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DOE OSTI2025

Accelerating the discovery of low-energy structure configurations: A computational approach that integrates first-principles calculations, Monte Carlo sampling, and Machine Learning

Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys considered candidate PFMs is key because it determines the most stable arrangement of atoms within the alloy, directly influencing its phase stability, structural integrity, and thermo-mechanical properties. However, since the search space grows exponentially with the number of atoms considered, obtaining such MECs using computationally expensive first-principles DFT calculations often results in a cumbersome task. To escape the above compromise between physical fidelity and computational efficiency, we have developed a novel physics-based data-driven approach that combines Monte Carlo sampling, first-principles DFT calculations, and Machine Learning to accelerate the discovery of MECs in multi-component alloys. More specifically, we have leveraged well-established Cluster Expansion (CE) techniques with Local Outlier Factor models to establish strategies that enhance the reliability of the CE method. In this work, we demonstrated the capabilities of the proposed approach for the particular case of a tungsten-based quaternary high-entropy alloy. However, the method is applicable to other types of alloys and enables a wide range of applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Engineered Endosymbionts that Modulate Primary Macrophage Function and Attenuate Tumor Growth by Shifting the Tumor Microenvironment

Modulating gene expression in macrophages can be used to improve tissue regeneration and redirect tumor microenvironments (TMEs) toward positive therapeutic outcomes. We have developed Bacillus subtilis as an engineered endosymbiont (EES) capable of residing inside the eukaryotic host cell cytoplasm and controlling the fate of macrophages. Secretion of mammalian transcription factors (TFs) from B. subtilis that expresses listeriolysin O (LLO; allowing the EES to escape destruction by the macrophage) modulated expression of surface markers, cytokines, and chemokines, indicating functional changes in a macrophage/monocyte cell line. The engineered B. subtilis LLO TF strains were evaluated in murine bone marrow-derived macrophages (BMDMs) by flow cytometry, chemokine/cytokine profiling, metabolic assays, and RNA-Seq delivery of TFs by the EES shifted BMDM gene expression, production of cytokine and chemokines, and metabolic patterns, indicating that the TF strains could guide primary macrophage function. Thereafter, the ability of the TF strains to alter the TME was characterized in vivo in an orthotopic murine model of triple-negative breast cancer to assess therapeutic effects. The TF strains altered the TME by shifting immune cell composition and attenuating tumor growth. Additionally, multiple doses of the TF strains were well-tolerated by the mice. The use of B. subtilis LLO TF strains as EES showed promise as a unique cancer immunotherapy by directing the immune function intracellularly. The uses of EES could be expanded to modulate other mammalian cells over a range of biomedical applications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Enhanced Selectivity for C 2 H 4 Production from C 2 H 6 on Partially Chlorinated IrO 2 (110) Surfaces

Modifying metal oxide surfaces to limit their oxidizing activity can provide a means of improving catalytic selectivity toward the partial oxidation of light alkanes. Here, in this study, we investigated the oxidation of C 2 H 6 on Cl-modified IrO 2 (110) surfaces using temperature-programmed reaction spectroscopy (TPRS) and first-principles microkinetic modeling. We find that substituting Cl for O in the IrO 2 (110) surface enhances the selectivity for C 2 H 6 conversion to C 2 H 4 during TPRS by suppressing extensive oxidation to CO x products, while also either enhancing C 2 H 4 production or altering it to a lesser extent, depending on the initial C 2 H 6 coverage. The C 2 H 4 selectivity increased with increasing C 2 H 6 and Cl coverage, but reached a limiting value below 50%. The Cl coverage changed negligibly during C 2 H 6 oxidation, and the surface reactivity decreased only marginally for Cl coverages up to 0.5 ML (monolayer). TPRS simulations using a microkinetic model predict C 2 H 4 and CO x product yields as a function of the Cl coverage that agree closely with the experimental results. According to the simulations, C 2 H 6 conversion to C 2 H 4 occurs on Cl-IrO 2 (110) by the hydrogenation of C 2 H 3 * species adsorbed in blocked states, in which neighboring sites are occupied only by unreactive HO and Cl species. The microkinetic modeling shows that H-hopping away from surface HO groups provides a relatively efficient route for C 2 H 3 * to escape blocked configurations and dehydrogenate, and that this process can limit the C 2 H 4 selectivity on Cl-IrO 2 (110) under the conditions studied. Overall, our results demonstrate that Cl-substitution into IrO 2 (110) enhances the selectivity for C 2 H 4 production from C 2 H 6 and provides insights into the reaction mechanism that can guide strategies to further improve the C 2 H 4 selectivity.

