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3P Program: Phenotyping X Prediction = Productivity (Final Scientific/Technical Report)

The goal of the 3P Program was to establish integrated, real-time phenotyping and to analyze above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the Sorghum gene pool. There were two overarching themes: 1) the development of a new crop improvement approach utilizing advances in high-throughput phenotyping (HTP), computing, and genomics for public dissemination and 2) leveraging this platform for sorghum crop improvement and commercialization. The Clemson team worked on creating genomic resources and using both statistical learning and high-throughput phenotyping in genomics-assisted breeding. Research was broadly interested in the genetics of carbon partitioning, with the aim of improving crop performance and achieving sustainability. The technology and resources created can be readily found in the public domain and serve to advance scientific understanding of crop genomics and breeding. Genomic prediction was able to identify top crosses to be made, and a hybrid prediction pipeline is in place to drive year-over-year genetic gain. Roots have long been ignored by plant breeders and agronomists, not because they are unimportant but because they are hard to measure. This is an untapped white space of potential insight and innovation. To address this, Hi Fidelity Genetics developed the RootTracker to measure roots in the field on a continuous basis. A database system called RootTracker Tracker was developed to handle data coming from the RootTrackers. In using this device, valuable data was observed for plant breeding, hydrochemical development, and other agricultural biology applications. Carnegie Mellon’s goal was developing new techniques to generate high-resolution 3D models of plants from data collected in the field. The idea was that more useful and more informative phenotypes could be extracted by resolving small features, such as seeds and flowers, and that by modeling in 3D, the spatial structure of plants could be examined. To achieve this, multiple images collected by a new small format structured light stereo imager were fused together. A sorghum panicle modeling pipeline was developed to allow the collection and processing of data. Carolina Seed Systems is an agricultural technology company focused on decarbonizing the agricultural system. Their technology pipeline serves to drive fundamental progress towards creation and distribution of carbon negative crops. The genomic and the engineering technology developed through the 3P Program was leveraged to deliver both value and sustainability from the grower to the consumer. Promising sorghum hybrids were scaled up and commercialized. The overall goal of our research was to integrate, create, and deploy genetic and engineering concepts and technologies to enhance crop productivity in a sustainable fashion. The combination of public and private partners allowed the basic research and hypothesis testing to be quickly accelerated for commercial application by the companies yet maintained that the core framework and academic insights remain in the public domain for continued market disruption, competition, and innovation.

59 BASIC BIOLOGICAL SCIENCES↗

A spatially regularized detector for emergent/re-emergent disease outbreaks

Early detection of outbreaks caused by emergent pathogens, using epidemiological surveillance data i.e., daily case counts, is difficult. This is because the data tend to be noisy during the early epoch of the outbreak. In contrast, the spread-rate of the disease tends to be well-behaved, as it depends only on the mixing patterns of the population and the characteristics of the pathogen, neither of which behave erratically in space-time. In this report, we explore whether the spread-rate can be used for epidemiological surveillance, conditional on case count data. Estimating the spread-rate from case count data allows us to exploit exogenous information, e.g., incubation period distributions etc., which can considerably smooth out any erratic temporal behavior. Further, epidemiological dynamics are spatially correlated, and if case counts are available for multiple areal units e.g., counties, these correlations could potentially be used to suppress noise in the early epoch data. These exogenous information and structure are not exploited by conventional syndromic surveillance detectors to extract a well-behaved latent variable for monitoring purposes. The technical challenge lies in the estimation of the spread-rate field jointly over a collection of areal units; further, the spread-rate varies over time. We develop a method based on mean-field variational inference to approximately estimate the spread-rate field, using a Gaussian Random Field Model for spatial regularization. The method is tested on the estimation of spread-rate in the thirty-three counties of New Mexico and detect the arrival of the Fall 2020 COVID-19 wave in September 2020. We find that the method is scalable, but underestimates the uncertainty in the estimated spread-rate field. We detect the arrival of the Fall 2020 wave a week ahead of conventional syndromic surveillance algorithms, but our simplistic detection algorithm, based on simple anomaly detection, suffers from a high false positive rate, similar to conventional detectors.

