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Local Regions (local + regions)

Distribution by Scientific Domains

Chemistry	50%

Selected Abstracts

Arbitrary placement of local meshes in a global mesh by the interface-element method (IEM)

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 15 2003
Hyun-Gyu KimArticle first published online: 25 FEB 200
Abstract A new method is proposed to place local meshes in a global mesh with the aid of the interface-element method (IEM). The interface-elements use moving least-square (MLS)-based shape functions to join partitioned finite-element domains with non-matching interfaces. The supports of nodes are defined to satisfy the continuity condition on the interfaces by introducing pseudonodes on the boundaries of interface regions. Particularly, the weight functions of nodes on the boundaries of interface regions span only neighbouring nodes, ensuring that the resulting shape functions are identical to those of adjoining finite-elements. The completeness of the shape functions of the interface-elements up to the order of basis provides a reasonable transfer of strain fields through the non-matching interfaces between partitioned domains. Taking these great advantages of the IEM, local meshes can be easily inserted at arbitrary places in a global mesh. Several numerical examples show the effectiveness of this technique for modelling of local regions in a global domain. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Piezospectroscopic Analysis of Interface Debonding in Thermal Barrier Coatings

JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 5 2000
Xiao Peng
One of the principal modes by which electron-beam-evaporated thermal barrier coatings fail is via the nucleation of local regions of debonding, which grow and link together until reaching a critically sized flaw for spontaneous buckling and spalling. This progressive-failure mode is used as a basis for analyzing the changes that can occur in photostimulated luminescence spectra that have been recorded from the thermally grown oxide. This process also provides a basis for the quantitative determination of the extent of local damage prior to spalling from an analysis of the shape of the luminescence spectra. [source]

Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins

PROTEIN SCIENCE, Issue 4 2010
Olivia Doppelt-Azeroual
Abstract Ligand,protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED-SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED-SMA is an automated and fast method to classify binding sites. It is based on MED-SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora-A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED-SMA approach is demonstrated as it gathers binding sites of proteins with similar structure-activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects. [source]

Pattern-recognition-based detection of planar objects in three-dimensional electron-density maps

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2008
Johan Hattne
A pattern-recognition-based method for the detection of planar objects in protein or DNA/RNA crystal structure determination is described. The procedure derives a set of rotation-invariant numeric features from local regions in the asymmetric unit of a crystallographic electron-density map. These features, primarily moments of various orders, capture different aspects of the local shape of objects in the electron density. Feature classification is achieved using a linear discriminant that is trained to optimize the contrast between planar and nonplanar objects. In five selected test cases with X-ray data spanning 2.0,3.0,Å resolution, the procedure identified the correct location and orientation for almost all of the double-ring and a majority of the single-ring planar groups. The accuracy of the location of the plane centres is of the order of 0.5,Å, even in moderately noisy density maps. [source]