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DOE OSTI2022

Operating a full tungsten actively cooled tokamak: overview of WEST first phase of operation

WEST is an MA class superconducting, actively cooled, full tungsten (W) tokamak, designed to operate in long pulses up to 1000 s. In support of ITER operation and DEMO conceptual activities, key missions of WEST are: (i) qualification of high heat flux plasma-facing components in integrating both technological and physics aspects in relevant heat and particle exhaust conditions, particularly for the tungsten monoblocks foreseen in ITER divertor; (ii) integrated steady-state operation at high confinement, with a focus on power exhaust issues. During the phase 1 of operation (2017–2020), a set of actively cooled ITER-grade plasma facing unit prototypes was integrated into the inertially cooled W coated startup lower divertor. Up to 8.8 MW of RF power has been coupled to the plasma and divertor heat flux of up to 6 MW m –2 were reached. Long pulse operation was started, using the upper actively cooled divertor, with a discharge of about 1 min achieved. This paper gives an overview of the results achieved in phase 1. Perspectives for phase 2, operating with the full capability of the device with the complete ITER-grade actively cooled lower divertor, are also described.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Offshore lightning more active and intense in U.S. East Coast wind areas than in North Sea

Fast winds over open areas off the U.S. East Coast resulted in many offshore areas being opened for wind power deployment. Yet lightning is active in this same general area. Lightning damage has been noted as the leading cause of unplanned downtime of wind farms. Here we use lightning observations from 2020–2022 to quantify lightning activity—U.S. East Coast Wind Lease and Wind Planning areas received about 14-times the lightning strokes and about 18-times the energy transfer compared to the operational wind farms in the North Sea. A strong north-south U.S. gradient of lightning exists : low off the coast of Maine, growing higher off Chesapeake Bay, and high south of Virginia. Very high lightning activity also occurs about 250 km from the U.S. coastline, which is 50–100 km outside currently designated Wind Areas but likely relevant to planning floating wind farms further from shore. International lightning protection standards, such as IEC 614200-24, use lightning stroke density and turbine top-height to estimate damage to wind turbines, but it remains unclear if such standards could protect U.S. offshore wind turbines in active lightning areas where the turbine top-height can be 100 m taller than the next tallest object for tens to hundreds of kilometers. This analysis suggests U.S. East Coast offshore wind farms will be subjected to much higher lightning stroke and lightning energy densities than the North Sea counterparts. Preparing the turbine designs in anticipation of these more active U.S. lightning risks will help foster wind’s growing contribution to a reliable and resilient low-carbon energy future.

lightning↗

DOE OSTI2020

Temporal Gating of Synaptic Competition in the Amygdala by Cannabinoid Receptor Activation

Abstract The acquisition of fear memories involves plasticity of the thalamic and cortical pathways to the lateral amygdala (LA). In turn, the maintenance of synaptic plasticity requires the interplay between input-specific synaptic tags and the allocation of plasticity-related proteins. Based on this interplay, weakly activated synapses can express long-lasting forms of synaptic plasticity by cooperating with strongly activated synapses. Increasing the number of activated synapses can shift cooperation to competition. Synaptic cooperation and competition can determine whether two events, separated in time, are associated or whether a particular event is selected for storage. The rules that determine whether synapses cooperate or compete are unknown. We found that synaptic cooperation and competition, in the LA, are determined by the temporal sequence of cortical and thalamic stimulation and that the strength of the synaptic tag is modulated by the endocannabinoid signaling. This modulation is particularly effective in thalamic synapses, supporting a critical role of endocannabinoids in restricting thalamic plasticity. Also, we found that the availability of synaptic proteins is activity-dependent, shifting competition to cooperation. Our data present the first evidence that presynaptic modulation of synaptic activation, by the cannabinoid signaling, functions as a temporal gating mechanism limiting synaptic cooperation and competition.

