On the beta-drift of an initially circular vortex patch

The nonlinear inviscid evolution of a vortex patch in a single-layer quasi-geostrophic fluid and within a background planetary vorticity gradient is examined numerically at unprecedented spatial resolution. The evolution is governed by two dimensionless parameters: the initial size (radius) of the vortex compared to the Rossby deformation radius, and the initial strength of the vortex compared to the variation of the planetary vorticity across the vortex. It is found that the zonal speed of a vortex increases with its strength. However, the meridional speed reaches a maximum at intermediate vortex strengths. Both large and weak vortices are readily deformed, often into elliptical and tripolar shapes. This deformation is shown to be related to an instability of the instantaneous vorticity distribution in the absence of the planetary vorticity gradient β. The extremely high numerical resolution employed reveals a striking feature of the flow evolution, namely the generation of very sharp vorticity gradients surrounding the vortex and extending downstream of it in time. These gradients form as the vortex forces background planetary vorticity contours out of its way as it propagates. The contours close to the vortex swirl rapidly around the vortex and homogenize, but at some critical distance the swirl is not strong enough and, instead, a sharp vorticity gradient forms. The region inside this sharp gradient is called the ‘trapped zone’, though it shrinks slowly in time and leaks. This leaking occurs in a narrow wake called the ‘trailing front’, another zone of sharp vorticity gradients, extending behind the vortex

Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules

Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES crystal structural data, the three dimensional structure of human YES was constructed based on template structure (PDB ID: 2H8H) obtained through homology search using MODELLER 9V7. The model was refined, energy minimized and assessed through PROCHECK. Active site residues of human YES were identified from the homology model in complex with template ligand AZD0530 and were further confirmed using CASTp. Five published inhibitors of YES family (Dasatinib, Bosutinib, SU6656, AZD0530 and CGP77675) were identified through literature search. High throughput virtual screening method at Ligand.Info was applied for these five inhibitors to establish a library of 1932 structural analogs. LigPrep was used to generate possible conformations of each ligand molecules from structural analog library. The ligand duplicates conformers, ligands having reactive functional group and poor ADME properties were rejected from the prepared dataset. Glide 5.5 was used to generate a grid box by picking the active site residues of human YES protein. Through sequential applications of stringent mode glide docking procedures from Glide HTVS to SP to XP respectively, 13 potential inhibitors were proposed. The docking complexes of each inhibitor with human YES protein were analyzed and lead ‘1’ molecule was identified to have higher binding affinity to human YES protein (XP Gscore: -12.07 Kcal/mol) compared to existing published inhibitors and other 12 lead molecules. The lead ‘1’ - human YES docking complex was highly stabilized through hydrogen bond network with amino acid residues Thr348, Asp358, Asp414 and Phe415. Moreover, from the results obtained we could decipher that lead ‘1’ molecule can be raised into potential inhibitors after binding assays, substantiated experimental investigations and passing several phases of clinical trials

Continuum Theory for Piezoelectricity in Nanotubes and Nanowires

We develop and solve a continuum theory for the piezoelectric response of one dimensional nanotubes and nanowires, and apply the theory to study electromechanical effects in BN nanotubes. We find that the polarization of a nanotube depends on its aspect ratio, and a dimensionless constant specifying the ratio of the strengths of the elastic and electrostatic interactions. The solutions of the model as these two parameters are varied are discussed. The theory is applied to estimate the electric potential induced along the length of a BN nanotube in response to a uniaxial stress.Comment: 4 pages in RevTex4, 2 epsf figure

Modelling of quantum information processing with Ehrenfest guided tra jectories: a case study

We apply a numerical method based on multi-configurational Ehrenfest tra jectories, and demonstrate converged results for the Choi fidelity of an entangling quantum gate between two two-level systems interacting through a set of bosonic modes. We consider both spin-boson and rotating wave Hamiltonians, for various numbers of mediating modes (from 1 to 100), and extend our treatment to include finite temperatures. Our results apply to two-level impurities interacting with the same band of a photonic crystal, or to two distant ions interacting with the same set of motional degrees of freedom.Comment: 12 pages, figures aplent

Spin-Filtering Multiferroic-Semiconductor Heterojunctions

We report on the structural and electronic properties of the interface between the multiferoic oxide YMnO$_3$ and wide band-gap semiconductor GaN studied with the Hubbard-corrected local spin density approximation (LSDA+U) to density-functional theory (DFT). We find that the band offsets at the interface between antiferromagnetically ordered YMnO$_3$ and GaN are different for spin-up and spin-down states. This behavior is due to the spin splitting of the valence band induced by the interface. The energy barrier depends on the relative orientation of the electric polarization with respect to the polarization direction of the GaN substrate suggesting an opportunity to create magnetic tunnel junctions in this materials system.Comment: 4 pages, 4 figure

Reply to Comment on "Dynamical corrections to the DFT-LDA electron conductance in nanoscale systems"

We reply to the comment by Jung, Bokes, and Godby (arXiv:0706.0140) on our paper Phys. Rev. Lett. 94, 186810 (2005). We show that the results in their comment should not be taken as an indication that the viscosity corrections to the conductance of real nanoscale structures are small. A more accurate treatment of the density and current density distribution and of the electronic correlations may yield much larger corrections in realistic systems.Comment: Reply to the comment by Jung et al (arXiv:0706.0140). 1 page, no figures, to appear in PR

Oral Administration of Peppermint in Wistar Albino Rats: Memory Boosting and Regaining

The studies on peppermint aroma fluence on cognition are numerous. However the knowledge about oral consumption of peppermint and cognition was inadequate. Hence the present study was undertaken to find out the effect of oral administration of peppermint spices in memory boosting and memory regaining on adult wistar rats. Here we investigate the influence of oral intake of peppermint on behavioral task performance by using T-maze and radial arm maze and physiological measures relative to a milk control group. We have observed significant memory boosting and memory regaining effects of peppermint when administered orally. This effect may be due to improvement of the blood flow to the brain and increasing the concentration power. Hence we recommend further research in this area by investigating compound metabolism to optimize quantification of memory performance following peppermint ingestion

Cobalt-Porphyrin Catalyzed Electrochemical Reduction of Carbon Dioxide in Water II: Mechanism from First Principles

We apply first principles computational techniques to analyze the two-electron, multi-step, electrochemical reduction of CO2 to CO in water using cobalt porphyrin as a catalyst. Density Functional Theory calculations with hybrid functionals and dielectric continuum solvation are used to determine the steps at which electrons are added. This information is corroborated with ab initio molecular dynamics simulations in an explicit aqueous environment which reveal the critical role of water in stabilizing a key intermediate formed by CO2 bound to cobalt. Using potential of mean force calculations, the intermediate is found to spontaneously accept a proton to form a carboxylate acid group at pH<9.0, and the subsequent cleavage of a C-OH bond to form CO is exothermic and associated with a small free energy barrier. These predictions suggest that the proposed reaction mechanism is viable if electron transfer to the catalyst is sufficiently fast. The variation in cobalt ion charge and spin states during bond breaking, DFT+U treatment of cobalt 3d orbitals, and the need for computing electrochemical potentials are emphasized.Comment: 33 pages, 7 figure