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At least 1,387 records · Page 77

The electronic structure, crystal fields, and magnetic anisotropy in RECo 5 magnets

The current progress in describing rare-earth-based magnets' electronic structure and magnetic properties is discussed. We use several currently popular electronic structure methods to show the typical values of critical parameters that define the physics of RECo 5 (RE = rare earth atom) materials. The magnetic moments and magnetic anisotropy of 4f atoms are obtained using several approaches, including anisotropic 4f-charge density-constrained DFT and DFT+HI methods. We also suggest the introduction of "penalty" functional for obtaining correct variational total energy in the traditional Hund's rule-constrained DFT-based techniques. The applicability and future extensions are discussed. The proposed combination of methods is potentially suitable for high-throughput computational searches of new rare-earth-containing magnetic materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes nosocomial infections for which there are limited treatment options. Penicillin-binding protein PBP3, a key therapeutic target, is an essential enzyme responsible for the final steps of peptidoglycan synthesis and is covalently inactivated by {beta}-lactam antibiotics. Here we disclose the first high resolution cocrystal structures of the P. aeruginosa PBP3 with both novel and marketed {beta}-lactams. These structures reveal a conformational rearrangement of Tyr532 and Phe533 and a ligand-induced conformational change of Tyr409 and Arg489. The well-known affinity of the monobactam aztreonam for P. aeruginosa PBP3 is due to a distinct hydrophobic aromatic wall composed of Tyr503, Tyr532, and Phe533 interacting with the gem-dimethyl group. The structure of MC-1, a new siderophore-conjugated monocarbam complexed with PBP3 provides molecular insights for lead optimization. Importantly, we have identified a novel conformation that is distinct to the high-molecular-weight class B PBP subfamily, which is identifiable by common features such as a hydrophobic aromatic wall formed by Tyr503, Tyr532, and Phe533 and the structural flexibility of Tyr409 flanked by two glycine residues. This is also the first example of a siderophore-conjugated triazolone-linked monocarbam complexed with any PBP. Energetic analysis of tightly and loosely held computed hydration sites indicates protein desolvation effects contribute significantly to PBP3 binding, and analysis of hydration site energies allows rank ordering of the second-order acylation rate constants. Taken together, these structural, biochemical, and computational studies provide a molecular basis for recognition of P. aeruginosa PBP3 and open avenues for future design of inhibitors of this class of PBPs.

59 BASIC BIOLOGICAL SCIENCES↗

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗

Squeezed bispectrum in the δ N formalism: local observer effect in field space

The prospects of future galaxy surveys for non-Gaussianity measurements call for the development of robust techniques for computing the bispectrum of primordial cosmological perturbations. In this paper, we propose a novel approach to the calculation of the squeezed bispectrum in multiple-field inflation. With use of the δ N formalism, our framework sheds new light on the recently pointed out difference between the squeezed bispectrum for global observers and that for local observers, while allowing one to calculate both. For local observers in particular, the squeezed bispectrum is found to vanish in single-field inflation. Furthermore, our framework allows one to go beyond the near-equilateral ('small hierarchy') limit, and to automatically include intrinsic non-Gaussianities that do not need to be calculated separately. The explicit computational programme of our method is given and illustrated with a few examples.

79 ASTRONOMY AND ASTROPHYSICS↗

The contribution of glacier melt to streamflow

Ongoing and projected future changes in glacier extent and water storage globally have lead to concerns about the implications for water supplies. However, the current magnitude of glacier contributions to river runoff is not well known, nor is the population at risk to future glacier changes. We estimate an upper bound on glacier melt contribution to seasonal streamflow by computing the energy balance of glaciers globally. Melt water quantities are computed as a fraction of total streamflow simulated using a hydrology model and the melt fraction is tracked down the stream network. In general, our estimates of the glacier melt contribution to streamflow are lower than previously published values. Nonetheless, we find that globally an estimated 225 (36) million people live in river basins where maximum seasonal glacier melt contributes at least 10% (25%) of streamflow, mostly in the High Asia region.

