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DOE OSTI2024

Simulating water dynamics related to pedogenesis across space and time: Implications for four-dimensional digital soil mapping

Digital soil mapping (DSM) relies on machine-learning and geostatistics to represent soil property observations across space. DSM techniques are powerful but often empirical, being limited to the quality and density of point samples. Water dynamics are closely related to soil variability, and the physics that govern water movement are well known. Hydrological properties can hence be simulated by physical models through space and time, unveiling key characteristics about soils. We propose the use of hydrologic models to map soils across the surface (2D), depth (1D), and time (1D)–which provides a 4D approach to digital soil mapping (4DSM). The Distributed Hydrology Soil Vegetation Model (DHSVM) was applied to a watershed currently under pasture. Moisture sensors and wells were installed at different depths in the watershed on summit, sideslope and toeslope positions to validate the model. DHSVM simulations of soil moisture distribution and depth to saturation were performed during the hydrological year (October 2008-September 2009). Clusters of similar pixels based on soil moisture values were determined using Dynamic Time Warping (DTW) to align temporal data and K-means. Clustering was performed both seasonally and for the entire year. Temporal patterns simulated by DHSVM matched measurements given by moisture sensors and wells. Seasonal clusters differed from the annual cluster. Distinct clusters were observed for each season and with depth, showing that spatiotemporal soil variability is lost when statically assessing soils. Spatiotemporal clusters corroborated field observations of fragipan occurrence not explicitly spatially mapped by Soil Survey Geographic Database (SSURGO). If a connection can be made between water and soils, static and dynamic soil variability can be predicted using physically based hydrologic models. Hydrologic models can benefit soil mapping by enabling reliable 4D simulation of water dynamics, which are fundamental to soil variability and soil classification and directly relate to biological, physical and chemical soil processes not captured by typical soil sampling protocols.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1999

Ice Thicknesses and Driving Stresses of Greenland Ice Sheet

Surface elevations from satellite radar altimetry (Geosat, Seasat, and ERS-1) and bedrock topography from airborne radar sounding (Simon Ekholm's Danish compilation) are combined to derive maps of the driving stresses in the Greenland ice sheet. The stress vector, tau = rho g h sin(alpha), is calculated using surface slope vectors, alpha, from surface elevations and ice thicknesses, h, from the difference between surface and basal elevations. Since the 5-km scale of the surface slope is only about 2 times the ice thickness, the stress maps show spatial variations indicative of longitudinal stress gradients associated with topographic undulations. Values of alpha generally vary from near zero at the ice divides to maxima values around 120 kpa, returning to near zero in a narrow band at the edges. The distribution of alpha's peaks at 60 kpa with an approximate sigma of +/- 20 kpa. Areas of very low alpha near the origin of the northeast ice stream may indicate small sub-glacial lakes. The profile of alpha, down the ice stream from near the ice divide, increases to a maximum of about 120 kpa near the margin, which is characteristic of East Antarctic outlet glaciers and in contrast to West Antarctic ice streams where alpha has maximum values 400 to 500 km inland from the grounding lines. Overall distributions of alpha values are compared with those for the Antarctic ice sheet and the Mars Northern ice cap.

Zwally, H. J.↗

DOE OSTI2022

Leveraging gradient weighted class activation mapping to improve classification effectiveness: Case study in transportation infrastructure characterization

Roadway â€œcornersâ€ are common for pedestrian use, whether designated with markings or not. Different types of markings have been deployed, ranging from simple parallel lines to more complex designs. Understanding the impact of different types of crosswalks is important for public safety. In this work we explore methods to improve the logging of marked crosswalk types. We used the Roadway Information Database from the Second Strategic Highway Research Project and used active learning methods with transfer learning to identify the crosswalk types (marked or unmarked). Upon completion we found our classifiers were unable to perform above roughly 94% correct classifications. To improve their efficacy, we separated the crosswalks into their â€œfine grainedâ€ types and used Gradient-Weighted Class Activation Mapping to isolate and study the features that classified the crosswalks. We compared this with sampled manually marked crosswalks and present findings. We believe this use case can represent a process to improve the active learning method for some visual machine learning applications.