Madeira, Natália↗

DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗

DOE OSTI2021

On the relation between active-region lifetimes and the autocorrelation function of light curves

ABSTRACT Rotational modulation of stellar light curves due to dark spots encloses information on spot properties and, thus, on magnetic activity. In particular, the decay of the autocorrelation function (ACF) of light curves is presumed to be linked to spot/active-region lifetimes, given that some coherence of the signal is expected throughout their lifetime. In the literature, an exponential decay has been adopted to describe the ACF. Here, we investigate the relation between the ACF and the active-region lifetimes. For this purpose, we produce artificial light curves of rotating spotted stars with different observation, stellar, and spot properties. We find that a linear decay and respective time-scale better represent the ACF than the exponential decay. We therefore adopt a linear decay. The spot/active-region time-scale inferred from the ACF is strongly restricted by the observation length of the light curves. For 1-yr light curves our results are consistent with no correlation between the inferred and the input time-scales. The ACF decay is also significantly affected by differential rotation and spot evolution: strong differential rotation and fast spot evolution contribute to a more severe underestimation of the active-region lifetimes. Nevertheless, in both circumstances the observed time-scale is still correlated with the input lifetimes. Therefore, our analysis suggests that the ACF decay can be used to obtain a lower limit of the active-region lifetimes for relatively long-term observations. However, strategies to avoid or flag targets with fast active-region evolution or displaying stable beating patterns associated with differential rotation should be employed.

Santos, A. R. G. (ORCID:0000000171956542)↗

DOE OSTI2022

Star-spots and magnetism: testing the activity paradigm in the Pleiades and M67

We measure star-spot filling fractions for 240 stars in the Pleiades and M67 open star clusters using APOGEE high-resolution H-band spectra. For this work, we developed a modified spectroscopic pipeline which solves for star-spot filling fraction and star-spot temperature contrast. We exclude binary stars, finding that the large majority of binaries in these clusters (80 per cent) can be identified from Gaia DR3 and APOGEE criteria – important for field star applications. Our data agree well with independent activity proxies, indicating that this technique recovers real star-spot signals. In the Pleiades, filling fractions saturate at a mean level of 0.248 ± 0.005 for active stars with a decline at slower rotation; we present fitting functions as a function of Rossby number. In M67, we recover low mean filling fractions of 0.030 ± 0.008 and 0.003 ± 0.002 for main sequence GK stars and evolved red giants, respectively, confirming that the technique does not produce spurious spot signals in inactive stars. Star-spots also modify the derived spectroscopic effective temperatures and convective overturn time-scales. Effective temperatures for active stars are offset from inactive ones by −109 ± 11 K, in agreement with the Pecaut & Mamajek empirical scale. Star-spot filling fractions at the level measured in active stars changes their inferred overturn time-scale, which biases the derived threshold for saturation. Finally, we identify a population of stars statistically discrepant from mean activity–Rossby relations and present evidence that these are genuine departures from a Rossby scaling. Our technique is applicable to the full APOGEE catalogue, with broad applications to stellar, galactic, and exoplanetary astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Modelling stellar activity with Gaussian process regression networks

ABSTRACT Stellar photospheric activity is known to limit the detection and characterization of extrasolar planets. In particular, the study of Earth-like planets around Sun-like stars requires data analysis methods that can accurately model the stellar activity phenomena affecting radial velocity (RV) measurements. Gaussian Process Regression Networks (GPRNs) offer a principled approach to the analysis of simultaneous time series, combining the structural properties of Bayesian neural networks with the non-parametric flexibility of Gaussian Processes. Using HARPS-N solar spectroscopic observations encompassing three years, we demonstrate that this framework is capable of jointly modelling RV data and traditional stellar activity indicators. Although we consider only the simplest GPRN configuration, we are able to describe the behaviour of solar RV data at least as accurately as previously published methods. We confirm the correlation between the RV and stellar activity time series reaches a maximum at separations of a few days, and find evidence of non-stationary behaviour in the time series, associated with an approaching solar activity minimum.

