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Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗

An extended numerical manifold method for unsaturated soil-water interaction analysis at micro-scale

To investigate unsaturated soil-water interaction at micro-scale, this work extends the numerical manifold method (NMM) by incorporating a soil-water coupling model considering specific capillary water distribution and capillary force calculation. The soil skeleton is constructed by a soil skeleton generation algorithm with random polygons. To more realistically capture the interaction between soil grains and capillary water, a capillary mechanics-based geometric algorithm is proposed to iteratively calculate the capillary water distribution. The capillary forces corresponding to the capillary water distribution are calculated based on the Young-Laplace equation. The proposed capillary water solving framework is first verified by reproducing the soil-water characteristic curve and the capillary water distribution of an ideal contact-disk model against analytical solutions. To further validate the ability of the capillary water solving framework to predict hydraulic behavior of the real soil, a laboratory test on the Toyoura sand is reproduced numerically. Then an ideal direct shear test is performed to further validate the two-way soil-water coupling procedure, in which a comparison between the numerical and analytical results regarding the shear strength and matric suction is presented. Finally, microscopic hydraulic and compression tests are conducted on two soil specimens with the same porosity and mean grain diameter but different uniformity coefficients. The results elucidate that the extended method is a potential tool to explore unsaturated soil behaviors at micro-scale.

58 GEOSCIENCES↗

Reinforcement learning for real-time process control in high-temperature superconductor manufacturing

With high efficiency and low energy loss, high-temperature superconductors (HTS) have demonstrated their profound applications in various fields, such as medical imaging, transportation, accelerators, microwave devices, and power systems. The high-field applications of HTS tapes have raised the demand for producing cost-effective tapes with long lengths in superconductor manufacturing. However, achieving the uniform and enhanced performance of a long HTS tape is challenging due to the unstable growth conditions in the manufacturing process. Although it is confirmed that the process parameters during the advanced metal organic chemical vapor deposition (A-MOCVD) process influence the uniformity of the produced HTS tapes, the high-dimensional process parameter signals and their complicated interactions make it difficult to develop an effective control policy. In this paper, we propose a local measure for the uniformity of HTS tapes to provide instant feedback for our control policy. Then, we model the manufacturing of HTS tapes as a Markov decision process (MDP) with continuous state and action spaces to assess the instant reward in real time in our feedback control model. As our MDP involves continuous and high-dimensional state and action spaces, a neural fitted Q-iteration (NFQ) algorithm is adopted to solve the MDP with artificial neural network (ANN) function approximation. The collinearity of process parameters can restrict our capability of adjusting the process parameters, which is addressed by the principal component analysis (PCA) in our method. The control policy adjusts the PCA of process parameters using the NFQ algorithm. In conclusion, based on our case studies on real A-MOCVD dataset, the obtained control policy increases the average uniformity of tapes by 5.6% and performs especially well on sample HTS tapes with a low uniformity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational Prediction of Water Sorption in Facilitated Transport Membranes

Polymeric facilitated transport membranes (FTMs) have emerged as an innovative class of promising carbon capture technology. Studies have shown that the transport properties of an FTM are significantly influenced by its water uptake. In order to better quantify FTM performance, we herein explore the potential of computational techniques to predict the equilibrium water uptake values of FTMs. Two prediction approaches were examined. First, the water sorption was explicitly simulated by iteratively conducting grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Second, the water sorption was predicted based on the chemical potential of the adsorbed water, which was calculated using the Widom insertion or continuous fractional component Monte Carlo (CFCMC) method. The chemical potential-based approach with CFCMC demonstrated good prediction of the equilibrium water uptake values of FTMs with poly(N-vinylformamide-co-vinylamine) as fixed-site carrier and 2-(1-piperazinyl)ethylamine sarcosinate as mobile carrier. The predicted water uptake values increased with increasing mobile carrier content and were in good agreement with the experimental values. Furthermore, the higher water uptake promoted the diffusion of CO 2 , N 2 , and mobile carrier as well as slightly stifled the sorption of N 2 . Such an approach significantly contributes to a more comprehensive theoretical evaluation of FTMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine learning interatomic potential for silicon-nitride (Si 3 N 4 ) by active learning