Karnowski, Thomas↗

DOE OSTI2022

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean ( Phaseolus vulgaris )

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks < 1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones

Klebsiella pneumoniae has become one of the most dangerous causative agents of hospital infections due to the acquisition of resistance to carbapenems, one of the last resort families of antibiotics. Resistance is usually mediated by carbapenemases coded for by different classes of genes. A prolonged outbreak of carbapenem-resistant K. pneumoniae infections has been recently described in northeastern Ohio. Most strains isolated from patients during this outbreak belong to MLST sequence type 258 (ST258). To understand more about this outbreak two isolates (strains 140 and 677), one of them responsible for a fatal infection, were selected for genome comparison analyses. Whole genome map and sequence comparisons demonstrated that both strains are highly related showing 99% average nucleotide identity. However, the genomes differ at the so-called high heterogeneity zone (HHZ) and other minor regions. This study identifies the potential value of the HHZ as a potential marker for K. pneumoniae clinical and epidemiological studies.

Evolutionary Biology↗

DOE OSTI2025

Bias correcting regional scale Earth system model projections: novel approach using empirical mode decomposition

Bias correction is a crucial step in using Earth system model outputs for assessments, as it adjusts systematic errors by comparing the model to observations. However, standard methods – ranging from mean-based linear scaling to distribution-based quantile mapping typically treat bias correction as a single-scale process, overlooking the fact that biases can manifest differently across daily, seasonal, and annual timescales. In this study, we propose a novel, timescale-aware bias-correction approach built on Empirical Mode Decomposition. By decomposing the meteorological signal into multiple oscillatory components and aggregating them to represent distinct timescales, we apply targeted corrections to each component, thereby preserving both short- and long-term structure in the data. Experimental illustrations show that the timescale-aware EMDBC framework matches the performance of conventional quantile-delta mapping (QDM) at the native daily scale and achieves progressively larger bias reductions at bi-weekly, seasonal, and annual scales. As a result, the proposed approach offers a more robust path to accurate and reliable Earth system projections, strengthening their utility for resilience and adaptation planning.

Ganguli, Arkaprabha [Argonne National Laboratory (↗

DOE OSTI2020

Dissolution of a cylindrical disk in Hele-Shaw flow: a conformal-mapping approach

Here we apply conformal mapping to find the evolving shapes of a dissolving cylinder in a potential flow. Similar equations can be used to describe melting in a flowing liquid phase. Results are compared with microfluidic experiments and numerical simulations. Shapes predicted by conformal mapping agree almost perfectly with experimental observations, after a modest (20 %) rescaling of the time. Finite-volume simulations show that the differences with experiment are connected to the underlying assumptions of the analytical model: potential flow and diffusion-limited dissolution. Approximate solutions of the equations describing the evolution of the shape of the undissolved solid can be derived from a Laurent expansion of the mapping function from the unit circle. Asymptotic expressions for the evolution of the area of the disk and the shift in its centre of mass have been derived at low and high Péclet number. Analytic approximations to the leading-order Laurent coefficients provide additional insight into the mechanisms underlying pore-scale dissolution.

58 GEOSCIENCES↗

NASA NTRS1973

Application of ERTS-1 imagery to detecting and mapping modern erosion features, and to monitoring erosional changes, in southern Arizona

The author has identified the following significant results. The red MSS band 5 gives the sharpest definition of modern arroyos. On the best images, modern arroy0s can be distinguished as narrow as 150 to 200 feet in reaches where their contrast with adjacent areas is only moderate, and as narrow as 60 to 75 feet where their contrast is high. Both the red and infrared bands show differences is soils and vegetation. In the late fall and winter imagery, band 7 generally is the most useful for mapping the areas of the more erodible soils. A map at 1:1,000,000 scale has been prepared that shows all the arroyos within the 17,000 square mile study area that have been identified from ERTS-1 images. Also, from U-2 color infrared airphotos, a 1:125,000 scale map has been made of a 50 mile reach along San Simon Wash, in southeastern Arizona. This map shows not only the arroyo channels and narrow flood plains that have developed since 1890, but also areas within a few miles of the wash that are severely guilled, severely sheet-eroded, and moderately sheet-eroded. Two important effects of the third largest recorded flood of the upper Gila River also have been determined from the ERTS-1 images. The inundated area is best displayed on band 7, and the areas of severe sand/gravel erosion/deposition show best on band 5.