59 BASIC BIOLOGICAL SCIENCES↗

Multimodal Atomic Force Microscopy for the Characterization of Metallic Particulates

This study investigates the utility of multimodal, or functional, atomic force microscopy (AFM) for the characterization of individual particles and particle ensembles. In single-particle analyses, AFM imaging modes provided orthogonal insights into mechanical and magnetic properties that are not accessible through conventional electron microscopy. Although the experiments were inherently delicate and time-intensive, with an observed sample loss rate of approximately 30%, these techniques enabled the qualitative differentiation of grain structures and magnetic domains, underscoring the challenges of experimental robustness. For particle ensembles, AFM enabled the extraction of reliable 2D and 3D particle size distributions. However, efforts to chemically differentiate particles based on mechanical property contrasts were limited by scaling effects and the qualitative nature of the data. Overall, multimodal AFM offers valuable complementary information, but its application requires careful consideration of methodological limitations, particularly for sample integrity, calibration, and scalability of mechanical and magnetic measurements. This report is organized to first address the application of AFM to single-particle analysis using various imaging modalities, followed by its potential role in ensemble-level particle screening and differentiation.

36 MATERIALS SCIENCE↗

Tritium Transport Phenomena in Molten-Salt Reactors

In this work, we review phenomena relevant to tritium transport in molten-salt reactors, which produce tritium from lithium and beryllium salts at significantly higher levels than other reactor types. Modeling of such phenomena began following MSRE operations, and these early models attempted to predict measured tritium distributions in the MSRE, accounting for turbulent mass-transport processes (using established heat transfer correlations), permeation through a variety of metal structures such as heat exchanger tubes, and transport to and from bubbles introduced into the salt by gas sparging. The models reasonably reproduced the MSRE data, but did so best when the permeability of structures was reduced by about a factor of 1,000. This issue does not appear to have been conclusively resolved, and all of the more recent attempts to model tritium transport in molten salts appear to make use of the same methodology. MSRE remains, however, essentially our only source of integral tritium transport data relevant to MSRs. Here, we generalize the MSRE approach to permeation in order to include potential rate-limiting effects at interfaces, as well the effects of added hydrogen. Appropriately non-dimensionalized, this system of equations identifies two dimensionless numbers whose relative values clearly delineate the conditions under which mass transport, surface effects, permeation, and hydrogen swamping are expected to become rate-limiting. We also describe the preliminary conceptual design of a forced convection FLiBe loop, into which tritium would be introduced for the purpose of providing validation data for such a model. The primary purpose of this is to investigate the coupled transport phenomena described above and identify those that are rate-limiting in MSRs. Additional test section configurations are described that would address other transport phenomena relevant to MSRs, including bubbly flows and graphite interactions.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

XPCA - R Implementation

Principal component analysis (PCA) is arguably the most popular tool in multivariate exploratory data analysis. We consider the question of how to handle heterogeneous variables that include continuous, binary, and ordinal. In the probabilistic interpretation of low-rank PCA, the data has a normal multivariate distribution and, therefore, normal marginal distributions for each column. If some marginals are continuous but not normal, the semiparametric copula-based principal component analysis (COCA) method is an alternative to PCA that combines a Gaussian copula with nonparametric marginals. If some marginals are discrete or semi-continuous, we present a new extended PCA (XPCA) method that also uses a Gaussian copula and nonparametric marginals and accounts for discrete variables in the likelihood calculation by integrating over appropriate intervals. Like PCA, the factors produced by XPCA can be used to find latent structure in data, build predictive models, and perform dimensionality reduction. We implement the new model, XPCA, and its ancestors PCA and COCA in both R and Python. This software provides implementations of XPCA, COCA, and probabilistic PCA in both R and Python. XPCA is written in arXiv report https://arxiv.org/abs/1808.07510. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. SAND2019-10591 M

Kincher-Winoto, Kina↗

XPCA -Python Implementation

Principal component analysis (PCA) is arguably the most popular tool in multivariate exploratory data analysis. We consider the question of how to handle heterogeneous variables that include continuous, binary, and ordinal. In the probabilistic interpretation of low-rank PCA, the data has a normal multivariate distribution and, therefore, normal marginal distributions for each column. If some marginals are continuous but not normal, the semiparametric copula-based principal component analysis (COCA) method is an alternative to PCA that combines a Gaussian copula with nonparametric marginals. If some marginals are discrete or semi-continuous, we present a new extended PCA (XPCA) method that also uses a Gaussian copula and nonparametric marginals and accounts for discrete variables in the likelihood calculation by integrating over appropriate intervals. Like PCA, the factors produced by XPCA can be used to find latent structure in data, build predictive models, and perform dimensionality reduction. We implement the new model, XPCA, and its ancestors PCA and COCA in both R and Python. This software provides implementations of XPCA, COCA, and probabilistic PCA in both R and Python. XPCA is written in arXiv report https://arxiv.org/abs/1808.07510. SAND2019-10591 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Kincher-Winoto, Kina↗

