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A new predictive computer simulation tool targeting the development of the H-mode pedestal at the plasma edge in tokamaks and the triggering and dynamics of edge localized modes (ELMs) is presented in this report. This tool brings together, in a coordinated and effective manner, several first-principles physics simulation codes, stability analysis packages, and data processing and visualization tools. A Kepler workflow is used in order to carry out an edge plasma simulation that loosely couples the kinetic code, XGC0, with an ideal MHD linear stability analysis code, ELITE, and an extended MHD initial value code such as M3D or NIMROD. XGC0 includes the neoclassical ion-electron-neutral dynamics needed to simulate pedestal growth near the separatrix. The Kepler workflow processes the XGC0 simulation results into simple images that can be selected and displayed via the Dashboard, a monitoring tool implemented in AJAX allowing the scientist to track computational resources, examine running and archived jobs, and view key physics data, all within a standard Web browser. The XGC0 simulation is monitored for the conditions needed to trigger an ELM crash by periodically assessing the edge plasma pressure and current density profiles using the ELITE code. If an ELM crash is triggered, the Kepler workflow launches the M3D code on a moderate-size Opteron cluster to simulate the nonlinear ELM crash and to compute the relaxation of plasma profiles after the crash. This process is monitored through periodic outputs of plasma fluid quantities that are automatically visualized with AVS/Express and may be displayed on the Dashboard. Finally, the Kepler workflow archives all data outputs and processed images using HPSS, as well as provenance information about the software and hardware used to create the simulation. The complete process of preparing, executing and monitoring a coupled-code simulation of the edge pressure pedestal buildup and the ELM cycle using the Kepler scientific workflow system is described in this paper.

Effects of regular treatments with the fungicides carbendazim and prochloraz applied to whole plots divided into subplots with different initial population mixtures of carbendazim-sensitive or carbendazim-resistant Tapesia yallundae or T acuformis were studied in successive crops of winter wheat from 1984/85 to 1999/2000. In unsprayed and carbendazim-sprayed whole plots, a stable coexistence of about 50% each of T yallundae and T acuformis developed within five seasons, but in whole plots sprayed with prochloraz or prochloraz plus carbendazim, the proportion of T acuformis increased to > 80%. A discrete time difference equation model was derived from knowledge of the biology of eyespot and competition theory to describe the population changes. The model was fitted to the data from treatments where coexistence occurred [subplots in unsprayed (1985-92) and carb endazim-sprayed (1985-89) whole plots], using nonlinear least squares regression. The optimized value of the resource overlap coefficient was small, suggesting niche differences between the two species. Populations were nearly 100% carbendazim-resistant in carbendazim-sprayed whole plots by July 1985 (one season) and in whole plots sprayed with prochloraz plus carbendazirn by July 1986 (two seasons). In prochloraz-sprayed whole plots, the proportion of carbendazim-resistant isolates decreased more rapidly than in unsprayed whole plots in the 1980s, but by July 1992 a shift in populations in unsprayed and prochloraz-sprayed whole plots towards predominantly carbendazim-resistant strains had occurred.

The understanding and predictive capability of transport physics and plasma confinement is reviewed from the perspective of achieving reactor-scale burning plasmas in the ITER tokamak, for both core and edge plasma regions. Very considerable progress has been made in understanding, controlling and predicting tokamak transport across a wide variety of plasma conditions and regimes since the publication of the ITER Physics Basis (IPB) document (1999 Nucl. Fusion 39 2137-2664). Major areas of progress considered here follow. (1) Substantial improvement in the physics content, capability and reliability of transport simulation and modelling codes, leading to much increased theory/experiment interaction as these codes are increasingly used to interpret and predict experiment. (2) Remarkable progress has been made in developing and understanding regimes of improved core confinement. Internal transport barriers and other forms of reduced core transport are now routinely obtained in all the leading tokamak devices worldwide. (3) The importance of controlling the H-mode edge pedestal is now generally recognized. Substantial progress has been made in extending high confinement H-mode operation to the Greenwald density, the demonstration of Type I ELM mitigation and control techniques and systematic explanation of Type I ELM stability. Theory-based predictive capability has also shown progress by integrating the plasma and neutral transport with MHD stability. (4) Transport projections to ITER are now made using three complementary approaches: empirical or global scaling, theory-based transport modelling and dimensionless parameter scaling (previously, empirical scaling was the dominant approach). For the ITER base case or the reference scenario of conventional ELMy H-mode operation, all three techniques predict that ITER will have sufficient confinement to meet its design target of Q = 10 operation, within similar uncertainties.

