3D ideal linear peeling ballooning theory in magnetic fusion devices

Nuclear fusion is the fundamental process that generates heat and light in the stars but it is also a promising potential candidate for the generation of energy by man. However, where in the center of stars the combination of extreme temperatures with extreme pressure is what drives light elements close enough together for them to fuse and release part of their combined mass as energy, on earth only extreme temperatures can be employed. Matter at these temperatures exists in the state of plasma, where the atoms are stripped clean of their electrons. In the resulting physical system the presence of long term electromechanical forces between the charged particles can lead to violent collective behavior. Therefore, the general question of confining hot plasma in a stable way is crucial in order to achieve fusion. One strategy of doing this is by employing powerful magnetic fields to guide the charged particles around a toroidal configuration. This work is about a class of instabilities that these configurations are susceptible to, called high-n instabilities. High-n instabilities are instabilities that have strong localization around the magnetic field lines that confine the plasma, and they have previously been identified as possible culprits for some significant processes that occur in magnetic configurations, such as the periodic release of energy through Edge-Localized Modes (ELMs), or even the complete loss of confinement during disruptions, during which a large amount of energy is released to the reactor walls, damaging them. However, whereas much work has been performed in this field, the analysis of high-n instabilities in realistic 3-D geometries, including the effects of the deformation of the plasma edge, has not yet been done yet in a systematic and dedicated manner. Therefore, in the first part of this work a suitable theoretical framework is developed. Here, the simplification can be made that only modes pertaining to the same field line couple, through their high-n nature. This reduces the dimensionality of the problem by one, but at the same time does not pose any limitations on the 3-D aspects of the instabilities. One of the results of the theory is a system of coupled ordinary differential equations that can be solved for an eigenvalue, the sign of which determines whether the mode formed by the corresponding eigenvector is unstable or not. The solution of these equations, however, is something that has to be done using numerical techniques, so to this end the numerical code PB3D is developed. This stands for Peeling-Ballooning in 3-D, two modes that are described well through high-n theory. PB3D can treat the stability of various equilibrium codes such a VMEC and HELENA in a modular way, is parallelized making use of the message-passing interface (MPI) and is optimized for speed. The code is verified making use of physical criteria and by comparisons with two other, well-established numerical codes that have ranges of applicability bordering on that of PB3D. The first one, MISHKA, is a general-n stability code for axisymmetric equilibria, whereas the second one, COBRA, can treat general 3-D cases, but only in the n→ ∞ limit, with a static edge. The successful introduction of PB3D paves the way for a multitude of potential applications concerning 3-D edge effects. It can be investigated, for example, how many previous findings concerning peeling-ballooning modes in axisymmetric configurations change or not when 3-D effects are introduced. The theory of high-n stability of axisymmetric equilibria, for example, in the past has shed light on the dynamics of ELMs, and how this changes by including 3-D effects is a topic of interest. This is true even more so as recently the relevance of ELM control has risen due to the potentially dangerous behavior of ELMs in the next generation nuclear fusion reactors. A strategy for controlling them also intrinsically relies on applying 3-D resonant magnetic perturbations. The study of these effects with PB3D is planned in the near future in the ITER Organization. Before that, in this work, as a first concrete application, the modification of the stability of the pedestal of a High-confinement plasma equilibrium configuration by a toroidal field ripple is considered. These so-called H-mode configurations are characterized by a steep pressure gradient near the plasma edge, called the pedestal, which increases the temperature and pressure attainable in the core. Therefore, they are often seen as vital in order to achieve fusion. In practice, however, a degradation of the pedestal size is often observed, due to 3-D modifications of the equilibrium, such as the periodic ripple in the toroidal magnetic field due to the discreteness of the toroidal field coils. It was observed here that the application of a toroidal ripple in the shape of the poloidal cross section in the order of a percent, lead to a substantial decrease in the highest possible pedestal pressure, in the order of 30-40%. This substantiates good qualitative agreement with experimental results, where degradations of similar magnitude were observed.This research was sponsored in part by DGICYT (Dirección General de Investigaciones Científicas y Tecnológicas) of Spain under Project No. ENE2012-38620-C02-02 and Project. No. ENE2015-68265, and also in part by EUROFUSION-WP14-EDU and through FUSENET mobility funding.Programa Oficial de Doctorado en Plasmas y Fusión NuclearPresidente: Nicolas Joost Lopes Cardozo.- Secretario: Eduardo Antonio Ahedo Galilea.- Secretario: Carlos Hidalgo Ver