Silicon nitride (Si 3 N 4 ) is an extensively used material in the automotive, aerospace, and semiconductor industries. However, its widespread use is in contrast to the scarce availability of reliable interatomic potentials that can be employed to study various aspects of this material on an atomistic scale, particularly its amorphous phase. In this work, we developed a machine learning interatomic potential, using an efficient active learning technique, combined with the Gaussian approximation potential (GAP) method. Our strategy is based on using an inexpensive empirical potential to generate an initial dataset of atomic configurations, for which energies and forces were recalculated with density functional theory (DFT); thereafter, a GAP was trained on these data and an iterative re-training algorithm was used to improve it by learning on-the-fly. When compared to DFT, our potential yielded a mean absolute error of 8 meV/atom in energy calculations for a variety of liquid and amorphous structures and a speed-up of molecular dynamics simulations by 3–4 orders of magnitude, while achieving a first-rate agreement with experimental results. Our potential is publicly available in an open-access repository.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Distribution System State Estimation Using a Multiple Iteration Extended Kalman Filter Approach

To support the operation of modern distribution systems, operators require real-time visibility into system states. Due to a lack of measurements and unbalanced operation, the state estimation in distribution systems is challenging as compared to transmission systems. This paper proposes the utilization of a Multiple Iteration - Extended Kalman Filter based approach for the distribution system state estimation. This modified version of the baseline extended Kalman filter iterates over the update step multiple times thereby reducing the estimation error. The proposed algorithm along with the auxiliary algorithms such as bad data detection is integrated into a co-simulation environment. Case studies show that the proposed state estimation method can result in a lesser estimation error as compared to the baseline approach.

Bhatti, Bilal Ahmad↗

Organic matter concentration and composition of experimentally burned open air and muffle furnace vegetation chars across differing burn severity and feedstock types from Pacific Northwest, USA (v4).

This dataset represents results from an experimental study designed to compare how the chemical composition of organic matter changes across different burn conditions and feedstock materials. The dataset provides both solid and dissolved phase bulk concentration and organic matter characterization data from experimentally generated chars. Chars were created in a closed muffle furnace or on an open burn table from four different feedstock species representing vegetation commonly impacted by fire regimes across the Pacific Northwest, USA. This data can be used to compare how different burn conditions may influence resultant organic matter chemistry and help further our understanding of potential biogeochemical impacts on river corridors post-fire. This dataset is comprised of one data package readme, one data dictionary (dd), one file level metadata (flmd), fourteen burn table videos, burn table video metadata and three folders containing (A) data; (B) metadata and protocols; and (C) photos. The folder names and the file name of the data package readme include a version number which will be updated with future iterations of this data package. The data folder includes (1) solid carbon and solid nitrogen; (2) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and total dissolved nitrogen (TN); (3) pH; (4) thermocouple time series temperature; (5) methods codes; (6) installation methods; (7) excitation emissions matrix (EEM) methods information; (8) a folder of excitation emissions matrix (EEM) fluorescence and absorbance spectra in dissolved organic matter and EEMs processing instructions; (9) solid state carbon-13 and solution state phosphorus nuclear magnetic resonance (13-C NMR and 31-P NMR) data and methods; (10) benzene polycarboxylic acid (BPCA) concentration and stable isotope data; (11) FTICR-MS methods; (12) Inductively coupled plasma (ICP) data for total calcium, magnesium, iron, aluminum, potassium, phosphorus, sodium, and sulfur along with sodium hydroxide-ethylenediaminetetraacetic acid (sodium hydroxide-EDTA) extractable calcium, magnesium, iron, aluminum, potassium, phosphorus, and sulfur; (13) a folder of phosphorus, carbon, and nitrogen X-ray absorption near edge structure (P-XANES, N-XANES, C-XANES) data for samples and standards; (14) P-XANES, N-XANES, C-XANES methods; (15) molybdate reactive phosphorus; and (16) folder of high resolution characterization of organic matter via 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains .txt data files and a subfolder containing instruments for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. The metadata and protocols folder includes (1) international geo-sample number (IGSN) mapping file (2) burn and laboratory metadata; (3) burn protocol; (4) laboratory protocol; (5) vegetation collection metadata; and (6) vegetation collection protocol. The folder contains photos of the solid chars. All files are .csv, .txt, .pdf, .jpg, .jpeg, .R, .ref, or .mp4. The data package was originally published October 2022 (v1). It was updated April 2023 (v2; new data files), September 2023 (v3; new and corrected data files), and September 2024 (v4; new and added/updated files). Metadata files were also updated to reflect these changes. See the change history section in the readme for more details.

54 ENVIRONMENTAL SCIENCES↗

Topology Optimization with a Manufacturability Objective

Part distortion and residual stress are critical factors for metal additive manufacturing (AM) because they can lead to high failure rates during both manufacturing and service. We present a topology optimization approach that incorporates a fast AM process simulation at each design iteration to provide predictions of manufacturing outcomes (i.e., residual stress, distortion, residual elastic energy) that can be optimized or constrained. The details of the approach and implementation are discussed, and an example design is presented that illustrates the efficacy of the method.