Morrison, R. B.↗

NASA NTRS1990

High resolution sub-millimetre mapping of starburst galaxies: Comparison with CO emission

Researchers present first results from a program of submillimeter continuum mapping of starburst galaxies, and comparison of their dust and CO emission. This project was prompted by surprising results from the first target, the nearby starburst M82, which shows in the dust continuum a morphology quite unlike that of its CO emission, in contrast to what might be expected if both CO and dust are accurately tracing the molecular hydrogen. Possible explanations for this striking difference are discussed. In the light of these results, the program has been extended to include sub-mm mapping of the nearby, vigorously star forming spirals, M83 and Maffei 2. The latter were also observed extensively in CO, in order to study excitation conditions in its central regions. The James Clerk Maxwell Telescope was used in these studies.

Smith, P. A.↗

DOE OSTI2024

Effect of different crystallographic properties on the electrical conductivity of two polymorphs of a spin crossover complex

In this study, the structure and transport properties of two polymorphs, nanoparticles and nanorods, of the iron(II) triazole [Fe(Htrz) 2 (trz)](BF 4 ) spin crossover complex were compared. Conductive atomic force microscopy was used to map the electrical conductivity of individual nanoparticles and nanorods. The [Fe(Htrz) 2 (trz)](BF 4 ) nanorods showed significantly higher conductivity compared to nanoparticles. This difference in electrical conductivity is partially associated to the different Fe–N bond lengths in each of the polymorphs, with an inverse relationship between Fe–N bond length and conductivity. Transport measurements were done on the nanorods for both high spin (at 380 K) and low spin (at 320 K) states under dark and illuminated conditions. The conductance is highest for the low spin state under dark conditions. In illumination, the conductance change is much diminished.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Mapping the Energy-Water Nexus around the Pacific Rim

The energy-water nexus has been mapped for almost 12,000 watersheds distributed across the 21-economies comprising the Asia-Pacific Economic Cooperation. Water consumption for energy production was estimated for 9 different sectors including thermoelectric and hydroelectric power; energy extraction including coal, oil, natural gas, uranium and unconventional oil/gas; and, energy processing including oil and biofuels. Conversely, the energy consumed providing water services was mapped for three sectors, drinking water, waste water and seawater desalination. These measures of resource use were put in context by drawing comparison with published measures of water risk. The objective of the mapping was to quantify the energy-water nexus and its variability at the subnational level, pinpoint potential vulnerabilities, and identify opportunities for international collaboration.

13 HYDRO ENERGY↗

DOE OSTI2018

Modeling the effects of molecular disorder on the properties of Frenkel excitons in organic molecular semiconductors

The Frenkel exciton model offers a convenient framework for simulating electronic excitations in organic conjugated systems that are too large to address with atomistic level electronic structure methods. Parameterization of this model is typically based on analytical expressions that incompletely describe the spatial and temporal correlations that are inherent to many condensed phase molecular systems. In this manuscript, we introduce a general procedure for including these correlations in the Frenkel exciton model, by mapping them directly from all-atom molecular configurations, for instance from classical molecular dynamics. Regardless of system morphology, this mapping automatically captures the spatial and temporal molecular correlations that are otherwise difficult or impossible to represent in terms of low-dimensional correlation functions. We apply this procedure to study the excited state properties of condensed phase materials made up of thiophene oligomers. We demonstrate that Frenkel model parameters can be mapped from a series of single molecule electronic structure calculations, and that for these materials efficient semi-empirical methods are sufficient to accurately reproduce experimental spectral measurements. By analyzing the statistics of model parameters derived from materials with different characteristic morphologies, we highlight failures in some assumptions that are commonly applied when generating model parameters. Finally, by simulating exciton dynamics on a mapped Frenekel exciton model, we demonstrate the ability to quantify the effect of material morphology on the dynamic properties of excitons.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Concentric Spherical GNN for 3D Representation Learning

