Computation of flow over a rotating body on unstructured Chimera mesh

Flow around moving boundary is ubiquitous in engineering applications. To increse the efficienly of the algorithm to handle moving boundaries is still a major challenge in Computational Fluid Dynamics (CFD). The Chimera grid method is one type of method to handle moving boundaries. A concept of domain de-composition has been proposed in this paper. In this method, sub-domains are meshed independently and governing equations are also solved separately on them. The Chimera grid method was originally used only on structured (curvilinear) meshes. However, in a problem which involves both moving boundary and complex geometry, the number of sub-domains required in a traditional (structured) Chimera method becomes fairly large. Thus the time required in the interior boundary locating, link-building and data exchanging also increases. The use of unstructured Chimera grid can reduce the time consumption significantly by the reduction of domain(block) number. Generally speaking, unstructured Chimera grid method has not been developed. In this paper, a well-known pressure correction scheme - SIMPLEC is modified and implemented on unstructured Chimera mesh. A new interpolation scheme regarding the pressure correction is proposed to prevent the possible decoupling of pressure. A moving-mesh finite volume approach is implemented in an inertial reference frame. This approach is then used to compute incompressible flow around a rotating circular and elliptic cylinder. These numerical examples demonstrate the capability of the proposed scheme in handling moving boundaries. The numerical results are in good agreement with other experimental and computational data in literature. The method proposed in this paper can be efficiently applied to more challenge cases such as free-falling objects or heavy particles in fluid.

A smoothing technique for discrete delta functions with application to immersed boundary method in moving boundary simulations.

The effects of complex boundary conditions on flows are represented by a volume force in the immersed boundary methods. The problem with this representation is that the volume force exhibits non-physical oscillations in moving boundary simulations. A smoothing technique for discrete delta functions has been developed in this paper to suppress the non-physical oscillations in the volume forces. We have found that the non-physical oscillations are mainly due to the fact that the derivatives of the regular discrete delta functions do not satisfy certain moment conditions. It has been shown that the smoothed discrete delta functions constructed in this paper have one-order higher derivative than the regular ones. Moreover, not only the smoothed discrete delta functions satisfy the first two discrete moment conditions, but also their derivatives satisfy one-order higher moment condition than the regular ones. The smoothed discrete delta functions are tested by three test cases: a one-dimensional heat equation with a moving singular force, a two-dimensional flow past an oscillating cylinder, and the vortex-induced vibration of a cylinder. The numerical examples in these cases demonstrate that the smoothed discrete delta functions can effectively suppress the non-physical oscillations in the volume forces and improve the accuracy of the immersed boundary method with direct forcing in moving boundary simulations.

Numerical simulation of condensation of bubbles under microgravity conditions by moving mesh method in the double-staggered grid

A numerical 2D method for simulation of two-phase flows including phase change under microgravity conditions is presented in this paper, with a level set method being coupled with the moving mesh method in the double-staggered grid systems. When the grid lines bend very much in a curvilinear grid, great errors may be generated by using the collocated grid or the staggered grid. So the double-staggered grid was adopted in this paper. The level set method is used to track the liquid-vapor interface. The numerical analysis is fulfilled by solving the Navier-Stokes equations using the SIMPLER method, and the surface tension force is modeled by a continuum surface force approximation. A comparison of the numerical results obtained with different numerical strategies shows that the double-staggered grid moving-mesh method presented in this paper is more accurate than that used previously in the collocated grid system. Based on the method presented in this paper, the condensation of a single bubble in the cold water under different level of gravity is simulated. The results show that the condensation process under the normal gravity condition is different from the condensation process under microgravity conditions. The whole condensation time is much longer under the normal gravity than under the microgravity conditions.

Acceleration of initially moving electrons by a copropagation intense laser pulse

Acceleration of an initially moving electron by a copropagation ultra-short ultra-intense laser pulse in vacuum is studied. It is shown that when appropriate laser pulse parameters and focusing conditions are imposed, the acceleration of electron by ascending front of laser pulse can be much stronger compared to the deceleration by descending part. Consequently, the electron can obtain significantly high net energy gain. We also report the results of the new scheme that enables a second-step acceleration of electron using laser pulses of peak intensity in the range of 10(19)-10(20) W mu m(2)/cm(2). In the first step the electron acceleration from rest is limited to energies of a few MeV, while in the second step the electron acceleration can be considerably enhanced to about 100 MeV energy.

