Rossby waves and two-dimensional turbulence in a large-scale zonal jet

The theory of homogeneous barotropic beta-plane turbulence is here extended to include effects arising from spatial inhomogeneity in the form of a zonal shear flow. Attention is restricted to the geophysically important case of zonal flows that are barotropically stable and are of larger scale than the resulting transient eddy field. Because of the presumed scale separation, the disturbance enstrophy is approximately conserved in a fully nonlinear sense, and the (nonlinear) wave-mean-flow interaction may be characterized as a shear-induced spectral transfer of disturbance enstrophy along lines of constant zonal wavenumber k. In this transfer the disturbance energy is generally not conserved. The nonlinear interactions between different disturbance components are turbulent for scales smaller than the inverse of Rhines's cascade-arrest scale κβ[identical with] (β0/2urms)½ and in this regime their leading-order effect may be characterized as a tendency to spread the enstrophy (and energy) along contours of constant total wavenumber κ [identical with] (k2 + l2)½. Insofar as this process of turbulent isotropization involves spectral transfer of disturbance enstrophy across lines of constant zonal wavenumber k, it can be readily distinguished from the shear-induced transfer which proceeds along them. However, an analysis in terms of total wavenumber K alone, which would be justified if the flow were homogeneous, would tend to mask the differences. The foregoing theoretical ideas are tested by performing direct numerical simulation experiments. It is found that the picture of classical beta-plane turbulence is altered, through the effect of the large-scale zonal flow, in the following ways: (i) while the turbulence is still confined to K Kβ, the disturbance field penetrates to the largest scales of motion; (ii) the larger disturbance scales K < Kβ exhibit a tendency to meridional rather than zonal anisotropy, namely towards v2 > u2 rather than vice versa; (iii) the initial spectral transfer rate away from an isotropic intermediate-scale source is significantly enhanced by the shear-induced transfer associated with straining by the zonal flow. This last effect occurs even when the large-scale shear appears weak to the energy-containing eddies, in the sense that dU/dy [double less-than sign] κ for typical eddy length and velocity scales.

The unsteady flow of a weakly compressible fluid in a thin porous layer. I: Two-dimensional theory

We consider the problem of determining the pressure and velocity fields for a weakly compressible fluid flowing in a two-dimensional reservoir in an inhomogeneous, anisotropic porous medium, with vertical side walls and variable upper and lower boundaries, in the presence of vertical wells injecting or extracting fluid. Numerical solution of this problem may be expensive, particularly in the case that the depth scale of the layer h is small compared to the horizontal length scale l. This is a situation which occurs frequently in the application to oil reservoir recovery. Under the assumption that epsilon=h/l<<1, we show that the pressure field varies only in the horizontal direction away from the wells (the outer region). We construct two-term asymptotic expansions in epsilon in both the inner (near the wells) and outer regions and use the asymptotic matching principle to derive analytical expressions for all significant process quantities. This approach, via the method of matched asymptotic expansions, takes advantage of the small aspect ratio of the reservoir, epsilon, at precisely the stage where full numerical computations become stiff, and also reveals the detailed structure of the dynamics of the flow, both in the neighborhood of wells and away from wells.

Theory of enhanced magnetic anisotropy induced by Pt adatoms on two-dimensional Co clusters supported on a Pt(111) substrate

Calculations are reported of the magnetic anisotropy energy of two-dimensional (2D) Co nanostructures on a Pt(111) substrate. The perpendicular magnetic anisotropy (PMA) of the 2D Co clusters strongly depends on their size and shape, and rapidly decreases with increasing cluster size. The PMA calculated is in reasonable agreement with experimental results. The sensitivity of the results to the Co-Pt spacing at the interface is also investigated and, in particular, for a complete Co monolayer we note that the value of the spacing at the interface determines whether PMA or in-plane anisotropy occurs. We find that the PMA can be greatly enhanced by the addition of Pt adatoms to the top surface of the 2D Co clusters. A single Pt atom can induce in excess of 5 meV to the anisotropy energy of a cluster. In the absence of the Pt adatoms the PMA of the Co clusters falls below 1 meV/Co atom for clusters of about 10 atoms whereas, with Pt atoms added to the surface of the clusters, a PMA of 1 meV/Co atom can be maintained for clusters as large as about 40 atoms. The effect of placing Os atoms on the top of the Co clusters is also considered. The addition of 5d atoms and clusters on the top of ferromagnetic nanoparticles may provide an approach to tune the magnetic anisotropy and moment separately.

The two-dimensional anharmonic oscillator II: the microwave spectrum of silyl isocyanate, SiH3NCO

The J + 1 ← J transitions (J = 2, 3, 4, 5, and 6) in the microwave spectrum of SiH3NCO have been assigned for the vibrational ground state and for the vibrational states v10 = 1, 2, and 3. The results for v10 = 0 confirm earlier work. The vibration-rotation constants show a remarkable variation with v10 and l10. To a large extent the anomalous behavior of these constants has been explained in terms of a strongly anharmonic potential function for the ν10 vibrational mode.

