Causality and heat transport in low magnetic shear Stellarators

Mención Internacional en el título de doctorLa Fusión Nuclear se ha convertido en el camino más prometedor para alcanzar una fuente de energía fiable y sostenible en un futuro próximo con un bajo impacto medioambiental. Cientos de millones de grados son necesarios para alcanzar las deseadas reacciones de Fusión Nuclear así que el plasma debe ser confinado usando fuertes campos magnéticos. Con estas enormes temperaturas el plasma está lejos del equilibrio y grandes gradientes de temperatura (y flujos de calor) aparecen. Durante décadas el transporte de calor ha sido uno de los temas principales en la búsqueda de un reactor de Fusión Nuclear eficiente. El elevado número de perdidas conlleva a una reducción del confinamiento y reduce la viabilidad de un reactor. Aun así, el transporte de calor todavía no se entiende totalmente por lo tanto queda mucho trabajo por delante. En esta tesis el transporte de calor en plasmas de fusión es analizado en el contexto de simulaciones MHD resistivas. Para ello usamos la técnica Transferencia de Entropía (TE). El Capítulo 2 introduce el modelo MHD usado para la simulación de plasmas de fusión y el Capítulo 3 describe el procedimiento de la Transferencia de Entropía. La TE es una técnica, del campo de la Teoría de la Información, la cual mide la propagación de información entre dos señales. La TE puede identificar si eventos pasados en una señal pueden ser usados para predecir eventos futuros en la otra señal. Su principal ventaja es que muestra la dirección del flujo de información. En este sentido, por causalidad nos referimos a que si la información está huyendo de A hacia B entonces A causa B. De esta manera hacemos una analogía entre la propagación de información y la propagación de calor. Los métodos más usados en el estudio del transporte de calor en plasmas experimentales de fusión son los métodos perturbativos. Estos han sido usados durante décadas en la mayoría de dispositivos de fusión. Muchos de estos experimentos usan un calentamiento externo modulado para determinar la respuesta del plasma y, de esta manera, analizar el transporte de calor. En modelos numéricos es relativamente fácil introducir una perturbación de calor en el plasma y estudiar su evolución temporal. No es el caso en plasmas experimentales donde lanzar un único pulso puede no ser viable y no es fácil de identificar debido al ruido de fondo. La estrategia presentada aquí, basada en la Transferencia de Entropía, muestra una nueva herramienta para analizar el transporte de calor. En recientes experimentos [1], el ECRH fue utilizado para calentar regiones internas del plasma para luego observar las perturbaciones espontaneas que se generaban durante el calentamiento. Se midió la temperatura electrónica en diferentes puntos radiales durante la presencia de perturbaciones espontaneas en el núcleo. Después la Transferencia de Entropía fue aplicada desde un punto de referencia en el núcleo a las diferentes señales distribuidas radialmente. De esta manera, la propagación radial de calor fue observada usando la TE. Sin embargo, esta propagación no era continua ni difusiva y mostraba regiones de atrapamiento donde las perturbaciones se frenaban. El Capítulo 4 resume algunos de los resultados experimentales observados y después aplica el mismo método de la Transferencia de Entropía a simulaciones numéricas de plasmas en el TJ-II. El modelo numérico nos permite entender la física subyacente e interpretar los resultados experimentales. El modelo es aplicado a diferentes casos y se obtienen conclusiones similares. Podemos identificar también regiones donde las perturbaciones mayormente son atrapadas y otras regiones donde el transporte radial es más rápido. Estas regiones de atrapamiento nos sugieren la presencia de (mini) barreras de transporte [2]. El mismo estudio de transporte de calor fue realizado en el W7-X [3]. A pesar de que el dispositivo W7-X tiene un mejor rendimiento y muchas diferencias con el TJ-II, tiene una característica común al ser un stellarator con una pequeña cizalla magnética. Debido a esa pequeña cizalla, modos de orden bajo pueden extenderse radialmente. La presencia de estas superficies racionales puede generar barreras de transporte. El Capítulo 5 introduce