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DOE OSTI2024

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers

This data package is associated with the publication “Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers” submitted to Science of the Total Environment. This data package includes the data necessary to replicate the analyses presented within the manuscript to investigate dissolved organic matter (DOM) development across broad spatial distances and within divergent biomes. Specifically, we included the Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data, geochemistry data, annotated metagenomic data, and results from ecological null modeling analyses in this data package. Additionally, we included the scripts necessary to generate the figures from the manuscript. Complete metagenomic data associated with this data package can be found at the National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. This dataset consists of (1) four folders; (2) a file-level metadata (flmd) file; (3) a data dictionary (dd) file; (4) a factor sheet describing samples; and (5) a readme. The FTICR Data folder contains (1) the processed Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data; (2) a transformation-weighted characteristics dendrogram generated from the FTICR-MS data; and (3) the script used to generate all FTICR-MS related figures. The Geochemical Data folder contains (1) the single geochemistry data file and (2) the R script responsible for generating associated figures. The Metagenomic Data folder contains (1) annotation information across different levels; (2) carbohydrate active enzyme (CAZyme) information from the dbCAN database (Yin et al., 2012); (3) phylogenetic tree data (FASTAs, alignments, and tree file); and (4) the scripts necessary to analyze all of these data and generate figures. The Null Modeling Data folder contains (1) data generated during null modeling for each river and all rivers combined and (2) the R scripts necessary to process the data. All files are .csv, .pdf, .tsv, .tre, .faa, .afa, .tree, or .R.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

A differentiable model of the evolution of dark matter halo concentration

ABSTRACT We introduce a new model of the evolution of the concentration of dark matter haloes, c(t). For individual haloes, our model approximates c(t) as a power law with a time-dependent index, such that at early times, concentration has a nearly constant value of c ≈ 3–4, and as cosmic time progresses, c(t) smoothly increases. Using large samples of halo merger trees taken from the Bolshoi–Planck and MultiDark Planck 2 cosmological simulations, we demonstrate that our three-parameter model can approximate the evolution of the concentration of individual haloes with a typical accuracy of 0.1 dex for $t\gtrsim 2\, {\rm Gyr}$ for all Bolshoi–Planck and MultiDark Planck 2 haloes of present-day peak mass $M_{0}\gtrsim 10^{11.5}\, {\rm M}_{\odot }$. We additionally present a new model of the evolution of the concentration of halo populations, which we show faithfully reproduces both average concentration growth and the diversity of smooth trajectories of c(t), including capturing correlations with halo mass and halo assembly history. Our publicly available source code, diffprof, can be used to generate Monte Carlo realizations of the concentration histories of cosmologically representative halo populations. diffprof is differentiable due to its implementation in the jax autodiff library, which facilitates the incorporation of our model into existing analytical halo model frameworks.

Stevanovich, Dash↗

DOE OSTI2020

Active layer depth and soil properties impact specific leaf area variation and ecosystem productivity in a boreal forest

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which dominant tree species changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Sensitivity of Pyrocumulus Convection to Tree Mortality During the 2020 Creek Fire in California

Abstract This study investigated the sensitivity of pyrocumulonimbus (PyroCb) induced by the California Creek fire of 2020 to the amount and type of surface fuels, within the WRF‐SFIRE modeling system. Satellite data were used to derive fire arrival times to constrain fire progression, and to augment the fuel characterization with better estimates of combustible vegetation accounting for tree mortality. Machine learning was employed to classify standing dead vegetation from aerial imagery, which was then added as a custom fuel class along with the standard Anderson fuel categories. Simulations using this new fuel class produced a larger and more vigorous PyroCb than the control run, however, still under‐predicted the cloud top. Additional augmentation of fuel mass to represent the accumulation of dead vegetation on the forest floor further improved the simulations, demonstrating the efficacy of representing both dead standing and fallen vegetation to produce more realistic PyroCb and smoke simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Distinguishing Orbiting and Infalling Dark Matter Particles with Machine Learning

Dark matter halos are typically defined as spheres that enclose some overdensity, but these sharp, somewhat arbitrary boundaries introduce nonphysical artifacts such as backsplash halos, pseudo-volution, and an incomplete accounting of halo mass. A more physically motivated alternative is to define halos as the collection of particles that are physically orbiting within their potential well. However, existing methods to classify particles as orbiting or infalling suffer from trade-offs between accuracy, computational cost, and generalizability across cosmologies. We present an efficient, yet accurate, supervised machine learning approach using decision trees. The classification is based on only the particle radii and velocities at two epochs. Compared to detailed analysis of particle trajectories, we find that our model matches the classification of 97% of particles. Consequently, we are able to quickly and accurately reproduce the density profiles of the orbiting and infalling components out to many virial radii. We demonstrate that our model generalizes to a significantly different cosmology that lies outside the training data set. We make publicly available both our final model and the code to train similar models.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1993

