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At least 829 records · Page 46

Encoder–decoder neural network for solving the nonlinear Fokker–Planck–Landau collision operator in XGC

An encoder–decoder neural network has been used to examine the possibility for acceleration of a partial integro-differential equation, the Fokker–Planck–Landau collision operator. This is part of the governing equation in the massively parallel particle-in-cell code XGC, which is used to study turbulence in fusion energy devices. The neural network emphasizes physics-inspired learning, where it is taught to respect physical conservation constraints of the collision operator by including them in the training loss, along with the ℓ 2 loss. In particular, network architectures used for the computer vision task of semantic segmentation have been used for training. A penalization method is used to enforce the ‘soft’ constraints of the system and integrate error in the conservation properties into the loss function. During training, quantities representing the particle density, momentum and energy for all species of the system are calculated at each configuration vertex, mirroring the procedure in XGC. This simple training has produced a median relative loss, across configuration space, of the order of 10 –4 , which is low enough if the error is of random nature, but not if it is of drift nature in time steps. The run time for the current Picard iterative solver of the operator is O(n 2 ), where n is the number of plasma species. As the XGC1 code begins to attack problems including a larger number of species, the collision operator will become expensive computationally, making the neural network solver even more important, especially since its training only scales as O(n). Here, a wide enough range of collisionality has been considered in the training data to ensure the full domain of collision physics is captured. An advanced technique to decrease the losses further will be subject of a subsequent report. Eventual work will include expansion of the network to include multiple plasma species.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Implementation of higher-order velocity mapping between marker particles and grid in the particle-in-cell code XGC

The global total-f gyrokinetic particle-in-cell code XGC, used to study transport in magnetic fusion plasmas or to couple with a core gyrokinetic code while functioning as an edge gyrokinetic code, implements a five-dimensional continuum grid to perform the dissipative operations, such as plasma collisions, or to exchange the particle distribution function information with a core code. To transfer the distribution function between marker particles and a rectangular two-dimensional velocity-space grid, XGC employs a bilinear mapping. The conservation of particle density and momentum is accurate enough in this bilinear operation, but the error in the particle energy conservation can become undesirably large and cause non-negligible numerical heating in a steep edge pedestal. In the present work we update XGC to use a novel mapping technique, based on the calculation of a pseudo-inverse, to exactly preserve moments up to the order of the discretization space. Here we describe the details of the implementation and we demonstrate the reduced interpolation error for a tokamak test plasma using first- and second-order elements with the pseudo-inverse method and comparing with the bilinear mapping.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Geometric electrostatic particle-in-cell algorithm on unstructured meshes

We present a geometric particle-in-cell (PIC) algorithm on unstructured meshes for studying electrostatic perturbations with frequency lower than electron gyrofrequency in magnetized plasmas. In this method, ions are treated as fully kinetic particles and electrons are described by the adiabatic response. The PIC method is derived from a discrete variational principle on unstructured meshes. To preserve the geometric structure of the system, the discrete variational principle requires that the electric field is interpolated using Whitney 1-forms, the charge is deposited using Whitney 0-forms and the electric field is computed by discrete exterior calculus. The algorithm has been applied to study the ion Bernstein wave (IBW) in two-dimensional magnetized plasmas. The simulated dispersion relations of the IBW in a rectangular region agree well with theoretical results. In a two-dimensional circular region with fixed boundary condition, the spectrum and eigenmode structures of the IBW are obtained from simulations. We compare the energy conservation property of the geometric PIC algorithm derived from the discrete variational principle with that of previous PIC methods on unstructured meshes. The comparison shows that the new PIC algorithm significantly improves the energy conservation property.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An unconditionally stable, time-implicit algorithm for solving the one-dimensional Vlasov–Poisson system

The development of an implicit, unconditionally stable, numerical method for solving the Vlasov–Poisson system in one dimension using a phase-space grid is presented. The algorithm uses the Crank–Nicolson discretization scheme and operator splitting allowing for direct solution of the finite difference equations. This method exactly conserves particle number, enstrophy and momentum. A variant of the algorithm which does not use splitting also exactly conserves energy but requires the use of iterative solvers. This algorithm has no dissipation and thus fine-scale variations can lead to oscillations and the production of negative values of the distribution function. We find that overall, the effects of negative values of the distribution function are relatively benign. We consider a variety of test cases that have been used extensively in the literature where numerical results can be compared with analytical solutions or growth rates. We examine higher-order differencing and construct higher-order temporal updates using standard composition methods.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Verifying raytracing/Fokker–Planck lower-hybrid current drive predictions with self-consistent full-wave/Fokker–Planck simulations

