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At least 685 records · Page 38

JGI Plant Transformation Workshop, May 20-21, 2025

Domestic biomass crops such as sorghum, switchgrass, Miscanthus, and poplar can provide United States industries with renewable feedstocks while also supporting low-input farming systems and strengthening supply chains for biofuels, biochemicals and biomaterials. The U.S. leads globally in biomass crop genomics, yet progress in engineering traits is constrained by slow, genotype-dependent transformation methods and lengthy Design-Build-Test-Learn (DBTL) cycles. At a May 2025 workshop, a panel of experts recommended establishing a DOE Plant Transformation Capability (PTC) to overcome these barriers. The PTC would unite two missions: advancing research to achieve genotype-independent, automated methods, and delivering scalable transformation services through a user-facility model. With expected gains of 10–100x in efficiency, including transformation and cost reduction, the PTC would accelerate the path from discovery to engineered plants, expand community access and training, and support downstream applications and workflows including field trials and regulatory navigation. By enabling rapid and predictable crop engineering, the PTC would strengthen U.S. supply chains, enhance industrial competitiveness, and ensure that DOE’s genomic investments deliver national impact.

09 BIOMASS FUELS↗

Oracle-Preserving Latent Flows

A fundamental task in data science is the discovery, description, and identification of any symmetries present in the data. We developed a deep learning methodology for the simultaneous discovery of multiple non-trivial continuous symmetries across an entire labeled dataset. The symmetry transformations and the corresponding generators are modeled with fully connected neural networks trained with a specially constructed loss function, ensuring the desired symmetry properties. The two new elements in this work are the use of a reduced-dimensionality latent space and the generalization to invariant transformations with respect to high-dimensional oracles. The method is demonstrated with several examples on the MNIST digit dataset, where the oracle is provided by the 10-dimensional vector of logits of a trained classifier. We find classes of symmetries that transform each image from the dataset into new synthetic images while conserving the values of the logits. We illustrate these transformations as lines of equal probability (“flows”) in the reduced latent space. These results show that symmetries in the data can be successfully searched for and identified as interpretable non-trivial transformations in the equivalent latent space.

97 MATHEMATICS AND COMPUTING↗

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling

Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N 2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A ( Candidatus Atelocyanobacterium thalassa ). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N 2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems.

59 BASIC BIOLOGICAL SCIENCES↗

A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN

Rust fungi comprise thousands of species, many of which cause disease on important crop plants. The flax rust fungus Melampsora lini has been a model species for the genetic dissection of plant immunity since the 1940s; however, the highly fragmented and incomplete reference genome has so far hindered progress in effector gene discovery. Here, we generated a fully phased, chromosome-scale assembly of the two nuclear genomes of M. lini strain CH5, resolving an additional 320 Mbp of the sequence. The 482-Mbp dikaryotic genome is at least 79% repetitive, with a large proportion (approximately 40%) of the genome comprising young, highly similar transposable elements. The assembly resolves the known effector gene loci, some of which carry complex duplications that were collapsed in the previous assembly. Using a genetic map followed by manual correction of gene models, we identified the AvrM3 and AvrN genes, which encode unusually large fungal effector proteins and trigger defense responses when co-expressed with the corresponding resistance genes. We located the genes linked to the tetrapolar mating system on chromosomes 4 and 9, but in contrast to the cereal rusts that have one pheromone receptor gene per haplotype, in flax rust, three pheromone receptor genes were found, with two of them closely linked on one haplotype. Taken together, we show that a high-quality assembly is crucial for resolving complex gene loci, and given the increasing number of fungal effectors of large size, the commonly applied criterion for effector candidates of being small proteins needs to be reconsidered.

