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DOE OSTI2024

No constraint on long-term tropical land carbon-climate feedback uncertainties from interannual variability

Unraveling drivers of the interannual variability of tropical land carbon cycle is critical for understanding land carbon-climate feedbacks. Here we utilize two generations of factorial model experiments to show that interannual variability of tropical land carbon uptake under both present and future climate is consistently dominated by terrestrial water availability variations in Earth system models. The magnitude of this interannual sensitivity of tropical land carbon uptake to water availability variations under future climate shows a large spread across the latest 16 models (2.3 ± 1.5 PgC/yr/Tt H 2 O), which is constrained to 1.3 ± 0.8 PgC/yr/Tt H 2 O using observations and the emergent constraint methodology. However, the long-term tropical land carbon-climate feedback uncertainties in the latest models can no longer be directly constrained by interannual variability compared with previous models, given that additional important processes are not well reflected in interannual variability but could determine long-term land carbon storage. Our results highlight the limited implication of interannual variability for long-term tropical land carbon-climate feedbacks and help isolate remaining uncertainties with respect to water limitations on tropical land carbon sink in Earth system models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Combined Plasmonic Au-nanoparticle and Conducting Metal Oxide High-temperature Optical Sensing with LSTO

<span style="color: rgba(0, 0, 0, 0.79); font-family: "Source Sans Pro", source-sans-pro, museo_sans300, museo-sans, Arial, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">Fiber optic sensor technology offers several advantages for harsh-environment applications. However, the development of optical gas sensing layers that are stable under harsh environmental conditions is an ongoing research challenge. In this work, electronically conducting metal oxide lanthanum-doped strontium titanate (LSTO) films embedded with gold nanoparticles are examined as a sensing layer for application in reducing gas flows at high temperature (600–800 °C). A strong localized surface plasmon resonance (LSPR) based response to hydrogen is demonstrated in the visible region of the spectrum, while a Drude free electron-based response is observed in the near-IR. Characteristics of these responses are studied both on planar glass substrates and on silica fibers. Charge transfer between the oxide film and the gold nanoparticles is explored as a possible mechanism governing the Au LSPR response and is considered in terms of the corresponding properties of the conducting metal oxide-based matrix phase. Principal component analysis is applied to the combined plasmonic and free-carrier based response over a range of temperatures and hydrogen concentrations. It is demonstrated that the combined visible and near-IR response of these films provides improved versatility for multiwavelength interrogation, as well as improved discrimination of important process parameters (concentration and temperature) through application of multivariate analysis techniques.</span>

Wuenschell, Jeffrey K.↗

DOE OSTI2025

Electrosome assembly: Structural insights from high voltage-activated calcium channel (CaV)–chaperone interactions

Ion channels are multicomponent complexes (termed here as“electrosomes”) that conduct the bioelectrical signals required for life. It has been appreciated for decades that assembly is critical for proper channel function, but knowledge of the factors that undergird this important process has been lacking. Although there are now exemplar structures of representatives of most major ion channel classes, there has been no direct structural information to inform how these complicated, multipart complexes are put together or whether they interact with chaperone proteins that aid in their assembly. Recent structural characterization of a complex of the endoplasmic membrane protein complex (EMC) chaperone and a voltage-gated calcium channel (CaV) assembly intermediate comprising the pore-forming CaVα1 and cytoplasmic CaVβ subunits offers the first structural view into the assembly of a member of the largest ion channel class, the voltagegated ion channel (VGIC) superfamily. The structure shows how the EMC remodels the CaVα1/CaVβ complex through a set of rigid body movements for handoff to the extracellular CaVα2δ subunit to complete channel assembly in a process that involves intersubunit coordination of a divalent cation and ordering of CaVα1 elements. These findings set a new framework for deciphering the structural underpinnings of ion channel biogenesis that has implications for understanding channel function, how drugs and disease mutations act, and for investigating how other membrane proteins may engage the ubiquitous EMC chaperone.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Shock-reshock of zirconium to explore the effect of microstructure on the alpha-omega phase transformation

