐old male presenting with urine leakage on coughing or abdominal strain beginning from his early twenties. A congenital type bulbar urethral diverticulum is diagnosed by voiding cystourethrography and cystourethroscopy. Endoscopic unroofing of the diverticulum freed the patient from stress urinary incontinence after the surgery. Neurourol. Urodynam. 26:271–273, 2007. © 2006 Wiley‐Liss, Inc.
Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis
Authors: Nguyen Phuong H. 
Published: October 2006

AbstractEmploying the recently developed hierarchical nonlinear principal component analysis (NLPCA) method of Saegusa et al. (Neurocomputing 2004;61:57–70 and IEICE Trans Inf Syst 2005;E88‐D:2242–2248), the complexities of the free energy landscapes of several peptides, including triglycine, hexaalanine, and the C‐terminal β‐hairpin of protein G, were studied. First, the performance of this NLPCA method was compared with the standard linear principal component analysis (PCA). In particular, we compared two methods according to (1) the ability of the dimensionality reduction and (2) the efficient representation of peptide conformations in low‐dimensional spaces spanned by the first few principal components. The study revealed that NLPCA reduces the dimensionality of the considered systems much better, than did PCA. For example, in order to get the similar error, which is due to representation of the original data of β‐hairpin in low dimensional space, one needs 4 and 21 principal components of NLPCA and PCA, respectively. Second, by representing the free energy landscapes of the considered systems as a function of the first two principal components obtained from PCA, we obtained the relatively well‐structured free energy landscapes. In contrast, the free energy landscapes of NLPCA are much more complicated, exhibiting many states which are hidden in the PCA maps, especially in the unfolded regions. Furthermore, the study also showed that many states in the PCA maps are mixed up by several peptide conformations, while those of the NLPCA maps are more pure. This finding suggests that the NLPCA should be used to capture the essential features of the systems. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Optimization of the hydrochloric acid concentration used for trifluoroacetate removal from synthetic peptides
Authors: Andrushchenko Valery V. , Vogel Hans J. , Prenner Elmar J. 
Published: October 2006

AbstractTrifluoroacetate (CF3COO−, or TFA) is almost always present in commercially synthesized peptides. Unfortunately, it has a strong infrared (IR) absorption band at 1673 cm−1, significantly overlapping or even completely obscuring the amide I band of a peptide. In such cases TFA must be removed from the solution in order to be able to use IR absorption spectroscopy for peptide secondary structure determination. The most convenient and widely used procedure involves peptide lyophilization from a 0.1 M HCl solution. In our studies of the tryptophan‐rich antimicrobial peptide indolicidin, we have found that caution should be taken when using this HCl concentration. High HCl concentrations (>10 mM in unbuffered solutions and > 50 mM in buffered solutions) may modify the peptide structure and reduce its thermal stability, thereby interfering with subsequent structural investigations of the peptide. Our results indicate that HCl concentrations between 2 and 10 mM are adequate to remove essentially all TFA impurities without any modification of the peptide secondary structure. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd.