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DOE OSTI2020

Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana

Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant–microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Fiber-optic diagnostic system for future accelerator magnets

The next generation high energy physics accelerators will require magnetic fields at ~20 T. HTS coils will be an essential component of future accelerator magnets and several efforts are currently dedicated on designing 20 T HTS- LTS hybrid magnets. Among the existing challenges, there is the lack of a robust quench detection system for hybrid magnet technology. Another big challenge is represented by the high number of training quenches required by Nb3Sn magnets to reach performance level. In this framework it is important to find a tool that allow local real-time monitoring of magnet strain and temperature. In this paper, we propose the use of fiber optics sensors for diagnostic and quench detection in future accelerator superconducting magnets. Discrete and distributed fiber optic sensors have demonstrated to be a promising tool. The goal is to instrument hundreds of accelerator superconducting magnets and to move beyond the proof-of-concept level. Significant developments are still needed. Here, we are going to present the most recent results and discuss the most urgent technical developments in order to make those sensors a robust and reliable diagnostic tool for accelerator superconducting magnets over the next 10 year. We foresee that discrete fiber sensors will be a stable diagnostic probe for superconducting magnets over the next 3 to 5 years. More R&D work will be necessary for distributed fibers. The most urgent needs are the increase of sample rate and sensitivity. Close collaboration with vendors will be necessary to improve mechanical properties and fabrication processes in order to produce hundreds of meters of fiber and instrument a large number of accelerator superconducting magnets. Those R&D efforts will last up to 10 years with a founding level that spans between 5-10 M$.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Laser‐Powder Melt Pool Solidification Dynamics and Microstructural Engineering of Ti‐5553 Microlattices

The fine geometric and topological control afforded by additive manufacturing technologies has enabled the manufacture of architected materials across length scales, and enabling tunable mechanical performance as a function of local and global design. Progress has been made to tune the mechanical response of architected materials through geometry, but understanding how the geometry and processing conditions will inform the microstructure remains a challenge due to the rapid solidification in laser powder bed fusion. This study uses in situ X-ray imaging and electron backscatter diffraction microscopy to demonstrate that the melt pool size, microstructure morphology, and elastic strain distribution is influenced by a combination of lattice geometry and laser processing conditions. These results indicate that within larger melt pools the local thermal gradients are sufficient to enable a columnar-to-equiaxed transition across the melt pool. Furthermore, the solidification mechanisms producing these microstructures are examined across the first 5 ms of melting and solidification, described via in situ high-speed X-ray imaging and mirrored via multiphysics simulation.

additive manufacturing↗

DOE OSTI2025

An attention-based neural ordinary differential equation framework for modeling inelastic processes

To preserve strictly conservative behavior as well as model the variety of dissipative behavior displayed by solid materials, we propose a significant enhancement to the internal state variable-neural ordinary differential equation (ISV-NODE) framework. In this data-driven, physics-constrained modeling framework internal states are inferred rather than prescribed. The ISV-NODE consists of: (a) a stress model dependent on observable deformation and inferred internal state, and (b) a model of the evolution of the internal states. The enhancements to ISV-NODE proposed in this work are multifold: (a) a partially input convex neural network stress potential provides polyconvexity in terms of observed strain while leaving the inferred state unconstrained, and (b) an internal state flow model uses common latent features to inform novel attention-based gating and drives the flow of internal state only in dissipative regimes. We demonstrated that this architecture can accurately model dissipative and conservative behavior across an isotropic, isothermal elastic-viscoelastic-elastoplastic spectrum with three exemplars, while maintaining fundamental principles by design.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model

Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.