Raytracing/Fokker–Planck (FP) simulations used to model lower-hybrid current drive (LHCD) often fail to reproduce experimental results, particularly when LHCD is weakly damped. A proposed reason for this discrepancy is the lack of ‘full-wave’ effects, such as diffraction and interference, in raytracing simulations and the breakdown of the raytracing approximation. Previous studies of LHCD using non-Maxwellian full-wave/FP simulations have been performed, but these simulations were not self-consistent and enforced power conservation between the FP and full-wave code using a numerical rescaling factor. Here, we have created a fully self-consistent full-wave/FP model for LHCD that is automatically power conserving. This was accomplished by coupling an overhauled version of the non-Maxwellian TORLH full-wave solver and the CQL3D FP code using the Integrated Plasma Simulator. We performed converged full-wave/FP simulations of Alcator C-Mod discharges and compared them with raytracing. We found that excellent agreement in the power deposition profiles from raytracing and TORLH could be obtained, however, TORLH had somewhat lower current drive efficiency and broader power deposition profiles in some cases. This discrepancy appears to be a result of numerical limitations present in the TORLH model and a small amount of diffractional broadening of the TORLH wave spectrum. Our results suggest full-wave simulation of LHCD is likely not necessary as diffraction and interference represented only a small correction that could not account for the differences between simulations and experiment.

Physics↗

The gyrokinetic field invariant and electromagnetic temperature-gradient instabilities in ‘good-curvature’ plasmas

Curvature-driven instabilities are ubiquitous in magnetised fusion plasmas. By analysing the conservation laws of the gyrokinetic system of equations, we demonstrate that the well-known spatial localisation of these instabilities to regions of ‘bad magnetic curvature’ can be explained using the conservation law for a sign-indefinite quadratic quantity that we call the gyrokinetic field invariant. Its evolution equation allows us to define the local effective magnetic curvature whose sign demarcates the regions of ‘good’ and ‘bad’ curvature, which, under some additional simplifying assumptions, can be shown to correspond to the inboard (high-field) and outboard (low-field) sides of a tokamak plasma, respectively. We find that, given some reasonable assumptions, electrostatic curvature-driven modes are always localised to the regions of bad magnetic curvature, regardless of the specific character of the instability. More importantly, we also deduce that any mode that is unstable in the region of good magnetic curvature must be electromagnetic in nature. As a concrete example, we present the magnetic-drift mode, a novel good-curvature electromagnetic instability, and compare its properties with the well-known electron-temperature-gradient instability. Finally, we discuss the relevance of the magnetic drift mode for high-β fusion plasmas, and in particular its relationship with microtearing modes.

fusion plasma↗

Confinement performance predictions for a high field axisymmetric tandem mirror

This paper presents a Hammir tandem mirror confinement performance analysis based on Realta Fusion’s first-of-a-kind model for axisymmetric magnetic mirror fusion performance. This model uses an integrated end plug simulation model including, heating, equilibrium and transport combined with a new formulation of the plasma operation contours (POPCONs) technique for the tandem mirror central cell. Using this model in concert with machine learning optimization techniques, it is shown that an end plug utilizing high temperature superconducting magnets and modern neutral beams enables a classical tandem mirror pilot plant producing a fusion gain Q > 5. The approach here represents an important advance in tandem mirror design. The high-fidelity end plug model enables calculations of heating and transport in the highly non-Maxwellian end plug to be made more accurately. The detailed end plug modelling performed in this work has highlighted the importance of classical radial transport and neutral beam absorption efficiency on end plug viability. The central cell POPCON technique allows consideration of a wide range of parameters in the relatively simple near-Maxwellian central cell, facilitating the selection of more optimal central cell plasmas. These advances make it possible to find more conservative classical tandem mirror fusion pilot plant operating points with lower temperatures, neutral beam energies and end plug performance requirements than designs in the literature. Despite being more conservative, it is shown that these operating points have sufficient confinement performance to serve as the basis of a viable fusion pilot plant provided that they can be stabilized against magnetohydrodynamic and trapped particle modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development of Steady-State and Dynamic Mass and Energy Constrained Neural Networks for Distributed Chemical Systems Using Noisy Transient Data

The paper presents the development of algorithms for mass and energy constrained neural network models that can exactly conserve the overall mass and energy of distributed chemical process systems, even though the noisy transient data used for optimal model training violate the same. In contrast to approximately satisfying mass and energy balance constraints of a system by soft penalization of objective function, algorithms have been developed for solving equality-constrained nonlinear optimization problems, thus providing the guarantee of exactly satisfying the system mass and energy conservation laws. For developing dynamic mass-energy constrained network models for distributed systems, hybrid series and parallel dynamic-static neural networks have been leveraged. The developed algorithms for solving both the training and forward problems are validated using both steady-state and dynamic data in the presence of various noise characteristics. The developed data-driven algorithms are flexible to exactly satisfy mass and energy balance constraints for dynamic chemical processes if the system holdup information is available. The proposed network structures and algorithms are applied to the development of data-driven lumped and distributed models of an adiabatic superheater/reheater system, a nonisothermal continuous stirred tank reactor, as well as an electrically heated plug-flow reactor system where one form of energy gets transformed to another. It has been observed that the mass-energy constrained neural networks yield a root mean squared error of <1% with respect to the system truth for the case studies evaluated in this work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent Advances in Cladding Material Extraction from Fuels in Nuclear Fuel Cycles