The two-dimensional anharmonic oscillator III: the CCC bending mode of C3O2

Newly observed data on the rotational constants of carbon suboxide in excited vibrational states of the low-wavenumber bending vibration ν7 have been successfully interpreted in terms of the two-dimensional anharmonic oscillator wavefunctions associated with this vibration. By combining these results with published infrared and Raman spectra the vibrational assignment has been extended and a refined bending potential for ν7 has been derived: this has a minimum at a bending angle of about 24° at the central C atom, with an energy maximum at the linear configuration some 23 cm−1 above the minimum. From similar data on the combination and hot bands of ν7 with ν4 (1587 cm−1) and ν2 (786 cm−1) the effective ν7 bending potential has also been determined in the one-quantum excited states of ν4 and ν2. The effective ν7 potential shows significant changes from the ground vibrational state; the central hump in the ν7 potential surface is increased to about 50 cm−1 in the v4 = 1 state, and decreased to about 1 cm−1 in the v2 = 1 state. In the light of these results vibrational assignments are suggested for most of the observed bands in the infrared and Raman spectra of C3O2.

The two-dimensional anharmonic oscillator I: vibration-rotation constants of fulminic acid, HCNO

The lowest-wavenumber vibration of HCNO and DCNO, ν5, is known to involve a largeamplitude low-frequency anharmonic bending of the CH bond against the CNO frame. In this paper the anomalous vibrational dependence of the observed rotational constants B(v5, l5), and of the observed l-doubling interactions, is interpreted according to a simple effective vibration-rotation Hamiltonian in which the appropriate vibrational operators are averaged in an anharmonic potential surface over the normal coordinates (Q5x, Q5y). All of the data on both isotopes are interpreted according to a single potential surface having a minimum energy at a slightly bent configuration of the HCN angle ( 170°) with a maximum at the linear configuration about 2 cm−1 higher. The other coefficients in the Hamiltonian are also interpreted in terms of the structure and the harmonic and anharmonic force fields; the substitution structure at the “hypothetical linear configuration” determined in this way gives a CH bond length of 1.060 Å, in contrast to the value 1.027 Å determined from the ground-state rotational constants. We also discuss the difficulties in rationalizing our effective Hamiltonian in terms of more fundamental theory, as well as the success and limitations of its use in practice.

Two-dimensional anharmonic oscillator: application to 2,5-dihydrofuran

A program has been developed to calculate the energy levels and corresponding wavefunctions for a two‐dimensional anharmonic potential surface of at least C2v symmetry. This program has been employed to explain the high resolution splittings observed in the far infrared spectrum of 2,5‐dihydrofuran. The magnitude of the cross term connecting the ring‐twisting and ring‐puckering modes of 2,5‐dihydrofuran is sufficiently large to be significant. The potential surface determined also suggests that the ring‐twisting mode may be slightly anharmonic.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye and analysed by two-dimensional difference gel electrophoresis. Gel images analysed off-line, using the DeCyder image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes, Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

4,4 '-Dipyridyl-N,N '-dioxide complexes of metal-thiocyanate/selenocyanate: pi-stacked molecular rods as three-dimensional support for two-dimensional polymeric sheets and intra/interchain S center dot center dot center dot S interaction dependent architecture of the R-2(2)(8) synthon driven assembly of one-dimensional polymeric chains

Three supramolecular complexes of Co(II) using SCN-/SeCN- in combination with 4,4'-dipyridyl-N,N'-dioxide (dpyo), i.e., {[Co(SCN)(2)(dpyo)(2)].(dpyo)}(n) ( 1), {[Co(SCN)(2)(dpyo)(H2O)(2)].(H2O)}(n) ( 2), {[Co(SeCN)(2)(dpyo)(H2O)(2)]center dot(H2O)}(n) ( 3), have been synthesized and characterized by single-crystal X-ray analysis. Complex 1 is a rare example of a dpyo bridged two-dimensional (2D) coordination polymer, and pi-stacked dpyo supramolecular rods are generated by the lattice dpyo, passing through the rhombic grid of stacked layers, resulting in a three-dimensional (3D) superstructure. Complexes 2 and 3 are isomorphous one-dimensional (1D) coordination polymers [-Co-dpyo-Co-] that undergo self-assembly leading to a bilayer architecture derived through an R-2(2)(8) H-bonding synthon between coordinated water and dpyo oxygen. A reinvestigation of coordination polymers [Mn(SCN)(2)(dpyo)( H2O)(MeOH)](n) ( 4) and {[Fe(SCN)(2)(dpyo)(H2O)(2)]center dot(H2O)}(n) ( 5) reported recently by our group [ Manna et al. Indian J. Chem. 2006, 45A, 1813] reveals brick wall topology rather than bilayer architecture is due to the decisive role of S center dot center dot center dot S/Se center dot center dot center dot Se interactions in determining the helical nature in 4 and 5 as compared to zigzag polymeric chains in 2 and 3, although the same R-2(2)(8) synthon is responsible for supramolecular assembly in these complexes.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.