Camacho, J. D. (ORCID:0000000151215560)↗

DOE OSTI2024

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗

DOE OSTI2020

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation

Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO 4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl–AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl•ATP•(Mn 2+ ) 2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn 2+ . The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Temporal Characterization of Tritium Smear Activities

Tritium collection efficiency varies as a function of smear media. The use of porous smear materials leads to an increase in the measured tritium activity as a function of time when the measurement is performed with liquid scintillation counters. Operational inclusion of the efficiency differences and the time dependence of the tritium smear activity is necessary to preclude inadvertently releasing materials or areas. Thomas Jefferson National Laboratory Radiological Control Department identified a contaminated stainless steel containment vessel that previously housed a target containing more than 37 TBq of tritium. The item was systematically sectioned and surveyed to compare three smear types: water-wetted cotton swabs, water-wetted paper smears, and ethanol-wetted Styrofoam wipes (NUC-Wipes™). The total activity of each section was determined using repeated decontamination. The time dependence of the measured activity was also studied. The measured activity of both paper smears and cotton swabs showed significant time dependence. The cotton swabs also showed significantly reduced collection efficiency. Given the widespread use of both of these media in routine contamination surveys, site operational limits were derived using fitted curves for time dependence and average efficiency results. In conclusion, the use of these more restrictive limits allows for rapid measurement of tritium smears while ensuring regulatory compliance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Competition between energy- and entropy-driven activation in glasses

In simplified models of glasses we clarify the existence of two different kinds of coexisting activated dynamics, with one of the two dominating over the other. One is the energy barrier hopping that is typically used to understand activation, and the other, which we call entropic activation, is driven by the scarcity of convenient directions in phase space. When entropic activation dominates, the height of the energy barriers is no longer the primary factor governing the system's slowdown. In our analysis, dominance of one mechanism over the other depends on temperature and the shape of the density of states. Herein, we also find that at low temperatures a phase transition between the two kinds of activation can occur. Our observations are used to provide a scenario that can harmonize the facilitation and thermodynamic pictures of the slowdown of glasses into a single description.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Vortex Lattices in Active Nematics with Periodic Obstacle Arrays

Here, we numerically model a two-dimensional active nematic confined by a periodic array of fixed obstacles. Even in the passive nematic, the appearance of topological defects is unavoidable due to planar anchoring by the obstacle surfaces. We show that a vortex lattice state emerges as activity is increased, and that this lattice may be tuned from “ferromagnetic” to “antiferromagnetic” by varying the gap size between obstacles. We map the rich variety of states exhibited by the system as a function of distance between obstacles and activity, including a pinned defect state, motile defects, the vortex lattice, and active turbulence. We demonstrate that the flows in the active turbulent phase can be tuned by the presence of obstacles, and explore the effects of a frustrated lattice geometry on the vortex lattice phase.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Decoupled Active and Reactive Power Control without PLL Requirement for Differential Buck Converter

This paper presents a decoupled active and reactive power control for the differential buck converter. This control does not require phase locked loop (PLL) for synchronization. Also, it achieves active and reactive power control in a simple single control loop structure. The differential buck converter has the capability to compensate the double line frequency power ripple without relying on additional hardware. Particularly, the Common Mode (CM) operation is used for active double line frequency power ripple absorption. Whereas, the Differential Mode (DM) operation is used as an active and reactive power exchanging port between the converter and the grid at the point of common coupling (PCC). The motivation behind this paper proposal are: (i) to avoid PLL induced instabilities, especially, when connecting the differential buck converter with weak grid, and (ii) direct active and reactive power control for the differential buck in a single loop control. The theoretical analyses are verified with a 5 kW converter with only 50 μF decoupling capacitor connected to a weak grid.