Scaling of the H-mode pedestal in tokamak plasmas with type I ELMs and dependence of the pedestal properties and the resulting divertor head load width with the plasma elongation and plasma current are investigated using the kinetic neoclassical XGC0 code for DIII-D and Alcator C-Mod tokamaks. The simulations in this study use realistic diverted geometry and are self-consistent with the inclusion of kinetic neoclassical physics, theory-based anomalous transport models with the E×B flow shearing effects, as well as an MHD ELM triggering criterion. Scalings for the pedestal width and height are developed as a function of the scanned plasma parameters. The nonlinear interplay between anomalous and neoclassical effects motivates the development of a self-consistent simulation model that includes neoclassical and anomalous effects simultaneously. It is demonstrated that the divertor heat load width depend on the plasma currents. In the development of this dependence, effects of neutral collisions and anomalous transport are taken into account. Changes in the neoclassical divertor heat load fluxes associated with the introduction of the neutral collision and anomalous transport effects are described. За допомогою кінетичного неокласичного коду XGC0 для розрядів в токамаках DIII-D і Alcator C-Mod досліджено скейлінг п’єдесталу в плазмі, що перебуває в режимі поліпшеного утримання, з прикордонними локалізованими модами (ПЛМ) першого типу, властивості п’єдесталу і потоку тепла на дивертор в залежності від витягнутості плазми та струму плазми. У розрахунках використовуються: реалістична геометрія дивертора, кінетична модель для неокласичних ефектів, модель аномального транспорту, яка враховує ефекти шира (ExB)-потоків, і умови збудження ПЛМ-нестійкостей. У результаті розрахунків отримані скейлінгі для ширини і висоти п’єдесталу як функції параметрів плазми. Нелінійна взаємодія неокласичних ефектів і ефектів, пов'язаних з аномальним транспортом, є мотивацією для розробки самоузгодженої чисельної моделі, яка одночасно включає ефекти аномального і неокласичного транспорту. Показано, що потоки тепла на дивертор залежать від плазмових струмів. Також представлено результати дослідження залежності напівширини профілів тепла на дивертор від ефектів, пов'язаних з аномальним транспортом і зіткненнями з нейтральними частинками. С помощью кинетического неоклассического кода XGC0 для разрядов в токамаках DIII-D и Alcator C-Mod исследованы скэйлинг пьедестала в плазме, находящейся в режиме улучшенного удержания, с приграничными локализованными модами (ПЛМ) первого типа, и зависимость свойств пьедестала и потока тепла на дивертор от вытянутости плазмы и тока плазмы. В расчетах используются: реалистичная геометрия дивертора, кинетическая модель для неоклассических эффектов, модель аномального транспорта, которая учитывает эффекты шира (ExB)-потоков, и условия возбуждения ПЛМ-неустойчивостей. В результате расчетов получены скэйлинги для ширины и высоты пьедестала как функции параметров плазмы. Нелинейное взаимодействие неоклассических эффектов и эффектов, связанных с аномальным транспортом, является мотивацией разработки самосогласованной численной модели, которая одновременно включает эффекты аномального и неоклассического транспорта. Показано, что потоки тепла на дивертор зависят от плазменных токов. Также представлены результаты исследования зависимости полуширины профилей тепла на дивертор от эффектов, связанных с аномальным транспортом и столкновениями с нейтральными частицами.

A reservoir of infection of Tapesia yallundae may exist after harvest in bases of cereal stems due to the presence of apothecia capable of discharging infective ascospores. Apothecia of T. yallundae developed in a seasonal pattern on winter barley inoculated with the pathogen, with maximum numbers of apothecia produced on stubble 5-7 months after harvest. A similar pattern of development was observed on infected winter wheat. However, the peak in numbers of mature apothecia was observed 2 months later than in winter barley. Apothecia capable of discharging ascospores were present for up to 6 months on stubble. Apothecia of T. acuformis were not detected on spring or winter barley, or spring or winter wheat stubble, despite inoculation of growing crops with isolates of compatible mating type.

Isolates of Fusarium avenaceum, mostly from crops of white lupin or wheat, were tested for pathogenicity on white lupin and wheat plants and compared by DNA tests and, in a limited study, vegetative compatibility. Most of the 80 isolates were pathogenic on both plant species after inoculation on shoot bases. Disease severity was greater at higher incubation temperatures that ranged from 15/10 degrees C to 25/20 degrees C (day/night temperatures). Isolates from lupin crops tended to be more pathogenic, on average, on lupins than on cereals. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer region of the rDNA distinguished two groups of isolates that occurred in different proportions among isolates from lupins and cereal crops. Random amplified polymorphic DNA (RAPD)-PCR analyses indicated considerable genetic variation among isolates, but there was some similarity among groups of isolates from populations in the same field. Genetic diversity was confirmed by a high degree of vegetative incompatibility among 20 isolates using nitrate nonutilizing mutants. There were no relationships among pathogenicity, RFLP group, RAPD group and vegetative compatibility group.

Communities of fungi on roots increased in diversity between second and third cereals, and were more diverse on winter wheat than on winter barley in a field experiment conducted over 3 years. Seed treatment with formulations containing fluquinconazole or fluquinconazole plus prochloraz had little effect on these communities, which include potentially beneficial, antagonistic fungi. Seed treatment decreased take-all and increased yield of wheat, especially in the second wheat in which take-all was building up, and in the third wheat when take-all was at its peak. It was less effective in the fourth wheat when take-all appeared to be in decline in plots that had no seed treatment throughout the experiment, and in barley, in which take-all was usually less severe. Take-all increased in untreated fourth wheat crops grown after third wheat crops that had been treated, suggesting that treatment had delayed take-all build-up and eventual progress into take-all decline.

Diagnostic and quantitative polymerase chain reaction (PCR) provided clarification of the causes of symptoms and the extent of infection by eyespot (Tapesia spp.) and sharp eyespot (Rhizoctonia cerealis) on winter wheat at early growth stages. Disease assessments made before stem extension, when decisions to apply fungicides are usually made, often did not agree with the pathogen diagnoses using PCR, suggesting that such early visual diagnoses may be unreliable. Visual and PCR diagnoses made on stems in summer generally supported each other, but there were often discrepancies in relating disease severity to amounts of pathogen present when determined by regression analyses of incidence or severity of symptoms on amount of pathogen DNA. Mixed symptoms caused by different pathogens may sometimes have been confounded. Relationships between symptoms and DNA of eyespot pathogens were less clear on some cultivars, often those with least disease. Sharp eyespot symptoms had a stronger relationship to DNA of its pathogen. Significant regressions often accounted for a small percentage of the variance, suggesting either that pathogens not assayed were contributing to symptoms or that lesions were in some cases persisting longer into the season than pathogen DNA. The frequency of pathogen detection before stem extension was a poor predictor of the amounts of pathogen DNA measured later in the season.