Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Interaction of a vortex ring with a single bubble: bubble and vorticity dynamics

The interaction of a single bubble with a single vortex ring in water has been studied experimentally. Measurements of both the bubble dynamics and vorticity dynamics have been done to help understand the two-way coupled problem. The circulation strength of the vortex ring (Gamma) has been systematically varied, while keeping the bubble diameter (D-b) constant, with the bubble volume to vortex core volume ratio (V-R) also kept fixed at about 0.1. The other important parameter in the problem is a Weber number based on the vortex ring strength. (We = 0.87 rho(Gamma/2 pi a)(2)/(sigma/D-b); a = vortex core radius, sigma = surface tension), which is varied over a large range, We = 3-406. The interaction between the bubble and ring for each of the We cases broadly falls into four stages. Stage I is before capture of the bubble by the ring where the bubble is drawn into the low-pressure vortex core, while in stage II the bubble is stretched in the azimuthal direction within the ring and gradually broken up into a number of smaller bubbles. Following this, in stage III the bubble break-up is complete and the resulting smaller bubbles slowly move around the core, and finally in stage IV the bubbles escape. Apart from the effect of the ring on the bubble, the bubble is also shown to significantly affect the vortex ring, especially at low We (We similar to 3). In these low-We cases, the convection speed drops significantly compared to the base case without a bubble, while the core appears to fragment with a resultant large decrease in enstrophy by about 50 %. In the higher-We cases (We > 100), there are some differences in convection speed and enstrophy, but the effects are relatively small. The most dramatic effects of the bubble on the ring are found for thicker core rings at low We (We similar to 3) with the vortex ring almost stopping after interacting with the bubble, and the core fragmenting into two parts. The present idealized experiments exhibit many phenomena also seen in bubbly turbulent flows such as reduction in enstrophy, suppression of structures, enhancement of energy at small scales and reduction in energy at large scales. These similarities suggest that results from the present experiments can be helpful in better understanding interactions of bubbles with eddies in turbulent flows.

Effective Degradation of Aqueous Nitrobenzene Using the SrFeO3-delta Photocatalyst under UV Illumination and Its Kinetics and Mechanistic Studies

In this article, the SrFeO3-delta photocatalyst was synthesized by a solution combustion method and applied for the photocatalytic degradation of aqueous nitrobenzene in the presence and absence of H2O2. The SrFeO3-delta photocatalyst was characterized by XRD, FT-IR, FE-SEM, TEM, TG-DTG, XPS, and UV visible spectroscopy. The band gap energy of SrFeO3-delta was found to be 3.75 eV which lies in the UV region. The XPS results indicate that the oxidation state of Sr and Fe in SrFeO3-delta was 2+ and 3+, respectively, and the surface atomic ratio of Sr and Fe is 0.995. The photocatalytic activity reveals that the degradation of nitrobenzene over the SrFeO3-delta catalyst itself (UV/SFO) is superior compared to SrFeO3-delta in the presence of H2O2 (UV/SFO/H2O2) with a degradation efficiency of 99-96%. The degradation of nitrobenzene obeys first-order kinetics in both UV/SFO and UV/SFO/H2O2 processes. The decrease in degradation efficiency with UV/SFO/H2O2 was attributed due to the formation of strontium carbonate on the photocatalyst surface.

Peptide delta-Turn: Literature Survey and Recent Progress

Among the various types of a-peptide folding motifs, delta-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the d-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.

Local structure of boundary layer transition in experiments with a single streamwise vortex

Transition induced by an isolated streamwise vortex embedded in a flat plate boundary layer was studied experimentally. The vortex was created by a gentle hill with a Gaussian profile that spanned on half of the width of a flat plate mounted in a low turbulence wind tunnel. PIV and hot-wire anemometry data were taken. Transition occurs as a non-inclined shear layer breaks up into a sequence of vortices, close to the boundary layer edge. The passing frequency of these vortices scales with square of the freestream velocity, similar to that in single-roughness induced transition. Quadrant analysis of streamwise and wall-normal velocity fluctuations show large ejection events in the outer layer. (C) 2015 Elsevier Inc. All rights reserved.