AI agent↗

DOE OSTI2021

Intrinsic and extrinsic effects on the fracture toughness of ductile metallic glasses

The potential application of metallic glasses (MGs) as structural materials demands accurate measurements of their toughness and the understanding of the underlying factors affecting it. Currently, it is challenging to precisely measure the toughness of MGs, especially ductile MGs. Measured toughness values are widely scattered, even for MGs with identical compositions. That is attributed to the combined effect of intrinsic and extrinsic factors including processing, sample geometries, and loading conditions. A fundamental understanding of the influences of these elements is thus of great significance. In the present study, molecular dynamics simulations are performed to investigate the influence of intrinsic and extrinsic effects on the fracture toughness of CuZr MGs. In particular, focused is placed on the effects of cooling rate, notch shape and size, strain rate, and temperature. The results indicate that the fracture toughness of a MG scales with the cooling rate used to prepare it. This is attributed to increased free volume content generated at high cooling rates, which enhances plastic deformation and amplifies the associated energy dissipation during plastic deformation events. Fracture toughness also increases with the strain rate, arguably due to strain rate-induced crack extension delay. Overall, the results demonstrate that the largest fracture toughness are achieved when MG samples are fabricated at high cooling rates and subjected to high strain rate deformation. In addition, results suggest that the fracture toughness decreases with increasing temperature, due to the significant decrease in strength. Here, the correlations revealed between these crucial intrinsic and extrinsic parameters and the calculated MG fracture toughness support the development of a framework to understand the root of the discrepancies in the measurement of the toughness of MGs and provide insights into the design of tough MGs for structural applications.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Emerged Metallicity in Molecular Ferromagnetic Wires

Supramolecular engineering bridges molecular assembly with macromolecular charge-transfer salts, promising the design to construct supramolecular architectures that integrate cooperative properties difficult or impossible to find in conventional lattices. Here, we report the crystal engineering design and kinetic growth of one-dimensional supramolecular wires composed of bis(ethylenedithio)tetrathiafulvalene (ET + ) cation and polymeric Cu[N(CN) 2 ] 2 – anion. A bulk ferromagnetic order is discovered for filling up the gap where strong ferromagnetism is missing in such ET molecule-based charge-transfer salts. Metallicity is induced by electric current from the semiconducting wire, which is attributed to strain effect by tuning its close molecular contact. This structural feature is evidenced through the combination of various mechanistic spectroscopic studies. Further, electric dipole is established from the close molecular contacts and is suggestive to stabilize ferromagnetic spin interaction through anions bridging spin sites. The breakthrough shown here provides a pathway to explore low-dimensional supramolecular materials exhibiting strong electron correlation, metallicity, and ferromagnetism.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Multiscale modeling of metal-hydride interphases—quantification of decoupled chemo-mechanical energies

Abstract The quantification of interphase properties between metals and their corresponding hydrides is crucial for modeling the thermodynamics and kinetics of the hydrogenation processes in solid-state hydrogen storage materials. In particular, interphase boundary energies assume a pivotal role in determining the kinetics of nucleation, growth, and coarsening of hydrides, alongside accompanying morphological evolution during hydrogenation. The total interphase energy arises from both chemical bonding and mechanical strains in these solid-state systems. Since these contributions are usually coupled, it is challenging to distinguish via conventional computational approaches. Here, a comprehensive atomistic modeling methodology is developed to decouple chemical and mechanical energy contributions using first-principles calculations, of which feasibility is demonstrated by quantifying chemical and elastic strain energies of key interfaces within the FeTi metal-hydride system. Derived materials parameters are then employed for mesoscopic micromechanical analysis, predicting crystallographic orientations in line with experimental observations. The multiscale approach outlined verifies the importance of the chemo-mechanical interplay in the morphological evolution of growing hydride phases, and can be generalized to investigate other systems. In addition, it can streamline the design of atomistic models for the quantitative evaluation of interphase properties between dissimilar phases and allow for efficient predictions of their preferred phase boundary orientations.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale molecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗

DOE OSTI2022

Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and a preferred host for production of other biofuels. That said, rewiring the metabolism of S. cerevisiae to produce other fermentation products, such as isobutanol, remains an academic challenge. Many studies report aerobic production of isobutanol, but ethanol remains a substantial by-product under these conditions due to the Crabtree effect. These studies indicate that the native isobutanol pathway is incapable of carrying sufficient flux to displace ethanol. In this report, we screened a combinatorial library of pathway enzymes to identify an isobutanol pathway cassette capable of supporting the growth of a non-ethanol producing S. cerevisiae . We began by identifying a diverse set of isobutanol pathway enzyme homologs and combined each open reading frame with varied-strength promoters in a combinatorial, pooled fashion. We applied a growth-coupled screen where a functional isobutanol pathway restored NAD + regeneration during glucose catabolism that is otherwise repressed via the Crabtree effect. Using this screen, we isolated a cassette consisting of a mosaic of bacterial and cytosol-localized fungal enzymes that conferred under aerobic conditions the ability to produce 364 mg/L isobutanol (8.8% of the theoretical maximum yield). We next shifted the cofactor usage of the isolated ketol-acid reductoisomerase enzyme in the cassette from NADPH to NADH-preferring to improve redox balance. The approach used herein isolated isobutanol producing strains that approach the best in the literature without producing substantial ethanol titers. Still, the best isolated cassette was insufficient to support anaerobic growth in the absence of ethanol fermentation - indicating the presence of further fundamental gaps in our understanding of yeast fermentation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Bioinspired mechanically interlocking holey graphene@SiO 2 anode

Mechanically interlocking structures that can enhance adhesion at the interface and regulate the stress distribution have been widely observed in biological systems. Inspired by the biological structures in the wings of beetles, we synthesized a holey graphene@SiO 2 anode with strong mechanical interlocking, characterized it electrochemically, and explained its performance by finite element analysis and density functional calculations. The mechanically interlocking structure enhances lithium-ion (Li + ) storage by transmitting the strain from SiO 2 to the holey graphene and by a mechano-electrochemical coupling effect. The interlocking fit hinders the abscission of SiO 2 and the distinctive structure reduces the stress and strain of SiO 2 during (de)lithiation. The positive mechano-electrochemical coupling effect preserves the amount of electrochemically active phase (Li x Si) during cycles and facilitates Li + diffusion. Therefore, the capacity shows only a slight attenuation after 8000 cycles (cycling stability), and the specific capacity is ~1200 mA h g –1 at 5 A/g (rate-performance). This study furnishes a novel way to design high-performance Li + /Na + /K + /Al 3+ anodes with large volume expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Superlattice-Structured Films by Magnetron Sputtering as New Era Electrodes for Advanced Lithium-ion Batteries

Sustaining sound structures in Si-based anodes is extremely challenging because of the high volumetric expansion that occurs upon cycling. To maintain high capacities over cycles, new designs rely on engineering-specific hierarchical geometries and/or optimized composite compositions such that at least one of the multiple elements serves as buffer and/or electron conductive pathways in the electrodes. In this paper, we report an innovative design in which alternating layers of periodic atomic structures involving multiple elements form a new anode material for lithium-ion batteries. In this work, a superlattice-structured amorphous film made using Si, Mo, and Cu is fabricated by a simple and scalable magnetron sputtering process for the first time. This continuous and repetitive superlattice formation along the film thickness provides a homogeneous stress-strain distribution. The Mo-Cu layer in the superlattice acts as an inactive-conductive layer and as a backbone to handle the volume expansion of active Si upon cycling. This nano-functional superlattice approach enables harnessing the high energy density of Si while maintaining its structural stability. As a result, the electrode exhibits high specific capacity and capacity retention even at high cycling rates. The possible use of the film in a full cell is also evaluated by cycling it vs. the LiMn 1.5 Ni 0.5 O 4 cathode. The full cell maintains a stable capacity of about 900 mAh g anode -1 over 150 cycles, at ~600 mA g -1 rate. The remarkable performance of this nano-functional superlattice film is found to be promising as anodes for applications that require high energy, long calendar life, and excellent abuse tolerance such as electric vehicle batteries.

