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In tokamak experiments, sufficiently strong E × B flow shear reduces turbulent transport, thereby improving the prospects for fusion power plants. It is therefore of great importance to efficiently explore parameter space to find where strong plasma flow can be achieved. To this end, we propose a new, physically motivated quasi-linear model for estimating momentum transport from turbulence in the presence of toroidal flow shear and plasma shaping. The method gives good estimates of momentum transport for up–down asymmetric geometries as well as low magnetic shear and tight aspect ratio. The results are benchmarked with high-fidelity nonlinear GENE simulations, demonstrating that it provides a fast and accurate estimate of momentum transport.

Microturbulence can produce stationary fine-scale radial corrugations on the plasma density and temperature gradients in magnetic confinement fusion devices. We study the effect of these corrugations, focusing on electron temperature gradient (ETG) transport in the tokamak pedestal, and report three main findings. 1) In the presence of a sinusoidal background temperature gradient corrugation, each ETG mode splits into three distinct eigenvalues, with one being the original, one being more unstable and one being less unstable. 2) Despite the presence of more unstable linear modes, nonlinear gyrokinetic simulations show a significant reduction in fluxes. 3) Profile shearing associated with the fine-scale background corrugations is identified as the saturation mechanism explaining the reduction in fluxes. It originates from the radial variation of the mode’s own phase velocity (proportional to the local diamagnetic drift velocity and the pressure gradient), and not from externally generated flows or E × B zonal flows. Fine-scale profile shearing could be a ubiquitous turbulence saturation mechanism in fusion plasmas.

In this work, we highlight an issue that may reduce the accuracy of many local nonlinear gyrokinetic simulations – turbulent self-interaction through the parallel boundary condition. Given a sufficiently long parallel correlation length, individual turbulent eddies can span the full domain and ‘bite their own tails’, thereby altering their statistical properties. Such self-interaction is only modelled accurately when the simulation domain corresponds to a full flux surface, otherwise it is artificially strong. For Cyclone Base Case parameters and typical domain sizes, we find that this mechanism modifies the heat flux by approximately 40 % and it can be even more important. The effect is largest when using kinetic electrons, low magnetic shear and strong turbulence drive (i.e. steep background gradients). It is found that parallel self-interaction can be eliminated by increasing the parallel length and/or the binormal width of the simulation domain until convergence is achieved.

We report a whole-genome comparison of gene content in allelic BAC contigs from two maize inbred lines. Genic content polymorphisms involve as many as 10,000 sequences and are mainly generated by DNA insertions. The termini of eight of the nine genic insertions that we analyzed shared the structural hallmarks of helitron rolling-circle transposons 1 , 2 , 3 . DNA segments defined by helitron termini contained multiple gene-derived fragments and had a structure typical of nonautonomous helitron-like transposons. Closely related insertions were found in multiple genomic locations. Some of these produced transcripts containing segments of different genes, supporting the idea that these transposition events have a role in exon shuffling and the evolution of new proteins. We identified putative autonomous helitron elements and found evidence for their transcription. Helitrons in maize seem to continually produce new nonautonomous elements responsible for the duplicative insertion of gene segments into new locations and for the unprecedented genic diversity. The maize genome is in constant flux, as transposable elements continue to change both the genic and nongenic fractions of the genome, profoundly affecting genetic diversity.

Based on the analysis of a large number of high-fidelity nonlinear gyrokinetic simulations, we propose a novel strategy to improve confinement in spherical tokamak plasmas by combining up-down asymmetric flux surface shaping with the Low Momentum Diffusivity (LMD) regime. We show that the intrinsic momentum flux driven by up-down asymmetry creates strong flow shear in the LMD regime that can significantly reduce energy transport, increasing the critical gradient by up to 25%. In contrast to traditional methods for generating flow shear, such as neutral beam injection, this approach requires no external momentum source and is expected to scale well to large fusion devices. The experimental applicability of this strategy in spherical tokamaks is addressed via simulations by considering actual equilibria from Mega Ampere Spherical Tokamak and a preliminary equilibrium from SMART.

Allelic chromosomal regions totaling more than 2.8 Mb and located on maize (Zea mays) chromosomes 1L, 2S, 7L, and 9S have been sequenced and compared over distances of 100 to 350 kb between the two maize inbred lines Mo17 and B73. The alleles contain extended regions of nonhomology. On average, more than 50% of the compared sequence is noncolinear, mainly because of the insertion of large numbers of long terminal repeat (LTR)-retrotransposons. Only 27 LTR-retroelements are shared between alleles, whereas 62 are allele specific. The insertion of LTR-retrotransposons into the maize genome is statistically more recent for nonshared than shared ones. Most surprisingly, more than one-third of the genes (27/72) are absent in one of the inbreds at the loci examined. Such nonshared genes usually appear to be truncated and form clusters in which they are oriented in the same direction. However, the nonshared genome segments are gene-poor, relative to regions shared by both inbreds, with up to 12-fold difference in gene density. By contrast, miniature inverted terminal repeats (MITEs) occur at a similar frequency in the shared and nonshared fractions. Many times, MITES are present in an identical position in both LTRs of a retroelement, indicating that their insertion occurred before the replication of the retroelement in question. Maize ESTs and/or maize massively parallel signature sequencing tags were identified for the majority of the nonshared genes or homologs of them. In contrast with shared genes, which are usually conserved in gene order and location relative to rice (Oryza sativa), nonshared genes violate the maize colinearity with rice. Based on this, insertion by a yet unknown mechanism, rather than deletion events, seems to be the origin of the nonshared genes. The intergenic space between conserved genes is enlarged up to sixfold in maize compared with rice. Frequently, retroelement insertions create a different sequence environment adjacent to conserved genes.