Multi-GPU immersed boundary method hemodynamics simulations

Large-scale simulations of blood flow that resolve the 3D deformation of each comprising cell are increasingly popular owing to algorithmic developments in conjunction with advances in compute capability. Among different approaches for modeling cell-resolved hemodynamics, fluid structure interaction (FSI) algorithms based on the immersed boundary method are frequently employed for coupling separate solvers for the background fluid and the cells within one framework. GPUs can accelerate these simulations; however, both current pre-exascale and future exascale CPU-GPU heterogeneous systems face communication challenges critical to performance and scalability. In this paper, we describe, to our knowledge, the largest distributed GPU-accelerated FSI simulations of high hematocrit cell-resolved flows with over 17 million red blood cells. We compare scaling on a fat node system with six GPUs per node and on a system with a single GPU per node. Through comparison between the CPU- and GPU-based implementations, we identify the costs of data movement in multiscale multi-grid FSI simulations on heterogeneous systems and show it to be the greatest performance bottleneck on the GPU.

97 MATHEMATICS AND COMPUTING↗

The Role of the U.S. Electric Distribution System in Serving Data Center and Other Large Loads

The rapid expansion of data centers in the United States is reshaping how the electric distribution system must plan for and accommodate large load interconnections. This report evaluates the role of the distribution grid in serving these loads, from small edge facilities to hyperscale campuses. Using national datasets, utility filings, and industry studies, we assess demand growth, reliability requirements, interconnection thresholds, and infrastructure needs at substations and feeders. The analysis highlights the mismatch between fast data center development timelines and slower utility planning and construction cycles, as well as strategies such as phased energization, on-site generation, hosting capacity maps, and structured interconnection frameworks. While focused on data centers, the insights also apply to other high-density loads such as advanced manufacturing, hydrogen production, and electrified transportation. The report concludes with approaches to align planning processes, transparency tools, and regulatory frameworks so utilities can manage new large loads in ways that support a reliable and resilient grid.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

The Complete Calibration of the Color–Redshift Relation (C3R2) Survey: Survey Overview and Data Release 1

A key goal of the Stage IV dark energy experiments Euclid , LSST, and WFIRST is to measure the growth of structure with cosmic time from weak lensing analysis over large regions of the sky. Weak lensing cosmology will be challenging: in addition to highly accurate galaxy shape measurements, statistically robust and accurate photometric redshift (photo- z ) estimates for billions of faint galaxies will be needed in order to reconstruct the three-dimensional matter distribution. Here we present an overview of and initial results from the Complete Calibration of the Color–Redshift Relation (C3R2) survey, which is designed specifically to calibrate the empirical galaxy color–redshift relation to the Euclid depth. These redshifts will also be important for the calibrations of LSST and WFIRST . The C3R2 survey is obtaining multiplexed observations with Keck (DEIMOS, LRIS, and MOSFIRE), the Gran Telescopio Canarias (GTC; OSIRIS), and the Very Large Telescope (VLT; FORS2 and KMOS) of a targeted sample of galaxies that are most important for the redshift calibration. We focus spectroscopic efforts on undersampled regions of galaxy color space identified in previous work in order to minimize the number of spectroscopic redshifts needed to map the color–redshift relation to the required accuracy. We present the C3R2 survey strategy and initial results, including the 1283 high-confidence redshifts obtained in the 2016A semester and released as Data Release 1.

79 ASTRONOMY AND ASTROPHYSICS↗

Path-space variational inference for non-equilibrium coarse-grained systems

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structure and Oxygen Evolution Activity of β-NiOOH: Where Are the Protons?