Schaner, Neil↗

Power Profile Monitoring and Tracking Evolution of System-Wide HPC Workloads

The power & energy demands of HPC machines have grown significantly. Modern exascale HPC systems require tens of megawatts of combined power for computing resources and cooling facilities at full capacity. The current energy trend is not sustainable for future HPC systems, and there is a need to work toward the energy efficiency aspect of HPC performance. Energy awareness of the HPC applications at the job level is essential for running an efficient HPC system. This work aims to develop a pipeline to provide a production-level system-wide overview of the HPC workloads' power profile while handling evolving workloads exhibiting new power trends. We developed an open-set classification model for HPC jobs based on the properties of power profiles to continuously provide a system-wide holistic view of recently completed jobs. The pipeline helps continuously monitor the job-level power usage pattern of HPC and enables us to capture the new trends in applications' power behavior. We employed a comprehensive set of techniques to generate job-level data, custom-designed feature extraction methods to extract critical features from jobs' power profiles, clustering techniques powered by generative modeling, and open-set classification for identifying job profiles into known classes or an unknown set. With extensive evaluations, we demonstrate the effectiveness of each component in our pipeline. We provide an analysis of the resulting clusters that characterize the power profile landscape of the Summit supercomputer from more than 60K jobs executed in a year. The open-set classification classifies the known data sets into known classes with high accuracy and identifies unknown data noints with over 85% accuracy.

Karimi, Ahmad Maroof↗

SU-E-T-347: Validation of the Condensed History Algorithm of Geant4 Using the Fano Test

Purpose: To validate the condensed history algorithm and physics of the Geant4 Monte Carlo toolkit for simulations of ionization chambers (ICs). This study is the first step to validate Geant4 for calculations of photon beam quality correction factors under the presence of a strong magnetic field for magnetic resonance guided linac system applications. Methods: The electron transport and boundary crossing algorithms of Geant4 version 9.6.p02 were tested under Fano conditions using the Geant4 example/application FanoCavity. User-defined parameters of the condensed history and multiple scattering algorithms were investigated under Fano test conditions for three scattering models (physics lists): G4UrbanMscModel95 (PhysListEmStandard-option3), G4GoudsmitSaundersonMsc (PhysListEmStandard-GS), and G4WentzelVIModel/G4CoulombScattering (PhysListEmStandard-WVI). Simulations were conducted using monoenergetic photon beams, ranging from 0.5 to 7 MeV and emphasizing energies from 0.8 to 3 MeV. Results: The GS and WVI physics lists provided consistent Fano test results (within ±0.5%) for maximum step sizes under 0.01 mm at 1.25 MeV, with improved performance at 3 MeV (within ±0.25%). The option3 physics list provided consistent Fano test results (within ±0.5%) for maximum step sizes above 1 mm. Optimal parameters for the option3 physics list were 10 km maximum step size with default values for other user-defined parameters: 0.2 dRoverRange, 0.01 mm final range, 0.04 range factor, 2.5 geometrical factor, and 1 skin. Simulations using the option3 physics list were ∼70 – 100 times faster compared to GS and WVI under optimal parameters. Conclusion: This work indicated that the option3 physics list passes the Fano test within ±0.5% when using a maximum step size of 10 km for energies suitable for IC calculations in a 6 MV spectrum without extensive computational times. Optimal user-defined parameters using the option3 physics list will be used in future IC simulations to calculate beam quality correction factors under the presence of a magnetic field. Elekta-MD Anderson Research Agreement.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets—from soil and seawater microbiomes—to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon’s abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.

59 BASIC BIOLOGICAL SCIENCES↗

Impurity lattice Monte Carlo for hypernuclei

Abstract We consider the problem of including $$\varLambda $$ Λ hyperons into the ab initio framework of nuclear lattice effective field theory. In order to avoid large sign oscillations in Monte Carlo simulations, we make use of the fact that the number of hyperons is typically small compared to the number of nucleons in the hypernuclei of interest. This allows us to use the impurity lattice Monte Carlo method, where the minority species of fermions in the full nuclear Hamiltonian is integrated out and treated as a worldline in Euclidean projection time. The majority fermions (nucleons) are treated as explicit degrees of freedom, with their mutual interactions described by auxiliary fields. This is the first application of the impurity lattice Monte Carlo method to systems where the majority particles are interacting. Here, we show how the impurity Monte Carlo method can be applied to compute the binding energies of the light hypernuclei. In this exploratory work we use spin-independent nucleon–nucleon and hyperon–nucleon interactions to test the computational power of the method. We find that the computational effort scales approximately linearly in the number of nucleons. The results are very promising for future studies of larger hypernuclear systems using chiral effective field theory and realistic hyperon–nucleon interactions, as well as applications to other quantum many-body systems.