Dynamics of the baryonic component in hierarchical clustering universes

I present self-consistent 3-D simulations of the formation of virialized systems containing both gas and dark matter in a flat universe. A fully Lagrangian code based on the Smoothed Particle Hydrodynamics technique and a tree data structure has been used to evolve regions of comoving radius 2-3 Mpc. Tidal effects are included by coarse-sampling the density of the outer regions up to a radius approx. 20 Mpc. Initial conditions are set at high redshift (z greater than 7) using a standard Cold Dark Matter perturbation spectrum and a baryon mass fraction of 10 percent (omega(sub b) = 0.1). Simulations in which the gas evolves either adiabatically or radiates energy at a rate determined locally by its cooling function were performed. This allows us to investigate with the same set of simulations the importance of radiative losses in the formation of galaxies and the equilibrium structure of virialized systems where cooling is very inefficient. In the absence of radiative losses, the simulations can be rescaled to the density and radius typical of galaxy clusters. A summary of the main results is presented.

Navarro, Julio↗

DOE OSTI2021

On the influence of halo mass accretion history on galaxy properties and assembly bias

Halo assembly bias is the secondary dependence of the clustering of dark matter haloes on their assembly histories at fixed halo mass. This established dependence is expected to manifest itself on galaxy clustering, a potential effect commonly known as galaxy assembly bias. Using the IllustrisTNG300 magnetohydrodynamical simulation, in this work we analyse the dependence of the properties and clustering of galaxies on the specific mass accretion history of their hosting haloes (sMAH). We first show that several halo and galaxy properties strongly correlate with the slope of the sMAH (β) at fixed halo mass. Haloes with increasingly steeper β increment their masses faster early on, and their hosted galaxies present larger stellar-to-halo mass ratios, lose their gas faster, reach the peak of their star formation histories at higher redshift, and become quenched earlier. We also demonstrate that β provides a more stable link to these key galaxy formation properties than other broadly employed halo proxies, such as formation time. Finally, we measure the secondary dependence of galaxy clustering on β at fixed halo mass. By tracing back the evolution of individual haloes, we show that the amplitude of the galaxy assembly bias signal for the progenitors of z = 0 galaxies increases with redshift, reaching a factor of 2 at z = 1 for haloes of Mhalo = 10 11.5 –10 12 h –1 M ⊙ . The measurement of the evolution of assembly bias along the merger tree provides a new theoretical perspective to the study of secondary bias. Our findings have also important implications for the generation of mock catalogues for upcoming cosmological surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Baryon $\sigma$ terms in SU(3) BChPT x 1/N c

ChPT and the 1/N c expansion provide systematic frameworks for the strong interactions at low energy. A combined framework of both expansions has been developed and applied for baryons with three light-quark-flavors. The small scale expansion of the combined approach is identified as the ξ-expansion, in which the power counting of the expansions is linked according to O(p) = O(1/N c ) = O(ξ). The physical baryon masses as well as lattice QCD baryon masses for different quark mass masses are analyzed to O(ξ 3 ) in that framework. σ terms are addressed using the Feynman Hellmann theorem. For the nucleon, a useful connection between the deviation of the Gell-Mann-Okubo relation and the σ term σ 8N associated with the scalar density $\bar{u}u+\bar{d}d-2\bar{s}s$ is identified. In particular, the deviation from the tree level relation σ 8N = $\frac{1}{3}$(2m N -m Σ -m Ξ ), which gives rise to the so called σ-term puzzle, is studied in the ξ-expansion. A large correction non-analytic in ξ results for that relation, making plausible the resolution of the puzzle. Issues with the determination of the strangeness σ terms are discussed, emphasizing the need for lattice calculations at smaller m s for better understanding the range of validity of the effective theory. The analysis presented here leads to σ πN = 69(10) MeV and σ πΔ = 60(10) MeV.

Fernando, Ishara P.↗

DOE OSTI2021

Canopy position influences the degree of light suppression of leaf respiration in abundant tree genera in the Amazon Forest