25 ENERGY STORAGE↗

DOE OSTI2023

Rapid and robust squashed spore/colony PCR of industrially important fungi

Fungi have been utilized for centuries in medical, agricultural, and industrial applications. Development of systems biology techniques has enabled the design and metabolic engineering of these fungi to produce novel fuels, chemicals, and enzymes from renewable feedstocks. Many genetic tools have been developed for manipulating the genome and creating mutants rapidly. However, screening and confirmation of transformants remain an inefficient step within the design, build, test, and learn cycle in many industrial fungi because extracting fungal genomic DNA is laborious, time-consuming, and involves toxic chemicals. In this study we developed a rapid and robust technique called “Squash-PCR” to break open the spores and release fungal genomic DNA as a template for PCR. The efficacy of Squash-PCR was investigated in eleven different filamentous fungal strains. Clean PCR products with high yields were achieved in all tested fungi. Spore age and type of DNA polymerase did not affect the efficiency of Squash-PCR. However, spore concentration was found to be the crucial factor for Squash-PCR in Aspergillus niger, with the dilution of starting material often resulting in higher PCR product yield. We then further evaluated the applicability of the squashing procedure for nine different yeast strains. We found that Squash-PCR can be used to improve the quality and yield of colony PCR in comparison to direct colony PCR in the tested yeast strains. The developed technique will enhance the efficiency of screening transformants and accelerate genetic engineering in filamentous fungi and yeast.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Factors that Impact the Redox Kinetics Associated with Sr1-xAxFeO3 (A = Ca, Ba) in Air Separations Technologies

Perovskite oxides, including SrFeO3-δ, have garnered significant interest for their impressive oxygen storage thermodynamics and kinetics. While traditional oxygen production is performed through cryogenic separation methods at the industrial scale, oxygen carrier-based separations have offered an attractive alternative at the modular scale. Perovskites are considered ideal oxygen carriers, with their structural flexibility minimizing both the thermodynamic barrier and the structural strain related to the oxygen uptake/release cycle. Our latest work has identified a few major factors that directly impact the oxygen release thermodynamics and kinetics for Sr1-xAxFeO3-δ (A = Ca, Ba) materials including elemental composition, crystallographic symmetry, surface area, and pretreatment conditions. This presentation will discuss these factors using Sr1¬-xCaxFeO3 and Ba1-xSrxFeO3 to illustrate their individual and collective impacts on the design of high-performance oxygen carriers when operating at 300-700 °C. Additionally, we will discuss how each of these factors can be leveraged for the numerous catalytic applications also dependent on the redox properties of mixed metal oxides.

Popczun, Eric↗

DOE OSTI2020

Chapter 16: Connecting Microbial Genotype with Phenotype in the Omics Era

Although rational design-based metabolic engineering has been applied widely to obtain promising microbial biocatalysts, conventional strategies such as adaptive laboratory evolution (ALE) and mutagenesis are still efficient approaches to improve microorganisms for exceptional features such as a broad spectrum of substrate utilization, robustness of cell growth, as well as high titer, yield, and productivity of the target products. In this chapter, we describe the procedure to generate mutant strains with desired phenotypes using ALE and a new mutagenesis approach of Atmosphere and Room Temperature Plasma (ARTP). In addition, we discuss the methodology to combine next-generation sequencing (NGS)-based genome-resequencing and RNA-Seq transcriptomics approaches to characterize the mutant strains and connect the phenotypes with their corresponding genotypic changes.