Synthesis and Photoluminescence Properties of Eu3+ activated Ce0.5Al0.5O2-delta Nanophosphors for WLEDs Application

A series of Eu3+ activated Ce0.5Al0.5O2-delta nanophosphors have been synthesized by the nitrate - citrate gel combustion method. All the compounds crystallized in the cubic fluorite CeO2 structure with space group Fm-3m (No. 225). FESEM revealed the flakes-like morphology. The average particle size was estimated from TEM studies and found to be in the range 15-25 nm. The values were in good agreement with the Scherer's method. In photoluminescence (PL) spectra, the D-5(0) -> F-7(2) (612 nm) transition dominates than other transitions which indicates that the Eu3+ ions occupy a site without inversion center. CIE chromaticity diagram confirmed that these nanophosphors can be useful in the fabrication of red component in white light emitting diodes (WLEDs).

Instabilities in unsteady boundary layers with reverse flow

Instabilities arising in unsteady boundary layers with reverse flow have been investigated experimentally. Experiments are conducted in a piston driven unsteady water tunnel with a shallow angle diffuser placed in the test section. The ratio of temporal (Pi(t)) to spatial (Pi(x)) component of the pressure gradient can be varied by a controlled motion of the piston. In all the experiments, the piston velocity variation with time is trapezoidal consisting of three phases: constant acceleration from rest, constant velocity and constant deceleration to rest. The adverse pressure gradient (and reverse flow) are due to a combination of spatial deceleration of the free stream in the diffuser and temporal deceleration of the free stream caused by the piston deceleration. The instability is usually initiated with the formation of one or more vortices. The onset of reverse flow in the boundary layer, location and time of formation of the first vortex and the subsequent flow evolution are studied for various values of the ratio Pi(x) (Pi(x) + Pi(t)) for the bottom and the top walls. Instability is due to the inflectional velocity profiles of the unsteady boundary layer. The instability is localized and spreads to the other regions at later times. At higher Reynolds numbers growth rate of instability is higher and localized transition to turbulence is observed. Scalings have been proposed for initial vortex formation time and wavelength of the instability vortices. Initial vortex formation time scales with convective time, delta/Delta U, where S is the boundary layer thickness and Delta U is the difference of maximum and minimum velocities in the boundary layer. Non-dimensional vortex formation time based on convective time scale for the bottom and the top walls are found to be 23 and 30 respectively. Wavelength of instability vortices scales with the time averaged boundary layer thickness. (C) 2015 Elsevier Masson SAS. All rights reserved.

Potency and pharmacokinetics of broad spectrum and isoform-specific p110 gamma and delta inhibitors in cancers

Emerging data on cancer suggesting that target-based therapy is promising strategy in cancer treatment. PI3K-AKT pathway is extensively studied in many cancers; several inhibitors target this pathway in different levels. Recent finding on this pathway uncovered the therapeutic applications of PI3K-specific inhibitors; PI3K, AKT, and mTORC broad spectrum inhibitors. Noticeably, class I PI3K isoforms, p110 and p110 catalytic subunits have rational therapeutic application than other isoforms. Therefore, three classes of inhibitors: isoform-specific, dual-specific and broad spectrum were selected for molecular docking and dynamics. First, p110 structure was modelled; active site was analyzed. Then, molecular docking of each class of inhibitors were studied; the docked complexes were further used in 1.2ns molecular dynamics simulation to report the potency of each class of inhibitor. Remarkably, both the studies retained the similar kind of protein ligand interactions. GDC-0941, XL-147 (broad spectrum); TG100-115 (dual-specific); and AS-252424, PIK-294 (isoform-specific) were found to be potential inhibitors of p110 and p110, respectively. In addition to that pharmacokinetic properties are within recommended ranges. Finally, molecular phylogeny revealed that p110 and p110 are evolutionarily divergent; they probably need separate strategies for drug development.

Influence of the upwelling events on the delta C-13 and delta O-18 of the benthic bivalve shells of the South Western Continental Margin of India

In this study, the influence of the spatial and temporal variability of upwelling intensity and the associated biological productivity observed during different phases of summer monsoon along the southwestern continental margin of India (SWCMI) on the delta C-13 and delta O-18 of the inorganic biogenic carbonate shells was investigated. Multispecies benthic bivalve shells (1-5 mm) separated from ten surface sediment samples of SWCMI (off 12 degrees N, 10 degrees N and 9 degrees N) collected during the onset (OSM) and peak (PSM) phase of the summer monsoon of 2009 were analysed for delta C-13 and delta O-18. Sea surface temperature along the study region indicates prominent upwelling in PSM than in OSM. A comparison of analytical and predicted values for delta O-18 in the bivalve shells confirmed their in situ origin during both the sampling periods. During PSM, the delta C-13 values in the benthic bivalve shells were more depleted in C-13 than during OSM which recorded lower values of delta C-13 in dissolved inorganic carbon of bottom waters expected in the study region in PSM due to the upwelled waters, high surface productivity and the associated high degradation of the organic matter in the subsurface and bottom waters. However, this depletion of delta C-13 was not observed in benthic bivalve shells obtained from 10 degrees N, since it is influenced by high export fluxes of carbon from the Cochin estuary since early monsoon months.