An improved recycling and recovery process for the cladding material from spent nuclear fuels is very important toward confirming nuclear energy to support ongoing sustainable development of nuclear management by reducing waste and conserving resources. Nuclear spent fuel cladding materials such as zirconium alloys have economic values and can be recovered, and their recovery eliminates problems in waste disposal and conserves valuable resources. Over 110 published reports and journal articles are reviewed and summarized herein, with a main focus on documenting recovery techniques used to recover cladding materials from spent nuclear fuel and recent developments. Several recovery techniques which are used at present times, such as mechanical separation, chemical dissolution, and hydrometallurgical processes have been covered with examples and discussions. Difficulties within the recovery process are also discussed, and most probable areas for future research in improving efficiency and sustainability of recovering cladding material are identified and discussed at the end. Here, this review could be an important document to the field of spent nuclear fuel reprocessing, recovering valuables and thereby offering guidance on how to effectively manage, safely handle, and reduce nuclear waste. In addition to reducing the volume and radiotoxicity of high-level waste, this review also highlights the potential economic benefit of recovering zirconium from spent fuel cladding by relating typical zirconium metal prices to the mass of cladding per tonne of spent fuel, illustrating that the recoverable material value is non-negligible compared with back-end fuel-cycle costs.

Mondal, Kunal [Oak Ridge National Laboratory (ORNL↗

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗

Parameterizing Perennial Bioenergy Crops in Version 5 of the Community Land Model Based on Site‐Level Observations in the Central Midwestern United States

Abstract With projected expansion of biofuel production at a global scale, there is a pressing need to develop adequate representation of bioenergy crops in land surface models to help effectively quantify the biogeophysical and biogeochemical effects of its associated land use changes. This study implements two new perennial bioenergy crops, Miscanthus and switchgrass, into the Community Land Model Version 5 based on site‐level observations from the midwestern United States by modifying parameters associated with photosynthesis, phenology, allocation, decomposition, and carbon cost of nitrogen uptake and integrating concomitantly land management practices. Sensitivity analyses indicate that carbon and energy fluxes of the perennial crops are most sensitive to photosynthesis and phenology parameters. Validation of simulated fluxes against site‐level measurements demonstrates that the model is capable of capturing the overall patterns of energy and carbon fluxes, as well as physiological transitions from leaf emergence to senescence. Compared to annual crops, perennial crops feature longer growing season, greater leaf areas, and higher productivity, leading to increased transpiration, lower annual runoff, and larger carbon uptake. The model simulations suggest that with higher CO 2 assimilation rates and lower demands for nutrients and water, high‐yielding perennial crops are promising alternatives of bioenergy feedstocks compared to traditional annual crops not only for mitigating climate change but also for environmental conservation purposes by reducing fertilizer application and therefore alleviating surface‐ and ground‐water contaminations. Although the local‐scale simulations shed light on potential benefits of using perennial grasses as bioenergy feedstocks, quantifying consequences of their plantations at larger scales warrants additional investigation.

Cheng, Yanyan↗

Assessing Adaptive Irrigation Impacts on Water Scarcity in Nonstationary Environments—A Multi‐Agent Reinforcement Learning Approach

Abstract One major challenge in water resource management is to balance the uncertain and nonstationary water demands and supplies caused by the changing anthropogenic and hydroclimate conditions. To address this issue, we developed a reinforcement learning agent‐based modeling (RL‐ABM) framework where agents (agriculture water users) are able to learn and adjust water demands based on their interactions with the water systems. The intelligent agents are created by a reinforcement learning algorithm adapted from the Q‐learning algorithm. We illustrated this framework in a case study where the RL‐ABM is two‐way coupled with the Colorado River Simulation System (CRSS), a long‐term planning model used for the administration of the Colorado River Basin, for assessing agriculture water uses impacts on water scarcity. Seventy‐eight intelligent agents are simulated, which can be grouped into three categories based on their parameter values: the “aggressive” (swift actions; low regrets), the “forward‐looking conservative” (mild actions; high regrets; fast learning), and the “myopic conservative” (mild actions; median regrets; slow learning). The ABM‐CRSS results showed that the major reservoirs in the Upper Colorado Basin might experience more frequent water shortages due to the increasing water uses compared to the original CRSS results. If the drought continues, the case study also demonstrates that agents can learn and adjust their demands.