Phase transformations play an important role in the mechanical behavior of materials subjected to extreme loading conditions. A series of shock-reshock experiments were fielded to determine whether the phase transitions in materials are significantly enhanced or inhibited by preexisting microstructural features. Polycrystalline zirconium samples were shock loaded using gas-gun plate impact and soft recovered to examine microstructure using electron backscatter diffraction (EBSD). Drive conditions were varied to study the (hcp) alpha to (hexagonal) omega solidsolid phase transformation. Recovered samples were then subjected to a second shock loading event to determine the change in material behavior as a function of pre-shock microstructure. Crystallography of phase fragments in the final microstructure showed that prior twinning (formed during the shock to a peak stress below the transition threshold) appeared to suppress omega formation/retention after reshock. Conversely, when a material was initially shocked into the omega phase field, retained-omega was not found to have a large impact on subsequent omega formation during reshock. This suggests that nucleation and growth of omega phase are important processes, and the relative activity of nucleation vs. growth processes is modified by a pre-existing substructure. Additionally, orientation relationships reveal a reverse transformation pathway (omega to alpha) dominates the final microstructure, suggesting significant grain growth in the omega phase field is possible even for dynamic timescales.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Platform for probing radiation transport properties of hydrogen at conditions found in the deep interiors of red dwarfs

We describe an experimental concept at the National Ignition Facility for specifically tailored spherical implosions to compress hydrogen to extreme densities (up to ∼800× solid density, electron number density ne∼4×1025 cm−3) at moderate temperatures (T∼200 eV), i.e., to conditions, which are relevant to the interiors of red dwarf stars. The dense plasma will be probed by laser-generated x-ray radiation of different photon energy to determine the plasma opacity due to collisional (free–free) absorption and Thomson scattering. The obtained results will benchmark radiation transport models, which in the case for free–free absorption show strong deviations at conditions relevant to red dwarfs. This very first experimental test of free–free opacity models at these extreme states will help to constrain where inside those celestial objects energy transport is dominated by radiation or convection. Moreover, our study will inform models for other important processes in dense plasmas, which are based on electron–ion collisions, e.g., stopping of swift ions or electron–ion temperature relaxation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Pulsed power to control growth of silicon nanoparticles in low temperature flowing plasmas

Low-temperature plasmas have seen increasing use for synthesizing high-quality, mono-disperse nanoparticles (NPs). Recent work has highlighted that an important process in NP growth in plasmas is particle trapping—small, negatively charged nanoparticles become trapped by the positive electrostatic potential in the plasma, even if only momentarily charged. In this article, results are discussed from a computational investigation into how pulsing the power applied to an inductively coupled plasma (ICP) reactor may be used for controlling the size of NPs synthesized in the plasma. The model system is an ICP at 1 Torr to grow silicon NPs from an Ar/SiH 4 gas mixture. This system was simulated using a two-dimensional plasma hydrodynamics model coupled to a three-dimensional kinetic NP growth and trajectory tracking model. The effects of pulse frequency and pulse duty cycle are discussed. We identified separate regimes of pulsing where particles become trapped for one pulsed cycle, a few cycles, and many cycles—each having noticeable effects on particle size distributions. For the same average power, pulsing can produce a stronger trapping potential for particles when compared to continuous wave power, potentially increasing particle mono-dispersity. Pulsing may also offer a larger degree of control over particle size for the same average power. Experimental confirmation of predicted trends is discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Physics-based model of irradiation creep for ferritic materials under fusion energy operation conditions

Irradiation creep is known to be an important process for structural materials in nuclear environments, potentially leading to creep failure at temperatures where thermal creep is generally negligible. While there is a great deal of data for irradiation creep in steels and zirconium alloys in light water reactor conditions, much less is known for first wall materials under fusion energy conditions. Lacking suitable fusion neutron sources for detailed experimentation, modeling, and simulation can help bridge the dose-rate and spectral-effects gap and produce quantifiable expectations for creep deformation of first wall materials under standard fusion conditions. In this paper, we develop a comprehensive model for irradiation creep created from merging a crystal plasticity representation of the dislocation microstructure and a defect evolution simulator that accounts for the entire cluster dimensionality space. Both approaches are linked by way of a climb velocity that captures dislocation-biased defect absorption and a dislocation strengthening term that reflects the accumulation of defect clusters in the system. Here, we carry out our study in Fe under first wall fusion reactor conditions, characterized by a fusion neutron spectrum with average recoil energies of 20 keV and a damage dose rate of ≈3×10 –7 dpa/s at temperatures between 300 and 800 K.

36 MATERIALS SCIENCE↗

DOE OSTI2021

IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

Significance Polycomb Repressive Complex 2 (PRC2) methylates histones to regulate multicellular development, maintenance of stem cell identity, X-chromosome inactivation, and other important processes. Given these essential roles, there is significant interest in identifying components that function with PRC2 to establish and maintain transcriptionally repressive heterochromatin. Here we document an unexpected new role for a well-studied and conserved chromatin remodeling factor, ISWI. We found that the Neurospora ISWI homolog is required for normal facultative heterochromatin structure and gene repression at PRC2 target regions, and we defined requirements for ATP-dependent catalytic activity and accessory regulatory proteins. These findings provide mechanistic insights into the formation and function of facultative heterochromatin in a model eukaryote.

