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Advances in 3D transient plasma dynamics and control through MHD and hybrid fluid-kinetic simulations with JOREK

Transient phenomena and their control are of high relevance in magnetic confinement fusion plasmas to guarantee a stable and safe plasma operation. Interpretative simulations can maximize the insights gained from experiments on present machines and predictive simulations can help in the preparation of design, mitigation techniques and operational scenarios for future devices. In this article, we provide an overview of recent advances and novel scientific results obtained with the 3D non-linear hybrid fluid-kinetic code JOREK, covering physics of plasma transients from the core to the scrape-off layer (SOL) both for tokamak and stellarator devices. Substantial progress was made in the physics understanding, model validation with experiments and experiment interpretation, thus, giving confidence for predictions to devices like DTT, ITER and DEMO. The topics addressed comprise a wide range: the edge physics of new operation scenarios and edge localized mode suppression; major disruptions with a focus on runaway electrons and vertical displacement events as well as disruption mitigation by shattered pellet injection; the physics mechanisms and operational limits of the flux pumping regime for sawtooth control; MHD limits of stellarators and work towards incorporating advanced edge/SOL/exhaust dynamics; continuing improvements of the code for more efficient hybrid simulations on conventional and accelerated high performance computing architectures.

disruptions↗

Integrated operation scenarios: Chapter 6 of the special issue: on the path to tokamak burning plasma operation

Here we report the progress of the development and optimization of operational scenarios for ITER and beyond, focusing upon baseline, hybrid, and steady-state scenarios since 2007. This includes advancements made by the integrated operation scenarios (IOS) topical group of the international tokamak physical activity as well as contributions from the broader tokamak community. The key area of research involves developing IOSs that encompass tokamak physics, operation, and technology by utilizing integrated modeling and control strategies. This requires leveraging available actuators to simultaneously control plasma position and shape, MHD activities that could lead to disruptions, transport, plasma-wall interaction and power exhaust, fuel cycle, fusion burn, and tritium breeding. The control extends from the plasma initiation phase, through the current ramp-up, flattop, start and end of the fusion burn, and current ramp-down, to the plasma termination phase. A review of the currently developed scenarios and modeling is provided in terms of (i) optimizing plasma initiation in ITER, (ii) preparing for the low activation phase to fully commission all tokamak systems and establish and validate physics and scenario conditions in preparation for deuterim-tritium (DT) operation, (iii) developing and preparing baseline and hybrid scenarios to demonstrate the feasibility of achieving these regimes within device constraints, (iv) exploring steady-state scenarios to meet ITER’s steady-state goals, (v) evaluating and preparing actuators for ITER, (vi) developing integrated control solutions using shared actuators. The most notable achievements include; (i) the development of ITER demonstration discharges by matching various dimensionless parameters, (ii) the development of scenarios in an ITER-like tungsten environment and DT operation, and (iii) the development of scenarios in superconducting tokamaks, enabling long-pulse operations with similar coil constraints to ITER. Along with these significant achievements, outstanding issues and recommendations for further research and development are provided. Importantly, this study goes beyond simply updating the ITER Physics Basis; it carries profound implications for the broader field of burning plasma research, offering valuable insights and guidance for the next generation of fusion experiments and devices.

ITER↗

Rapid and efficient in planta genome editing in sorghum using foxtail mosaic virus‐mediated sgRNA delivery

SUMMARY The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single‐guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR‐associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase ( PDS ), Magnesium‐chelatase subunit I ( MgCh ), 4‐hydroxy‐3‐methylbut‐2‐enyl diphosphate reductase , orthologs of maize Lemon white1 ( Lw1 ) or GFP . The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

54 ENVIRONMENTAL SCIENCES↗

Data for Rapid and Efficient in planta Genome Editing in Sorghum Using Foxtail Mosaic Virus-mediated sgRNA Delivery

The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single-guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR-associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase (PDS), Magnesium-chelatase subunit I (MgCh), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, orthologs of maize Lemon white1 (Lw1) or GFP. The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

Feedstock Production↗

Data for "Viral-mediated Delivery of Morphogenic Regulators Enables Leaf Transformation in Sorghum bicolor (L.)"