Hung, Fengwei↗

Verifying Ray Tracing Amplitude Methods for Global Magnetospheric Modeling

Abstract Ray tracing is a commonly used method for modeling the propagation of electromagnetic waves in Earth's magnetosphere. To apply ray tracing results to global models of wave‐particle interaction such as energetic electron scattering, it is useful to map the discrete rays to a volume filling mesh. However, some methods have inherent losses of energy from the wave source, or do not account for the full range of wave properties within a sample volume. We have developed and tested a 3D magnetospheric ray tracing code “MESHRAY” which resolves these issues. MESHRAY uses the conservation of Poynting flux through ray triplets with finite volume to determine the local field amplitudes. Electromagnetic wave energy density from all ray data points is mapped to a mesh and verified against the wave source power for energy conservation varying time step length, number of rays, and total time steps. We find that the method is self‐consistent and numerically robust. We further investigate whether the neglect of phase information and superposition has a significant impact on the accuracy of mapping wave intensity to a mesh. We find excellent agreement between the analytic solution for waves emitted by a line source in a plane‐stratified medium and an equivalent ray tracing solution. When phase information is excluded, ray tracing reproduces an average amplitude spread over regions of coherent constructive and destructive interference. This may be an important consideration for interpolating ray tracing results of longer wavelength waves such as magnetosonic, electromagnetic ion cyclotron, or ULF waves.

79 ASTRONOMY AND ASTROPHYSICS↗

Using Convex Optimization to Efficiently Apportion Tracer and Pollutant Sources From Point Concentration Observations

Abstract Rivers transport elements, minerals, chemicals, and pollutants produced in their upstream basins. A sample from a river is a mixture of all of its upstream sources, making it challenging to pinpoint the contribution from each individual source. Here, we show how a nested sample design and convex optimization can be used to efficiently unmix downstream samples of a well‐mixed, conservative tracer in a steady state system into the contributions of their upstream sources. Our approach is significantly faster than previous methods. We represent the river's sub‐catchments, defined by sampling sites, using a directed acyclic graph. This graph is used to build a convex optimization problem which, thanks to its convexity, can be quickly solved to global optimality—in under a second on desktop hardware for data sets of ∼100 samples or fewer. Uncertainties in the upstream predictions can be generated using Monte Carlo resampling. We provide an open‐source implementation of this approach in Python. The inputs required are straightforward: a table containing sample locations and observed tracer concentrations, along with a D8 flow‐direction raster map. As a case study, we use this method to map the elemental geochemistry of sediment sources for rivers draining the Cairngorms mountains, UK. This method could be extended to non‐conservative and non‐steady state tracers. We also show, theoretically, how multiple tracers could be simultaneously inverted to recover upstream run‐off or erosion rates as well as source concentrations. Overall, this approach can provide valuable insights to researchers in various fields, including water quality, geochemical exploration, geochemistry, hydrology, and wastewater epidemiology.

Barnes, Richard↗

Blue Carbon Stocks Along the Pacific Coast of North America Are Mainly Driven by Local Rather Than Regional Factors

Coastal wetlands, including seagrass meadows, emergent marshes, mangroves, and temperate tidal swamps, can efficiently sequester and store large quantities of sediment organic carbon (SOC). However, SOC stocks may vary by ecosystem type and along environmental or climate gradients at different scales. Quantifying such variability is needed to improve blue carbon accounting, conservation effectiveness, and restoration planning. We analyzed SOC stocks in 1,284 sediment cores along >6,500 km of the Pacific coast of North America that included large environmental gradients and multiple ecosystem types. Tidal wetlands with woody vegetation (mangroves and swamps) had the highest mean stocks to 1 m depth (357 and 355 Mg ha −1 , respectively), 45% higher than marshes (245 Mg ha −1 ), and more than 500% higher than seagrass (68 Mg ha −1 ). Unvegetated tideflats, though not often considered a blue carbon ecosystem, had noteworthy stocks (148 Mg ha −1 ). Stocks increased with tidal elevation and with fine (<63 μm) sediment content in several ecosystems. Stocks also varied by dominant plant species within individual ecosystem types. At larger scales, marsh stocks were lowest in the Sonoran Desert region of Mexico, and swamp stocks differed among climate zones; otherwise stocks showed little correlation with ecoregion or latitude. More variability in SOC occurred among ecosystem types, and at smaller spatial scales (such as individual estuaries), than across regional climate gradients. These patterns can inform coastal conservation and restoration priorities across scales where preserving stored carbon and enhancing sequestration helps avert greenhouse gas emissions and maintains other vital ecosystem services.

emergent marsh↗

X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release

Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na+/substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na + binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.

Science & Technology - Other Topics↗

Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life

Abstract Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S 0 )-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S 0 reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.

59 BASIC BIOLOGICAL SCIENCES↗