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Multiple Structures (multiple + structure)
Selected AbstractsInterface handling for three-dimensional higher-order XFEM-computations in fluid,structure interactionINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 7 2009Ursula M. Mayer Abstract Three-dimensional higher-order eXtended finite element method (XFEM)-computations still pose challenging computational geometry problems especially for moving interfaces. This paper provides a method for the localization of a higher-order interface finite element (FE) mesh in an underlying three-dimensional higher-order FE mesh. Additionally, it demonstrates, how a subtetrahedralization of an intersected element can be obtained, which preserves the possibly curved interface and allows therefore exact numerical integration. The proposed interface algorithm collects initially a set of possibly intersecting elements by comparing their ,eXtended axis-aligned bounding boxes'. The intersection method is applied to a highly reduced number of intersection candidates. The resulting linearized interface is used as input for an elementwise constrained Delaunay tetrahedralization, which computes an appropriate subdivision for each intersected element. The curved interface is recovered from the linearized interface in the last step. The output comprises triangular integration cells representing the interface and tetrahedral integration cells for each intersected element. Application of the interface algorithm currently concentrates on fluid,structure interaction problems on low-order and higher-order FE meshes, which may be composed of any arbitrary element types such as hexahedra, tetrahedra, wedges, etc. Nevertheless, other XFEM-problems with explicitly given interfaces or discontinuities may be tackled in addition. Multiple structures and interfaces per intersected element can be handled without any additional difficulties. Several parallelization strategies exist depending on the desired domain decomposition approach. Numerical test cases including various geometrical exceptions demonstrate the accuracy, robustness and efficiency of the interface handling. Copyright © 2009 John Wiley & Sons, Ltd. [source] Identification of Lmo1 as part of a Hox-dependent regulatory network for hindbrain patterningDEVELOPMENTAL DYNAMICS, Issue 9 2007Christelle Matis Abstract The embryonic functions of Hox proteins have been extensively investigated in several animal phyla. These transcription factors act as selectors of developmental programmes, to govern the morphogenesis of multiple structures and organs. However, despite the variety of morphogenetic processes Hox proteins are involved in, only a limited set of their target genes has been identified so far. To find additional targets, we used a strategy based upon the simultaneous overexpression of Hoxa2 and its cofactors Pbx1 and Prep in a cellular model. Among genes whose expression was upregulated, we identified LMO1, which codes for an intertwining LIM-only factor involved in protein,DNA oligomeric complexes. By analysing its expression in Hox knockout mice, we show that Lmo1 is differentially regulated by Hoxa2 and Hoxb2, in specific columns of hindbrain neuronal progenitors. These results suggest that Lmo1 takes part in a Hox paralogue 2,dependent network regulating anteroposterior and dorsoventral hindbrain patterning. Developmental Dynamics 236:2675,2684, 2007. © 2007 Wiley-Liss, Inc. [source] Collateral desmitis of the distal interphalangeal joint in conjunction with concurrent ossification of the cartilages of the foot in nine horsesEQUINE VETERINARY EDUCATION, Issue 9 2008T. S. Mair Summary The purpose of this study was to describe the frequency of occurrence of severe ossification of the collateral cartilages (sidebone) coexistent with collateral desmitis of the distal interphalangeal joint (DIPJ) in lame horses. Sidebone was diagnosed and graded on standard radiographs and soft tissue injuries of the foot were diagnosed using standing low-field magnetic resonance imaging (MRI). Of 15 horses with forelimb lameness and severe sidebone, 9 had evidence of concurrent collateral desmitis of the DIPJ. All 15 horses had damage to other structures (including the deep digital flexor tendon, distal sesamoidean impar ligament, collateral sesamoidean ligament, navicular bone and distal phalanx) within the affected feet as identified on MRI. The clinical and pathophysiological significance of concurrent collateral desmitis of the DIPJ and sidebone is currently uncertain. However, this study shows that injuries to multiple structures within the foot are common and that collateral desmitis of the distal interphalangeal joint is frequently seen in lame horses in conjunction with severe ossification of the collateral cartilages. [source] Mining protein dynamics from sets of crystal structures using "consensus structures"PROTEIN SCIENCE, Issue 4 2010Gerard J. P. van Westen Abstract In this work, we describe two novel approaches to utilize the dynamic structure information implicitly contained in large crystal structure data sets. The first approach visualizes both consistent as well as variable ligand-induced changes in ligand-bound compared with apo protein crystal structures. For this purpose, information was mined from B-factors and ligand-induced residue displacements in multiple crystal structures, minimizing experimental error and noise. With this approach, the mechanism of action of non-nucleoside reverse transcriptase inhibitors (NNRTIs) as an inseparable combination of distortion of protein dynamics and conformational changes of HIV-1 reverse transcriptase was corroborated (a combination of the previously proposed "molecular arthritis" and "distorted site" mechanisms). The second approach presented here uses "consensus structures" to map common binding features that are present in a set of structures of NNRTI-bound HIV-1 reverse transcriptase. Consensus structures are based on different levels of structural overlap of multiple crystal structures and are used to analyze protein,ligand interactions. The structures are shown to yield information about conserved hydrogen bonding interactions as well as binding-pocket flexibility, shape, and volume. From the consensus structures, a common wild type NNRTI binding pocket emerges. Furthermore, we were able to identify a conserved backbone hydrogen bond acceptor at P236 and a novel hydrophobic subpocket, which are not yet utilized by current drugs. Our methods introduced here reinterpret the atom information and make use of the data variability by using multiple structures, complementing classical 3D structural information of single structures. [source] Multiple crystal structures of actin dimers and their implications for interactions in the actin filamentACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2008Michael R. Sawaya The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing precisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The reappearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199,205 and 287,291 are highlighted. [source] Hydration of the Calcium Dication: Direct Evidence for Second Shell Formation from Infrared SpectroscopyCHEMPHYSCHEM, Issue 15 2007Matthew F. Bush Abstract Infrared laser action spectroscopy in a Fourier-transform ion cyclotron resonance mass spectrometer is used in conjunction with ab initio calculations to investigate doubly charged, hydrated clusters of calcium formed by electrospray ionization. Six water molecules coordinate directly to the calcium dication, whereas the seventh water molecule is incorporated into a second solvation shell. Spectral features indicate the presence of multiple structures of Ca(H2O)72+ in which outer-shell water molecules accept either one (single acceptor) or two (double acceptor) hydrogen bonds from inner-shell water molecules. Double-acceptor water molecules are predominately observed in the second solvent shells of clusters containing eight or nine water molecules. Increased hydration results in spectroscopic signatures consistent with additional second-shell water molecules, particularly the appearance of inner-shell water molecules that donate two hydrogen bonds (double donor) to the second solvent shell. This is the first reported use of infrared spectroscopy to investigate shell structure of a hydrated multiply charged cation in the gas phase and illustrates the effectiveness of this method to probe the structures of hydrated ions. [source] | ||||||||||