A high-order Godunov scheme for global 3D MHD accretion disks simulations. I. The linear growth regime of the magneto-rotational instability

We employ the PLUTO code for computational astrophysics to assess and compare the validity of different numerical algorithms on simulations of the magneto-rotational instability in 3D accretion disks. In particular we stress on the importance of using a consistent upwind reconstruction of the electro-motive force (EMF) when using the constrained transport (CT) method to avoid the onset of numerical instabilities. We show that the electro-motive force (EMF) reconstruction in the classical constrained transport (CT) method for Godunov schemes drives a numerical instability. The well-studied linear growth of magneto-rotational instability (MRI) is used as a benchmark for an inter-code comparison of PLUTO and ZeusMP. We reproduce the analytical results for linear MRI growth in 3D global MHD simulations and present a robust and accurate Godunov code which can be used for 3D accretion disk simulations in curvilinear coordinate systems

Modelling of the effect of ELMs on fuel retention at the bulk W divertor of JET

Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York

High-resolution array comparative genomic hybridisation (aCGH) analysis of DNA copy number aberrations (CNAs) was performed on breast carcinomas in premenopausal women from Western New York (WNY) and from Gomel, Belarus, an area exposed to fallout from the 1986 Chernobyl nuclear accident. Genomic DNA was isolated from 47 frozen tumour specimens from 42 patients and hybridised to arrays spotted with more than 3000 BAC clones. In all, 20 samples were from WNY and 27 were from Belarus. In total, 34 samples were primary tumours and 13 were lymph node metastases, including five matched pairs from Gomel. The average number of total CNAs per sample was 76 (range 35–134). We identified 152 CNAs (92 gains and 60 losses) occurring in more than 10% of the samples. The most common amplifications included gains at 8q13.2 (49%), at 1p21.1 (36%), and at 8q24.21 (36%). The most common deletions were at 1p36.22 (26%), at 17p13.2 (26%), and at 8p23.3 (23%). Belarussian tumours had more amplifications and fewer deletions than WNY breast cancers. HER2/neu negativity and younger age were also associated with a higher number of gains and fewer losses. In the five paired samples, we observed more discordant than concordant DNA changes. Unsupervised hierarchical cluster analysis revealed two distinct groups of tumours: one comprised predominantly of Belarussian carcinomas and the other largely consisting of WNY cases. In total, 50 CNAs occurred significantly more commonly in one cohort vs the other, and these included some candidate signature amplifications in the breast cancers in women exposed to significant radiation. In conclusion, our high-density aCGH study has revealed a large number of genetic aberrations in individual premenopausal breast cancer specimens, some of which had not been reported before. We identified a distinct CNA profile for carcinomas from a nuclear fallout area, suggesting a possible molecular fingerprint of radiation-associated breast cancer

FACT Prevents the Accumulation of Free Histones Evicted from Transcribed Chromatin and a Subsequent Cell Cycle Delay in G1

The FACT complex participates in chromatin assembly and disassembly during transcription elongation. The yeast mutants affected in the SPT16 gene, which encodes one of the FACT subunits, alter the expression of G1 cyclins and exhibit defects in the G1/S transition. Here we show that the dysfunction of chromatin reassembly factors, like FACT or Spt6, down-regulates the expression of the gene encoding the cyclin that modulates the G1 length (CLN3) in START by specifically triggering the repression of its promoter. The G1 delay undergone by spt16 mutants is not mediated by the DNA–damage checkpoint, although the mutation of RAD53, which is otherwise involved in histone degradation, enhances the cell-cycle defects of spt16-197. We reveal how FACT dysfunction triggers an accumulation of free histones evicted from transcribed chromatin. This accumulation is enhanced in a rad53 background and leads to a delay in G1. Consistently, we show that the overexpression of histones in wild-type cells down-regulates CLN3 in START and causes a delay in G1. Our work shows that chromatin reassembly factors are essential players in controlling the free histones potentially released from transcribed chromatin and describes a new cell cycle phenomenon that allows cells to respond to excess histones before starting DNA replication