algunas observaciones experimentales de la Ref [3] y luego nuestro modelo numérico es usado para interpretar esos resultados experimentales. Usando el método TE observamos, otra vez, regiones donde las perturbaciones de calor están atrapadas o regiones con un transporte mayor. En los Capítulos 4 and 5 el transporte de calor se estudia cualitativamente. La Transferencia de Entropía permite identificar regiones radiales en el plasma con diferente transporte de calor. Sin embargo, en el Capítulo 6, usamos la Transferencia de Entropía para estudiar cuantitativamente el transporte radial de calor. La técnica es capaz de estimar una difusividad efectiva en diferentes puntos radiales. La TE es comparada con otros métodos para demonstrar su efectividad. El Capítulo 7 describe la emergencia de barreras de transporte y vórtices turbulentos. Las inestabilidades resistivas de intercambio dan lugar a vórtices turbulentos los cuales siguen las líneas de campo magnético. Por consiguiente, esos vórtices turbulentos pueden desarrollar una estructura filamentaria. La contribución total de los diferentes vórtices turbulentos e inestabilidades en el plasma puede generar un flujo poloidal promedio el cual puede dar lugar a la formación de barreras de transporte. Los vórtices turbulentos, relacionados con las barreras de transporte, deben poderse encontrar como estructuras filamentarias dentro del plasma. En el Capítulo 8 la topología de las estructuras filamentarias en el TJ-II es analizada usando la técnica de la Transferencia de Entropía. Primero, algunos de los resultados experimentales en el TJII se resumen, después usando nuestras simulaciones numéricas interpretamos esos resultados. Centrándonos en el potencial electrostático podemos observar que hay estructuras (filamentarias) siguiendo las líneas de campo magnético en superficies radiales. Con el método TE, la periodicidad, longitud, ancho radial y velocidad de los filamentos se puede calcular. Luego encontramos que donde se observan las zonas radiales de atrapamiento (Capítulo 4) hay estructuras filamentarias. Asociamos la presencia de esos filamentos con las barreras de transporte. Finalmente, el Capítulo 9 reproduce algunos de los estudios del anterior capítulo pero para el dispositivo W7-X. Usando nuestras simulaciones numéricas, estudiamos algunas de las propiedades de las estructuras filamentarias y obtenemos conclusiones similares. Este trabajo puede ser usado en futuros experimentos para interpretar sus resultados.Nuclear Fusion is becoming the most promising way to achieve a reliable and sustainable source of energy in the coming future with a low environmental impact. Hundreds of millions degrees are required to obtain the desired Nuclear Fusion reactions so plasma must be confined using strong magnetic fields. Under such large temperatures plasma is far away from equilibrium and high temperature gradients (and heat uxes) appear. For several decades, heat transport has been one of the main issues to achieve the goal of an efficient nuclear fusion reactor. High losses yields to a poor confinement and reduce the viability of a reactor. Even though, heat transport is not yet well understood and still much work is necessary. In this thesis heat transport in fusion plasmas is analyzed in the framework of resistive MHD simulations. To do so, we use the Transfer Entropy (TE) technique. Chapter 2 introduces the MHD model used to simulate fusion plasmas and the Transfer Entropy approach is described in Chapter 3. The TE is a technique, from Information theory field, which measures the information propagation between two time signals. The TE can identify if previous events in one signal can be used to predict future events in another signal. Its main advantage is that it shows the direction of that information ow. In this sense, by causality we mean that if the information is owing from A to B then A causes B. Therefore, we make an analogy between the information propagation and heat propagation. The most used methods to study heat transport in experimental fusion plasmas are the perturbative methods. They have been used during decades in most fusion devices. Most of the experiments use external heating modulation to determine the plasma response and, in this way, analyze heat transport. In numerical models is