Instabilities in the oscillatory flow of a complex fluid.

The dynamics of a fluid in a vertical tube, subjected to an oscillatory pressure gradient, is studied experimentally for both a Newtonian and a viscoelastic shear-thinning fluid. Particle image velocimetry is used to determine the two-dimensional velocity fields in the vertical plane of the tube axis, in a range of driving amplitudes from 0.8 to 2.5 mm and of driving frequencies from 2.0 to 11.5 Hz. The Newtonian fluid exhibits a laminar flow regime, independent of the axial position, in the whole range of drivings. For the complex fluid, instead, the parallel shear flow regime exhibited at low amplitudes [Torralba, Phys. Rev. E 72, 016308 (2005)] becomes unstable at higher drivings against the formation of symmetric vortices, equally spaced along the tube. At even higher drivings the vortex structure itself becomes unstable, and complex nonsymmetric structures develop. Given that inertial effects remain negligible even at the hardest drivings (Re < 10(-1)), it is the complex rheology of the fluid that is responsible for the instabilities observed. The system studied represents an interesting example of the development of shear-induced instabilities in nonlinear complex fluids in purely parallel shear flow.

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene. (C) 2004 Elsevier Inc. All rights reserved.

Liver cytochrome oxidase P4501A1 purification of Acipenser persicus and designing ELISA for measuring

Moon oxygenases related to cytochrome P450s are the molecular Biomarkers which have important role in Biotransformation of endogenous and exogenous compounds and catalazyin of many biological reactions. One of the important isoenzyme is cytochrome P4501A. This isoenzyme involved in metabolism of environment pollutnts such as PAHs. Because of its inducibility, it has a key tool for impact assesment of contaminants in aquatic environment. In this study, at first, that fractions containing Acipenser persicus and Huso huso isoenzyme were purified, and after that Antibodies against them were prepared. For isolation of isoenzyme fraction, Microsomes were prepared from fish liver using differential centrifugation at high speeds. microsomes were solubiized by cholat sodium and Emulgen. Extraction of this isoenzyme was done with the combinatuion of ionexchange chromatography and gelfiltration or chromatofocusing chromatography. Ion exchange chromatography and gel filtration were applied in DEAE sepharose fast flow and sephacryl S200 respectively and chromatofocusing was done at poly buffer 74 and 94 exchanger. The results of SDS-PAGE Showed that the molecular weight of isoenzyme was about 58±1 KDa. Furthermore the inmunoblotting results confirmed this subject. Isoenzyme activigy based on EROD (Ethoxyresorofin o-deethylase) reaction showed about 20-26 fold increase in enzyme activity of treated fish than control fish. The results of Elisa, Using monoclonal anti cod P4501A demonstrated the inducibility and highly elevated of its activity in treated sample more than the control fish. Mean while, the fish sample were showed the strong reaction to polyclonal antibody against beluga P4501A1 prepared in our Lab compared to monoclonal anti body.

DT-MRI data visualisation using the dual tree Complex Wavelet transform

In this paper a novel visualisation method for diffusion tensor MRI datasets is introduced. This is based on the use of Complex Wavelets in order to produce "stripy" textures which depict the anisotropic component of the diffusion tensors. Grey-scale pixel intensity is used to show the isotropic component. This paper also discusses enhancements of the technique for 3D visualisation. © 2004 IEEE.

Complex wavelets and shift invariance

Recently we have developed a new form of discrete wavelet transform, which generates complex coefficients by using a dual tree of wavelet filters to obtain their real and imaginary parts. This introduces limited redundancy (2 m:1 for m-dimensional signals) and allows the transform to provide approximate shift invariance and directionally selective filters (properties lacking in the traditional wavelet transform) while preserving the usual properties of perfect reconstruction and computational efficiency with good well-balanced frequency responses. In this paper we analyse why the new transform can be designed to be shift invariant, and describe how to estimate the accuracy of this approximation and design suitable filters to achieve this.

Biologically-inspired object recognition system with features from complex wavelets

In this paper, a novel cortex-inspired feed-forward hierarchical object recognition system based on complex wavelets is proposed and tested. Complex wavelets contain three key properties for object representation: shift invariance, which enables the extraction of stable local features; good directional selectivity, which simplifies the determination of image orientations; and limited redundancy, which allows for efficient signal analysis using the multi-resolution decomposition offered by complex wavelets. In this paper, we propose a complete cortex-inspired object recognition system based on complex wavelets. We find that the implementation of the HMAX model for object recognition in [1, 2] is rather over-complete and includes too much redundant information and processing. We have optimized the structure of the model to make it more efficient. Specifically, we have used the Caltech 5 standard dataset to compare with Serre's model in [2] (which employs Gabor filter bands). Results demonstrate that the complex wavelet model achieves a speed improvement of about 4 times over the Serre model and gives comparable recognition performance. © 2011 IEEE.