Beryllium global erosion and deposition at JET-ILW simulated with ERO2.0

The recently developed Monte-Carlo code ERO2.0 is applied to the modelling of limited and diverted discharges at JET with the ITER-like wall (ILW). The global beryllium (Be) erosion and deposition is simulated and compared to experimental results from passive spectroscopy. For the limiter configuration, it is demonstrated that Be self-sputtering is an important contributor (at least 35%) to the Be erosion. Taking this contribution into account, the ERO2.0 modelling confirms previous evidence that high deuterium (D) surface concentrations of up to ∼50% atomic fraction provide a reasonable estimate of Be erosion in plasma-wetted areas. For the divertor configuration, it is shown that drifts can have a high impact on the scrape-off layer plasma flows, which in turn affect global Be transport by entrainment and lead to increased migration into the inner divertor. The modelling of the effective erosion yield for different operational phases (ohmic, L- and H-mode) agrees with experimental values within a factor of two, and confirms that the effective erosion yield decreases with increasing heating power and confinement

Investigation of deuterium trapping and release in the JET ITER-like wall divertor using TDS and TMAP

Selected set of samples from JET ITER-Like Wall (JET-ILW) divertor tiles exposed both in 2013–2014 and 2011–2014 has been analysed using Thermal Desorption Spectrometry (TDS). The deuterium (D) amounts obtained with TDS were compared with Ion Beam Analysis (IBA) and Secondary Ion Mass Spectrometry (SIMS) data. The highest amount of D was found on the top part of inner divertor which has regions with the thickest deposited layers. This area resides deep in the scrape-off layer. Changes in plasma configurations between the first (2011–2012) and the second (2013–2014) JET-ILW campaign altered the material migration towards the inner and the outer divertor corner increasing the amount of deposition in the shadowed areas of the divertor base tiles. D retention on the outer divertor tiles is clearly smaller than on the inner divertor tiles. Experimental TDS spectra for samples from the top part of inner divertor and from the outer strike point region were modelled using TMAP program. Experimental deuterium profiles obtained with SIMS have been used and the detrapping and the activation energies have been adjusted. Analysis of the results of the TMAP simulations enabled to determine the nature of traps in different sample

EDGE2D-EIRENE simulations of the influence of isotope effects and anomalous transport coefficients on near scrape-off layer radial electric field

EDGE2D-EIRENE (the ‘code’) simulations show that radial electric field, E$_{r}$, in the near scrape-off layer (SOL) of tokamaks can have large variations leading to a strong local E×B shear greatly exceeding that in the core region. This was pointed out in simulations of JET plasmas with varying divertor geometry, where the magnetic configuration with larger predicted near SOL E$_{r}$ was found to have lower H-mode power threshold, suggesting that turbulence suppression in the SOL by local E×B shear can be a player in the L–H transition physics (Delabie et al 2015 42nd EPS Conf. On Plasma Physics (Lisbon, Portugal, 22–26 June 2015) paper O3.113 (http://ocs.ciemat.es/ EPS2015PAP/pdf/O3.113.pdf), Chankin et al 2017 Nucl. Mater. Energy 12 273). Further code modeling of JET plasmas by changing hydrogen isotopes (H–D–T) showed that the magnitude of the near SOL E$_{r}$ is lower in H cases in which the H-mode threshold power is higher (Chankin et al 2017 Plasma Phys. Control. Fusion 59 045012). From the experiment it is also known that hydrogen plasmas have poorer particle and energy confinement than deuterium plasmas, consistent with the code simulation results showing larger particle diffusion coefficients at the plasma edge, including SOL, in hydrogen plasmas (Maggi et al 2018 Plasma Phys. Control. Fusion 60 014045). All these experimental observations and code results support the hypothesis that the near SOL E×B shear can have an impact on the plasma confinement. The present work analyzes neutral ionization patterns of JET plasmas with different hydrogen isotopes in L-mode cases with fixed input power and gas puffing rate, and its impact on target electron temperature, T$_{e}$, and SOL E$_{r}$. The possibility of a self-feeding mechanism for the increase in the SOL E$_{r}$ via the interplay between poloidal E×B drift and target T$_{e}$ is discussed. It is also shown that reducing anomalous turbulent transport coefficients, particle diffusion and electron and ion heat conductivities, leads to higher peak target T$_{e}$ and larger E$_{r}$, suggesting the possibility of a positive feedback loop, under an implicitly made assumption that the E×B shear in the SOL is capable of suppressing turbulence