Evidence of Electron Heating by Alpha Particles in JET Deuterium-Tritium Plasmas.

The fusion-born alpha particle heating in magnetically confined fusion machines is a high priority subject for studies. The self-heating of thermonuclear fusion plasma by alpha particles was observed in recent deuterium-tritium (D-T) experiments on the joint European torus. This observation was possible by conducting so-called "afterglow" experiments where transient high fusion yield was achieved with neutral beam injection as the only external heating source, and then termination of the heating at peak performance. This allowed the first direct evidence for electron heating of plasmas by fusion-born alphas to be obtained. Interpretive transport modeling of the relevant D-T and reference deuterium discharges is consistent with the alpha particle heating observation.

Genetic control of N-glycosylation of human blood plasma proteins.

Glycosylation is an important protein modification, which influences the physical and chemical properties as well as biological function of these proteins. Large-scale population studies have shown that the levels of various plasma protein N-glycans are associated with many multifactorial human diseases. Observed associations between protein glycosylation levels and human diseases have led to the conclusion that N-glycans can be considered a potential source of biomarkers and therapeutic targets. Although biochemical pathways of glycosylation are well studied, the understanding of the mechanisms underlying general and tissue-specific regulation of these biochemical reactions in vivo is limited. This complicates both the interpretation of the observed associations between protein glycosylation levels and human diseases, and the development of glycan-based biomarkers and therapeutics. By the beginning of the 2010s, high-throughput methods of N-glycome profiling had become available, allowing research into the genetic control of N-glycosylation using quantitative genetics methods, including genome-wide association studies (GWAS). Application of these methods has made it possible to find previously unknown regulators of N-glycosylation and expanded the understanding of the role of N-glycans in the control of multifactorial diseases and human complex traits. The present review considers the current knowledge of the genetic control of variability in the levels of N-glycosylation of plasma proteins in human populations. It briefly describes the most popular physical-chemical methods of N-glycome profiling and the databases that contain genes involved in the biosynthesis of N-glycans. It also reviews the results of studies of environmental and genetic factors contributing to the variability of N-glycans as well as the mapping results of the genomic loci of N-glycans by GWAS. The results of functional in vitro and in silico studies are described. The review summarizes the current progress in human glycogenomics and suggests possible directions for further research.

Fusion product measurements by nuclear diagnostics in the Joint European Torus deuterium-tritium 2 campaign (invited).

A new deuterium-tritium experimental, DTE2, campaign has been conducted at the Joint European Torus (JET) between August 2021 and late December 2021. Motivated by significant enhancements in the past decade at JET, such as the ITER-like wall and enhanced auxiliary heating power, the campaign achieved a new fusion energy world record and performed a broad range of fundamental experiments to inform ITER physics scenarios and operations. New capabilities in the area of fusion product measurements by nuclear diagnostics were available as a result of a decade long enhancement program. These have been tested for the first time in DTE2 and a concise overview is provided here. Confined alpha particle measurements by gamma-ray spectroscopy were successfully demonstrated, albeit with limitations at neutron rates higher than some 1017 n/s. High resolution neutron spectroscopy measurements with the magnetic proton recoil instrument were complemented by novel data from a set of synthetic diamond detectors, which enabled studies of the supra-thermal contributions to the neutron emission. In the area of escaping fast ion diagnostics, a lost fast ion detector and a set of Faraday cups made it possible to determine information on the velocity space and poloidal distribution of the lost alpha particles for the first time. This extensive set of data provides unique information for fundamental physics studies and validation of the numerical models, which are key to inform the physics and scenarios of ITER.

The Nernst effect in Corbino geometry.