Ni oxides and oxyhydroxides (NiO x ) have been studied for a long time as cathode materials for alkaline batteries and electrocatalysts for the oxygen evolution reaction (OER). Yet, understanding of the connection between their atomic and electronic structures and electrochemical performance or stability is still incomplete. In this work, we use first-principles density functional theory (DFT) calculations to revisit the structure, electronic properties, and OER activity of β-NiOOH, the catalytically active phase of NiO x . Following extensive DFTbased screening, we identify a hitherto overlooked structure characterized by a uniform distribution of H atoms on the NiO 2 layers. All the Ni 3+ cations in this structure exhibit an identical t g 6 e g 1 electronic configuration with an occupied 3d z2 orbital. Comparison of the calculated bond lengths with extended X-ray absorption fine structure (EXAFS) data unequivocally supports this structure relative to all other low-energy configurations. Based on this structure, we uncover and detail defect-dominated OER mechanisms on the basal β-NiOOH (001) surface, with overpotentials as low as 0.39 V. The present results should provide a valuable contribution to ongoing efforts for understanding and developing enhanced transition-metal hydroxide catalysts for the OER.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A small core in Vesta inferred from Dawn’s observations

Vesta’s large-scale interior structure had previously been constrained primarily using the gravity and shape data from the Dawn mission. However, these data alone still allow a wide range of possibilities for the differentiation state of the body. The moment of inertia is arguably the most diagnostic parameter related to the radial density distribution of a planetary body, making it crucial for assessing the body’s state of internal differentiation. Determining the moment of inertia requires additional measurements of the amplitudes of small rotational motions, such as precession and nutation. Here we report an updated estimate of the moment of inertia of Vesta inferred from Dawn’s Doppler tracking via the Deep Space Network and onboard imaging data. The recovered value for Vesta’s normalized polar moment of inertia is $\overline{C}$/MR 2 = 0.4208 ± 0.0047 (where M is the mass of Vesta and R is the reference radius), which is only 6.6% lower than the homogeneous value of 0.4505. This value, combined with the gravity field and global shape, suggests that Vesta’s interior has limited density stratification beneath its howardite–eucrite–diogenite-dominated crust. We propose two possible origin scenarios that are consistent with the observed constraints. In the first scenario, Vesta’s interior did not undergo full differentiation due to late accretion. In the second scenario, Vesta originated as an impact remnant of a larger differentiated body re-accreted with non-chondritic bulk composition produced from a catastrophic impact. Vesta did not experience complete differentiation in either scenario, suggesting that its current state reflects a complex interplay between its accretion timing, thermal evolution, redistribution of 26 Al bearing melt and/or impact processes.

CNEOS 2014-01-08 bolide↗

Structural constraint integration in a generative model for the discovery of quantum materials

Billions of organic molecules have been computationally generated, yet functional inorganic materials remain scarce due to limited data and structural complexity. Here, in this work, we introduce Structural Constraint Integration in a GENerative model (SCIGEN), a framework that enforces geometric constraints, such as honeycomb and kagome lattices, within diffusion-based generative models to discover stable quantum materials candidates. SCIGEN enables conditional sampling from the original distribution, preserving output validity while guiding structural motifs. This approach generates ten million inorganic compounds with Archimedean and Lieb lattices, over 10% of which pass multistage stability screening. High-throughput density functional theory calculations on 26,000 candidates shows over 95% convergence and 53% structural stability. A graph neural network classifier detects magnetic ordering in 41% of relaxed structures. Furthermore, we synthesize and characterize two predicted materials, TiPd 0.22 Bi 0.88 and Ti 0.5 Pd 1.5 Sb, which display paramagnetic and diamagnetic behaviour, respectively. Our results indicate that SCIGEN provides a scalable path for generating quantum materials guided by lattice geometry.

36 MATERIALS SCIENCE↗

Effect of rare earth size on network structure and glass forming ability in binary aluminum garnets

Rare earth aluminate glasses are potentially useful for optical, luminescence, and laser applications. As reluctant glass formers, these materials exhibit unconventional atomic structures. To better understand how their structures correlate with glass formation, we investigate two rare earth aluminum garnet melts, La 3 Al 5 O 12 (LAG) and Yb 3 Al 5 O 12 (YbAG), which represent the relative extremes of good and poor glass forming ability in rare earth aluminates. Structural models have been refined to high-energy X-ray diffraction data over 1340–2740 K. Both melts contain mixtures of AlO 4 , AlO 5 , and AlO 6 polyhedra, with larger fractions of [5] Al and [6] Al in YbAG. Extrapolation of the Al–O coordination distributions to the glass transition match closely with 27 Al nuclear magnetic resonance measurements of (La 1−z Y z ) 3 Al 5 O 12 glasses, z = 0 to 1. During cooling, the mean coordination numbers increase for La–O in LAG from 6.45(8) to 6.98(8) and for Yb–O in YbAG from 6.02(8) to 6.21(8). Linkedness among Al–O polyhedra at ∼2450 K is mostly corner-sharing, with 9% edge-sharing in LAG and 19% in YbAG. Among [4] Al units, both melts have 6% edge-sharing that convert to all corner-sharing upon cooling. Network connectivity is compared using a newly defined metric, K n , that is similar to the Q n distribution but that accounts for the edge-sharing and triply bonded oxygen present in these melts. The lower glass forming ability in YbAG as compared to LAG correlates with more edge-sharing, associated with the larger fractions of [5] Al and [6] Al, and lower connectivity among [4] Al units.