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome

Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin bio-synthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula x Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement

Acute sterfte bij het rund: autopsieprotocol en retrsospectieve studie

Sudden death is defined as the unexpected death of an apparently healthy animal within 24 hours after onset of the symptoms. In literature, many causes of sudden death have been reported. In the field, it is very difficult to confirm the exact cause of sudden death only by necropsy. Nevertheless, an exact diagnosis is requested in case of insurance expertise or herd health problems. In the present article, a practical protocol for approaching sudden death in cattle is proposed. The protocol is based on information available in the literature and on a retrospective necropsy series of sudden death cases in cattle in Flanders (n=124). The most common causes were enterotoxemia (23.7%), acute pneumonia (9.3%) and Taxus baccata intoxication (6.8%)

PB3D: a new code for edge 3-D ideal linear peeling-ballooning stability

A new numerical code PB3D (Peeling-Ballooning in 3-D) is presented. It implements and solves the intermediate-to-high-n ideal linear magnetohydrodynamic stability theory extended to full edge 3-D magnetic toroidal configurations in previous work [1]. The features that make PB3D unique are the assumptions on the perturbation structure through intermediate-to-high mode numbers n in general 3-D configurations, while allowing for displacement of the plasma edge. This makes PB3D capable of very efficient calculations of the full 3-D stability for the output of multiple equilibrium codes. As first verification, it is checked that results from the stability code MISHKA [2], which considers axisymmetric equilibrium configurations, are accurately reproduced, and these are then successfully extended to 3-D configurations, through comparison with COBRA [3], as well as using checks on physical consistency. The non-intuitive 3-D results presented serve as a tentative first proof of the capabilities of the code

PB3D: A new code for edge 3-D ideal linear peeling-ballooning stability

A new numerical code PB3D (Peeling-Ballooning in 3-D) is presented. It implements and solves the intermediate-to-high-n ideal linear magnetohydrodynamic stability theory extended to full edge 3-D magnetic toroidal configurations in previous work [1]. The features that make PB3D unique are the assumptions on the perturbation structure through intermediate-to-high mode numbers n in general 3-D configurations, while allowing for displacement of the plasma edge. This makes PB3D capable of very e cient calculations of the full 3-D stability for the output of multiple equilibrium codes. As first verification, it is checked that results from the stability code MISHKA [2], which considers axisymmetric equilibrium configurations, are accurately reproduced, and these are then successfully extended to 3-D configurations, through comparison with COBRA [3], as well as using checks on physical consistency. The non-intuitive 3-D results presented serve as a tentative first proof of the capabilities of the code.This research was sponsored in part by DGICYT (Dirección General de Investigaciones Científicas y Tecnológicas) of Spain under Project No. ENE2015-6826

Three-dimensional linear peeling-ballooning theory in magnetic fusion devices

Ideal magnetohydrodynamics theory is extended to fully 3D magnetic configurations to investigate the linear stability of intermediate to high n peeling-ballooning modes, with n the toroidal mode number. These are thought to be important for the behavior of edge localized modes and for the limit of the size of the pedestal that governs the high confinement H-mode. The end point of the derivation is a set of coupled second order ordinary differential equations with appropriate boundary conditions that minimize the perturbed energy and that can be solved to find the growth rate of the perturbations. This theory allows of the evaluation of 3D effects on edge plasma stability in tokamaks such as those associated with the toroidal ripple due to the finite number of toroidal field coils, the application of external 3D fields for elm control, local modification of the magnetic field in the vicinity of ferromagnetic components such as the test blanket modules in ITER, etc.This research was sponsored in part by DGICYT (Dirección General de Investigaciones Científicas y Tecnológicas) of Spain under Project No. ENE2012-38620-C02-02 and also in part by Comunidad de Madrid Project No. S2009/ENE-1679.Publicad

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies

Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high resolutioncommunity profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula x Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non target DNA and retrieval of bacterial OTUs

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=bijp20The attached document is the author's final accepted/submitted version of the journal article. You are advised to consult the publisher's version if you wish to cite from it

Method of plant tissue culture and regeneration

Plants may be regenerated from stomatal cells or protoplasts of such cells. Prior to regeneration the cells or protoplasts may be genetically transformed by the introduction of hereditary material most preferably by a DNA construct which is free of genes which specify resistance to antibiotics. The regeneration step may include callus formation on a hormone-free medium. The method is particularly suitable for sugar beet