Leaf respiration in the dark (R dark ) and light (R day ) is poorly characterized in diverse tropical ecosystems, and little to no information exists on the degree of light suppression in common tree species within the Amazon basin, and their dependences upon plant functional traits and position within the canopy. We quantified R dark and apparent R day using the Kok method and measured key leaf traits in 26 tree individuals of different species distributed in three different canopy positions: canopy, lower canopy, and understory. To explore the relationships between the leaf traits we used the standardized major axis (SMA). We found that canopy trees had significantly higher rates of R dark and R day than trees in the understory. The difference between R dark and R day (the light suppression of respiration) was greatest in the understory (68 ± 9%, 95% CI) and lower canopy (49 ± 9%, 95% CI) when compared to the canopy (37 ± 10%, 95% CI). We also found that R day was significantly and strongly correlated with R dark (p < 0.001) for all the canopy positions. Also, leaf mass per area (LMA) and leaf Phosphorus concentration (P) had a significant relationship with R dark (p < 0.001; p = 0.003), respectively. In addition, a significant relationship was found for LMA in the canopy and lower canopy positions (p = 0.009; p = 0.048) while P was only significant in the canopy (p = 0.044). Finally, no significant relationship was found between R dark and nitrogen, sugars, and starch. Our results highlight the importance of including representation of the light suppression of leaf respiration in terrestrial biosphere models and also of accounting for vertical gradients within forest canopies and connections with functional traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Constraint on the total width of the Higgs boson from Higgs boson and four-top-quark measurements in pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

This Letter presents a constraint on the total width of the Higgs boson (Γ H ) using a combined measurement of on-shell Higgs boson production and the production of four top quarks, which involves contributions from off-shell Higgs boson-mediated processes. This method relies on the assumption that the tree-level Higgs-top Yukawa coupling strength is the same for on-shell and off-shell Higgs boson production processes, thereby avoiding any assumptions about the relationship between on-shell and off-shell gluon fusion Higgs production rates, which were central to previous measurements. The result is based on up to 140 fb -1 of proton–proton collisions at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV collected with the ATLAS detector at the Large Hadron Collider. The observed (expected) 95% confidence level upper limit on Γ H is 450 MeV (75 MeV). Additionally, considering the constraint on the Higgs-top Yukawa coupling from loop-induced Higgs boson production and decay processes further yields an observed (expected) upper limit of 160 MeV (55 MeV).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Raw leaf gas exchange data in the Amazon basin, 2014-2016

This data package contains raw leaf gas exchange data used to support the publication "Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin," Phytochemistry, in-press. Data was collected from 162 individuals, distributed among 25 botanical families and 113 species, from four sites in the Amazon. The data was collected using a modified portable photosynthesis system for environmental control coupled to a thermal desorption tube for volatile isoprenoid collections. Collected TD tube samples were analysed in Manaus, Brazil, using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). The dataset includes both photosynthesis and isoprene/monoterpene emission rates from leaves under standard environmental conditions as well as controlled light response curves. For detailed methods and raw data, refer to the publication and related material cited in Dataset References.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Color-octet scalars in Dirac gaugino models with broken R symmetry

In this work we study the collider phenomenology of color-octet scalars ( sgluons ) in supersymmetric models with Dirac gaugino masses that feature an explicitly broken R symmetry ( R - broken models ). We construct such models by augmenting minimal R -symmetric models with a fairly general set of supersymmetric and softly supersymmetry-breaking operators that explicitly break R symmetry. We then compute the rates of all significant two-body decays and highlight new features that appear as a result of R symmetry breaking, including enhancements to extant decay rates, novel tree- and loop-level decays, and improved cross sections of single sgluon production. We demonstrate in some detail how the familiar results from minimal R -symmetric models can be obtained by restoring R symmetry. In parallel to this discussion, we explore constraints on these models from the Large Hadron Collider. We find that, in general, R symmetry breaking quantitatively affects existing limits on color-octet scalars, perhaps closing loopholes for light CP-odd (pseudoscalar) sgluons while opening one for a light CP-even (scalar) particle. Qualitatively, however, we find that — much as for minimal R -symmetric models, despite stark differences in phenomenology — scenarios with broken R symmetry and two sgluons below the TeV scale can be accommodated by existing searches.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Detection of Diversion in a Realistic Heat Pipe Microreactor Using Supervised Machine Learning

Microreactors (MRs) pose new challenges for international safeguards. Here, their small size and mass reproducibility make them ideal for deployment in greater numbers and in remote locations, making the job of safeguards inspectors more challenging. Machine learning (ML) is currently being applied to many fields to augment human performance and increase automation; in particular, ML could be used to provide insight for international inspectors to help detect the diversion of nuclear fuel from MR cores. Four ML model types (k-nearest neighbors, decision tree, random forest, and histogram-based gradient boosted ensemble) were trained on integrated flux and critical control drum angle data generated with Serpent 2 for a realistic heat pipe MR design, achieving nearly 100% binary classification accuracy of nominal and diversion core configurations by the end of 1 full power year for three of the four model types. Regression model variants were also trained, using the same input data, for predicting the number of fuel pins diverted. Root-mean-square errors below 5% of the total number of fuel pins were achieved by the 1 full power year mark for all models.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Measuring the electron Yukawa coupling via resonant s-channel Higgs production at FCC-ee

