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  • Engineering General  (39)
  • Life Sciences (General)  (19)
  • 1
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 17 (1993), S. 1019-1033 
    ISSN: 0271-2091
    Keywords: Convergence behaviour ; Element-by-element data structure ; GMRES ; ORTHOMIN ; Mesh density ; Penalty function model ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The ability of two types of Conjugate Gradient like iterative solvers (GMRES and ORTHOMIN) to resolve large-scale phenomena as a function of mesh density and convergence tolerance limit is investigated. The flow of an incompressible fluid inside a sudden expansion channel is analysed using three meshes of 400, 1600 and 6400 bilinear elements. The iterative solvers utilize the element-by-element data structure of the finite element technique to store and maintain the data at the element level. Both the mesh density and the penalty parameter are found to influence the choice of the convergence tolerance limit needed to obtain accurate results. An empirical relationship between the element size, the penalty parameter, and the convergence tolerance is presented. This relationship can be used to predict the proper choice of the convergence tolerance for a given penalty parameter and element size.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 35 (1992), S. 807-833 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: Numerical simulation of forming processes is studied using the Navier-Stokes equations and the energy equation governing viscous, incompressible fluids. A review of various important aspects of forming processes is also reviewed for completeness. A penalty finite element model of the equations is developed. The finite element model is used to study the effectiveness of various constitutive models developed for metal forming and polymer processing. The element-by-element (EBE) data structure with efficient iterative solution methods is used to solve the large systems of equations that arise in the analysis of complex 3-D problems. Numerical results for problems representative of various forming processes (e.g. extrusion and solidification) are presented.
    Additional Material: 20 Ill.
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  • 3
    Publication Date: 2011-08-24
    Description: Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 277; 6; 4206-14
    Format: text
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  • 4
    Publication Date: 2011-08-24
    Description: Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 277; 12; 9840-52
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  • 5
    Publication Date: 2011-08-24
    Description: Calcium is essential for pollen germination and pollen tube growth. A large body of information has established a link between elevation of cytosolic Ca(2+) at the pollen tube tip and its growth. Since the action of Ca(2+) is primarily mediated by Ca(2+)-binding proteins such as calmodulin (CaM), identification of CaM-binding proteins in pollen should provide insights into the mechanisms by which Ca(2+) regulates pollen germination and tube growth. In this study, a CaM-binding protein from maize pollen (maize pollen calmodulin-binding protein, MPCBP) was isolated in a protein-protein interaction-based screening using (35)S-labeled CaM as a probe. MPCBP has a molecular mass of about 72 kDa and contains three tetratricopeptide repeats (TPR) suggesting that it is a member of the TPR family of proteins. MPCBP protein shares a high sequence identity with two hypothetical TPR-containing proteins from Arabidopsis. Using gel overlay assays and CaM-Sepharose binding, we show that the bacterially expressed MPCBP binds to bovine CaM and three CaM isoforms from Arabidopsis in a Ca(2+)-dependent manner. To map the CaM-binding domain several truncated versions of the MPCBP were expressed in bacteria and tested for their ability to bind CaM. Based on these studies, the CaM-binding domain was mapped to an 18-amino acid stretch between the first and second TPR regions. Gel and fluorescence shift assays performed with CaM and a CaM-binding synthetic peptide further confirmed MPCBP binding to CaM. Western, Northern, and reverse transcriptase-polymerase chain reaction analysis have shown that MPCBP expression is specific to pollen. MPCBP was detected in both soluble and microsomal proteins. Immunoblots showed the presence of MPCBP in mature and germinating pollen. Pollen-specific expression of MPCBP, its CaM-binding properties, and the presence of TPR motifs suggest a role for this protein in Ca(2+)-regulated events during pollen germination and growth.
    Keywords: Life Sciences (General)
    Type: The Journal of biological chemistry (ISSN 0021-9258); Volume 275; 45; 35457-70
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  • 6
    Publication Date: 2011-08-24
    Description: Calmodulin (CaM), a key calcium sensor in all eukaryotes, regulates diverse cellular processes by interacting with other proteins. To isolate CaM binding proteins involved in ethylene signal transduction, we screened an expression library prepared from ethylene-treated Arabidopsis seedlings with 35S-labeled CaM. A cDNA clone, EICBP (Ethylene-Induced CaM Binding Protein), encoding a protein that interacts with activated CaM was isolated in this screening. The CaM binding domain in EICBP was mapped to the C-terminus of the protein. These results indicate that calcium, through CaM, could regulate the activity of EICBP. The EICBP is expressed in different tissues and its expression in seedlings is induced by ethylene. The EICBP contains, in addition to a CaM binding domain, several features that are typical of transcription factors. These include a DNA-binding domain at the N terminus, an acidic region at the C terminus, and nuclear localization signals. In database searches a partial cDNA (CG-1) encoding a DNA-binding motif from parsley and an ethylene up-regulated partial cDNA from tomato (ER66) showed significant similarity to EICBP. In addition, five hypothetical proteins in the Arabidopsis genome also showed a very high sequence similarity with EICBP, indicating that there are several EICBP-related proteins in Arabidopsis. The structural features of EICBP are conserved in all EICBP-related proteins in Arabidopsis, suggesting that they may constitute a new family of DNA binding proteins and are likely to be involved in modulating gene expression in the presence of ethylene.