42 ENGINEERING↗

Energy Storage Impacts in Resilience Hubs and Other Critical Infrastructure: An Assessment Guide for Developers and Practitioners

Battery energy storage systems (BESS) deployed behind the meter at resilience hubs and other critical infrastructure can provide economic and operational value during normal operations—such as lower and more predictable energy costs—as well as resilience and security benefits during power disruptions by maintaining essential services. However, existing evaluation approaches tend to focus narrowly on engineering performance or rely on broad socio-economic frameworks that are not well suited to behind-the-meter storage. As a result, developers, utilities, and funders often lack consistent methods for defining success, quantifying benefits, and comparing outcomes across projects. This report presents a practitioner-oriented impact assessment framework for evaluating behind-the-meter BESS at resilience hubs and critical infrastructure facilities. The framework is organized into five iterative components—developing an action plan, defining project goals, identifying metrics, collecting data and measuring outcomes, and reporting and using results—and includes a structured metric architecture spanning six impact categories. Designed for real-world constraints such as limited staffing and uneven data availability, the framework was developed, applied, and refined through real projects, and is illustrated with case studies across diverse deployment contexts.

Impact Assessment↗

The XFaster Power Spectrum and Likelihood Estimator for the Analysis of Cosmic Microwave Background Maps

We present the XFaster analysis package, XFaster is a fast, iterative angular power spectrum estimator based on a diagonal approximation to the quadratic Fisher matrix estimator. XFaster uses Monte Carlo simulations to compute noise biases and filter transfer functions and is thus a hybrid of both Monte Carlo and quadratic estimator methods. In contrast to conventional pseudo-C ℓ based methods, the algorithm described here requires a minimal number of simulations, and does not require them to be precisely representative of the data to estimate accurate covariance matrices for the bandpowers. The formalism works with polarization-sensitive observations and also data sets with identical, partially overlapping, or independent survey regions. The method was first implemented for the analysis of BOOMERanG data (Netterfield et al. 2002; Jones et al. 2006), and also used as part of the Planck analysis (Rocha et al. 2011). Here, we describe the full, publicly available analysis package, written in Python, as developed for the analysis of data from the 2015 flight of the SPIDER instrument (SPIDER Collaboration 2021). The package includes extensions for self-consistently estimating null spectra and for estimating fits for Galactic foreground contributions. We show results from the extensive validation of XFaster using simulations, and its application to the SPIDER data set.

79 ASTRONOMY AND ASTROPHYSICS↗

A Regularized Variance-Reduced Modified Extragradient Method for Stochastic Hierarchical Games

We consider an N -player hierarchical game in which the i th player’s objective comprises of an expectation-valued term, parametrized by rival decisions, and a hierarchical term. Such a framework allows for capturing a broad range of stochastic hierarchical optimization problems, Stackelberg equilibrium problems, and leader-follower games. We develop an iteratively regularized and smoothed variance-reduced modified extragradient framework for iteratively approaching hierarchical equilibria in a stochastic setting. We equip our analysis with rate statements, complexity guarantees, and almost-sure convergence results. We then extend these statements to settings where the lower-level problem is solved inexactly and provide the corresponding rate and complexity statements. Our model framework encompasses many game theoretic equilibrium problems studied in the context of power markets. We present a realistic application to the study of virtual power plants, emphasizing the role of hierarchical decision making and regularization. Preliminary numerics suggest that empirical behavior compares well with theoretical guarantees.

Tikhonov regularization↗

More Than 30 000-fold Field Enhancement of Terahertz Nanoresonators Enabled by Rapid Inverse Design

The rapid development of 6G communications using terahertz (THz) electromagnetic waves has created a demand for highly sensitive THz nanoresonators capable of detecting these waves. Among the potential candidates, THz nanogap loop arrays show promising characteristics but require significant computational resources for accurate simulation. This requirement arises because their unit cells are 10 times smaller than millimeter wavelengths, with nanogap regions that are 1 000 000 times smaller. To address this challenge, we propose a rapid inverse design method using physics-informed machine learning, employing double deep Q-learning with an analytical model of the THz nanogap loop array. In ~39 h on a middle-level personal computer, our approach identifies the optimal structure through 200 000 iterations, achieving an experimental electric field enhancement of 32 000 at 0.2 THz, 300% stronger than prior results. In conclusion, our analytical model-based approach significantly reduces the amount of computational resources required, offering a practical alternative to numerical simulation-based inverse design for THz nanodevices.

