Numerical simulation of a self-similar cascade of filament instabilities in the surface quasigeostrophic system.

We provide numerical evidence for the existence of a cascade of filament instabilities in the surface quasigeostrophic system for rotating, stratified flow near a horizontal boundary. The cascade involves geometrically shrinking spatial and temporal scales and implies the singular collapse of the filament width to zero in a finite time. The numerical method is both spatially and temporally adaptive, permitting the accurate simulation of the evolution over an unprecedented range of spatial scales spanning over ten orders of magnitude. It provides the first convincing demonstration of the cascade, in which the large separation of scales between subsequent instabilities has made previous numerical simulation difficult.

Jet sharpening by turbulent mixing.

Jets or localized strong currents in planetary atmospheres, as well as in the Earth's oceans, are often associated with sharp potential-vorticity gradients owing to the inherent balance exhibited by these flows. Here, we explore and quantify jet sharpening in a simple idealized single-layer quasi-geostrophic model on a mid-latitude ß-plane. The advantages of this idealization are that just two parameters control the flow development (the Rossby deformation length and the amplitude of the initial random flow perturbation), and that numerical experiments can comprehensively and accurately cover the parameter space. These experiments, carried out at unprecedented numerical resolution, reveal how an initially broad jet is sharpened, and the role played by coherent vortices in the vicinity of jets.

Unifying scaling theory for vortex dynamics in two-dimensional turbulence.

We present a scaling theory for unforced inviscid two-dimensional turbulence. Our model unifies existing spatial and temporal scaling theories. The theory is based on a self-similar distribution of vortices of different sizes A. Our model uniquely determines the spatial and temporal scaling of the associated vortex number density which allows the determination of the energy spectra and the vortex distributions. We find that the vortex number density scales as n(A,t)-t(-2/3)/A, which implies an energy spectrum E-k(-5), significantly steeper than the classical Batchelor-Kraichnan scaling. High-resolution numerical simulations corroborate the model.

Nonrobustness of the two-dimensional turbulent inverse cascade.

The inverse energy cascade in two-dimensional Navier-Stokes turbulence is examined in the quasisteady regime, with small-scale, band-limited forcing at scale kf-1, with particular attention to the influence of forcing Reynolds number Re on the energy distribution at large scales. The strength of the inverse energy cascade, or fraction of energy input that is transferred to larger scales, increases monotonically toward unity with increasing Re proportional, variantkmax2kf2, where kmax is the maximum resolved wave number. Moreover, as Re increases beyond a critical value, for which a direct enstrophy cascade to small scales is first realized, the energy spectrum in the energy-cascading range steepens from a k-53 to k-2 dependence. The steepening is interpreted as the result of a greater tendency for coherent vortex formation in cases when forcing scales are adequately resolved. In spectral space, it is associated with nonlocality of the inverse energy transfer.

Steps in predicting the relationship of yield on fungicide dose.

ABSTRACT A set of hypothetical steps has been defined, which links fungicide dose to marketable yield, whereby (i) increasing dose decreases symptom area, according to a dose-response curve, (ii) decreased symptom area increases crop green area index (GAI), (iii) increasing GAI increases fractional interception of photosynthetically active radiation, (iv) increased fractional interception increases crop dry matter accumulation, and (v) yield increases, depending on the partitioning of dry matter to the marketable fraction. One equation represented all five steps. By integrating this equation for light interception during the yield forming period and differentiating with respect to the ratio of fungicide cost over yield value, an analytical solution was obtained for the economic optimum dose. Taking published ranges of parameter values for the Septoria tritici wheat pathosystem as an example, yield-response curves and optimum doses were biologically plausible when compared with data from four field experiments. The analytical and empirical results imply that the dose required to optimize economic return will vary substantially between sites, seasons, and cultivars. Sensitivity analyses identified parameters describing specific facets of disease severity, fungicide efficacy, and assimilate partitioning as most influential in determining the dose optimum.

Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporine.

The crystal structure of the kinase domain of C-terminal Src kinase (CSK) has been determined by molecular replacement, co-complexed with the protein kinase inhibitor staurosporine (crystals belong to the space group P21212 with a=44.5 A, b=120.6 A, c=48.3 A). The final model of CSK has been refined to an R-factor of 19.9 % (Rfree=28.7 %) at 2.4 A resolution. The structure consists of a small, N-terminal lobe made up mostly of a beta-sheet, and a larger C-terminal lobe made up mostly of alpha-helices. The structure reveals atomic details of interactions with staurosporine, which binds in a deep cleft between the lobes. The polypeptide chain fold of CSK is most similar to c-Src, Hck and fibroblast growth factor receptor 1 kinase (FGFR1K) and most dissimilar to insulin receptor kinase (IRK). Interactions between the N and C-terminal lobe are mediated by the bound staurosporine molecule and by hydrogen bonds. In addition, there are several water molecules forming lobe-bridging hydrogen bonds, which may be important for maintaining the catalytic integrity of the kinase. Furthermore, the conserved Lys328 and Glu267 residues utilise water in the formation of a molecular pivot which is essential in allowing relative movement of the N and C-terminal lobes. An analysis of the residues around the ATP-binding site reveals structural differences with other protein tyrosine kinases. Most notable of these are different orientations of the conserved residues Asp332 and Phe333, suggesting that inhibitor binding proceeds via an induced fit. These structural observations have implications for understanding protein tyrosine kinase catalytic mechanisms and for the design of ATP-mimicking inhibitors of protein kinases.

The design and synthesis of inhibitors of the cysteinyl protease, Der p I.

Prototype irreversible inhibitors of the cysteinyl protease Der p I were designed, synthesised and evaluated in vitro. Candidates were designed using a modular approach, whereby a peptide sequence was appended with known thiophilic moieties. This hinged on utilizing peptide sequences from substrate specificity data compiled using proprietary RAPiD technology.