Melampsora↗

On-the-fly autonomous control of neutron diffraction via physics-informed Bayesian active learning

We demonstrate the first live, autonomous control over neutron diffraction experiments by developing and deploying ANDiE: the autonomous neutron diffraction explorer. Neutron scattering is a unique and versatile characterization technique for probing the magnetic structure and behavior of materials. However, instruments at neutron scattering facilities in the world is limited, and instruments at such facilities are perennially oversubscribed. We demonstrate a significant reduction in experimental time required for neutron diffraction experiments by implementation of autonomous navigation of measurement parameter space through machine learning. Prior scientific knowledge and Bayesian active learning are used to dynamically steer the sequence of measurements. We show that ANDiE can experimentally determine the magnetic ordering transition of both MnO and Fe 1.09 Te all while providing a fivefold enhancement in measurement efficiency. Furthermore, in a hypothesis testing post-processing step, ANDiE can determine transition behavior from a set of possible physical models. ANDiE's active learning approach is broadly applicable to a variety of neutron-based experiments and can open the door for neutron scattering as a tool of accelerated materials discovery.

36 MATERIALS SCIENCE↗

Benchmarking the PCMCI Causal Discovery Algorithm for Spatiotemporal Systems

Causal discovery algorithms construct hypothesized causal graphs that depict causal dependencies among variables in observational data. While powerful, the accuracy of these algorithms is highly sensitive to the underlying dynamics of the system in ways that have not been fully characterized in the literature. In this report, we benchmark the PCMCI causal discovery algorithm in its application to gridded spatiotemporal systems. Effectively computing grid-level causal graphs on large grids will enable analysis of the causal impacts of transient and mobile spatial phenomena in large systems, such as the Earth’s climate. We evaluate the performance of PCMCI with a set of structural causal models, using simulated spatial vector autoregressive processes in one- and two-dimensions. We develop computational and analytical tools for characterizing these processes and their associated causal graphs. Our findings suggest that direct application of PCMCI is not suitable for the analysis of dynamical spatiotemporal gridded systems, such as climatological data, without significant preprocessing and downscaling of the data. PCMCI requires unrealistic sample sizes to achieve acceptable performance on even modestly sized problems and suffers from a notable curse of dimensionality. This work suggests that, even under generous structural assumptions, significant additional algorithmic improvements are needed before causal discovery algorithms can be reliably applied to grid-level outputs of earth system models.

54 ENVIRONMENTAL SCIENCES↗

Adaptable Standards for Discovery, Access, and Usability of Oak Ridge National Laboratory’s Data Portals and Catalogs

Oak Ridge National Laboratory (ORNL) is leveraging its established capabilities and subject matter expertise in data curation, governance, management, national security, and risk assessment and mitigation to support the US Department of Energy (DOE) Grid Modernization Initiative. Using standards modeled by the National Institute of Standards and Technology (NIST), the Data Curation Network (DCN), the Oak Ridge Leadership Computing Facility (OLCF), and other leading organizations in the fields of energy research, high-performance computing, and national and homeland security, ORNL seeks to provide a federated approach to research data discovery, use, and interoperability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Inverse design of nanoporous crystalline reticular materials with deep generative models

Reticular frameworks are crystalline porous materials that form via the self-assembly of molecular building blocks in different topologies, with many having desirable properties for gas storage, separation, catalysis, biomedical applications and so on. The notable variety of building blocks makes reticular chemistry both promising and challenging for prospective materials design. Here we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder for the generative design of reticular materials. We demonstrate the automated design process with a class of metal–organic framework (MOF) structures and the goal of separating carbon dioxide from natural gas or flue gas. Our model shows high fidelity in capturing MOF structural features. Here, we show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported.

36 MATERIALS SCIENCE↗

Defect graph neural networks for materials discovery in high-temperature clean-energy applications

We present a graph neural network approach that fully automates the prediction of defect formation enthalpies for any crystallographic site from the ideal crystal structure, without the need to create defected atomic structure models as input. Here we used density functional theory reference data for vacancy defects in oxides, to train a defect graph neural network (dGNN) model that replaces the density functional theory supercell relaxations otherwise required for each symmetrically unique crystal site. Interfaced with thermodynamic calculations of reduction entropies and associated free energies, the dGNN model is applied to the screening of oxides in the Materials Project database, connecting the zero-kelvin defect enthalpies to high-temperature process conditions relevant for solar thermochemical hydrogen production and other energy applications. The dGNN approach is applicable to arbitrary structures with an accuracy limited principally by the amount and diversity of the training data, and it is generalizable to other defect types and advanced graph convolution architectures. In conclusion, it will help to tackle future materials discovery problems in clean energy and beyond.