Learning 3D representations that generalize well to arbitrarily oriented inputs is a challenge of practical importance in applications varying from computer vision to physics and chemistry. We propose a novel multi-resolution convolutional architecture for learning over concentric spherical feature maps, of which the single sphere representation is a special case. Our hierarchical architecture is based on alternatively learning to incorporate both intra-sphere and inter-sphere information. We show the applicability of our method for two different types of 3D inputs, mesh objects, which can be regularly sampled, and point clouds, which are irregularly distributed. We also propose an efficient mapping of point clouds to concentric spherical images, thereby bridging spherical convolutions on grids with general point clouds. We demonstrate the effectiveness of our approach in improving state-of-the-art performance on 3D classification tasks with rotated data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

SU-F-R-36: Validating Quantitative Radiomic Texture Features for Oncologic PET: A Digital Phantom Study

Purpose: Radiomic texture features derived from the oncologic PET have recently been brought under intense investigation within the context of patient stratification and treatment outcome prediction in a variety of cancer types; however, their validity has not yet been examined. This work is aimed to validate radiomic PET texture metrics through the use of realistic simulations in the ground truth setting. Methods: Simulation of FDG-PET was conducted by applying the Zubal phantom as an attenuation map to the SimSET software package that employs Monte Carlo techniques to model the physical process of emission imaging. A total of 15 irregularly-shaped lesions featuring heterogeneous activity distribution were simulated. For each simulated lesion, 28 texture features in relation to the intensity histograms (GLIH), grey-level co-occurrence matrices (GLCOM), neighborhood difference matrices (GLNDM), and zone size matrices (GLZSM) were evaluated and compared with their respective values extracted from the ground truth activity map. Results: In reference to the values from the ground truth images, texture parameters appearing on the simulated data varied with a range of 0.73–3026.2% for GLIH-based, 0.02–100.1% for GLCOM-based, 1.11–173.8% for GLNDM-based, and 0.35–66.3% for GLZSM-based. For majority of the examined texture metrics (16/28), their values on the simulated data differed significantly from those from the ground truth images (P-value ranges from <0.0001 to 0.04). Features not exhibiting significant difference comprised of GLIH-based standard deviation, GLCO-based energy and entropy, GLND-based coarseness and contrast, and GLZS-based low gray-level zone emphasis, high gray-level zone emphasis, short zone low gray-level emphasis, long zone low gray-level emphasis, long zone high gray-level emphasis, and zone size nonuniformity. Conclusion: The extent to which PET imaging disturbs texture appearance is feature-dependent and could be substantial. It is thus advised that use of PET texture parameters for predictive and prognostic measurements in oncologic setting awaits further systematic and critical evaluation.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2017

Kepler Planet Detection Metrics: Per-Target Flux-Level Transit Injection Tests of TPS for Data Release 25