Frame, Dillon↗

Application of Plasma Waveguides to High Energy Accelerators

The eventual success of laser-plasma based acceleration schemes for high-energy particle physics will require the focusing and stable guiding of short intense laser pulses in reproducible plasma channels. For this goal to be realized, many scientific issues need to be addressed. These issues include an understanding of the basic physics of, and an exploration of various schemes for, plasma channel formation. In addition, the coupling of intense laser pulses to these channels and the stable propagation of pulses in the channels require study. Finally, new theoretical and computational tools need to be developed to aid in the design and analysis of experiments and future accelerators. Here we propose a 3-year renewal of our combined theoretical and experimental program on the applications of plasma waveguides to high-energy accelerators. During the past grant period we have made a number of significant advances in the science of laser-plasma based acceleration. We pioneered the development of clustered gases as a new highly efficient medium for plasma channel formation. Our contributions here include theoretical and experimental studies of the physics of cluster ionization, heating, explosion, and channel formation. We have demonstrated for the first time the generation of and guiding in a corrugated plasma waveguide. The fine structure demonstrated in these guides is only possible with cluster jet heating by lasers. The corrugated guide is a slow wave structure operable at arbitrarily high laser intensities, allowing direct laser acceleration, a process we have explored in detail with simulations. The development of these guides opens the possibility of direct laser acceleration, a true miniature analogue of the SLAC RF-based accelerator. Our theoretical studies during this period have also contributed to the further development of the simulation codes, Wake and QuickPIC, which can be used for both laser driven and beam driven plasma based acceleration schemes. We will continue our development of advanced simulation tools by modifying the QuickPIC algorithm to allow for the simulation of plasma particle pick-up by the wake fields. We have also performed extensive simulations of plasma slow wave structures for efficient THz generation by guided laser beams or accelerated electron beams. We will pursue experimental studies of direct laser acceleration, and THz generation by two methods, ponderomotive-induced THz polarization, and THz radiation by laser accelerated electron beams. We also plan to study both conventional and corrugated plasma channels using our new 30 TW in our new lab facilities. We will investigate production of very long hydrogen plasma waveguides (5 cm). We will study guiding at increasing power levels through the onset of laser-induced cavitation (bubble regime) to assess the role played by the preformed channel. Experiments in direct acceleration will be performed, using laser plasma wakefields as the electron injector. Finally, we will use 2-colour ionization of gases as a high frequency THz source (<60 THz) in order for femtosecond measurements of low plasma densities in waveguides and beams.

43 PARTICLE ACCELERATORS↗

Embedded Sensor Development in Metallic Structures for the Transformational Challenge Reactor

The ability to make minimally intrusive measurements of process conditions has tremendous potential for improving system performance and control in applications such as nuclear power generation. Towards this end, emerging and evolving advanced manufacturing methods, such as additive manufacturing, present new opportunities for more seamlessly integrating sensing with structure. This technical report summarizes the progress of work performed to assess the feasibility of embedding commercial off-the-shelf (COTS) sensors in a metallic reactor core using advanced manufacturing methods. The progress of four research and development tasks are documented: 1) A survey of COTS sensors for nuclear applications that are candidates for embedded fabrication, 2) Development of a conceptual framework for investigating the feasibility of sensor embedment, 3) Definition of structural geometries and other characteristics that will represent compelling proof-of-concept, and 4) Preliminary prototyping of embedded sensors. For the purposes of this initial study, nuclear grade K-type thermocouples were selected for investigation of embedment methodologies. This sensor was selected as an initial candidate because it represents one of the simplest sensor configurations that can provide useful process information. A selective laser melting (SLM) additive manufacturing process was used to fabricate structures with complexity representative of the core design of the transformational challenge reactor (TCR) and methods were developed to embed a thermocouple with a complex two-dimensional routing path. There are many challenges associated with embedding sensors during the additive manufacturing process including securing the sensor in the structure, relocating the part in the additive machine if using a “pick and place” sensor placement method, mitigating the potential for powder contamination, optimizing energy deposition parameters to build as closely as possible around the sensor path and improve structural integrity of the part, and tuning energy deposition to mitigate thermally induced warpage of the sensor and part as well as potential for damaging the sensing device. Preliminary results indicate that it is feasible to integrate the sensor while minimally compromising the structural integrity of the part and preserving sensor performance. This first phase of this work focused on developing a workflow for embedding sensors and controlling energy deposition during the additive manufacturing process to better understand the build characteristics around the sensor. Future work will perform more in-depth characterization of prototype parts using X-ray computed tomography and scanning electron microscopy to better understand fabricated structures, performance testing of embedded sensors in high temperature environments, adding new embedded measurement modalities, embedding devices with dissimilar materials in contact with additive powders, and the development of methods for embedding sensors with three-dimensional routing paths.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