relatively easy to introduce a heat perturbation in the plasma and study its time evolution. That is not the case in experimental plasmas where to set a single pulse can be not feasible and it is not easy to identify it due to the background noise. The approach presented here, based on the Transfer Entropy, illustrates a new tool to analyze heat transport. In recent experiments [1], the ERCH was used to heat inner locations of the plasma and then observe the spontaneous perturbations generated by the heating. The electron temperature was measured at different radial locations during the presence of spontaneous perturbations in the core. Then the Transfer Entropy was applied from a reference point in the core to the different signals radially distributed. In this way, radial heat propagation was observed using TE. However this propagation was neither continuous nor diffusive and showed trapping regions where perturbations were slowed down. Chapter 4 sums up some of the experimental observations and then apply the same Transfer Entropy approach to numerical simulations of TJ-II plasmas. The numerical model allows us to understand the underlying physics and interpret the experimental results. The model is applied to different cases and similar conclusions are obtained. We can identify as well regions were the perturbations are mostly trapped and other regions were radial transport is faster. This trapping regions are suggesting the presence of (mini) transport barriers [2]. The same study of heat transport was done in the W7-X [3]. In spite of the fact that the W7-X device has a better performance and many differences with the TJ-II, it has a common characteristic of being a stellarator with low magnetic shear. Due the low shear, low order modes may extend in a wider radial region. The presence of these rational surfaces may generate transport barriers. Chapter 5 introduces some of the experimental observations in Ref. [3] and then our numerical model is used in order to interpret these experiment results. Using the TE approach we observe, again, regions where heat perturbations are trapped or regions with enhanced transport. In Chapters 4 and 5 the heat transport is studied qualitatively. The Transfer Entropy allows to identify radial regions in the plasma with different heat transport. However, in Chapter 6, we use the Transfer Entropy to quantitatively study that radial heat transport. The technique is able to estimate an effective diffusivity at different radial locations. The TE is compared with other approaches to demonstrate its effectiveness. Chapter 7 describes the emergence of transport barriers and turbulent vortices. Resistive interchange instabilities yield to turbulent vortices which follow the magnetic field lines. Therefore, those turbulent vortices may have a filamentary structure. The total contribution of the different turbulent vortices and fluctuations in the plasma may generate an average poloidal ow which in turn can lead to the formation of transport barriers. The turbulent vortices, related to the transport barriers, should be found as filamentary structures in the plasma. In Chapter 8, the topology of filamentary structures in TJ-II is analyzed using the Transfer Entropy technique. First, some of the experimental results in TJ-II are summarized and then our numerical simulations are used to interpret these results. Focusing on the electrostatic potential we can observe that there are (filamentary) structures following the magnetic field lines in radial surfaces. By the TE approach, periodicity, length, radial width and velocity of filaments can be calculated. Then, we find that where we observed trapping radial regions (Chapter 4), there are filamentary structures. We associate the presence of these filaments with the transport barriers. Finally, Chapter 9 reproduces some of the studies from the previous chapter but for the W7-X device. Using our numerical simulations, some of the properties of the filamentary structures are studied and similar conclusions are obtained. This work may be used in future experiments to interpret the results.Programa Oficial de Doctorado en Plasmas y Fusión Nuclear por la Universidad Carlos III de MadridPresidente: Luis Conde López.- Secretario: Luis Raúl Sánchez Fernández.- Vocal: Peter Beye

