A high-density and high-confinement tokamak plasma regime for fusion energy.

The tokamak approach, utilizing a toroidal magnetic field configuration to confine a hot plasma, is one of the most promising designs for developing reactors that can exploit nuclear fusion to generate electrical energy1,2. To reach the goal of an economical reactor, most tokamak reactor designs3-10 simultaneously require reaching a plasma line-averaged density above an empirical limit-the so-called Greenwald density11-and attaining an energy confinement quality better than the standard high-confinement mode12,13. However, such an operating regime has never been verified in experiments. In addition, a long-standing challenge in the high-confinement mode has been the compatibility between a high-performance core and avoiding large, transient edge perturbations that can cause very high heat loads on the plasma-facing-components in tokamaks. Here we report the demonstration of stable tokamak plasmas with a line-averaged density approximately 20% above the Greenwald density and an energy confinement quality of approximately 50% better than the standard high-confinement mode, which was realized by taking advantage of the enhanced suppression of turbulent transport granted by high density-gradients in the high-poloidal-beta scenario14,15. Furthermore, our experimental results show an integration of very low edge transient perturbations with the high normalized density and confinement core. The operating regime we report supports some critical requirements in many fusion reactor designs all over the world and opens a potential avenue to an operating point for producing economically attractive fusion energy.

Spectrally resolved polarization angle across the motional Stark effect spectrum.

A new diagnostic technique has been developed that couples a spectrometer and an image-intensified camera into the traditional motional Stark effect (MSE) system on DIII-D. The image-intensified camera syncs with the photo-elastic modulators to spectrally resolve the Stokes parameters across the Stark multiplet. Polarization dependent phase shift, likely from a plasma facing mirror, leads to the spectropolarimeter measuring a variation in the polarization angle across the MSE spectrum of ∼8°.

Four-dimensional calibration turntable of the motional Stark effect diagnostic on EAST.

The motional Stark effect (MSE) diagnostic is applied to measure the safety factor q and current density profile of a tokamak device, which are important parameters in realizing the high-performance and long-pulse steady state of a tokamak. A single-channel MSE diagnostic based on dual photoelastic modulators, whose sightline meets with the neutral beam injection at a major radius of R = 2.12 m, has been built for the D window of the Experimental Advanced Superconducting Tokamak (EAST). According to the requirements of MSE diagnostic polarimetric calibration, a high-precision four-dimensional calibration turntable, driven by four stepping motors and controlled by software running on the computer, was designed for EAST. The turntable allows us to rapidly calibrate the MSE diagnostic in a series of positions and angles during EAST maintenance. The turntable can move in four dimensions of translation, yaw, pitch, and roll of the polarizer and can create linearly polarized light at any given angle with accuracy of ∼0.05° for the MSE system offline calibration. The experimental results of the MSE diagnostic calibration in the laboratory show that the turntable has the advantages of high positioning accuracy, flexible spatial movement, and convenient control and fully meets the calibration requirements of an MSE diagnosis system.

Asymmetries in the motional Stark effect emission on the DIII-D tokamak.

Spectrometer measurements and filter upgrades to a motional Stark effect polarimeter measuring the outer half-radius of the DIII-D tokamak helped to identify asymmetries in the polarization angle of Stark-split emission. The measured polarization angle of the π components differs and is not orthogonal to the σ component. These differences persist over a range of densities and with low levels of background light. It is suggested that the difference in the polarization angle between components is from a change in the ellipticity of the emitted light across the Stark components coupled with imperfect polarization preservation from an in-vessel mirror.

Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing.

Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence.

High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation.

The human leukocyte antigen (HLA) class I and class II loci are the most polymorphic genes in the human genome; distinguishing the thousands of HLA alleles is challenging. Next generation sequencing of exonic amplicons with the 454 genome sequence (GS) FLX System and Conexio Assign ATF 454 software provides high resolution, high throughput HLA genotyping for eight class I and class II loci. HLA typing of potential donors for unrelated bone marrow donor registries typically uses a subset of these loci at high sample throughput and low cost per sample. The Fluidigm Access Array System enables the incorporation of 48 different multiplex identifiers (MIDs) corresponding to 48 genomic DNA samples with up to 48 different primer pairs in a microfluidic device generating 2304 parallel polymerase chain reactions (PCRs). Minimal volumes of reagents are used. During genomic PCR, in this 4-primer system, the outer set of primers containing the MID and the 454 adaptor sequences are incorporated into an amplicon generated by the inner HLA target-specific primers each containing a common sequence tag at the 5' end of the forward and reverse primers. Pools of the resulting amplicons are used for emulsion PCR and clonal sequencing on the 454 Life Sciences GS FLX System, followed by genotyping with Conexio software. We have genotyped 192 samples with 100% concordance to known genotypes using 8 primer pairs (covering exons 2 and 3 of HLA-A, B and C, and exon 2 of DRB1, 3/4/5 and DQB1) and 96 MIDs in a single GS FLX run. An average of 166 reads per amplicon was obtained. We have also genotyped 96 samples at high resolution (14 primer pairs covering exons 2, 3, and 4 of the class I loci and exons 2 of DRB1, 3/4/5, DQA1, DQB1, DPB1, and exon 3 of DQB1), recovering an average of 173 sequence reads per amplicon.