    Keywords: Life Sciences (General)
    Type: Biochemical and biophysical research communications (ISSN 0006-291X); Volume 279; 3; 762-9
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  • 7
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 2 (1982), S. 151-171 
    ISSN: 0271-2091
    Keywords: Penalty method ; Incompressible Flow ; Finite Elements ; Convergence ; Existence ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In this paper the penalty function method is reviewed in the general context of solving constrained minimization problems. Mathematical properties, such as the existence of a solution to the penalty problem and convergence of the solution of a penalty problem to the solution of the original problem, are studied for the general case. Then the results are extended to a penalty function formulation of the Stokes and Navier-Stokes equations. Conditions for the equivalence of two penalty-finite element models of fluid flow are established, and the theoretical error estimates are verified in the case of Stokes's problem.
    Additional Material: 2 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 10 (1990), S. 373-400 
    ISSN: 0271-2091
    Keywords: Comparison ; Experimental ; Simulation ; Planar entry flow ; Viscoelastic ; Convergence ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The goal of this research was to determine whether there is any interaction between the type of constitutive equation used and the degree of mesh refinement, as well as how the type of constitutive equation might affect the convergence and quality of the solution, for a planar 4:1 contraction in the finite eiement method. Five constitutive equations were used in this work: the Phan-Thien-Tanner (PTT), Johnson-Segalman (JS), White-Metzner (WM), Leonov-like and upper convected Maxwell (UCM) models. A penalty Galerkin finite element technique was used to solve the system of non-linear differential equations. The constitutive equations were fitted to the steady shear viscosity and normal stress data for a polystyrene melt. In general it was found that the convergence limit based on the Deborah number De and the Weissenberg number We varied from model to model and from mesh to mesh. From a practical point of view it was observed that the wall shear stress in the downstream region should also be indicated at the point where convergence is lost, since this parameter reflects the throughput conditions. Because of the dependence of convergence on the combination of mesh size and constitutive equation, predictions of the computations were compared with birefringence data obtained for the same polystyrene melt flowing through a 4:1 planar contraction. Refinement in the mesh led to better agreement between the predictions using the PTT model and flow birefringence, but the oscillations became worse in the corner region as the mesh was further refined, eventually leading to the loss of convergence of the numerical algorithm. In comparing results using different models at the same wall shear stress conditions and on the same mesh, it was found that the PTT model gave less overshoot of the stresses at the re-entrant corner. Away from the corner there were very small differences between the quality of the solutions obtained using different models. All the models predicted solutions with oscillations. However, the values of the solutions oscillated around the experimental birefringence data, even when the numerical algorithm would not converge. Whereas the stresses are predicted to oscillate, the streamlines and velocity field remained smooth. Predictions for the existence of vortices as well as for the entrance pressure loss (ΔPent) varied from model to model. The UCM and WM models predicted negative values for ΔPent.
    Additional Material: 19 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 7 (1987), S. 1325-1342 
    ISSN: 0271-2091
    Keywords: Convective Heat Transfer ; Finite Elements ; Navier-Stokes Equations ; Numerical Results ; Penalty Model ; Staggered Cylinders ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The two-dimensional Navier-Stokes equations and the energy equation governing steady laminar incompressible flow are solved by a penalty finite-element model for flow across finite depth, five-row deep, staggered bundles of cylinders. Pitch to diameter ratios of 1·5 and 2·0 are considered for cylinders in equilateral triangular and square arrangements. Reynolds numbers studied range from 100 to 400, and a Prandtl number of 0·7 is used. Velocity vector fields, streamline patterns, vorticity, pressure and temperature contours, local and average Nusselt numbers, pressure and shear stress distributions around the cylinder walls and drag coefficients are presented. The results obtained agree well with available experimental and numerical data.
    Additional Material: 10 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    International Journal for Numerical and Analytical Methods in Geomechanics 6 (1982), S. 441-459 
    ISSN: 0363-9061
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Notes: The present study is a continuation of the numerical modelling of geologic structures by the authors (see J. N. Reddy et al., Finite-element modelling of folding and faulting, this journal). The present paper is concerned with the computation of the stress and fracture density distributions in single layer folds by the finite-element method. It was found that variations in fracture patterns are related to several variables: (i) the viscosity of the competent layer, (ii) the ratio of the viscosity of the competent layer to the viscosity of the matrix, (iii) the cohesive strength of the material, and (iv) the boundary velocities during deformation. The fracture prediction is based on the Mohr-Coulomb criterion, which is a function of the stresses only. Prediction of fracture density is based on a function of the strain energy. It is found that there is a good correlation between the computer predicted fractures and the fracture pattern produced by the expermental buckiing of rock-beams. Itis, concluded that the viscosity ratio controls the location of fractures in single layer folds.
    Additional Material: 17 Ill.
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