Khan, Ahmad↗

DOE OSTI2024

Temporal mismatches in flight activity patterns between Pipistrellus kuhlii and Prays oleae in olive farms: Implications for biocontrol services potential

Abstract Biocontrol services are widely recognized to provide key incentives for bat conservation. However, we have virtually no information on whether and how disruptions in bat‐mediated biocontrol services are driven by mismatches between the temporal activity patterns of insectivorous bats and insect pests. We investigated the temporal relationship between the nightly activity patterns of the common pipistrelle bat ( Pipistrellus kuhlii ) and the olive fruit moth ( Prays oleae ). Temporal mismatches between species pairs were estimated as the time difference (expressed as a percentage of the night) at which P. kuhlii and P. oleae reached 50% of their abundance. The study was carried out during spring, summer, and fall between 2017 and 2019 in 60 olive farms representing increasing levels of structural simplification (as a surrogate of agricultural intensification). Olive farms were classified as exhibiting high (i.e. HIGH olive farms; n = 27), intermediate (MID; n = 18), and low (LOW; n = 15) structural complexity. Temporal mismatches between the activity levels of P. kuhlii and P. oleae varied between seasons and types of olive farms, being comparatively lower in summer than in spring and fall. Furthermore, summer was the only season in which temporal mismatches between species pairs differed between types of olive farms, with higher temporal mismatches found in LOW than in HIGH and MID olive farms. Overall, our work demonstrates the existence of temporal mismatches between the nightly activity patterns of P. kuhlii and P. oleae . Furthermore, it demonstrates that the structural simplification of olive farms increases temporal mismatches between species pairs, particularly in summer when bat‐mediated biocontrol services are most needed. Synthesis and applications . Future research should consider mismatches between the temporal activity patterns of insectivorous bats and insect pests. Otherwise, the actual impact of agricultural intensification on bat‐mediated biocontrol services as well as the economic impact of their loss on the agriculture industry might be underestimated. To enhance biocontrol services, we propose increasing the availability of suitable roosting and foraging sites as well as conserving areas of remnant native woodland and scattered hollow‐bearing trees.

Herrera, José M.↗

DOE OSTI2022

Structural basis for the calmodulin-mediated activation of eukaryotic elongation factor 2 kinase

Translation is a tightly regulated process that ensures optimal protein quality and enables adaptation to energy/nutrient availability. The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K), a key regulator of translation, specifically phosphorylates the guanosine triphosphatase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis. eEF-2K activation requires calmodulin binding and autophosphorylation at the primary stimulatory site, T348. Biochemical studies predict a calmodulin-mediated activation mechanism for eEF-2K distinct from other calmodulin-dependent kinases. Here, we resolve the atomic details of this mechanism through a 2.3-Å crystal structure of the heterodimeric complex of calmodulin and the functional core of eEF-2K (eEF-2K TR ). This structure, which represents the activated T348-phosphorylated state of eEF-2K TR , highlights an intimate association of the kinase with the calmodulin C-lobe, creating an “activation spine” that connects its amino-terminal calmodulin-targeting motif to its active site through a conserved regulatory element.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Craspase is a CRISPR RNA-guided, RNA-activated protease

The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.

Science & Technology - Other Topics↗

DOE OSTI2023

Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity

Here, a DNA polymerase with a single mutation and a divalent calcium cofactor catalyzes the synthesis of unnatural N3'→P5' phosphoramidate (NP) bonds to form NP-DNA. However, this template-directed phosphoryl transfer activity remains orders of magnitude slower than native phosphodiester synthesis. Here, we used time-resolved x-ray crystallography to show that NP-DNA synthesis proceeds with a single detectable calcium ion in the active site. Using insights from isotopic and elemental effects, we propose that one-metal-ion electrophilic substrate activation is inferior to the native two-metal-ion mechanism. We found that this deficiency in divalent activation could be ameliorated by trivalent rare earth and post–transition metal cations, substantially enhancing NP-DNA synthesis. Scandium(III), in particular, confers highly specific NP activity with kinetics enhanced by more than 100-fold over calcium(II), yielding NP-DNA strands up to 100 nucleotides in length.

59 BASIC BIOLOGICAL SCIENCES↗