16(th) IHIW : review of HLA typing by NGS.

Human leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA-based genotyping methods, including Sanger sequence-based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high-resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next-generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short- and long-range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele-calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.

16(th) IHIW: immunogenomic data-management methods. report from the immunogenomic data analysis working group (IDAWG).

SUMMARY: The goal of the immunogenomic data analysis working group (IDAWG) is to facilitate the consistent analysis of HLA and KIR data, and the sharing of those data among the immunogenomic and larger genomic communities. However, the data management approaches currently applied by immunogenomic researchers are not widely discussed or reported in the literature, and the effect of different approaches on data analyses is not known. With ASHI's support, the IDAWG developed a 45 question survey on HLA and KIR data generation, data management and data analysis practices. Survey questions detailed the loci genotyped, typing systems used, nomenclature versions reported, computer operating systems and software used to manage and transmit data, the approaches applied to resolve HLA ambiguity and the methods used for basic population-level analyses. Respondents were invited to demonstrate their HLA ambiguity resolution approaches in simulated data sets. By May 2012, 156 respondents from 35 nations had completed the survey. These survey respondents represent a broad sampling of the Immunogenomic community; 52% were European, 30% North American, 10% Asian, 4% South American and 4% from the Pacific. The project will continue in conjunction with the 17th Workshop, with the aim of developing community data sharing standards, ambiguity resolution documentation formats, single-task data Management tools and novel data analysis methods and applications. While additional project details and plans for the 17th IHIW will be forthcoming, we welcome the input and participation in these projects from the histocompatibility and immunogenetics community.

Pedestal magnetic field measurements using a motional Stark effect polarimeter.

Temperature-controlled, 0.15 nm interference filters were installed on an edge-viewing system of the motional Stark effect (MSE) polarimeter on the DIII-D tokamak. The upgraded system provides a factor of two reduction in the bandpass compared to the previous design, and linear control of the bandpass, which is unaltered by wavelength tuning. With the new system, there is a reduced dependence of the inferred polarization angle on the filter wavelength calibration. Recent measurements from the calibrated edge-viewing system show increased agreement with other MSE arrays.

Magnetohydrodynamic interference with the edge pedestal motional Stark effect diagnostic on DIII-D.

Accurate measurement of internal magnetic field direction using motional Stark effect (MSE) polarimetry in the edge pedestal is desired for nearly all tokamak scenario work. A newly installed 500 kHz 32-channel digitizer on the MSE diagnostic of DIII-D allows full spectral information of the polarimeter signal to be recovered for the first time. Fourier analysis of this data has revealed magnetohydrodynamic (MHD) fluctuations in the plasma edge pedestal at ρ ≥ 0.92. By correlating edge localized mode fluctuations seen on lock-in amplifier outputs with MSE spectrograms, it has been shown that edge pedestal tearing mode fluctuations cause interference with MSE second harmonic instrument frequencies. This interference results in unrecoverable errors in the real-time polarization angle measurement that are more than an order of magnitude larger than typical polarimeter uncertainties. These errors can cause as much as a 38% difference in local q. By using a redundant measure of the linear polarization found at the fourth harmonic photo-elastic modulator (PEM) frequency, MHD interference can be avoided. However, because of poorer signal-to-noise the fourth harmonic signal computed polarization angle shows no improvement over the MHD polluted second harmonics. MHD interference could be avoided in future edge pedestal tokamak polarimeters by utilizing PEMs with higher fundamental frequencies and a greater separation between their frequencies.

A multi-site study using high-resolution HLA genotyping by next generation sequencing.

The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution.

Measurements of the internal magnetic field using the B-Stark motional Stark effect diagnostic on DIII-D (inivited).

Results are presented from the B-Stark diagnostic installed on the DIII-D tokamak. This diagnostic provides measurements of the magnitude and direction of the internal magnetic field. The B-Stark system is a version of a motional Stark effect (MSE) diagnostic based on the relative line intensities and spacing of the Stark split D(α) emission from injected neutral beams. This technique may have advantages over MSE polarimetry based diagnostics in future devices, such as the ITER. The B-Stark diagnostic technique and calibration procedures are discussed. The system is shown to provide accurate measurements of B(θ)/B(T) and ∣B∣ over a range of plasma conditions. Measurements have been made with toroidal fields in the range of 1.2-2.1 T, plasma currents in the range 0.5-2.0 MA, densities between 1.7 and 9.0×10(19) m(-3), and neutral beam voltages between 50 and 81 keV. The viewing direction and polarization dependent transmission properties of the collection optics are found using an in situ beam into gas calibration. These results are compared to values found from plasma equilibrium reconstructions and the MSE polarimetry system on DIII-D.

A digital lock-in upgrade of the motional Stark effect diagnostic on DIII-D.

