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Rigid Geometry (rigid + geometry)

Distribution by Scientific Domains

Chemistry	40%

Selected Abstracts

Large eddy simulation of turbulent flows in complex and moving rigid geometries using the immersed boundary method

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 7 2005
Mayank Tyagi
Abstract A large eddy simulation (LES) methodology for turbulent flows in complex rigid geometries is developed using the immersed boundary method (IBM). In the IBM body force terms are added to the momentum equations to represent a complex rigid geometry on a fixed Cartesian mesh. IBM combines the efficiency inherent in using a fixed Cartesian grid and the ease of tracking the immersed boundary at a set of moving Lagrangian points. Specific implementation strategies for the IBM are described in this paper. A two-sided forcing scheme is presented and shown to work well for moving rigid boundary problems. Turbulence and flow unsteadiness are addressed by LES using higher order numerical schemes with an accurate and robust subgrid scale (SGS) stress model. The combined LES,IBM methodology is computationally cost-effective for turbulent flows in moving geometries with prescribed surface trajectories. Several example problems are solved to illustrate the capability of the IBM and LES methodologies. The IBM is validated for the laminar flow past a heated cylinder in a channel and the combined LES,IBM methodology is validated for turbulent film-cooling flows involving heat transfer. In both cases predictions are in good agreement with measurements. LES,IBM is then used to study turbulent fluid mixing inside the complex geometry of a trapped vortex combustor. Finally, to demonstrate the full potential of LES,IBM, a complex moving geometry problem of stator,rotor interaction is solved. Copyright © 2005 John Wiley & Sons, Ltd. [source]

A Dinuclear Double-Stranded Oxido Complex of ReV with a Bis(benzene- o -dithiolato) Ligand

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 27 2009
Jorge S. Gancheff
Abstract The reaction of [ReOCl3(PPh3)2] with 1,2-bis(2,3-dimercaptobenzamido)ethane (H4 - 1) in the presence of Na2CO3 in methanol under anaerobic conditions affords the dinuclear ReV oxido complex [PPh4]2[ReO(1)]2 containing two distorted square-pyramidal {ReVOS4} units bridged by the ligand strands in a double-stranded fashion. The coordinationgeometry around the metal centers is similar to the one observed for [ReO(bdt)2],. The ReS4 planes are arranged in a coplanar fashion and are not twisted around the metal,metal vector, which prevents the complex to adopt a helical structure. Luminescence studies show the presence of emission bands, which are assigned to singlet-singlet transitions exhibiting very fast decays (ca. 10 ns). Theoretical Density Functional (DFT) studies on geometry and electronic properties were performed employing the hybrid B3LYP and PBE1PBE functionals. While the general trends observed in the experimental data are well reproduced in all cases, a good agreement was obtained using PBE1PBE, in particular for the Re,S bonds. Natural Bond Orbitals (NBO) analysis indicates the presence of polarized Re,O and Re,S bonds, both of them polarized toward the non-metal. The calculation show that the molecular orbitals of the ReV are doubly degenerated, the occupied 5d orbital of rhenium lying beneath occupied sulfur-based MOs due to the rigid geometry imposed by the C,C backbone of the bis(benzene- o -dithiolato) ligands. The origin of all absorption bands is ascribed to a ligand-to-metal charge transfer (LMCT), in which occupied sulfur-based orbitals and unoccupied rhenium-centered orbitals are involved.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source]

Large eddy simulation of turbulent flows in complex and moving rigid geometries using the immersed boundary method

Real-space protein-model completion: an inverse-kinematics approach

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2005
Henry Van Den Bedem
Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12,15 residues in areas of weak or ambiguous electron density, even at medium to low resolution. [source]