Testbed for the Pellet Launching System for JT-60SA

As part of the European contribution to the large size superconducting tokamak project JT-60SA, a new Pellet Launching System (PLS) is designed and built. The aims of the PLS are to provide efficient fuelling to the plasma and to control and mitigate Edge Localised Modes (ELMs). Two pellet sources, one for fuelling pellets, one for pacing pellets, are delivering pellets to a centrifuge launcher. The centrifuge enables precise launch of pellets according to already proven control schemes. Furthermore, this system opens a way towards a test bed for the EU-DEMO fuelling system. The new PLS has to be completed and commissioned first at the IPP Garching pellet lab and then to be shipped to QST Naka site after having demonstrated its performance. This dedicated test bed has been set up, providing suitable vacuum conditions to operate the PLS in similar conditions (except magnetic field and radiation). Maximum hydrogen throughput is about 400 mbar·L/s per pellet source. Safety issues must be considered for hydrogen inventory of pellet sources (∼100 bar·L each). In a first step, the pellet sources will be put on a test vessel providing inherent safety by a huge volume (10 m³) which makes sure that the hydrogen concentration is below 1% under all circumstances. A hydrogen safety survey prior to assembly confirmed the concept to be followed by an assessment after the installation in order to get the required license for operation. The PLS as a whole, for the time being equipped with two pellet sources, is to be certified according to explosion prevention rules (ATEX) as a product to be shipped to Naka site. To obtain this, an appropriate declaration of explosion zones inside the vacuum system and the use of suitable and certified equipment is mandatory. Such, the integration of this system can be planned and assessed on a clear technical and regulatory basis

SeqAn An efficient, generic C++ library for sequence analysis

<p>Abstract</p> <p>Background</p> <p>The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use.</p> <p>Results</p> <p>To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use.</p> <p>Conclusion</p> <p>We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.</p

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

[Abstract] The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at −25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinan

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)

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

Impact of ICRF on the scrape-off layer and on plasma wall interactions: From present experiments to fusion reactor

Recent achievements in studies of the effects of ICRF (Ion Cyclotron Range of Frequencies) power on the SOL (Scrape-Off Layer) and PWI (Plasma Wall Interactions) in ASDEX Upgrade (AUG), Alcator C-Mod, and JET-ILW are reviewed. Capabilities to diagnose and model the effect of DC biasing and associated impurity production at active antennas and on magnetic field connections to antennas are described. The experiments show that ICRF near-fields can lead not only to E×B convection, but also to modifications of the SOL density, which for Alcator C-Mod are limited to a narrow region near antenna. On the other hand, the SOL density distribution along with impurity sources can be tailored using local gas injection in AUG and JET-ILW with a positive effect on reduction of impurity sources. The technique of RF image current cancellation at antenna limiters was successfully applied in AUG using the 3-strap AUG antenna and extended to the 4-strap Alcator C-Mod field-aligned antenna. Multiple observations confirmed the reduction of the impact of ICRF on the SOL and on total impurity production when the ratio of the power of the central straps to the total antenna power is in the range 0.6<P$_{cen}$/P$_{total}$<0.8. Near-field calculations indicate that this fairly robust technique can be applied to the ITER ICRF antenna, enabling the mode of operation with reduced PWI. On the contrary, for the A2 antenna in JET-ILW the technique is hindered by RF sheaths excited at the antenna septum. Thus, in order to reduce the effect of ICRF power on PWI in a future fusion reactor, the antenna design has to be optimized along with design of plasmafacing components

Impact of fast ions on density peaking in JET: fluid and gyrokinetic modeling

The effect of fast ions on turbulent particle transport, driven by ion temperature gradient (ITG)/ trapped electron mode turbulence, is studied. Two neutral beam injection (NBI) heated JET discharges in different regimes are analyzed at the radial position ρ$_{t}$=0.6, one of them an L-mode and the other one an H-mode discharge. Results obtained from the computationally efficient fluid model EDWM and the gyro-fluid model TGLF are compared to linear and nonlinear gyrokinetic GENE simulations as well as the experimentally obtained density peaking. In these models, the fast ions are treated as a dynamic species with a Maxwellian background distribution. The dependence of the zero particle flux density gradient (peaking factor) on fast ion density, temperature and corresponding gradients, is investigated. The simulations show that the inclusion of a fast ion species has a stabilizing influence on the ITG mode and reduces the peaking of the main ion and electron density profiles in the absence of sources. The models mostly reproduce the experimentally obtained density peaking for the L-mode discharge whereas the H-mode density peaking is significantly underpredicted, indicating the importance of the NBI particle source for the H-mode density profile

Current Research into Applications of Tomography for Fusion Diagnostics

Retrieving spatial distribution of plasma emissivity from line integrated measurements on tokamaks presents a challenging task due to ill-posedness of the tomography problem and limited number of the lines of sight. Modern methods of plasma tomography therefore implement a-priori information as well as constraints, in particular some form of penalisation of complexity. In this contribution, the current tomography methods under development (Tikhonov regularisation, Bayesian methods and neural networks) are briefly explained taking into account their potential for integration into the fusion reactor diagnostics. In particular, current development of the Minimum Fisher Regularisation method is exemplified with respect to real-time reconstruction capability, combination with spectral unfolding and other prospective tasks