The use of lock-in amplifiers for phase sensitive detection of motional Stark effect (MSE) diagnostic signals is of critical importance to real-time internal current profile measurements in tokamak plasmas. A digital lock-in (DLI) upgrade utilizing field programable gate array firmware has been installed on the MSE system of the DIII-D tokamak for the eventual replacement of largely obsolete analog units. While the new digital system has shown a small reduction in electronic noise over the analog, the main advantages are reduced cost, hardware simplicity, compact size, and phase tracking during plasma operations. DLI recovery of MSE polarization angles was accomplished through use of reference processing to produce only photoelastic modulator (PEM) second harmonic frequencies and electronic signal processing to maximize the fidelity of the recovered signal. A simplified discrete analytical solution was found that accurately describes the new DLI hardware. The DLI algorithm was found to cause a prohibitively large oscillating artifact atop the demodulated signal. The artifact was caused by the accumulator interval not containing an exact integer number of PEM multiplier periods. Successful MSE measurements require the minimization of this oscillating artifact amplitude. The analytical solution was used to select an appropriate accumulator interval that both reduces the artifact and maintains the greatest temporal resolution possible. Sample EFIT equilibria reconstructions and corresponding safety factor profiles showed very close agreement between the analog and digital lock-ins.

Evidence for fast-ion transport by microturbulence.

Cross-field diffusion of energetic ions by microturbulence is measured during neutral-beam injection into the DIII-D tokamak. Fast-ion D(alpha), neutron, and motional Stark effect measurements diagnose the fast-ion distribution function. As expected for transport by plasma turbulence, anomalies relative to the classical prediction are greatest in high temperature plasmas, at low fast-ion energy, and at larger minor radius. Theoretical estimates of fast-ion diffusion are comparable to experimental levels.

Magnetic-flux pumping in high-performance, stationary plasmas with tearing modes.

Analysis of the change in the magnetic field pitch angles during edge localized mode events in high performance, stationary plasmas on the DIII-D tokamak shows rapid (<1 ms) broadening of the current density profile, but only when a m/n=3/2 tearing mode is present. This observation of poloidal magnetic-flux pumping explains an important feature of this scenario, which is the anomalous broadening of the current density profile that beneficially maintains the safety factor above unity and forestalls the sawtooth instability.

Measurements of the internal magnetic field on DIII-D using intensity and spacing of the motional Stark multiplet.

We describe a version of a motional Stark effect (MSE) diagnostic based on the relative line intensities and spacing of Stark split D(alpha) emission from the neutral beams. This system, named B-Stark, has been recently installed on the DIII-D tokamak. To find the magnetic pitch angle, we use the ratio of the intensities of the pi(3) and sigma(1) lines. These lines originate from the same upper level and so are not dependent on the level populations. In future devices, such as ITER, this technique may have advantages over diagnostics based on MSE polarimetry. We have done an optimization of the viewing direction for the available ports on DIII-D to choose the installation location. With this placement, we have a near optimal viewing angle of 59.6 degrees from the vertical direction. All hardware has been installed for one chord, and we have been routinely taking data since January 2007. We fit the spectra using a simple Stark model in which the upper level populations of the D(alpha) transition are treated as free variables. The magnitude and direction of the magnetic field obtained using this diagnostic technique compare well with measurements from MSE polarimetry and EFIT.

Overview of equilibrium reconstruction on DIII-D using new measurements from an expanded motional Stark effect diagnostic.

Motional Stark effect (MSE) measurements constrain equilibrium reconstruction of DIII-D tokamak plasmas using the equilibrium code EFIT. In 2007, two new MSE arrays were brought online, bringing the system to three core arrays, two edge arrays, and 64 total channels. We present the first EFIT reconstructions using this expanded system. Safety factor and E(R) profiles produced by fitting to data from the two new arrays and one of the other three agree well with independent measurements. Comparison of the data from the three arrays that view the core shows that one of the older arrays is inconsistent with the other two unless the measured calibration factors for this array are adjusted. The required adjustments depend on the toroidal field and plasma current direction, and on still other uncertain factors that change as the plasma evolves. We discuss possible sources of calibration error for this array.

Optimization of the optical design of the ITER MSE diagnostic.

The motional Stark effect (MSE) diagnostic will be essential for the study of advanced scenarios on ITER and its design is currently underway with initial emphasis on the optical design. Optical performance, as measured by photon throughput and minimization of polarization aberrations, will be critical to the success of the diagnostic. Consequently, the initial design work has been focused heavily on this area. In order meet the ITER MSE diagnostic design requirements, two approaches for the measurement are under consideration. The first is based on standard polarimeter techniques to measure the polarization of the emitted light, whereas the second measures the Stark splitting from which absolute value(B) can be inferred, where absolute value(B) is the magnitude of the total magnetic field. The base line design of the optical system is centered on the first approach. Emphasis in this case is placed on minimizing the polarization aberrations of the optical relay system. Motivation for the second method results from concern that the optical properties of the plasma-facing mirror, particularly its diattenuation and retardance, will degrade with plasma exposure. The second approach, while less sensitive to aberrations induced by plasma exposure effects, requires greater optical throughput in order to measure the complete Stark spectrum. We have developed an optimized optical design applicable to both measurement techniques. A summary of the design is presented and design issues are discussed.