Between a plasma and a solid target lies a positively charged sheath of several Debye lengths $\\lambda _{D}$ width, typically much smaller than the characteristic length scale $L$ of the main plasma. This scale separation implies that the asymptotic limit $\\epsilon = \\lambda _{D} / L \\rightarrow 0$ is useful to solve for the plasma-sheath system. In this limit, the Bohm criterion must be satisfied at the sheath entrance. A new derivation of the kinetic criterion, admitting a general ion velocity distribution, is presented. It is proven that, for $\\epsilon \\rightarrow 0$, the distribution of the velocity component normal to the target, $v_x$, and its first derivative must vanish for $|v_x| \\rightarrow 0$ at the sheath entrance. These two conditions can be subsumed into a third integral one after it is integrated by parts twice. A subsequent interchange of the limits $\\epsilon \\rightarrow 0$ and $|v_x| \\rightarrow 0$ is invalid, leading to a divergence which underlies the misconception that the criterion gives undue importance to slow ions.

Linear and nonlinear local gyrokinetic simulations of the high power high current JT-60SA scenario are presented, based on inputs from predictive transport modelling. Carbon impurities and fast ions are included in the simulations as well as electromagnetic effects. High frequency modes associated with fast ions are found in linear and nonlinear simulations and identified as Toroidal Alfven Eigenmodes (TAEs). In the absence of TAEs, turbulent transport is found to mainly be driven by the ion temperature gradient mode. In this case, fast particles are found not to have a significant effect on the heat flux. The total heat flux at half normalized minor radius is found to be higher than expected based on the assumed total heating power. A modest 10% decrease of the ion and electron temperature gradients (ETGs) is sufficient to match the expected value. On the other hand, simulations at other radial positions demonstrate heat fluxes lower than expected, consistent with the previous study of a similar scenario and an increase of the ion and ETGs by about 20%–30% is necessary to recover the expected heat flux.

The gyrokinetic delta-f particle-in-cell (PIC) approach is known to be successful for simulating turbulence in the core of magnetic fusion plasmas, where fluctuations are relatively small and therefore the unperturbed particle distribution function, usually represented by a stationary Maxwellian f0, remains a good choice of a control variate for reducing statistical sampling noise. However, towards the plasma edge, characterized by low density and temperature and strong gradients, relative deviation amplitudes typically become large, so that the essential assumption of |δf/f0| << 1 underlying the delta-f PIC approach will not be valid, where δf is the fluctuating part of distribution. This motivates the study of the limits of the delta-f approach in a simplified system mimicking the plasma edge. To this end, simulations are run using GK-engine, which is a delta-f PIC code that solves the nonlinear gyrokinetic equation in a sheared slab geometry, using B-spline finite elements to represent the self-consistent electrostatic field. Initial radial density and ion temperature profiles exhibiting high logarithmic gradients representing plasma edge conditions are used. In order to avoid practical problems of particles exiting the simulation domain as the ion temperature profile relaxes, all profiles are mirrored at domain-centre and periodic boundary conditions are imposed. The validity of the delta-f approach is measured by statistical noise estimates, while monitoring relative deviation levels of temperature via the kinetic energy. In particular, the effect of background profile gradients on these measures is investigated. As a first step towards reducing the amplitude of the deviation δf, an adaptive Maxwellian f0 is implemented, whose time dependent temperature profiles are obtained by locally relaxing kinetic energy accumulating in δf into f0.

Self-interaction is the process by which a microinstability eigenmode that is extended along the direction parallel to the magnetic field interacts non-linearly with itself. This effect is particularly significant in gyrokinetic simulations accounting for kinetic passing electron dynamics and is known to generate stationary $E\\times B$ zonal flow shear layers at radial locations near low-order mode rational surfaces (Weikl et al. Phys. Plasmas, vol. 25, 2018, 072305). We find that self-interaction, in fact, plays a very significant role in also generating fluctuating zonal flows, which is critical to regulating turbulent transport throughout the radial extent. Unlike the usual picture of zonal flow drive in which microinstability eigenmodes coherently amplify the flow via modulational instabilities, the self-interaction drive of zonal flows from these eigenmodes are uncorrelated with each other. It is shown that the associated shearing rate of the fluctuating zonal flows therefore reduces as more toroidal modes are resolved in the simulation. In simulations accounting for the full toroidal domain, such an increase in the density of toroidal modes corresponds to an increase in the toroidal system size, leading to a finite system size effect that is distinct from the well-known profile shearing effect.