97 MATHEMATICS AND COMPUTING↗

Towards Automated Design of Corrosion Resistant Alloy Coatings with an Autonomous Scanning Droplet Cell

We present an autonomous scanning droplet cell platform designed for on-demand alloy electrodeposition and real-time electrochemical characterization. Automation and machine learning are currently driving rapid innovation in high-throughput and autonomous materials design and discovery. We present two alloy design vignettes: one focusing on a multi-objective corrosion resistant alloy optimization and a study highlighting the complexity of the multimodal characterization needed to provide insight into the underlying structural and chemical factors that drive observed material behavior. This motivates a close coupling between autonomous research platforms and scientific machine learning methodology that blends mechanistic physical models and black box machine learning models. Lastly, we reflect on our early efforts in on-demand alloy deposition, highlighting some of the challenges. This emerging research area presents new opportunities to accelerate materials synthesis, evaluation, and hence discovery and design.

36 MATERIALS SCIENCE↗

TOI-1235 b: A Keystone Super-Earth for Testing Radius Valley Emergence Models around Early M Dwarfs

Small planets on close-in orbits tend to exhibit envelope mass fractions of either effectively zero or up to a few percent depending on their size and orbital period. Models of thermally driven atmospheric mass loss and of terrestrial planet formation in a gas-poor environment make distinct predictions regarding the location of this rocky/nonrocky transition in period–radius space. Here we present the confirmation of TOI-1235 b (P = 3.44 days, r{sub p}=1.738{sub −0.076}{sup +0.087} R{sub ⊕}), a planet whose size and period are intermediate between the competing model predictions, thus making the system an important test case for emergence models of the rocky/nonrocky transition around early M dwarfs (R {sub s} = 0.630 ± 0.015 R{sub ⊙}, M {sub s} = 0.640 ± 0.016 M{sub ⊙}). We confirm the TESS planet discovery using reconnaissance spectroscopy, ground-based photometry, high-resolution imaging, and a set of 38 precise radial velocities (RVs) from HARPS-N and HIRES. We measure a planet mass of 6.91{sub −0.85}{sup +0.75} M{sub ⊕}, which implies an iron core mass fraction of 20{sub −12}{sup +15}% in the absence of a gaseous envelope. The bulk composition of TOI-1235 b is therefore consistent with being Earth-like, and we constrain an H/He envelope mass fraction to be <0.5% at 90% confidence. Our results are consistent with model predictions from thermally driven atmospheric mass loss but not with gas-poor formation, suggesting that the former class of processes remains efficient at sculpting close-in planets around early M dwarfs. Our RV analysis also reveals a strong periodicity close to the first harmonic of the photometrically determined stellar rotation period that we treat as stellar activity, despite other lines of evidence favoring a planetary origin (P=21.8{sub −0.8}{sup +0.9} days, m{sub p}sin i=13.0{sub −5.3}{sup +3.8} M{sub ⊕}) that cannot be firmly ruled out by our data.

79 ASTRONOMY AND ASTROPHYSICS↗

Imaging grain microstructure in a model ceramic energy material with optically generated coherent acoustic phonons

Characterization of microstructure, chemistry and function of advanced energy materials remains a challenge for instrumentation science with tremendous opportunity for new discoveries. This active area of research is starting to make considerable strides with examples ranging from methodologies that employ bright X-rays, electron microscopy and optical spectroscopy. However, further development of instruments, capable of multimodal measurements, is necessary to fully reveal complex microstructure evolution in realistic environments and dynamical systems that are far from equilibrium. In this regard, laser-based instruments have a unique advantage as multiple measurement methodologies are easily combined into a single instrument using standard optics. A new pump-probe method that uses optically generated acoustic phonons is expanding standard optical characterization by providing depth resolved information. Here we report on a noteworthy extension of this pump-probe method to image grain microstructure in ceria. Rich information regarding the orientation of individual crystallites is obtained by monitoring acoustic phonon velocities and noting how the polarization of the probe beam influences the detected signal amplitude. When paired with other optical microscopies, this methodology will provide new perspectives for optical characterization of ceramic materials.