IrO2↗

DOE OSTI2025

Intracellular Biomacromolecule Delivery by Stimuli-Responsive Protein Vesicles Loaded by Hydrophobic Ion Pairing

Proteins can perform ideal therapeutic functions. However, their large size and significant surface hydrophilicity and charge prohibit them from reaching intracellular targets. These chemical features also render them poorly encapsulated by nanoparticles used for intracellular delivery. In this work, a novel combination of protein vesicles and hydrophobic ion pairing (HIP) was used to load protein cargo and achieve cytosolic delivery to overcome the limitations of previous protein vesicle properties. Protein vesicles are thermally self-assembling nanoparticles made from elastin-like polypeptide (ELP) fused to an arginine-rich leucine zipper and a globular protein fused to a glutamate-rich leucine zipper. To impart stimuli-responsive disassembly, physiological stability, and small size, the ELP sequence was modified to include histidine and tyrosine residues. HIP was used to load and release protein cargo requiring endosomal escape for cytosolic function. HIP vesicles enabled delivery of cytochrome c, a cytosolically active protein, and a significant reduction in viability in both a traditional two-dimensional (2D) human cancer cell line culture and a biomimetic three-dimensional (3D) organoid model of acute myeloid leukemia. By examining the uptake of positively and negatively charged fluorescent protein cargos loaded by HIP, this work revealed the necessity of HIP for cytosolic cargo delivery and how HIP loading influences protein vesicle self-assembly and disassembly using microscopy, small-angle X-ray scattering, and nanoparticle tracking analysis. HIP protein vesicles have the potential to broaden the use of intracellular proteins as therapeutics for various diseases and extend protein vesicles to deliver other biomacromolecules, as the strategy developed here resulted in the first cytosolic protein cargo delivery using protein vesicles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Cell-Free Systems Biology: Characterizing Central Metabolism of Clostridium thermocellum with a Three-Enzyme Cascade Reaction

Genetic approaches have been traditionally used to understand microbial metabolism, but this process can be slow in nonmodel organisms due to limited genetic tools. An alternative approach is to study metabolism directly in the cell lysate. This avoids the need for genetic tools and is routinely used to study individual enzymatic reactions but is not generally used to study systems-level properties of metabolism. Here we demonstrate a new approach that we call “cell-free systems biology”, where we use well-characterized enzymes and multienzyme cascades to serve as sources or sinks of intermediate metabolites. This allows us to isolate subnetworks within metabolism and study their systems-level properties. To demonstrate this, we worked with a threeenzyme cascade reaction that converts pyruvate to 2,3-butanediol. Although it has been previously used in cell-free systems, its pH dependence was not well characterized, limiting its utility as a sink for pyruvate. We showed that improved proton accounting allowed better prediction of pH changes and that active pH control allowed 2,3-butanediol titers of up to 2.1 M (189 g/L) from acetoin and 1.6 M (144 g/L) from pyruvate. The improved proton accounting provided a crucial insight that preventing the escape of CO 2 from the system largely eliminated the need for active pH control, dramatically simplifying our experimental setup. We then used this cascade reaction to understand limits to product formation in Clostridium thermocellum, an organism with potential applications for cellulosic biofuel production. We showed that the fate of pyruvate is largely controlled by electron availability and that reactions upstream of pyruvate limit overall product formation.