We study the manifestation of the Nernst effect in the Corbino disk subjected to the normal external magnetic field and to the radial temperature gradient. The Corbino geometry offers a precious opportunity for the direct measurement of the magnetization currents that are masked by kinetic contributions to the Nernst current in the conventional geometry. The magnetization currents, also referred to as the edge currents, are independent on the conductivity of the sample which is why they can be conveniently described within the thermodynamic approach. They can be related to the Landau thermodynamic potential for an infinite system. We demonstrate that the observable manifestation of this, purely thermodynamic, Nernst effect consists in the strong oscillations of the magnetic field measured in the center of the disk as a function of the external field. The oscillations depend on the temperature difference at the edges of the disk. Dirac fermions and 2D electrons with a parabolic spectrum are characterized by oscillations of different phase and frequency. We predict qualitatively different power dependencies of the magnitude of the Nernst signal on the chemical potential for normal and Dirac carriers.

The GWAS-MAP platform for aggregation of results of genome-wide association studies and the GWAS-MAP|homo database of 70 billion genetic associations of human traits.

Hundreds of genome-wide association studies (GWAS) of human traits are performed each year. The results of GWAS are often published in the form of summary statistics. Information from summary statistics can be used for multiple purposes - from fundamental research in biology and genetics to the search for potential biomarkers and therapeutic targets. While the amount of GWAS summary statistics collected by the scientific community is rapidly increasing, the use of this data is limited by the lack of generally accepted standards. In particular, the researchers who would like to use GWAS summary statistics in their studies have to become aware that the data are scattered across multiple websites, are presented in a variety of formats, and, often, were not quality controlled. Moreover, each available summary statistics analysis tools will ask for data to be presented in their own internal format. To address these issues, we developed GWAS-MAP, a high-throughput platform for aggregating, storing, analyzing, visualizing and providing access to a database of big data that result from region- and genome-wide association studies. The database currently contains information on more than 70 billion associations between genetic variants and human diseases, quantitative traits, and "omics" traits. The GWAS-MAP platform and database can be used for studying the etiology of human diseases, building predictive risk models and finding potential biomarkers and therapeutic interventions. In order to demonstrate a typical application of the platform as an approach for extracting new biological knowledge and establishing mechanistic hypotheses, we analyzed varicose veins, a disease affecting on average every third adult in Russia. The results of analysis confirmed known epidemiologic associations for this disease and led us to propose a hypothesis that increased levels of MICB and CD209 proteins in human plasma may increase susceptibility to varicose veins.

A network-based conditional genetic association analysis of the human metabolome.

Background: Genome-wide association studies have identified hundreds of loci that influence a wide variety of complex human traits; however, little is known regarding the biological mechanism of action of these loci. The recent accumulation of functional genomics ("omics"), including metabolomics data, has created new opportunities for studying the functional role of specific changes in the genome. Functional genomic data are characterized by their high dimensionality, the presence of (strong) statistical dependency between traits, and, potentially, complex genetic control. Therefore, the analysis of such data requires specific statistical genetics methods. Results: To facilitate our understanding of the genetic control of omics phenotypes, we propose a trait-centered, network-based conditional genetic association (cGAS) approach for identifying the direct effects of genetic variants on omics-based traits. For each trait of interest, we selected from a biological network a set of other traits to be used as covariates in the cGAS. The network can be reconstructed either from biological pathway databases (a mechanistic approach) or directly from the data, using a Gaussian graphical model applied to the metabolome (a data-driven approach). We derived mathematical expressions that allow comparison of the power of univariate analyses with conditional genetic association analyses. We then tested our approach using data from a population-based Cooperative Health Research in the region of Augsburg (KORA) study (n = 1,784 subjects, 1.7 million single-nucleotide polymorphisms) with measured data for 151 metabolites. Conclusions: We found that compared to single-trait analysis, performing a genetic association analysis that includes biologically relevant covariates can either gain or lose power, depending on specific pleiotropic scenarios, for which we provide empirical examples. In the context of analyzed metabolomics data, the mechanistic network approach had more power compared to the data-driven approach. Nevertheless, we believe that our analysis shows that neither a prior-knowledge-only approach nor a phenotypic-data-only approach is optimal, and we discuss possibilities for improvement.

Entropy spikes as a signature of Lifshitz transitions in the Dirac materials.