The Future Circular Collider (FCC-ee) offers the unique opportunity of studying the Higgs Yukawa coupling to the electron, $y_\mathrm {e}$ , via resonant s -channel production, $\mathrm {e^+e^-}\rightarrow \mathrm {H}$ , in a dedicated run at $\sqrt{s} = m_\mathrm {H}$ . The signature for direct Higgs production is a small rise in the cross sections for particular final states, consistent with Higgs decays, over the expectations for their occurrence due to Standard Model (SM) background processes involving $\mathrm {Z}^*$ , $\gamma ^*$ , or t -channel exchanges alone. Performing such a measurement is remarkably challenging for four main reasons. First, the low value of the e $^\pm $ mass leads to a tiny $y_\mathrm {e}$ coupling and correspondingly small cross section: $\sigma _\mathrm {ee\rightarrow H} \propto m_\mathrm {e}^2 = 0.57$ fb accounting for initial-state $\gamma $ radiation. Second, the $\mathrm {e^+e^-}$ beams must be monochromatized such that the spread of their centre-of-mass (c.m.) energy is commensurate with the narrow width of the SM Higgs boson, $\varGamma _\mathrm {H} = 4.1$ MeV, while keeping large beam luminosities. Third, the Higgs mass must also be known beforehand with a few-MeV accuracy in order to operate the collider at the resonance peak, $\sqrt{s} = m_\mathrm {H}$ . Last but not least, the cross sections of the background processes are many orders-of-magnitude larger than those of the Higgs decay signals. A preliminary generator-level study of 11 Higgs decay channels using a multivariate analysis, which exploits boosted decision trees to discriminate signal and background events, identifies two final states as the most promising ones in terms of statistical significance: $\mathrm {H}\rightarrow gg$ and $\mathrm {H}\rightarrow \mathrm {W}\mathrm {W}^*\!\rightarrow \ell \nu $ + 2 jets. For a benchmark monochromatization with 4.1-MeV c.m. energy spread (leading to $\sigma _\mathrm {ee\rightarrow H} = 0.28$ fb) and 10 ab $^{-1}$ of integrated luminosity, a $1.3\sigma $ signal significance can be reached, corresponding to an upper limit on the e $^\pm $ Yukawa coupling at 1.6 times the SM value: |y e | < 1.6|y e SM | at 95% confidence level, per FCC-ee interaction point per year. Directions for future improvements of the study are outlined.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1993

Numerical experiments with model monophyletic and paraphyletic taxa

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

Non-NASA Center↗

NASA NTRS2016

CME Flux Rope and Shock Identifications and Locations: Comparison of White Light Data, Graduated Cylindrical Shell Model, and MHD Simulations

Coronal mass ejections (CMEs) are major transient phenomena in the solar corona that are observed with ground-based and spacecraft-based coronagraphs in white light or with in situ measurements by spacecraft. CMEs transport mass and momentum and often drive shocks. In order to derive the CME and shock trajectories with high precision, we apply the graduated cylindrical shell (GCS) model to fit a flux rope to the CME directed toward STEREO A after about 19:00 UT on 29 November 2013 and check the quality of the heliocentric distance-time evaluations by carrying out a three-dimensional magnetohydrodynamic (MHD) simulation of the same CME with the Block Adaptive Tree Solar-Wind Roe Upwind Scheme (BATS-R-US) code. Heliocentric distances of the CME and shock leading edges are determined from the simulated white light images and magnetic field strength data. We find very good agreement between the predicted and observed heliocentric distances, showing that the GCS model and the BATS-R-US simulation approach work very well and are consistent. In order to assess the validity of CME and shock identification criteria in coronagraph images, we also compute synthetic white light images of the CME and shock. We find that the outer edge of a cloud-like illuminated area in the observed and predicted images in fact coincides with the leading edge of the CME flux rope and that the outer edge of a faint illuminated band in front of the CME leading edge coincides with the CME-driven shock front.

Schmidt, J. M.↗

NASA NTRS1989

Automated model formulation for time-varying flexible structures

Presented here is an identification technique that uses the sensor information to choose a new model out of a finite set of discrete model space, in order to follow the observed changes to the given time varying flexible structure. Boundary condition sets or other information on model variations are used to organize the set of possible models laterally into a search tree with levels of abstraction used to order the models vertically within branches. An object-oriented programming approach is used to represent the model set in the search tree. A modified A (asterisk) best first search algorithm finds the model where the model response best matches the current observations. Several extensions to this methodology are discussed. Methods of possible integration of rules with the current search algorithm are considered to give weight to interpreted trends that may be found in a series of observations. This capability might lead, for instance, to identifying a model that incorporates a progressive damage rather than with incorrect paramenters such as added mass. Another new direction is to consider the use of noisy time domain sensor feedback rather than frequency domain information in the search algorithm to improve the real-time capability of the developed procedure.

Glass, B. J.↗