Using the local gyrokinetic code, GS2, to investigate global ITG modes in tokamaks. (I) s-α{\alpha} model with profile and flow shear effects

This paper combines results from a local gyrokinetic code with analytical theory to reconstruct the global eigenmode structure of the linearly unstable ion-temperature-gradient (ITG) mode with adiabatic electrons. The simulations presented here employ the s-${\alpha}$ tokamak equilibrium model. Local gyrokinetic calculations, using GS2 have been performed over a range of radial surfaces, x, and for ballooning phase angle, p, in the range -${\pi} {\leq} p {\leq\pi}$, to map out the complex local mode frequency, ${\Omega_0(x, p) = \omega_0(x, p) + i\gamma_0(x, p)}$. Assuming a quadratic radial profile for the drive, namely ${\eta_i = L_n/L_T}$, (holding constant all other equilibrium profiles such as safety factor, magnetic shear etc.), ${\Omega_0(x, p)}$ has a stationary point. The reconstructed global mode then sits on the outboard mid plane of the tokamak plasma, and is known as a conventional or isolated mode, with global growth rate, ${\gamma}$ ~ Max[${\gamma_0(x, p)}$], where ${\gamma_0(x, p)}$ is the local growth rate. Taking the radial variation in other equilibrium profiles (e.g safety factor q(x)) into account, removes the stationary point in ${\Omega_0(x, p)}$ and results in a mode that peaks slightly away from the outboard mid-plane with a reduced global growth rate. Finally, the influence of flow shear has also been investigated through a Doppler shift, ${\omega_0 \rightarrow \omega_0 + n\Omega^{\prime}x}$, where n is the toroidal mode number and ${\Omega^{\prime}}$ incorporates the effect of flow shear. The equilibrium profile variation introduces an asymmetry to the growth rate spectrum with respect to the sign of ${\Omega^{\prime}}$, consistent with recent global gyrokinetic calculations.Comment: 10 pages, 8 figures and 1 tabl

Kinetic instabilities that limit {\beta} in the edge of a tokamak plasma: a picture of an H-mode pedestal

Plasma equilibria reconstructed from the Mega-Amp Spherical Tokamak (MAST) have sufficient resolution to capture plasma evolution during the short period between edge-localized modes (ELMs). Immediately after the ELM steep gradients in pressure, P, and density, ne, form pedestals close to the separatrix, and they then expand into the core. Local gyrokinetic analysis over the ELM cycle reveals the dominant microinstabilities at perpendicular wavelengths of the order of the ion Larmor radius. These are kinetic ballooning modes (KBMs) in the pedestal and microtearing modes (MTMs) in the core close to the pedestal top. The evolving growth rate spectra, supported by gyrokinetic analysis using artificial local equilibrium scans, suggest a new physical picture for the formation and arrest of this pedestal.Comment: Final version as it appeared in PRL (March 2012). Minor improvements include: shortened abstract, and better colour table for figures. 4 pages, 6 figure

Glycogen and its metabolism: some new developments and old themes

Glycogen is a branched polymer of glucose that acts as a store of energy in times of nutritional sufficiency for utilization in times of need. Its metabolism has been the subject of extensive investigation and much is known about its regulation by hormones such as insulin, glucagon and adrenaline (epinephrine). There has been debate over the relative importance of allosteric compared with covalent control of the key biosynthetic enzyme, glycogen synthase, as well as the relative importance of glucose entry into cells compared with glycogen synthase regulation in determining glycogen accumulation. Significant new developments in eukaryotic glycogen metabolism over the last decade or so include: (i) three-dimensional structures of the biosynthetic enzymes glycogenin and glycogen synthase, with associated implications for mechanism and control; (ii) analyses of several genetically engineered mice with altered glycogen metabolism that shed light on the mechanism of control; (iii) greater appreciation of the spatial aspects of glycogen metabolism, including more focus on the lysosomal degradation of glycogen; and (iv) glycogen phosphorylation and advances in the study of Lafora disease, which is emerging as a glycogen storage disease

Redox Switch for the Inhibited State of Yeast Glycogen Synthase Mimics Regulation by Phosphorylation