The Radial Propagation of Heat in Strongly Driven Non-Equilibrium Fusion Plasmas

Heat transport is studied in strongly heated fusion plasmas, far from thermodynamic equilibrium. The radial propagation of perturbations is studied using a technique based on the transfer entropy. Three different magnetic confinement devices are studied, and similar results are obtained. "Minor transport barriers" are detected that tend to form near rational magnetic surfaces, thought to be associated with zonal flows. Occasionally, heat transport "jumps" over these barriers, and this "jumping" behavior seems to increase in intensity when the heating power is raised, suggesting an explanation for the ubiquitous phenomenon of "power degradation" observed in magnetically confined plasmas. Reinterpreting the analysis results in terms of a continuous time random walk, "fast" and "slow" transport channels can be discerned. The cited results can partially be understood in the framework of a resistive Magneto-HydroDynamic model. The picture that emerges shows that plasma self-organization and competing transport mechanisms are essential ingredients for a fuller understanding of heat transport in fusion plasmas.Research sponsored in part by the Ministerio de Economía y Competitividad of Spain under Project No. ENE2015-68206-P and ENE2015-68265-P. This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training program 2014-2018 and 2019-2020 under Grant Agreement No. 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission

The impact of rational surfaces on radial heat transport in TJ-II

Autor colectivo: TJ-II TeamIn this work, we study the outward propagation of temperature perturbations. For this purpose, we apply an advanced analysis technique, transfer entropy, to ECE measurements performed in ECR heated discharges at the low-shear stellarator TJ-II. We observe that the propagation of these perturbations is not smooth, but is slowed down at specific radial positions, near 'trapping zones' characterized by long time lags with respect to the perturbation origin. We also detect instances of rapid or instantaneous (non-local) propagation, in which perturbations appear to 'jump over' specific radial regions. The analysis of perturbations introduced in a resistive magneto-hydrodynamic model of the plasma leads to similar results. The radial regions corresponding to slow radial transport are identified with maxima of the flow shear associated with rational surfaces (mini-transport barriers). The non-local interactions are ascribed to MHD mode coupling effects

Filaments in the edge confinement region of TJ-II

Autor colectivo: TJ-II TeamFloating potential measurements from two remote reciprocating probes in the plasma edge region of the TJ-II stellarator are analyzed using the transfer entropy, revealing the spatial dimensions and propagation properties of filamentary structures. The results are corroborated by performing simulations with a resistive MHD model and analyzing data from synthetic diagnostics. The transfer entropy captures the rotation of the filaments and allows the calculating of their rotation velocity. This deduced velocity was compared to the (known) poloidal velocity of the plasma and showed a relatively good agreement

Discovery of circulating miRNAs as biomarkers of chronic Chagas heart disease via a small RNA-Seq approach

Circulating miRNAs; Biomarkers; Chronic Chagas heart diseasemiARN circulantes; Biomarcadores; Enfermedad cardíaca crónica de ChagasmiRNAs circulants; Biomarcadors; Malaltia cardíaca crònica de ChagasChagas disease affects approximately 7 million people worldwide in Latin America and is a neglected tropical disease. Twenty to thirty percent of chronically infected patients develop chronic Chagas cardiomyopathy decades after acute infection. Identifying biomarkers of Chagas disease progression is necessary to develop better therapeutic and preventive strategies. Circulating microRNAs are increasingly reliable biomarkers of disease and therapeutic targets. To identify new circulating microRNAs for Chagas disease, we performed exploratory small RNA sequencing from the plasma of patients and performed de novo miRNA prediction, identifying potential new microRNAs. The levels of the new microRNAs temporarily named miR-Contig-1519 and miR-Contig-3244 and microRNAs that are biomarkers for nonchagasic cardiomyopathies, such as miR-148a-3p and miR-224-5p, were validated by quantitative reverse transcription. We found a specific circulating microRNA signature defined by low miR-Contig-3244, miR-Contig-1519, and miR-148a-3 levels but high miR-224-5p levels for patients with chronic Chagas disease. Finally, we predicted in silico that these altered circulating microRNAs could affect the expression of target genes involved in different cellular pathways and biological processes, which we will explore in the future.The funding was supported by Agencia Nacional e Promoción Científica y Tecnológica, PICT 2013-1892, Secretaría de Ciencia y Tecnología, Universidad Nacional de Rosario, 1MED410, Ministerio de Economía y competitividad and Fondo Europeo de Desarrollo Regional, SAF2016-75988-R (MINECO/FEDER), SAF2015-63868-R (MINECO/FEDER), Red de Investigación de Centros de Enfermedades Tropicales, RICET RD12/0018/0004, Consejería de Sanidad, Comunidad de Madrid, S-2010/BMD-2332, Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación and Fondo Europeo de Desarrollo Regional, PGC2018-096132-B-I00

Discovery of circulating miRNAs as biomarkers of chronic Chagas heart disease via a small RNA-Seq approach