A dilation-driven vortex flow in sheared granular materials explains a rheometric anomaly

Granular flows occur widely in nature and industry, yet a continuum description that captures their important features is yet not at hand. Recent experiments on granular materials sheared in a cylindrical Couette device revealed a puzzling anomaly, wherein all components of the stress rise nearly exponentially with depth. Here we show, using particle dynamics simulations and imaging experiments, that the stress anomaly arises from a remarkable vortex flow. For the entire range of fill heights explored, we observe a single toroidal vortex that spans the entire Couette cell and whose sense is opposite to the uppermost Taylor vortex in a fluid. We show that the vortex is driven by a combination of shear-induced dilation, a phenomenon that has no analogue in fluids, and gravity flow. Dilatancy is an important feature of granular mechanics, but not adequately incorporated in existing models.

Control of vortex shedding at moderate Reynolds numbers

The suppression method of vortex shedding from a circular cylinder has been studied experimentally in the Reynolds number range from 300 to 1600. The test is performed in a water channel. The model cylinder is 1 cm in diameter and 38 cm in length. A row of small rods of 0.18 cm in diameter and 1.5 cm in length are perpendicularly connected to the surface of the model cylinder and distributed along the meridian, The distance between the neighboring rods and the angle of attack of the rods can be changed so that the suppression effect on vortex shedding can be adjusted. The results show that vortex shedding can be suppressed effectively if the distance between the neighboring rods is smaller than 3 times and the cylinder diameter and the angle of attack is in the range of 30degreesless than or equal tobeta<90&DEG;.

Experimental Study on Vortex-Induced Vibrations of a Pipeline Near a Plane Boundary in Steady Flow

对单向水流作用下近壁管道横向涡激振动进行了实验模拟,重点探讨了管道与壁面间隙比(e/D)对管道涡激振动幅值和涡激振动频率响应特性的影响规律.实验结果表明,管道与壁面间隙宽度对管道涡激振动特性有较明显影响.在较大间隙比(e/D＞0.66)下,管道振幅随着Vr数的增大先快速增长到最大值,然后平缓下降;在振动初期(即Vr数较小时),管道振动频率变化基本符合Strouhal规律;在振动中后期(即Vr数较大时),管道振动频率变化不符合Strouhal规律,而在管道固有频率附近缓慢增长.在较小间隙比(e/D＜0.30)下,管道振幅随Vr数的增大先平缓上升到最大值,随后较快速下降;在振动初期,管道振动频率变化不遵循Strouhal规律;在整个振动范围内,与较大间隙比情况相比,随着Vr数增加,管道振动频率增长幅度明显较大.

Rossby Vortex Simulation on a Paraboloidal Coordinate System Using the Lattice Boltzmann Method

In this paper, we apply our compressible lattice Boltzmann model to a rotating parabolic coordinate system to simulate Rossby vortices emerging in a layer of shallow water flowing zonally in a rotating paraboloidal vessel. By introducing a scaling factor, nonuniform curvilinear mesh can be mapped to a flat uniform mesh and then normal lattice Boltzmann method works. Since the mass per unit area on the two-dimensional (2D) surface varies with the thickness of the water layer, the 2D flow seems to be "compressible" and our compressible model is applied. Simulation solutions meet with the experimental observations qualitatively. Based on this research, quantitative solutions and many natural phenomena simulations in planetary atmospheres, oceans, and magnetized plasma, such as the famous Jovian Giant Red Spot, the Galactic Spiral-vortex, the Gulf Stream, and the Kuroshio Current, etc,, can be expected.

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.

Vortex breaking and cutting in type II superconductors.

In technological superconductors, the Lorentz force on the flux vortices is opposed by inhomogeneous pinning and so the critical current may be controlled by a combination of vortex entanglement, cutting, and cross-joining. To understand the roles of these processes we report measurements of structures in which a weak pinning layer is sandwiched between two strongly pinning leads. Quantitative modeling of the results demonstrates that in such systems the critical current is limited by the deformation of individual vortices and not by subsequent cross-joining processes.