Generation of large-scale vortex dislocations in a three-dimensional wake-type flow

Numerical study of three-dimensional evolution of wake-type flow and vortex dislocations is performed by using a compact finite diffenence-Fourier spectral method to solve 3-D incompressible Navier-Stokes equations. A local spanwise nonuniformity in momentum defect is imposed on the incoming wake-type flow. The present numerical results have shown that the flow instability leads to three-dimensional vortex streets, whose frequency, phase as well as the strength vary with the span caused by the local nonuniformity. The vortex dislocations are generated in the nonuniform region and the large-scale chain-like vortex linkage structures in the dislocations are shown. The generation and the characteristics of the vortex dislocations are described in detail.

Numerical analysis and comparison of three metal-oxide-type super-resolution near field structures

Based on the Fresnel-Kirchkoff diffraction theory, we build up a Gaussian diffraction model of metal-oxide-type super-resolution near field structure (super-RENS), which can describe far field optical properties. The spectral contrast induced by refractive index and the structural changes in AgOx, PtOx and PdOx thin films, which are the key functional layers in super-RENS, are studied by using this model. Comparison results indicate that the spectral contrast intensively on laser-induced distribution and change of the refractive index in the metal-oxide films. The readout mechanism of the metal-oxide-type super-RENS optical disc is further clarified. This Gaussian diffraction model can be used as a simple and effective method for choosing proper active materials in super-RENS.

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.

The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

Photoinduced voltage shift in a three-barrier, two-well resonant tunneling structure integrated with a 1.2-mu m-thick n-type GaAs layer

By integrating a three-barrier, two-well resonant tunneling structure with a 1.2-mu m-thick, slightly doped n-GaAs layer, a photoinduced voltage shift on the order of magnitude of 100 mV in resonant current peaks has been verified at an irradiance of low light power density. The 1.2-mu m-thick, slightly doped n-GaAs layer manifests itself of playing an important role in enhancing photoelectric sensitivity. (c) 2005 Elsevier B.V. All rights reserved.

Cflec-4, a multidomain C-type lectin involved in immune defense of Zhikong scallop Chlamys farreri

C-type lectins are a superfamily of carbohydrate-recognition proteins which play crucial roles in the innate immunity. In this study, a novel multidomain C-type lectin gene from scallop Chlamys farreri (designated as Cflec-4) was cloned by RACE approach based on EST analysis. The full-length cDNA of Cflec-4 was of 2086 bp. The open reading frame was of 1830 bp and encoded a polypeptide of 609 amino acids, including a signal sequence and four dissimilar carbohydrate-recognition domains (CRDs). The deduced amino acid sequence of CflecA shared high similarities to other C-type lectin family members. The phylogenetic analysis revealed the divergence between the three N-terminal CRDs and the C-terminal one, suggesting that the four CRDs in Cflec-4 originated by repeated duplication of different primordial CRD. The potential tertiary structure of each CRD in Cflec-4 was typical double-loop structure with Ca2+-binding site 2 in the long loop region and two conserved disulfide bridges at the bases of the loops. The tissue distribution of Cflec-4 mRNA was examined by fluorescent quantitative real-time PCR. In the healthy scallops, the Cflec-4 transcripts could be only detected in gonad and hepatopancreas, whereas in the Listonella anguillarum challenged scallops, it could be also detected in hemocytes. These results collectively suggested that CflecA was involved in the immune defense of scallop against pathogen infection and provided new insight into the evolution of C-type lectin superfamily. (C) 2009 Elsevier Ltd. All rights reserved.

Structure of Vortex Dislocations in a Wake-type Flow

Structure and dynamical processes of vortex dislocations in a kind of wake-type flow are described clearly by vortex lines, which are directly constructed from data of three-dimensional direct numerical simulations of the flow evolution.

Low-Dimensional Dynamical Systems for a Wake-Type Shear Flow with Vortex Dislocations

Low-dimensional systems are constructed to investigate dynamics of vortex dislocations in a wake-type shear flow. High-resolution direct numerical simulations are employed to obtain flow snapshots from which the most energetic modes are extracted using proper orthogonal decomposition (POD). The first 10 modes are classified into two groups. One represents the general characteristics of two-dimensional wake-type shear flow, and the other is related to the three-dimensional properties or non-uniform characteristics along the span. Vortex dislocations are generated by these two kinds of coherent structures. The results from the first 20 three-dimensional POD modes show that the low- dimensional systems have captured the basic properties of the wake-type shear flow with vortex dislocation, such as two incommensurable frequencies and their beat frequency.

Numerical exploration of new features on three-dimensional transition of a cylinder wake

The three-dimensional transition of the wake flow behind a circular cylinder is studied in detail by direct numerical simulations using 3D incompressible N-S equations for Reynolds number ranging from 200 to 300. New features and vortex dynamics of the 3D transition of the wake are found and investigated. At Re = 200, the flow pattern is characterized by mode A instability. However, the spanwise characteristic length of the cylinder determines the transition features. Particularly for the specific spanwise characteristic length linear stable mode may dominate the wake in place of mode A and determine the spanwise phase difference of the primary vortices shedding. At Re = 250 and 300 it is found that the streamwise vortices evolve into a new type of mode - "dual vortex pair mode" downstream. The streamwise vortex structures switch among mode A, mode B and dual vortex pair mode from near wake to downstream wake. At Re = 250, an independent low frequency f(m) in addition to the vortex shedding frequency f(s) is identified. Frequency coupling between f(m) and f(s) occurs. These result in the irregularity of the temporal signals and become a key feature in the transition of the wake. Based on the formation analysis of the streamwise vorticity in the vicinity of cylinder, it is suggested that mode A is caused by the emergence of the spanwise velocity due to three dimensionality of the incoming flow past the cylinder. Energy distribution on various wave numbers and the frequency variation in the wake are also described.

Lattice type of fracture model for concrete

Concrete is usually described as a three-phase material, where matrix, aggregate and interface zones are distinguished. The beam lattice model has been applied widely by many investigators to simulate fracture processes in concrete. Due to the extremely large computational effort, however, the beam lattice model faces practical difficulties. In our investigation, a new lattice called generalized beam (GB) lattice is developed to reduce computational effort. Numerical experiments conducted on a panel subjected to uniaxial tension show that the GB lattice model can reproduce the load-displacement curves and crack patterns in agreement to what are observed in tests. Moreover, the effects of the particle overlay on the fracture process are discussed in detail. (C) 2007 Elsevier Ltd. All rights reserved.

Study of three elastic-plastic constitutive models by non-proportional finite deformations of OFHC copper

Experimental stress-strain data of OFHC copper first under torsion to 13% and then under torsion-tension to about 10% are used to study the characteristics of three elastic-plastic constitutive models: Chaboche's super-positional nonlinear model, Dafalias and Popov's two surface model and Watanabe and Atluri's version of the endochronic model. The three models, originally oriented for infinitesimal deformation, have been extended for finite deformation. The results show (a) the Mises-type yield surface used in the three models brings about significant departure of the predictions from the experimental data; (b) Chaboche's and Dafalias' models are easier than Watanabe and Atluri's model in determining the material parameters in them, and (c) Chaboche's and Watanabe & Atluri's models produce almost the same prediction to the data, while Dafalias' model cannot accurately predict the plastic deformations when a loading path changes in its direction. Copyright (C) 1996 Elsevier Science Ltd