We demonstrate theoretically that the characteristic feature of a 2D system undergoing N consequent Lifshitz topological transitions is the occurrence of spikes of entropy per particle s of a magnitude ±ln2/(J - 1/2) with 2 ≤ J ≤ N at low temperatures. We derive a general expression for s as a function of chemical potential, temperature and gap magnitude for the gapped Dirac materials. Inside the smallest gap, the dependence of s on the chemical potential exhibits a dip-and-peak structure in the temperature vicinity of the Dirac point. The spikes of the entropy per particles can be considered as a signature of the Dirac materials. These distinctive characteristics of gapped Dirac materials can be detected in transport experiments where the temperature is modulated in gated structures.

Population specific analysis of Yakut exomes.

We studied the genetic diversity of the Yakut population using exome sequencing. We performed comparative analysis of the Yakut population and the populations that are included in the "1000 Genomes" project and we identified the alleles specific to the Yakut population. We showed, that the Yakuts population is a separate cluster between Europeans and East Asians.

Fast ion energy distribution from third harmonic radio frequency heating measured with a single crystal diamond detector at the Joint European Torus.

Neutron spectroscopy measurements with a single crystal diamond detector have been carried out at JET, for the first time in an experiment aimed at accelerating deuterons to MeV energies with radio frequency heating at the third harmonic. Data are interpreted by means of the expected response function of the detector and are used to extract parameters of the highly non-Maxwellian distribution function generated in this scenario. A comparison with observations using a time of flight and liquid scintillator neutron spectrometers is also presented. The results demonstrate the capability of diamond detectors to contribute to fast ion physics studies at JET and are of more general relevance in view of the application of such detectors for spectroscopy measurements in the neutron camera of next step tokamak devices.

Determination of hydrogen/deuterium ratio with neutron measurements on MAST.

On MAST, compressional Alfvén eigenmodes can be destabilized by the presence of a sufficiently large population of energetic particles in the plasma. This dependence was studied in a series of very similar discharges in which increasing amounts of hydrogen were puffed into a deuterium plasma. A simple method to estimate the isotopic ratio nH/nD using neutron emission measurements is here described. The inferred isotopic ratio ranged from 0.0 to 0.6 and no experimental indication of changes in radial profile of nH/nD were observed. These findings are confirmed by TRANSP/NUBEAM simulations of the neutron emission.

Neutron spectrometry of JET discharges with ICRH-acceleration of helium beam ions.

Recent experiments at JET aimed at producing 4He ions in the MeV range through third harmonic ion cyclotron resonance heating (ICRH) acceleration of 4He beams in a 4He dominated plasma. MeV range D was also present through parasitic ICRH absorption on residual D. In this contribution, we analyze TOFOR neutron spectrometer data from these experiments. A consistent description of the data is obtained with d(d,n)3He and 9Be(α,n)12C neutron components calculated using Stix distributions for the fast D and 4He, taking finite Larmor radius effects into account and with a ICRH power partition of P(D)(RF) = 0.01×P(4He)(RF), in agreement with TOMCAT simulations.

Experimental study of the ion critical-gradient length and stiffness level and the impact of rotation in the JET tokamak.

Experiments were carried out in the JET tokamak to determine the critical ion temperature inverse gradient length (R/LTi=R|nablaTi|/Ti) for the onset of ion temperature gradient modes and the stiffness of Ti profiles with respect to deviations from the critical value. Threshold and stiffness have been compared with linear and nonlinear predictions of the gyrokinetic code GS2. Plasmas with higher values of toroidal rotation show a significant increase in R/LTi, which is found to be mainly due to a decrease of the stiffness level. This finding has implications on the extrapolation to future machines of present day results on the role of rotation on confinement.

Destabilizing effect of dynamical friction on fast-particle-driven waves in a near-threshold nonlinear regime.

The nonlinear evolution of waves excited by the resonant interaction with energetic particles, just above the instability threshold, is shown to depend on the type of relaxation process that restores the unstable distribution function. When dynamical friction dominates over diffusion in the phase space region surrounding the wave-particle resonance, an explosive evolution of the wave is found to be the only solution. This is in contrast with the case of dominant diffusion when the wave may exhibit steady-state, amplitude modulation, chaotic and explosive regimes near marginal stability. The experimentally observed differences between Alfvénic instabilities driven by neutral beam injection and those driven by ion-cyclotron resonance heating are interpreted.