Dynamic phase-mapping of domain nucleation on MgO : LiNbO3 crystal by digital holographic interferometry

The quantitative phase-mapping of the domain nucleation in MgO:LiNbO3 crystals is presented by using the digital holographic interferometry. An unexpected peak phase at the beginning of the domain nucleation is observed and it is lowered as the spreading of the domain nucleus. The existence of the nucleus changes the moving speed of the domain wall by pinning it for 3s. Such in-situ quantitative analysis of the domain nucleation process is a key to optimizing domain structure fabrication.

A new protein structure of P-II class snake venom metalloproteinases: it comprises metalloproteinase and disintegrin domains

A new metalloproteinase-disintegrin, named Jerdonitin, was purified from Trimeresurus jerdonii venom with a molecular weight of 36 kDa on SDS-PAGE. It dose-dependently inhibited ADP-induced human platelet aggregation with IC50 of 120 nM. cDNA cloning and sequencing revealed that Jerdonitin belonged to the class II of snake venom metalloproteinases (SVMPs) (P-II class). Different from other P-II class SVMPs, metalloproteinase and disintegrin domains of its natural protein were not separated, confirmed by internal peptide sequencing. Compared to other P-II class SVMPs, Jerdonitin has two additional cysteines (Cys219 and Cys238) located in the spacer domain and disintegrin domain, respectively. They probably form a disulfide bond and therefore the metalloproteinase and disintegrin domains cannot be separated by posttranslationally processing. In summary, comparison of the amino acid sequences of Jerdonitin with those of other P-II class SVMPs by sequence alignment and phylogenetic analysis, in conjunction with natural protein structure data, suggested that it was a new type of P-II class SVMPs. (C) 2003 Elsevier Inc. All rights reserved.

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Differential amplitude modulation of auditory evoked cortical potentials associated with brain state in the freely moving rhesus monkey

We simultaneously recorded auditory evoked potentials (AEP) from the temporal cortex (TCx), the dorsolateral prefrontal cortex (dPFCx) and the parietal cortex (PCx) in the freely moving rhesus monkey to investigate state-dependent changes of the AEP. AEPs obtained during passive wakefulness, active wakefulness (AW), slow wave sleep and rapid-eye-movement sleep (REM) were compared. Results showed that AEP from all three cerebral areas were modulated by brain states. However, the amplitude of AEP from dPFCx and PCx significantly appeared greater attenuation than that from the TCx during AW and REM. These results indicate that the modulation of brain state on AEP from all three cerebral areas investigated is not uniform, which suggests that different cerebral areas have differential functional contributions during sleep-wake cycle. (C) 2002 Elsevier Science Ireland Ltd.. All rights reserved.

A microelectrode drive for long term recording of neurons in freely moving and chaired monkeys

An electrode drive is described for recordings of neurons in freely moving and chaired monkeys during the performance of behavioural tasks. The electrode drives are implanted for periods of up to 6 months, and can advance up to 42 electrodes using 14 independent drive mechanisms. The drive samples 288 points within a 12 mm x 12 min region, with 15 min of electrode travel. Major advantages are that recordings are made in freely moving monkeys, and these recordings can be compared with those in chaired experiments; waveforms of single neurons are stable, enabling prolonged recordings of the same neurons across periods of days; recordings can be made throughout the brain, including the dorsolateral prefrontal cortex and hippocampus; the drive accommodates both sharp microelectrodes and fine wire assemblies such as tetrodes. (C) 2003 Elsevier Science B.V; All rights reserved.

Spatially directed movement and neuronal activity in freely moving monkey

The abilities to plan a series of movements and to navigate within the environment require the functions of the frontal and ventromedial temporal lobes, respectively. Neuropsychological studies posit the existence of egocentric (prefrontal) and allocentri

Neurophysiological recordings in freely moving monkeys

Recordings of neuronal activity in freely moving rats are common in experiments where electrical signals are transmitted using cables. Such techniques are not common in monkeys because their prehensile abilities are thought to preclude such techniques. Ho

Maze model to study spatial learning and memory in freely moving monkeys

Many types of mazes have been used in cognitive brain research and data obtained from those experiments, especially those from rodents' studies, support the idea that the hippocampus is related to spatial learning and memory. But the results from non-huma

The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b