adaptive laboratory evolution (ALE)↗

DOE OSTI2024

Elasticity-controlled jamming criticality in soft composite solids

Soft composite solids are made of inclusions dispersed within soft matrices. They are ubiquitous in nature and form the basis of many biological tissues. In the field of materials science, synthetic soft composites are promising candidates for building various engineering devices due to their highly programmable features. However, when the volume fraction of the inclusions increases, predicting the mechanical properties of these materials poses a significant challenge for the classical theories of composite mechanics. The difficulty arises from the inherently disordered, multi-scale interactions between the inclusions and the matrix. To address this challenge, we systematically investigated the mechanics of densely filled soft elastomers containing stiff microspheres. We experimentally demonstrate how the strain-stiffening response of the soft composites is governed by the critical scalings in the vicinity of a shear-jamming transition of the included particles. The proposed criticality framework quantitatively connects the overall mechanics of a soft composite with the elasticity of the matrix and the particles, and captures the diverse mechanical responses observed across a wide range of material parameters. The findings uncover a novel design paradigm of composite mechanics that relies on engineering the jamming properties of the embedded inclusions.

36 MATERIALS SCIENCE↗

DOE OSTI2026

In situ electric field X-ray total scattering reveals composition-dependent electromechanical strain mechanisms in (1 − x )BiFe 2/8 Ti 3/8 Mg 3/8 O 3 – x PbTiO 3 ceramics

Ferroelectric materials find many applications in energy and aerospace industries. A major challenge for ferroelectric materials is maintaining their properties at elevated temperatures. The (1 − x )BiFe 2/8 Ti 3/8 Mg 3/8 O 3 – x PbTiO 3 (BFTM–xPT) ferroelectric solid solution is a promising candidate for high-temperature applications as it has a high piezoelectric response while also maintaining its ferroelectric phase until a high Curie temperature (T C ) of 650 °C. In this work, we investigate the piezoelectric mechanism in BFTM–xPT, a novel high-T C ferroelectric ceramic. To elucidate the origin of its enhanced piezoelectric performance, relative to other piezoceramics of similar T C , in situ electric field X-ray total scattering experiments were performed. Total scattering combines Bragg scattering (diffraction) and diffuse scattering (pair distribution function), providing insight on various length scales. With information spanning different length scales, extrinsic contributions (i.e., domain wall motion and interphase boundary motion) can be separated from intrinsic contributions (i.e., piezoelectric lattice strain). We show that, for compositions within the morphotropic phase boundary (MPB, x = 0.325), the piezoelectric response is dominated by intrinsic piezoelectric lattice strain, whereas outside the MPB (x = 0.375) the major component of the piezoelectric response is from extrinsic mechanisms including an electric-field-induced phase transition and tetragonal domain wall motion. This article reveals that the origin of piezoelectric response in BFTM–xPT is composition-dependent and shows that high-performance materials may also be located outside the MPB. These findings can help guide material design to optimize properties for specific applications.

Richtik, Brooke N. [University of Calgary, AB (Can↗

DOE OSTI2024

Waning immunity and IgG4 responses following bivalent mRNA boosting

Messenger RNA (mRNA) vaccines were highly effective against the ancestral SARS-CoV-2 strain, but the efficacy of bivalent mRNA boosters against XBB variants was substantially lower. Here, we show limited durability of neutralizing antibody (NAb) responses against XBB variants and isotype switching to immunoglobulin G4 (IgG4) responses following bivalent mRNA boosting. Bivalent mRNA boosting elicited modest XBB.1-, XBB.1.5-, and XBB.1.16-specific NAbs that waned rapidly within 3 months. In contrast, bivalent mRNA boosting induced more robust and sustained NAbs against the ancestral WA1/2020 strain, suggesting immune imprinting. Following bivalent mRNA boosting, serum antibody responses were primarily IgG2 and IgG4 responses with poor Fc functional activity. In contrast, a third monovalent mRNA immunization boosted all isotypes including IgG1 and IgG3 with robust Fc functional activity. These data show substantial immune imprinting for the ancestral spike and isotype switching to IgG4 responses following bivalent mRNA boosting, with important implications for future booster designs and boosting strategies.

Science & Technology - Other Topics↗