Interaction between human interleukin-16 and CD4 receptor of HIV-1

AIM: To study the interaction between human interleukin-16 (IL-16) and the receptor CD4 (T-lymphocyte differentiation antigen) of human immunodeficiency virus type 1 (HIV-1). METHODS: Two structurally con served regions (SCRs) of human IL-16 were built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of human interleukin-1 (HIL-4) and HIL-2 as the templates. The coordinates for amino-terminal residue sequence, carboxyl-terminal residue sequences, and cytoplasm loops were generated using Biopolymer's LOOP SEARCH algorithm. RESULTS: HIL-16 first formed a homodimer, then contacted with CD4 dimer further forming a dimeric complex. Subsequently, the dimeric complex constructed the tetrameric complex by two disulfide bridges between the cysteines of HIL-16 (Cys31-Cys31). CONCLUSION: The interaction model is useful to propose the action mechanism of HIL-16 and is beneficial for rational designing of novel anti-HIV drugs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Change propagation analysis in complex technical systems

Understanding how and why changes propagate during engineering design is critical because most products and systems emerge from predecessors and not through clean sheet design. This paper applies change propagation analysis methods and extends prior reasoning through examination of a large data set from industry including 41,500 change requests, spanning 8 years during the design of a complex sensor system. Different methods are used to analyze the data and the results are compared to each other and evaluated in the context of previous findings. In particular the networks of connected parent, child and sibling changes are resolved over time and mapped to 46 subsystem areas. A normalized change propagation index (CPI) is then developed, showing the relative strength of each area on the absorber-multiplier spectrum between -1 and +1. Multipliers send out more changes than they receive and are good candidates for more focused change management. Another interesting finding is the quantitative confirmation of the "ripple" change pattern. Unlike the earlier prediction, however, it was found that the peak of cyclical change activity occurred late in the program driven by systems integration and functional testing. Patterns emerged from the data and offer clear implications for technical change management approaches in system design. Copyright © 2007 by ASME.

Large-eddy simulation of complex geometry jets

Computations are made for chevron and coflowing jet nozzles. The latter has a bypass ratio of 6:1. Also, unlike the chevron nozzle, the core flow is heated, making the inlet conditions reminiscent of those for a real engine. A large-eddy resolving approach is used with circa 12 × 10 6 cell meshes. Because the codes being used tend toward being dissipative the subgrid scale model is abandoned, giving what can be termed numerical large-eddy simulation. To overcome near-wall modeling problems a hybrid numerical large-eddy simulation-Reynolds-averaged Navier-Stokes related method is used. For y + ≤ 60 a Reynolds-averaged Navier-Stokes model is used. Blending between the two regions makes use of the differential Hamilton-Jabobi equation, an extension of the eikonal equation. For both nozzles, results show encouraging agreement with measurements of other workers. The eikonal equation is also used for ray tracing to explore the effect of the mean flow on acoustic ray trajectories, thus yielding a coherent solution strategy. © 2011 by Cambridge University.

Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy.

The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.

Probing the location of displayed cytochrome b562 on amyloid by scanning tunnelling microscopy.

Amyloid fibres displaying cytochrome b562 were probed using scanning tunnelling microscopy (STM) in vacuo. The cytochromes are electron transfer proteins containing a haem cofactor and could, in principle, mediate electron transfer between the tip and the gold substrate. If the core fibres were insulating and electron transfer within the 3D haem network was detected, then the electron transport properties of the fibre could be controlled by genetic engineering. Three kinds of STM images were obtained. At a low bias (<1.5 V) the fibres appeared as regions of low conductivity with no evidence of cytochrome mediated electron transfer. At a high bias, stable peaks in tunnelling current were observed for all three fibre species containing haem and one species of fibre that did not contain haem. In images of this kind, some of the current peaks were collinear and spaced around 10 nm apart over ranges longer than 100 nm, but background monomers complicate interpretation. Images of the third kind were rare (1 in 150 fibres); in these, fully conducting structures with the approximate dimensions of fibres were observed, suggesting the possibility of an intermittent conduction mechanism, for which a precedent exists in DNA. To test the conductivity, some fibres were immobilized with sputtered gold, and no evidence of conduction between the grains of gold was seen. In control experiments, a variation of monomeric cytochrome b562 was not detected by STM, which was attributed to low adhesion, whereas a monomeric multi-haem protein, GSU1996, was readily imaged. We conclude that the fibre superstructure may be intermittently conducting, that the cytochromes have been seen within the fibres and that they are too far apart for detectable current flow between sites to occur. We predict that GSU1996, being 10 nm long, is more likely to mediate successful electron transfer along the fibre as well as being more readily detectable when displayed from amyloid.

Complex study of transport AC loss in various 2G HTS racetrack coils

HTS racetrack coils are becoming important elements of an emerging number of superconducting devices such as generators or motors. In these devices the issue of AC loss is crucial, as performance and cooling power are derived from this quantity. This paper presents a comparative study of transport AC loss in two different types of 2G HTS racetrack coils. In this study, both experimental measurements and computer simulation approaches were employed. All the experiments were performed using classical AC electrical method. The finite-element computer model was used to estimate electromagnetic properties and calculate transport AC loss. The main difference between the characterized coils is covered inside tape architectures. While one coil uses tape based on RABITS magnetic substrate, the second coil uses a non-magnetic tape. Ferromagnetic loss caused by a magnetic substrate is an important issue involved in the total AC loss. As a result, the coil with the magnetic substrate surprised with high AC loss and rather low performance. © 2013 Elsevier B.V. All rights reserved.