36 MATERIALS SCIENCE↗

Surrogate Neural Architecture Codesign Package (SNAC-Pack)

Neural Architecture Search is a powerful approach for automating model design, but existing methods struggle to accurately optimize for real hardware performance, often relying on proxy metrics such as bit operations. We present Surrogate Neural Architecture Codesign Package (SNAC-Pack), an integrated framework that automates the discovery and optimization of neural networks focusing on FPGA deployment. SNAC-Pack combines Neural Architecture Codesign's multi-stage search capabilities with the Resource Utilization and Latency Estimator, enabling multi-objective optimization across accuracy, FPGA resource utilization, and latency without requiring time-intensive synthesis for each candidate model. We demonstrate SNAC-Pack on a high energy physics jet classification task, achieving 63.84% accuracy with resource estimation. When synthesized on a Xilinx Virtex UltraScale+ VU13P FPGA, the SNAC-Pack model matches baseline accuracy while maintaining comparable resource utilization to models optimized using traditional BOPs metrics. This work demonstrates the potential of hardware-aware neural architecture search for resource-constrained deployments and provides an open-source framework for automating the design of efficient FPGA-accelerated models.

Weitz, Jason [UC, San Diego] (ORCID:00090004631535↗

Bridging nuclear physics across energy scales: from neutrinoless double-beta decay to high-energy heavy-ion collisions

This paper exemplifies how connecting methods at disparate energy scales can illuminate fundamental questions. By demonstrating that nuclear wave function properties governing rare decay processes also influence collective behavior at extreme temperatures and densities, the authors have opened a new pathway for constraining physics beyond the Standard Model. With multiple ton-scale 0νββ experiments under construction, any method reducing NME uncertainties will directly impact our ability to interpret discoveries or constrain neutrino properties. The general principle—that collective phenomena in high-energy collisions can illuminate subtle features of many-body correlations in the colliding nuclei—may find applications across nuclear and particle physics. Furthermore, this intersection of nuclear structure theory, heavy-ion physics, and fundamental symmetry tests represents fertile ground for future discoveries in modern physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Identification of earth-abundant materials for selective dehydrogenation of light alkanes to olefins

Catalytic alkane dehydrogenation is of considerable importance in the synthesis of olefins industrially. However, discovery of highly active, selective, and stable heterogeneous catalysts to replace noble metal Pt remains challenging. By combining descriptor-based microkinetic modeling, high-throughput computations, machine-learning concepts, and experiments, we efficiently evaluated 1,998 bimetallic alloys and successfully identified Ni 3 Mo as one of the most promising catalysts in selective ethane dehydrogenation. This work will open new possibilities of using earth-abundant materials as catalysts for essential heterogeneous catalytic reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A study of resistive peeling–ballooning modes across spherical tokamaks

We investigate how non-ideal-magnetohydrodynamics (MHD) effects, in particular plasma resistivity, impact the peeling–ballooning stability thresholds in spherical tokamaks. This analysis follows the discovery of resistive kink-peeling modes in ELMing National Spherical Torus Experiment (NSTX) discharges. In the present study we extend this modeling to ELMing pulses in the Mega Ampere Spherical Tokamak (MAST) and MAST—Upgrade (MAST-U), where we find a clear resistive scaling for peeling–ballooning modes. While in NSTX ideal-MHD predicts stability for ELMing discharges, in MAST-U we find that the plasma is slightly unstable to peeling–ballooning modes, but is fully stabilized once diamagnetic effects are considered in terms of a growth rate normalization. A resistive power law scaling is calculated for these modes on MAST-U, which lies in between that of tearing modes and resistive interchange modes. A comparison between M3D-C1 and NIMROD shows reasonable agreement for this scaling. Resistivity destabilizes the modes and the peeling–ballooning unstable domain is considerably expanded in both, MAST and MAST-U. In addition to the MAST/-U pulses we also analyze resistive PB stability in a NSTX-similarity discharge on DIII-D. While having a different aspect ratio from NSTX, this discharge uses NSTX-like shaping parameters, toroidal field and plasma current. By considering these discharges alongside NSTX cases, we identify conditions influencing the onset of resistive peeling–ballooning modes. Furthermore, our findings indicate that magnetic shear in the pedestal region is closely linked to the emergence of resistive edge modes.

MAST-U↗