Kamei, Masayuki↗

DOE OSTI2026

Parametrically amplified Josephson plasma waves in YBa 2 Cu 3 O 6+ x : Evidence for local superconducting fluctuations up to the pseudogap temperature T ∗

Experiments that subject underdoped YBa 2 Cu 3 O 6+x (YBCO) to intense terahertz pulses at temperatures between the transition temperature T c and the pseudogap scale T ∗ have revealed a reflectivity edge that resembles that of the superconducting state, together with second harmonic generation of a probe pulse modulated at a similar frequency. These have been interpreted in terms of parametric amplification of the lower Josephson plasmon mode. Since this mode is often associated with coherent oscillations between bilayers in the YBCO structure, these experiments have led to the suggestion that the intense pump has created (or revealed) in-plane pair coherence up to T ∗ ≈ 400 K. In this paper we propose an alternative explanation by assuming the existence of local pair amplitude and phase at equilibrium for T c < T < T ∗ . The phase correlation spans only a few lattice constants and we do not assume any pump-induced enhancement of this correlation, either in-plane or between bilayers. Instead, the coherent drive, via a parametric amplification process, induces coherence in the Josephson currents between members of bilayers. When combined with a Floquet framework, the reflectivity data can be explained. The key point is that in the lower Josephson plasmon, the coupling between bilayers is mainly capacitive; the Josephson current between bilayers can be set to zero without strongly affecting the parametric amplification process. Importantly, while superconducting coherence may not be created by the pump, the pseudogap phase must possess a local pairing amplitude at equilibrium. Consequently, these experiments have strong implications for the understanding of the pseudogap phase.

parametric amplification↗

DOE OSTI2025

The impact of non-local parallel electron transport on plasma-impurity reaction rates in tokamak scrape-off layer plasmas

Abstract Plasma-impurity reaction rates are a crucial part of modelling tokamak scrape-off layer (SOL) plasmas. To avoid calculating the full set of rates for the large number of important processes involved, a set of effective rates are typically derived which assume Maxwellian electrons. However, non-local parallel electron transport may result in non-Maxwellian electrons, particularly close to divertor targets. Here, the validity of using Maxwellian-averaged rates in this context is investigated by computing the full set of rate equations for a fixed plasma background from kinetic and fluid SOL simulations. We consider the effect of the electron distribution as well as the impact of the electron transport model on plasma profiles. Results are presented for lithium, beryllium, carbon, nitrogen, neon and argon. It is found that electron distributions with enhanced high-energy tails can result in significant modifications to the ionisation balance and radiative power loss rates from excitation, on the order of 50%–75% for the latter. Fluid electron models with Spitzer-Härm or flux-limited Spitzer-Härm thermal conductivity, combined with Maxwellian electrons for rate calculations, can increase or decrease this error, depending on the impurity species and plasma conditions. Based on these results, we also discuss some approaches to experimentally observing non-local electron transport in SOL plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

LHC hadronic jet generation using convolutional variational autoencoders with normalizing flows

Abstract In high energy physics, one of the most important processes for collider data analysis is the comparison of collected and simulated data. Nowadays the state-of-the-art for data generation is in the form of Monte Carlo (MC) generators. However, because of the upcoming high-luminosity upgrade of the Large Hadron Collider (LHC), there will not be enough computational power or time to match the amount of needed simulated data using MC methods. An alternative approach under study is the usage of machine learning generative methods to fulfill that task. Since the most common final-state objects of high-energy proton collisions are hadronic jets, which are collections of particles collimated in a given region of space, this work aims to develop a convolutional variational autoencoder (ConVAE) for the generation of particle-based LHC hadronic jets. Given the ConVAE’s limitations, a normalizing flow (NF) network is coupled to it in a two-step training process, which shows improvements on the results for the generated jets. The ConVAE+NF network is capable of generating a jet in 18.30 ± 0.04 μ s , making it one of the fastest methods for this task up to now.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The Natural Products Magnetic Resonance Database (NP-MRD) for 2025

The Natural Products Magnetic Resonance Database or NP-MRD (https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction and retrieval of nuclear magnetic resonance (NMR) data on natural products. The NP-MRD was initially established to support compound de-replication and data dissemination for the natural products community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics and nutrition science fields. Indeed, since its launch in 2021, the NP-MRD has expanded enormously in size, scope and popularity. The current version of NP-MRD now contains nearly 7X more compounds (281,859 vs. 40,908) and 7X more NMR spectra (5.1 million vs. 817,000) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11,000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from a 165 spectra per year to more than 10,000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20,000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, important improvements to the visualization and display of NMR spectra, notable updates to the database’s spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD’s database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned.