21 terahertz time-domain spectroscopy↗

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si$_2$H$_6$ which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MHD, disruptions and control physics: Chapter 4 of the special issue: on the path to tokamak burning plasma operation

In this chapter, we review the progress in MHD stability, disruptions and control in magnetic fusion research that has occurred over the past (more than) one and a half decades since the publication by Hender et al in 2007 on the same topic as part of the update of ITER Physics Basis. During this period, remarkable progress has been achieved in the understanding of the basic physics and overall control of MHD instabilities through a wide spectrum of dedicated experiments, theory and modeling. The sawtooth activities are probably today one of the best understood of MHD events and very robust control schemes have been developed for reliable operation of tokamaks through core heating. Similarly, significant improvements have been achieved in understanding and control of neoclassical tearing modes, resistive wall modes or locked modes and their control through ECCD or error field control. The field of disruption prediction through application of artificial intelligence, machine learning or deep learning methods, which had already started at the time of the 2007 review, has progressed significantly due to general progress in these fields and application of newer, more sophisticated algorithms. However, although remarkable progress has been achieved in the field of Disruptions, their understanding, prediction, possible avoidance and mitigation still remain probably the most active fields of R&D globally in this field. This is especially because reactor grade machines like ITER and DEMO will be much less tolerant in respect of disruptions and runaway currents, and their occurrences must be either avoided altogether or minimized to an acceptable value without causing any significant hindrance to robust machine operations. This review is intended to present a broad spectrum of the R&D that has occurred in this field in support of ITER, which will also be of immense significance for all future machines, especially reactors like DEMO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Beyond Taylor’s hypothesis: a novel volumetric reconstruction of velocity and density fields for variable‑density and shear flows

Abstract This work presents a novel numerical procedure for reconstructing volumetric density and velocity fields from planar laser-induced fluorescence (PLIF) and stereoscopic particle image velocimetry (SPIV) data. This new method is theoretically and practically demonstrated to provide more accurate 3D vortical structures and density fields in high shear flows than reconstruction methods based on the mean convective velocity. While Taylor’s hypothesis of frozen turbulence is commonly applied by using the local mean streamwise velocity, the proposed algorithm uses the measured local instantaneous velocity for data convection. It consists of a step-by-step reconstruction based on a mixed Lagrangian–Eulerian solver that includes the 3D interpolation of scattered flow data and that relaxes the Taylor’s hypothesis by iterative enforcement of the incompressibility constraint on the velocity field. This methodology provides 3D fields with temporal resolution, spatial resolution, and accuracy comparable to that of real 3D snapshots, thus providing a practical alternative to tomographic measurements. The procedure is validated using numerical data of the constant-density channel flow available on the Johns Hopkins University Turbulence Database (JHTDB), showing the accurate reconstruction of the 3D velocity field. The algorithm is applied to an experimental dataset of PLIF and SPIV measurements of a variable-density jet flow, demonstrating its capability to provide 3D velocity and density fields that are more consistent with the Navier–Stokes equations compared to the mean flow convective method. Graphic abstract

42 ENGINEERING↗

The 1 → 3 massive splitting functions from QCD factorization and SCET

Splitting functions are universal functions describing the collinear dynamics of gauge theories, and as such are crucial ingredients for a wide variety of calculations in perturbative QCD. We present analytic results for the triple collinear splitting functions in QCD with a single massive parton. We derive the splitting functions using two distinct methods; first by expanding the squared matrix elements in the collinear limit, and secondly by using soft-collinear effective theory with massive quarks. We find agreement between these two approaches, providing a strong check of our results. Additionally, we also check all iterated and soft limits of our results, finding agreement with predictions from factorization. Our results provide an important ingredient for higher order perturbative calculations involving massive partons, and for the description of the collinear dynamics of heavy flavor jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modeling and experimental validation of dynamical effects in Bragg coherent x-ray diffractive imaging of finite crystals

Bragg coherent diffractive imaging (BCDI) is a noninvasive microscopy technique that can visualize the shape and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. Its strain imaging capability relies on Fourier transform–based iterative phase retrieval algorithms, which are mostly developed under the kinematical approximation. Such approximation prohibits the application of BCDI on larger crystals, which are commonly seen in most emerging functional materials. Understanding the dynamical effect in BCDI, as well as developing a validated method for modeling BCDI at the dynamical diffraction limit, is crucial for applying BCDI to hierarchical systems that contain micron-sized crystals and grains. Thus we report a comparative study on the impact of dynamical diffraction effects by comparing the reconstruction results from two measurements of the same crystal. Forward simulation is implemented to show subtle changes of interference fringes in the diffraction pattern due to the dynamical diffraction, and is compared directly with the experimental data.

36 MATERIALS SCIENCE↗

Few-shot leaf segmentation

In this work, we use few-shot learning to segment the body and vein architecture of Populus trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy, in some cases exceeding even human-level segmentation. The leaf and vein segmentations are subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the "vein density" trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code, we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes.

Lagergren, John [Oak Ridge National Lab. (ORNL), O↗