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom ( Bbm ), Wuschel2 ( Wus2 ), Wuschel-like homeobox protein 2a ( Wox2a ) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

gene editing↗

All the light we cannot see: Climate manipulations leave short and long‐term imprints in spectral reflectance of trees

Abstract Anthropogenic climate change, particularly changes in temperature and precipitation, affects plants in multiple ways. Because plants respond dynamically to stress and acclimate to changes in growing conditions, diagnosing quantitative plant‐environment relationships is a major challenge. One approach to this problem is to quantify leaf responses using spectral reflectance, which provides rapid, inexpensive, and nondestructive measurements that capture a wealth of information about genotype as well as phenotypic responses to the environment. However, it is unclear how warming and drought affect spectra. To address this gap, we used an open‐air field experiment that manipulates temperature and rainfall in 36 plots at two sites in the boreal‐temperate ecotone of northern Minnesota, USA. We collected leaf spectral reflectance (400–2400 nm) at the peak of the growing season for three consecutive years on juveniles (two to six years old) of five tree species planted within the experiment. We hypothesized that these mid‐season measurements of spectral reflectance capture a snapshot of the leaf phenotype encompassing a suite of physiological, structural, and biochemical responses to both long‐ and short‐time scale environmental conditions. We show that the imprint of environmental conditions experienced by plants hours to weeks before spectral measurements is linked to regions in the spectrum associated with stress, namely the water absorption regions of the near‐infrared and short‐wave infrared. In contrast, the environmental conditions plants experience during leaf development leave lasting imprints on the spectral profiles of leaves, attributable to leaf structure and chemistry (e.g., pigment content and associated ratios). Our analyses show that after accounting for baseline species spectral differences, spectral responses to the environment do not differ among the species. This suggests that building a general framework for understanding forest responses to climate change through spectral metrics may be possible, likely having broader implications if the common responses among species detected here represent a widespread phenomenon. Consequently, these results demonstrate that examining the entire spectrum of leaf reflectance for environmental imprints in contrast to single features (e.g., indices and traits) improves inferences about plant‐environment relationships, which is particularly important in times of unprecedented climate change.

Stefanski, Artur [Department of Forest Resources U↗

Process intensification approach to enhancing heat and mass transfer: Radio frequency (RF) assisted drying of paper and board

Conventional multi-cylinder drying of paper and board typically relies on both conductive drying from steam-heated cylinders and convective drying, where heated air flows over the paper web surface. Conduction primarily contributes to heat transfer, while convection is the main driver of mass transfer. However, conventional drying systems are heavily dependent on steam, usually powered by fossil fuels, and are often energy-inefficient with high levels of waste. Additionally, these surface-driven processes result in a lower percentage of energy absorption compared to the energy supplied, leading to significant energy losses. To improve this long-standing process, an experimental system was developed to investigate a process intensification approach involving the integration of Radio Frequency (RF) heating, a volumetric electromagnetic technology, alongside traditional conduction and convection drying methods. This study also emphasizes the use of sensors to continuously monitor key parameters such as moisture content, supply system temperatures, sample temperatures, air flows, and drying rates in real-time. The effect of RF as an auxiliary energy source in localized environments at varying moisture levels was explored to optimize industrial drying systems, quantify potential improvements, and provide insights for future studies. Experimental results from trials combining RF with convection and with the base case alternating conduction-convection drying processes are presented. It is shown that RF is a viable process intensification approach for paper drying improving the drying rate and energy intensity at higher moisture contents. These findings offer valuable insights for process intensification and contribute to the process development, modeling, and simulation of advanced paper drying techniques.

42 ENGINEERING↗

Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in Brassica napus

SUMMARY Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects of climate change on crop yields, we need to develop varieties that are more tolerant to water‐limited conditions. We aimed to determine how diverse crop types (winter/spring oilseed, tuberous, and leafy) of the allopolyploid Brassica napus , a species that contains the economically important rapeseed oilseed crop, respond to prolonged water limitation. We exposed plants to an 80% reduction in water and assessed growth and color on a high‐throughput phenotyping system over 4 weeks and ended the experiment with tissue collection for a time course transcriptomic study. We found an overall reduction in growth across cultivars but to varying degrees. Diel transcriptome analyses revealed significant accession‐specific changes in time‐of‐day regulation of photosynthesis, carbohydrate metabolism, and sulfur metabolism. Interestingly, there was extensive variation in which homoeologs from the two parental subgenomes responded to water limitation across crop types that could be due to differences in regulatory regions in these allopolyploid lines. Follow‐up experiments on select cultivars confirmed that plants maintained photosynthetic health during the prolonged water limitation while slowing growth. In two cultivars examined, we found significant time of day changes in levels of glucosinolates, sulfur‐ and nitrogen ‐rich specialized metabolites, consistent with the diel transcriptomic responses. These results suggest that these lines are adjusting their sulfur and nitrogen stores under water‐limited conditions through distinct time of day regulation.