Chagas disease affects approximately 7 million people worldwide in Latin America and is a neglected tropical disease. Twenty to thirty percent of chronically infected patients develop chronic Chagas cardiomyopathy decades after acute infection. Identifying biomarkers of Chagas disease progression is necessary to develop better therapeutic and preventive strategies. Circulating microRNAs are increasingly reliable biomarkers of disease and therapeutic targets. To identify new circulating microRNAs for Chagas disease, we performed exploratory small RNA sequencing from the plasma of patients and performed de novo miRNA prediction, identifying potential new microRNAs. The levels of the new microRNAs temporarily named miR-Contig-1519 and miR-Contig-3244 and microRNAs that are biomarkers for nonchagasic cardiomyopathies, such as miR-148a-3p and miR-224-5p, were validated by quantitative reverse transcription. We found a specific circulating microRNA signature defined by low miR-Contig-3244, miR-Contig-1519, and miR-148a-3 levels but high miR-224-5p levels for patients with chronic Chagas disease. Finally, we predicted in silico that these altered circulating microRNAs could affect the expression of target genes involved in different cellular pathways and biological processes, which we will explore in the future.The funding was supported by Agencia Nacional e Promoción Científica y Tecnológica, PICT 2013-1892, Secretaría de Ciencia y Tecnología, Universidad Nacional de Rosario, 1MED410, Ministerio de Economía y competitividad and Fondo Europeo de Desarrollo Regional, SAF2016-75988-R (MINECO/FEDER), SAF2015-63868-R (MINECO/FEDER), Red de Investigación de Centros de Enfermedades Tropicales, RICET RD12/0018/0004, Consejería de Sanidad, Comunidad de Madrid, S-2010/BMD-2332, Ministerio de Ciencia, Innovación y Universidades-Agencia Estatal de Investigación and Fondo Europeo de Desarrollo Regional, PGC2018-096132-B-I00, and PID2021-123389OB-I00

Ecological risk assessment of pesticides in the Mijares River (eastern Spain) impacted by citrus production using wide-scope screening and target quantitative analysis

The widespread use of pesticides, especially in agricultural areas, makes necessary to control their presence in surrounding surface waters. The current study was designed to investigate the occurrence and ecological risks of pesticides and their transformation products in a Mediterranean river basin impacted by citrus agricultural production. Nineteen sites were monitored in three campaigns distributed over three different seasons. After a qualitative screening, 24 compounds was selected for subsequent quantitative analysis. As expected, the lower section of the river was most contaminated, with total concentration >5 µg/L in two sites near to the discharge area of wastewater treatment plants. The highest concentrations were found in September, after agricultural applications and when the river flow is reduced. Ecological risks were calculated using two mixture toxicity approaches (Toxic Unit and multi-substance Potentially Affected Fraction), which revealed high acute and chronic risks of imidacloprid to invertebrates, moderate-to-high risks of diuron, simazine and 2,4-D for primary producers, and moderate-to-high risks of thiabendazole for invertebrates and fish. This study shows that intensive agricultural production and the discharge of wastewater effluents containing pesticide residues from post-harvest citrus processing plants are threatening freshwater biodiversity. Further actions are recommended to control pesticide use and to reduce emissions.Universitat Jaume I/[UJI-B2018-55]/UJI/EspañaMinistry of Science, Innovation and University/[RTI2018-097417-B-I00]//EspañaGeneralitat Valenciana[PROMETEO 2019/040]//EspañaUniversidad de Costa Rica/[OAICE-CAB-12-235-2016]/UCR/Costa RicaMinisterio de Ciencia e Innovación/[RYC2019-028132-I]/MICINN/EspañaMinistry of Economy and Competitiveness/[RYC-2017-22525]/MINECO/EspañaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro en Investigación en Contaminación Ambiental (CICA

Discovery of circulating miRNAs as biomarkers of chronic Chagas heart disease via a small RNA-Seq approach

Abstract Chagas disease affects approximately 7 million people worldwide in Latin America and is a neglected tropical disease. Twenty to thirty percent of chronically infected patients develop chronic Chagas cardiomyopathy decades after acute infection. Identifying biomarkers of Chagas disease progression is necessary to develop better therapeutic and preventive strategies. Circulating microRNAs are increasingly reliable biomarkers of disease and therapeutic targets. To identify new circulating microRNAs for Chagas disease, we performed exploratory small RNA sequencing from the plasma of patients and performed de novo miRNA prediction, identifying potential new microRNAs. The levels of the new microRNAs temporarily named miR-Contig-1519 and miR-Contig-3244 and microRNAs that are biomarkers for nonchagasic cardiomyopathies, such as miR-148a-3p and miR-224-5p, were validated by quantitative reverse transcription. We found a specific circulating microRNA signature defined by low miR-Contig-3244, miR-Contig-1519, and miR-148a-3 levels but high miR-224-5p levels for patients with chronic Chagas disease. Finally, we predicted in silico that these altered circulating microRNAs could affect the expression of target genes involved in different cellular pathways and biological processes, which we will explore in the future