Wilke, Stephen K. [Materials Development, Inc., Ar↗

Pore2Chip: All-in-one python tool for soil microstructure analysis and micromodel design

The Pore2Chip Python package is designed to create 2D micromodels using extracted data from 3D X-ray computed tomography (XCT) images. This package helps analyze soil structure and function, allowing for the investigation of hydro-biogeochemical processes that impact mineral extraction and reactivity, oxygen concentrations, and nutrient availability in disturbed or managed soils. Key metrics encompass pore size distributions, pore throat size distributions, and connectivity (pore coordination numbers). The final output is a 2D scalable SVG design representing a core or aggregate. Designs can be fabricated with methods such as laser etching, 3D printing, and photolithography.

lab-on-chip↗

A Semi-supervised Hybrid Machine Learning Framework for the Qualification of Resistance Spot Welds

• Industries requiring high structural integrity, including automotive, aerospace, and construction, place considerable significance on weld quality classification. • The inspection normally involves human expertise through predefined quality metrics that are subjective, error-prone, and time-intensive • The challenge to classification model development is the scarcity of labeled data and imbalanced distributions in the data that are labeled. • This work develops a new hybrid methodology that achieves clustering using KMeans++ together with supervised classification to overcome these challenges. • The ensemble-based classifiers were identified as optimal, with accuracy enhancements of up to 8% using the pseudo-labeled dataset. • The work provides practical insight into feature engineering and machine learning integration in industrial quality assurance applications.

Rogers, Jeremy K. [Savannah River National Laborat↗

Multiwavelength study of the star formation in the S237 H ii region

We present a detailed multiwavelength study of observations from X-ray, near-infrared, and centimeter wavelengths to probe the star formation processes in the S237 region. Multiwavelength images trace an almost sphere-like shell morphology of the region, which is filled with the 0.5–2 keV X-ray emission. The region contains two distinct environments—a bell-shaped cavity-like structure containing the peak of 1.4 GHz emission at center, and elongated filamentary features without any radio detection at edges of the sphere-like shell—where Herschel clumps are detected. Using the 1.4 GHz continuum and {sup 12}CO line data, the S237 region is found to be excited by a radio spectral type of B0.5V star and is associated with an expanding H ii region. The photoionized gas appears to be responsible for the origin of the bell-shaped structure. The majority of molecular gas is distributed toward a massive Herschel clump (M{sub clump} ∼ 260 M{sub ⊙}), which contains the filamentary features and has a noticeable velocity gradient. The photometric analysis traces the clusters of young stellar objects (YSOs) mainly toward the bell-shaped structure and the filamentary features. Considering the lower dynamical age of the H ii region (i.e., 0.2–0.8 Myr), these clusters are unlikely to be formed by the expansion of the H ii region. Our results also show the existence of a cluster of YSOs and a massive clump at the intersection of filamentary features, indicating that the collisions of these features may have triggered cluster formation, similar to those found in the Serpens South region.

79 ASTRONOMY AND ASTROPHYSICS↗

Angular Dependence of Drell-Yan in the SeaQuest Experiment using Deep Neural Network-Based Reconstruction

The SeaQuest and SpinQuest experiments at Fermilab were designed to probe the internal dynamics of protons and neutrons via the angular dependence of muons created by colliding 120 GeV protons into stationary targets. To do this, it is necessary to translate the detector data into coherent information about the particles detected in the experiment. This dissertation describes the development and implementation of QTracker, a neural network-based algorithm designed to reconstruct muons. The application of QTracker to experimental data yields improved reconstruction of muon tracks, allowing for a more precise investigation of the transverse momentum distributions and angular modulations in the Drell-Yan process. This work highlights the potential of neural network-based methods to advance particle tracking and enhance our understanding of nucleon structure.

Conover, Arthur↗