Quantifying the ability of a transiting planet survey to recover transit signals has commonly been accomplished through Monte-Carlo injection of transit signals into the observed data and subsequent running of the signal search algorithm (Gilliland et al., 2000; Weldrake et al., 2005; Burke et al., 2006). In order to characterize the performance of the Kepler pipeline (Twicken et al., 2016; Jenkins et al., 2017) on a sample of over 200,000 stars, two complementary injection and recovery tests are utilized:1. Injection of a single transit signal per target into the image or pixel-level data, hereafter referred to as pixel-level transit injection (PLTI), with subsequent processing through the Photometric Analysis (PA), Presearch Data Conditioning (PDC), Transiting Planet Search (TPS), and Data Validation (DV) modules of the Kepler pipeline. The PLTI quantification of the Kepler pipeline's completeness has been described previously by Christiansen et al. (2015, 2016); the completeness of the final SOC 9.3 Kepler pipeline acting on the Data Release 25 (DR25) light curves is described by Christiansen (2017).2. Injection of multiple transit signals per target into the normalized flux time series data with a subsequent transit search using a stream-lined version of the Transiting Planet Search (TPS) module. This test, hereafter referred to as flux-level transit injection (FLTI), is the subject of this document. By running a heavily modified version of TPS, FLTI is able to perform many injections on selected targets and determine in some detail which injected signals are recoverable. Significant numerical efficiency gains are enabled by precomputing the data conditioning steps at the onset of TPS and limiting the search parameter space (i.e., orbital period, transit duration, and ephemeris zero-point) to a small region around each injected transit signal.The PLTI test has the advantage that it follows transit signals through all processing steps of the Kepler pipeline, and the recovered signals can be further classified as planet candidates or false positives in the exact same manner as detections from the nominal (i.e., observed) pipeline run (Twicken et al., 2016, Thompson et al., in preparation). To date, the PLTI test has been the standard means of measuring pipeline completeness averaged over large samples of targets (Christiansen et al., 2015, 2016; Christiansen, 2017). However, since the PLTI test uses only one injection per target, it does not elucidate individual-target variations in pipeline completeness due to differences in stellar properties or astrophysical variability. Thus, we developed the FLTI test to provide a numerically efficient way to fully map individual targets and explore the performance of the pipeline in greater detail. The FLTI tests thereby allow a thorough validation of the pipeline completeness models (such as window function (Burke and Catanzarite, 2017a), detection efficiency (Burke Catanzarite, 2017b), etc.) across the spectrum of Kepler targets (i.e., various astrophysical phenomena and differences in instrumental noise). Tests during development of the FLTI capability revealed that there are significant target-to-target variations in the detection efficiency.

DR25↗

DOE OSTI2022

Nonlinear dimension reduction for surrogate modeling using gradient information

We introduce a method for the nonlinear dimension reduction of a high-dimensional function $u:{\mathbb{R}}^d\rightarrow{\mathbb{R}}$, $d\gg 1$. Our objective is to identify a nonlinear feature map $g:{\mathbb{R}}^d\rightarrow{\mathbb{R}}^m$, with a prescribed intermediate dimension $m\ll d$, so that $u$ can be well approximated by $f\circ g$ for some profile function $f:{\mathbb{R}}^m\rightarrow{\mathbb{R}}$. We propose to build the feature map by aligning the Jacobian $\nabla g$ with the gradient $\nabla u$, and we theoretically analyze the properties of the resulting $g$. Once $g$ is built, we construct $f$ by solving a gradient-enhanced least squares problem. Our practical algorithm uses a sample $\{{\textbf{x}}^{(i)},u({\textbf{x}}^{(i)}),\nabla u({\textbf{x}}^{(i)})\}_{i=1}^N$ and builds both $g$ and $f$ on adaptive downward-closed polynomial spaces, using cross validation to avoid overfitting. We numerically evaluate the performance of our algorithm across different benchmarks, and explore the impact of the intermediate dimension $m$. We show that building a nonlinear feature map $g$ can permit more accurate approximation of $u$ than a linear $g$, for the same input data set.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Forecast of Wildfire Potential Across California USA Using a Transformer

Wildfires are a major issue facing the United States, a matter further exacerbated by an ever-changing climate. In California alone, wildfires are responsible for billions of dollars in damages and take lives each year. Accurately predicting fire danger conditions allows preparation awareness before wildfires start. Transformers are a class of deep learning models designed to identify patterns in sequential datasets. In recent years, transformers have gained popularity through their impressive performance in natural language processing and other applications of signal recognition. This analysis demonstrates the ability of a transformer with a residual connection to forecast fire danger potential over the state of California. Wildland fire potential index (WFPI) maps collected from the US Geological Survey database from January 1st 2020 to December 31st 2023 were used to tune, train and evaluate the transformer. Meteorological inputs (provided by Daymet daily weather and climatological summaries), the normalized difference vegetation index (NDVI) (calculated from the Moderate Resolution Imaging Spectroradiometer (MODIS)), and outputs from the Scott and Burgman fire behavior fuel models (to characterize maps of fuel types), were used as inputs. Our results show that a transformer can effectively emulate the US Forest Service modeled WFPI maps of California USA for four week long forecasts over the month of July, 2023, with correlations ranging from 0.85 – 0.98.

Limber, Russell [ORNL]↗

DOE OSTI2023

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