Artifical Intelligence↗

DOE OSTI2022

Using kernel-based statistical distance to study the dynamics of charged particle beams in particle-based simulation codes

Measures of discrepancy between probability distributions (statistical distance) are widely used in the fields of artificial intelligence and machine learning. We describe how certain measures of statistical distance can be implemented as numerical diagnostics for simulations involving charged-particle beams. Related measures of statistical dependence are also described. The resulting diagnostics provide sensitive measures of dynamical processes important for beams in nonlinear or high-intensity systems, which are otherwise difficult to characterize. Here, the focus is on kernel-based methods such as maximum mean discrepancy, which have a well-developed mathematical foundation and reasonable computational complexity. Several benchmark problems and examples involving intense beams are discussed. While the focus is on charged-particle beams, these methods may also be applied to other many-body systems such as plasmas or gravitational systems.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Spatiotemporal Automatic Calibration of Infrastructure Lidar, Radar, and Camera with a Global Navigation Satellite System

Robust and accurate perception is important for modern intelligent transportation systems (ITS), which use sensors of various modalities for data fusion to create a digital twin of an intersection. Sensor calibration is an important process that creates a unified coordinate frame for the sensor output data so that it can be used for data fusion. Classical approaches for sensor calibration are time-consuming, require an overlapping field of view for feature matching, and are not feasible for ITS application as they cause disruptions in the flow of traffic. In this paper, we present a spatiotemporal automatic calibration approach to calibrate multiple infrastructure lidar, radar, and cameras installed at a traffic intersection. The approach uses global navigation satellite system (GNSS) positioning information shared by connected vehicles, and when the vehicle is detected by the sensor, we match the sensor detections with the GNSS coordinates. The proposed algorithm is evaluated with a real-world dataset utilizing detections from two radars, cameras, and lidars with a test vehicle instrumented with a post-processing kinematic (PPK)-corrected GNSS driving past the sensors installed at a four-way traffic intersection. The experimental results show that the proposed automatic calibration approach can achieve the transformation with a root mean squared error of less than 0.5 for radar and lidar and less than 2 for camera detections. The ability to rapidly calibrate sensors not only benefits initial installations, but can also be used for system health monitoring, while utilizing available connected vehicle data to test the real-time sensor fidelity and operational status.

ADVANCED PROPULSION SYSTEMS,ENERGY CONSERVATION, C↗

DOE OSTI2024

An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae)

ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages ofQuercusand relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors ofCastanea + Castanopsis,Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.

Biochemistry & Molecular Biology↗

DOE OSTI2020

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass ( Panicum virgatum )

Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. As such, to understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust ( Puccinia spp.) severity in switchgrass ( Panicum virgatum ) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.

09 BIOMASS FUELS↗

DOE OSTI2022

Separating Oil-Water Mixtures Using Bump Arrays

Particle separation is an important process step across many fields. One technique being applied for separating solids such as blood components or sand particles from carrier fluids is the use of arrays of aligned posts called deterministic lateral arrays to bump particles to one side in the flow stream to enhance separation. This technique may be useful for separation of deformable particles. The ability to efficiently separate two-phase industrial (oil/water) mixtures is key for future use of valuable resources. Over 1 trillion gallons of petroleum production water could be reclaimed annually for reuse in the drought-ridden western US states. The ability to reclaim this petroleum production water may be critical for the Central High Plains (Colorado, Kansas, Oklahoma, Texas, and New Mexico). Trends in just the High Plains area already lost 20 to 25% of the irrigated farming area due to insufficient ground water storage to irrigate, and farmland losses are expected to grow to 40%. Proving this technology is key to reuse of petroleum production water for crop irrigation or to replace water from currently failing aquifers in rich agricultural lands of the Central High Plains. We conducted experiments applying mesofluidic separation for flowing two-phase (oil/water) mixtures. Experiments were conducted using oils of differing viscosities with water as the carrier fluid; separation was achieved over a range of oil-water concentrations. We describe the results of these experiments in this paper.

oil-water separation, micelle, droplet separation,↗

DOE OSTI2024

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

ABSTRACT Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus . Furthermore, all Bermanella encoded and expressed genes for non-gaseous n -alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment. IMPORTANCE Microbial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based ‘omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Howe, Kathryn L.↗