Ricono, Angela [University of Minnesota St. Paul M↗

Validation of 3D MHD simulations of Ne/D 2 mixed shattered pellet injection in JET

Nonlinear 3D magnetohydrodynamic (MHD) modeling of shattered pellet injection (SPI) in JET tokamak plasmas is performed with the JOREK code. The study focuses on the validation of simulation result with respect to experimental observations, addressing in particular figures of merit for the efficiency of the SPI, as a technique to mitigate thermal loads by injecting radiative impurities like neon during the thermal quench (TQ) phase of disruptions. A set of JET pulses with neon/deuterium atomic mixture ratio in the shattered pellet varying from 10% to 100% provides the experimental data to be compared with. Simulations using different models for the ablation of solid fragments and the radiation of neon impurities are considered. Synthetic diagnostics are employed for a direct quantitative comparison with key JET diagnostic systems providing in particular radiation, electron temperature and density, and magnetic measurements. 3D radiation structures from MHD simulations are analyzed to estimate the toroidal asymmetry of radiation, which is difficult to measure in JET due to the presence of only two toroidally displaced multi-channel bolometry systems. JOREK simulations show that, before the TQ, the bulk of the radiation is concentrated in a toroidal region enclosing the radiating fragments that is missed by both multi-channel bolometers, suggesting a possible underestimation of the total radiation by such diagnostic systems in the pre-TQ phase. On the other hand, JOREK predicts that during the TQ the radiation becomes more toroidally symmetric, with positive implications for the heat load to plasma facing components.

JOREK↗

Saturation of fishbone instability through zonal flows driven by energetic particle transport in tokamak plasmas

Gyrokinetic and kinetic-MHD simulations are performed for the fishbone instability in the DIII-D discharge #178631, chosen for validation of first-principles simulations to predict the energetic particle (EP) transport in an ITER prefusion baseline scenario. Fishbone modes are found to generate zonal flows, which dominate the fishbone saturation. The underlying mechanisms of the two-way fishbone-zonal flows nonlinear interplay are discussed in details. Numerical and analytical analyses identify the fishbone-induced EP redistribution as the dominant generation mechanism for zonal flows. The zonal flows modify the nonlinear dynamics of phase space zonal structures, which reduces the amount of EPs able to resonate with the mode, leading to an early fishbone saturation. Simulation results including zonal flows agree quantitatively with DIII-D experimental measurements of the fishbone saturation amplitude and EP transport, supporting this novel saturation mechanism by self- generated zonal flows. Moreover, the wave-particle mode-locking mechanism is shown to determine quantitatively the fishbone frequency down-chirping, as evident in GTC simulation results in agreement with predictions from analytical theory. Finally, the
fishbone-induced zonal flows are possibly responsible for the formation of an ion-ITB in the DIII-D discharge. Based on the low EP transport and the large zonal flow shearing rates associated with the fishbone instability in gyrokinetic simulations of the ITER scenario, it is conjectured that high performance scenarios could be designed in ITER burning plasmas through fishbone-induced ITBs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

59 BASIC BIOLOGICAL SCIENCES↗

In-Field Testing of Components for Feedback and Control of the ITER Disruption Mitigation System

Here, the shattered pellet injection (SPI) method has been chosen as the disruption mitigation system (DMS) for ITER. To protect the device from plasma disruptions that cause damaging heat and electromagnetic loads, SPI is used to inject high-Z material into the plasma. The process of SPI utilizes cryogenic cooling to form solid pellets. Pellets are accelerated down a barrel and into an angled surface, causing the pellet to shatter prior to entering the tokamak chamber. For the DMS to function reliably, the 27 separate shattered pellet injectors planned for ITER must rely on many components to provide accurate feedback data and for control functions. Each component in the DMS is exposed to an elevated background magnetic field depending on its placement and proximity to the plasma chamber. A Helmholtz coil test stand that is operated at Oak Ridge National Laboratory was utilized to test the components in relevant background field levels to assess component performance. This paper details the test design and results for in-field component operation for a variety of components. This list includes the following components: two different network switches for camera connectivity, a VAT fast shutter valve intended to reduce the flow of SPI propellant gas into the torus, a solenoid control valve intended for use in the pellet formation process, pressure/vacuum switches to be used for feedback and control, a printed circuit board piezo pressure sensor to be used to measure breech pressure, and various relays for the high-voltage pulsed power supply used to drive the SPI propellant valve.