Accuracy of EFIT equilibrium reconstruction with internal diagnostic information at JET.

In tokamak experiments, equilibrium reconstruction codes are used to calculate the location of the last closed flux surface, to map diagnostic information, and to derive important properties like current density and safety factor. At JET, the equilibrium code EFIT is automatically executed after each discharge. For speed and robustness, intershot EFIT is based on magnetic probe measurements only. As a consequence, the intershot profiles of the safety factor can be wrong for a variety of plasma scenarios. Internal diagnostic information, the pitch angle as measured with the motional stark effect, Faraday rotation angles, as well as pressure profile information can increase the accuracy of the EFIT equilibrium. In this paper, the accuracy of the internal diagnostics at JET and their impact on the EFIT results are discussed in detail. The influence of control parameters like the form of the test functions for ff' and p' on the equilibrium is investigated. The q(min) from this analysis agrees with information from magnetohydrodynamics analysis (e.g., Alfvén cascades and sawtooth analysis) to within 10%-15%.

Anomalous absorption line in the magneto-optical response of graphene.

The intensity as well as position in energy of the absorption lines in the infrared conductivity of graphene, both exhibit features that are directly related to the Dirac nature of its quasiparticles. We show that the evolution of the pattern of absorption lines as the chemical potential is varied encodes the information about the presence of the anomalous lowest Landau level. The first absorption line related to this level always appears with full intensity or is entirely missing, while all other lines disappear in two steps. We demonstrate that if a gap develops, the main absorption line splits into two provided that the chemical potential is greater than or equal to the gap.

Unusual microwave response of dirac quasiparticles in graphene.

Recent experiments have proven that the quasiparticles in graphene obey a Dirac equation. Here we show that microwaves are an excellent probe of their unusual dynamics. When the chemical potential is small, the intraband response can exhibit a cusp around zero frequency Omega and this unusual line shape changes to Drude-like by increasing the chemical potential |mu|, with width linear in mu. The interband contribution at T=0 is a constant independent of Omega with a lower cutoff at 2mu. Distinctly different behavior occurs if interaction-induced phenomena in graphene cause an opening of a gap Delta. At a large magnetic field B, the diagonal and Hall conductivities at small Omega become independent of B but remain nonzero and show a structure associated with the lowest Landau level. This occurs because in the Dirac theory the energy of this level, E0 = +/-Delta, is field independent in sharp contrast to the conventional case.

Probing internal transport barriers with heat pulses in JET.

The first electron temperature modulation experiments in plasmas characterized by strong and long-lasting electron and ion internal transport barriers (ITB) have been performed in JET using ion cyclotron resonance heating in mode conversion scheme. The ITB is shown to be a well localized narrow layer with low heat diffusivity, characterized by subcritical transport and loss of stiffness. In addition, results from cold pulse propagation experiments suggest a second order transition process for ITB formation.

Unconventional integer quantum Hall effect in graphene.

Monolayer graphite films, or graphene, have quasiparticle excitations that can be described by (2+1)-dimensional Dirac theory. We demonstrate that this produces an unconventional form of the quantized Hall conductivity sigma(xy) = -(2e2/h)(2n+1) with n = 0, 1, ..., which notably distinguishes graphene from other materials where the integer quantum Hall effect was observed. This unconventional quantization is caused by the quantum anomaly of the n=0 Landau level and was discovered in recent experiments on ultrathin graphite films.

Monitoring Alfvén cascades with interferometry on the JET Tokamak.

A microwave interferometry technique is applied for the first time for detecting a discrete spectrum of Alfvén cascade (AC) eigenmodes excited with fast ions in reversed magnetic shear plasmas of the Joint European Torus. The interferometry measurements of plasma density perturbations associated with ACs show an unprecedented frequency and time resolution superior to that obtained with external magnetic coils. The measurements of ACs are used for monitoring the evolution of the safety factor and density of rational magnetic surfaces in the region of maximum plasma current.