Glycogen synthase (GS) is the rate limiting enzyme in the synthesis of glycogen. Eukaryotic GS is negatively regulated by covalent phosphorylation and allosterically activated by glucose-6-phosphate (G6P). To gain structural insights into the inhibited state of the enzyme, we solved the crystal structure of yGsy2-R589A/R592A to a resolution of 3.3 Å. The double mutant has an activity ratio similar to the phosphorylated enzyme and also retains the ability to be activated by G6P. When compared to the 2.88 Å structure of the wild-type G-6-P activated enzyme, the crystal structure of the low-activity mutant showed that the N-terminal domain of the inhibited state is tightly held against the dimer-related interface thereby hindering acceptor access to the catalytic cleft. Based on these two structural observations, we developed a reversible redox regulatory feature in yeast GS by substituting cysteine residues for two highly conserved arginine residues. When oxidized, the cysteine mutant enzyme exhibits activity levels similar to the phosphorylated enzyme, but cannot be activated by G-6-P. Upon reduction, the cysteine mutant enzyme regains normal activity levels and regulatory response to G-6-P activation

Comparison of BES measurements of ion-scale turbulence with direct, gyrokinetic simulations of MAST L-mode plasmas

Observations of ion-scale (k_y*rho_i <= 1) density turbulence of relative amplitude dn_e/n_e <= 0.2% are available on the Mega Amp Spherical Tokamak (MAST) using a 2D (8 radial x 4 poloidal channel) imaging Beam Emission Spectroscopy (BES) diagnostic. Spatial and temporal characteristics of this turbulence, i.e., amplitudes, correlation times, radial and perpendicular correlation lengths and apparent phase velocities of the density contours, are determined by means of correlation analysis. For a low-density, L-mode discharge with strong equilibrium flow shear exhibiting an internal transport barrier (ITB) in the ion channel, the observed turbulence characteristics are compared with synthetic density turbulence data generated from global, non-linear, gyro-kinetic simulations using the particle-in-cell (PIC) code NEMORB. This validation exercise highlights the need to include increasingly sophisticated physics, e.g., kinetic treatment of trapped electrons, equilibrium flow shear and collisions, to reproduce most of the characteristics of the observed turbulence. Even so, significant discrepancies remain: an underprediction by the simulations of the turbulence amplituide and heat flux at plasma periphery and the finding that the correlation times of the numerically simulated turbulence are typically two orders of magnitude longer than those measured in MAST. Comparison of these correlation times with various linear timescales suggests that, while the measured turbulence is strong and may be `critically balanced', the simulated turbulence is weak.Comment: 27 pages, 11 figure

The response of toroidal drift modes to profile evolution : A model for small-ELMs in tokamak plasmas?

We consider a time-dependent linear global electrostatic toroidal fluid ion-temperature gradient (ITG) model to study the evolution of toroidal drift modes in tokamak plasmas as the equilibrium flow-shear varies with time. While we consider the ITG mode as a specific example, the results are expected to be valid for most other toroidal microinstabilities. A key result is that when there is a position in the plasma with a maximum in the instability drive (e.g. ITG), there is a transient burst of stronger growth as the flow-shear evolves through a critical value. This transient burst is expected to drive a filamentary plasma eruption, reminiscent of small-ELMs. The amplitude of the dominant linear mode is initially peaked above or below the outboard midplane, and rotates through it poloidally as the flow-shear passes through the critical value. This theoretical prediction could provide an experimental test of whether this mechanism underlies some classes of small-ELMs

Salicylaldehyde hydrazones: buttressing of outer sphere hydrogen-bonding and copper-extraction properties

Salicylaldehyde hydrazones are weaker copper extractants than their oxime derivatives, which are used in hydrometallurgical processes to recover ~20 % of the world’s copper. Their strength, based on the extraction equilibrium constant Ke, can be increased by nearly three orders of magnitude by incorporating electron-withdrawing or hydrogen-bond acceptor groups (X) ortho to the phenolic OH group of the salicylaldehyde unit. Density functional theory calculations suggest that the effects of the 3-X substituents arise from a combination of their influence on the acidity of the phenol in the pH-dependent equilibrium, Cu2+ + 2Lorg ⇌ [Cu(L–H)2]org + 2H+, and on their ability to ‘buttress’ interligand hydrogen bonding by interacting with the hydrazone N–H donor group. X-ray crystal structure determination and computed structures indicate that in both the solid state and the gas phase, coordinated hydrazone groups are less planar than coordinated oximes and this has an adverse effect on intramolecular hydrogen-bond formation to the neighbouring phenolate oxygen atoms