Disruption mitigation↗

Introduction and overview: Chapter 1 of the special issue: on the path to tokamak burning plasma operation

The International Tokamak Physics Activity (ITPA) has developed a comprehensive overview of the results of its coordinated R&D activities in fusion physics and diagnostics implemented during the past two decades with the aim of developing an improved physics basis for the operation of tokamak burning plasma experiments. Here, an introduction is presented to key concepts in the physics of burning plasmas in tokamaks, together with an overview of the scope of the principal areas of physics R&D pursued by the ITPA Topical Physics Groups in which the critical issues, major areas of progress and most significant recent results are highlighted. This paper introduces the following collection of articles, which encompass detailed presentations of the progress achieved by the Topical Groups in preparing the physics basis for the operation of tokamak burning plasma experiments expected to come into operation in the 2030s.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Virus-induced gene editing of stomatal regulators in Nicotiana benthamiana enables rapid functional genomics

Virus-induced gene editing (VIGE) holds promise as a rapid and scalable approach for functional genomics in plants. Here, we apply a tobacco rattle virus (TRV)-based single-guide RNA (sgRNA) delivery system to target key regulators of stomatal development in Nicotiana benthamiana using transgenic Cas9-expressing lines. sgRNAs fused to a mobile RNA element and co-delivered with TRV enabled both somatic and heritable genome editing across orthologs of STOMAGEN, EPF2, YODA, and SPEECHLESS. Somatic editing frequencies reached up to 95%, and heritable tetra-allelic mutations were recovered in multiple target genes. Mutants exhibited significant, gene-specific changes in stomatal density, with corresponding effects on leaf temperature indicative of altered evaporative cooling. Additionally, sgRNAs fused to an AmCyan reporter enabled visualization of virus-infected tissues, allowing stomatal phenotyping in edited M0 sectors. This TRV-based platform facilitates functional assessment of genes influencing stomatal patterning and offers a powerful tool for dissecting gene function in a developmentally and physiologically relevant context.

60 APPLIED LIFE SCIENCES↗

Summary of the 5th IAEA technical meeting on fusion data processing, validation and analysis (FDPVA)

The purpose of the 5th International Atomic Energy Agency technical meeting on fusion data processing, validation and analysis (FDPVA) (Ghent University, Ghent, Belgium, 12–15 June 2023) was to provide a platform during which a set of topics relevant to FDPVA were discussed with the view of meeting the needs of next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucial for a knowledge-based understanding of the physical processes governing the dynamics of these plasmas. This paper presents the recent progress and achievements in the domain of plasma diagnostics data analysis and synthetic diagnostics reported at the meeting, including concept description of new devices; fusion databases; integrated data analysis; inverse problems; uncertainty propagation, verification and validation; probabilistic methods and machine learning. The relevant results underline trends observed in the current major fusion confinement devices.

fusion databases↗

Testing of Fusion Machine Components Against Cryogenic Pellet Impacts

Shattered pellet injection (SPI), currently the most effective method of disruption mitigation, is currently implemented on tokamaks worldwide for experimental purposes. Cryogenic pellets are formed and fired into an angled surface before entering the plasma. The impact with the angled surface causes the pellets to fragment into a cloud of particles with the purpose of increasing the surface area for ablation. As pellets traverse guide tubes, depending on design, there is a chance of an off-normal pellet impact. Pellet impacts are also, depending on design, possible in the plasma chamber if not fully ablated and assimilated, or if the fragment plume is not directed in the proper direction. This paper outlines a series of pellet impact tests on various tiles and components relevant to the ITER, JET, and ASDEX Upgrade SPI systems. In conclusion, testing was done to assess the potential damage from pellet and fragment plume impacts through high-speed imaging and the visual inspection of components.

Cryogenic pellets↗

Energetic particle physics: Chapter 7 of the special issue: on the path to tokamak burning plasma operation

We review the physics of energetic particles (EPs) in magnetically confined burning fusion plasmas with focus on advances since the last update of the ITER Physics Basis (Fasoli et al 2007 Nucl. Fusion 47 S264). Topics include basic EP physics, EP generation, diagnostics of EPs and instabilities, the interaction of EPs and thermal plasma instabilities, EP-driven instabilities, energetic particle modes (EPMs), and turbulence, linear and nonlinear stability and simulation of EP-driven instabilities and EPMs, 3D effects, scenario optimization strategies based on EP phase-space control, EPs in reduced field scenarios in ITER before DT, and the physics of runaway electrons. We describe the simulation and modeling of EPs in fusion plasmas, including instability drive and damping as well as EP transport, with a range of approaches from first-principles to reduced models, including gyrokinetic simulations, kinetic-MHD models, gyrofluid models, reduced models, and semi-analytical approaches.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