LLNL Response to the DOE ASCR RFI, "Stewardship of Software for Scientific and High-Performance Computing"

For decades, Lawrence Livermore National Laboratory (LLNL) has been engaged in significant research, development, and support for software to enable scientific computing and, particularly, the use of high performance computing (HPC) in the NNSA mission space. In particular, the move in the mid-1990’s to simulation as a leading component of stockpile stewardship through the ASCI and the successor ASC programs, as well as the need for reliable data acquisition and control software for the National Ignition Facility, have been important drivers in building expertise in production-quality software development at LLNL. LLNL has also been a leader in the DOE SciDAC FASTMath Institute and the DOE Exascale Computing Project (ECP), both of which have striven to make scientific computing software – in particular, the enabling technologies underpinning simulation capabilities – more widely adopted and sustainable. As such, we believe that our experience can inform the broader goal of software stewardship for scientific and high-performance computing. LLNL strongly supports the formation of a new DOE ASCR program element in software stewardship and sustainment. Historically, DOE ASCR has funded applied mathematics and computer science research that has led to the development of important new capabilities and algorithms that are expressed as artifacts in research software. Such frameworks, libraries, and tools have seldom been directly funded to address the important issues of code maintenance, documentation, robustness, and community building. Software engineering and support have typically been done on the side in support of the ASCR-driven research products. DOE funding priorities have been slow to recognize that good software engineering, the kind that ensures research investments have more adoption and longevity, requires significant resources. Based upon our experiences, we have prepared this response to highlight the concerns and issues we believe to be important as DOE ASCR considers its role in scientific software stewardship. We believe that role is important and will require a significant investment of new funding to legitimately support the technologies past and future DOE ASCR investments have and will produce to facilitate their uptake and adoption in the broader scientific computing community. Following a summary of our involvement in scientific software development, the remainder our response is organized around the nine topics specifically identified in the RFI.

97 MATHEMATICS AND COMPUTING↗

EQSIM: Exascale Predictions of Earthquake Effects on Critical Infrastructure

The great “San Francisco” earthquake of 1906 is one of the most recognized, and sobering, demonstrations of the havoc that can be caused by the sudden and violent movement of Earth’s tectonic plates. The estimated 7.9-magnitude quake and subsequent fires decimated the major metropolis and surrounding areas: buildings turned to ruins, hundreds of thousands of people left homeless, and a death toll exceeding 3,000. Today, as evidenced by the catastrophic 7.8-magnitude earthquake that struck Turkey in February 2023, these events still present a significant danger to life and economic security. To mitigate the potential devastation of future earthquakes and better prepare for these inevitable events, researchers are turning to high-performance computers to simulate the underlying geophysical processes and accurately quantify associated risks to critical infrastructure.

42 ENGINEERING↗

New Los Alamos Opacity Calculations

In 2015 Los Alamos National Laboratory (LANL) released a new set of OPLIB opacity tables for the elements hydrogen through zinc. The new LANL opacities are publicly available via our website and are already in use by the astrophysics community. In this contribution, we discuss the extension of our opacity calculations to elements beyond zinc. Such calculations are motivated by potential industrial applications (for elements such as Sn) as well as available experimental data with which to compare our calculations (for Ge and Br). After a short outline of our method for computing opacities for these elements, we make comparisons to available experimental data and find good agreement. Future plans are briefly discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗

Constraints on methane emissions in North America from future geostationary remote-sensing measurements

The success of future geostationary (GEO) satellite observation missions depends on our ability to design instruments that address their key scientific objectives. Here, an Observation System Simulation Experiment (OSSE) is performed to quantify the constraints on methane (CH 4 ) emissions in North America obtained from shortwave infrared (SWIR), thermal infrared (TIR), and multi-spectral (SWIR+TIR) measurements in geostationary orbit and from future SWIR low-Earth orbit (LEO) measurements. Furthermore, we used an efficient stochastic algorithm to compute the information content of the inverted emissions at high spatial resolution (0.5° × 0.7°) in a variational framework using the GEOS-Chem chemistry-transport model and its adjoint. Our results show that at sub-weekly timescales, SWIR measurements in GEO orbit can constrain about twice as many independent flux patterns than in LEO orbit, with a degree of freedom for signal (DOF) for the inversion of 266 and 115, respectively. Comparisons between TIR GEO and SWIR LEO configurations reveal that poor boundary layer sensitivities for the TIR measurements cannot be compensated for by the high spatiotemporal sampling of a GEO orbit. The benefit of a multi-spectral instrument compared to current SWIR products in a GEO context is shown for sub-weekly timescale constraints, with an increase in the DOF of about 50 % for a 3-day inversion. Our results further suggest that both the SWIR and multi-spectral measurements on GEO orbits could almost fully resolve CH 4 fluxes at a spatial resolution of at least 100 km × 100 km over source hotspots (emissions > 4 × 10 5 kg day -1 ). The sensitivity of the optimized emission scaling factors to typical errors in boundary and initial conditions can reach 30 and 50 % for the SWIR GEO or SWIR LEO configurations, respectively, while it is smaller than 5 % in the case of a multi-spectral GEO system. Our results demonstrate that multi-spectral measurements from a geostationary satellite platform would address the need for higher spatiotemporal constraints on CH 4 emissions while greatly mitigating the impact of inherent uncertainties in source inversion methods on the inferred fluxes.

54 ENVIRONMENTAL SCIENCES↗

US ATLAS and US CMS HPC and Cloud Blueprint

The Large Hadron Collider (LHC) at CERN houses two general purpose detectors - ATLAS and CMS - which conduct physics programs over multi-year runs to generate increasingly precise and extensive datasets. The efforts of the CMS and ATLAS collaborations lead to the discovery of the Higgs boson, a fundamental particle that gives mass to other particles, representing a monumental achievement in the field of particle physics that was recognized with the awarding of the Nobel Prize in Physics in 2013 to François Englert and Peter Higgs. These collaborations continue to analyze data from the LHC and are preparing for the high luminosity data taking phase at the end of the decade. The computing models of these detectors rely on a distributed processing grid hosted by more than 150 associated universities and laboratories worldwide. However, such new data will require a significant expansion of the existing computing infrastructure. To address this, both collaborations have been working for years on integrating High Performance Computers (HPC) and commercial cloud resources into their infrastructure and continue to assess the potential role of such resources in order to cope with the demands of the new high luminosity era. US ATLAS and US CMS computing management have charged the authors to provide a blueprint document looking at current and possibly future use of HPC and Cloud resources, outlining integration models, possibilities, challenges and costs. The document will address key questions such as the optimal use of resources for the experiments and funding agencies, the main obstacles that need to be overcome for resource adoption, and areas that require more attention.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Extending the subspace hybrid method for eigenvalue problems in reactor physics calculation

This paper presents an innovative hybrid Monte-Carlo-Deterministic method denoted by the SUBSPACE method designed for improving the efficiency of hybrid methods for reactor analysis applications. The SUBSPACE method achieves its high computational efficiency by taking advantage of the existing correlations between desired responses. Recently, significant gains in computational efficiency have been demonstrated using this method for source driven problems. Within this work the mathematical theory behind the SUBSPACE method is introduced and extended to address core wide level k-eigenvalue problems. The method's efficiency is demonstrated based on a three-dimensional quarter-core problem, where responses are sought on the pin cell level. The SUBSPACE method is compared to the FW-CADIS method and is found to be more efficient for the utilized test problem because of the reason that the FW-CADIS method solves a forward eigenvalue problem and an adjoint fixed-source problem while the SUBSPACE method only solves an adjoint fixed-source problem. Based on the favorable results obtained here, we are confident that the applicability of Monte Carlo for large scale reactor analysis could be realized in the near future. (authors)

97 MATHEMATICS AND COMPUTING↗

Inverse Design of Plasma Metamaterial Devices for Optical Computing

We apply inverse-design methods to produce two-dimensional plasma metamaterial (PMM) devices. Backpropagated finite-difference frequency-domain (FDFD) simulations are used to design waveguides and demultiplexers operating under both TE and TM modes. Demultiplexing and waveguiding are demonstrated for devices composed of plasma elements with reasonable plasma densities of approximately 7 GHz, allowing for future in situ training and experimental realization of these designs. We also explore the possible applicability of PMMs to nonlinear boolean operations for use in optical computing. Functionally complete logical connectives (or and and) are achieved in the TM mode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