09 BIOMASS FUELS↗

DOE OSTI2025

Atomistic Origin of Microsecond Carrier Lifetimes at Perovskite Grain Boundaries: Machine Learning-Assisted Nonadiabatic Molecular Dynamics

The polycrystalline nature of perovskites, stemming from their facile solution-based fabrication, leads to a high density of grain boundaries (GBs) and point defects. However, the impact of GBs on perovskite performance remains uncertain, with contradictory statements found in the literature. We developed a machine learning force field, sampled GB structures on a nanosecond time scale, and performed nonadiabatic (NA) molecular dynamics simulations of charge carrier trapping and recombination in stoichiometric and doped GBs. The simulations reveal long, microsecond carrier lifetimes, approaching experimental data, stemming from charge separation at the GBs and small NA coupling, 0.01–0.1 meV. Stoichiometric GBs exhibit transient trap states, which, however, are not particularly detrimental to the carrier lifetime. Halide dopants form interstitial defects in the bulk, but have a stabilizing influence on the GB structure by passivating undersaturated Pb atoms and reducing the transient trap state formation. On the contrary, excess Pb destabilizes GBs, allowing formation of persistent midgap states that trap charges. Still, the charge carrier lifetime reduces relatively little, because the midgap states decouple from the bands, and charges are more likely to escape back into bands upon a GB structural fluctuation. The atomistic study into the structural dynamics of perovskite GBs and its influence on charge carrier trapping and recombination provides valuable insights into the complex properties of perovskites and the intricate role of GBs in the material performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A More Transparent Infrared Window

The infrared window region (780–1,250 cm –1 , 12.8 to 8.0 μm) is of great importance to Earth's climate due to its high transparency and thermal energy. We present here a new investigation of the transparency of this spectral region based on observations by interferometers of downwelling surface radiance at two DOE Atmospheric Radiation Measurement program sites. We focus on the dominant source of absorption in this region, the water vapor continuum, and derive updated values of spectral absorption coefficients for both the self and foreign continua. Our results show that the self continuum is too strong in the previous version of Mlawer-Tobin_Clough-Kneizys-Davies (MT_CKD) water vapor continuum model, a result that is consistent with other recent analyses, while the foreign continuum is too weak in MT_CKD. In general, the weaker self continuum derived in this study results in an overall increase in atmospheric transparency in the window, although in atmospheres with low amounts of water vapor the transparency may slightly decrease due to the increase in foreign continuum absorption. These continuum changes lead to a significant decrease in downwelling longwave flux at the surface for moist atmospheres and a modest increase in outgoing longwave radiation. The increased fraction of surface-leaving radiation that escapes to space leads to a notable increase (~5–10%) in climate feedback, implying that climate simulations that use the new infrared window continuum will show somewhat less warming than before. This study also points out the possibly important role that aerosol absorption may play in the longwave radiative budget.

58 GEOSCIENCES↗

DOE OSTI2024

Unlocking the potential of biogas systems for energy production and climate solutions in rural communities

On-site conversion of organic waste into biogas to satisfy consumer energy demand has the potential to realize energy equality and mitigate climate change reliably. However, existing methods ignore either real-time full supply or methane escape when supply and demand are mismatched. Here, we show an improved design of community biogas production and distribution system to overcome these and achieve full co-benefits in developing economies. We take five existing systems as empirical examples. Mechanisms of synergistic adjusting out-of-step biogas flow rates on both the plant-side and user-side are defined to obtain consumption-to-production ratios of close to 1, such that biogas demand of rural inhabitants can be met. Furthermore, carbon mitigation and its viability under universal prevailing climates are illustrated. Coupled with manure management optimization, Chinese national deployment of the proposed system would contribute a 3.77% reduction towards meeting its global 1.5 °C target. Additionally, fulfilling others’ energy demands has considerable decarbonization potential.

09 BIOMASS FUELS↗

DOE OSTI2024

Upland Yedoma taliks are an unpredicted source of atmospheric methane

Landscape drying associated with permafrost thaw is expected to enhance microbial methane oxidation in arctic soils. Here we show that ice-rich, Yedoma permafrost deposits, comprising a disproportionately large fraction of pan-arctic soil carbon, present an alternate trajectory. Field and laboratory observations indicate that talik (perennially thawed soils in permafrost) development in unsaturated Yedoma uplands leads to unexpectedly large methane emissions (35–78 mg m -2 d -1 summer, 150–180 mg m -2 d -1 winter). Upland Yedoma talik emissions were nearly three times higher annually than northern-wetland emissions on an areal basis. Approximately 70% emissions occurred in winter, when surface-soil freezing abated methanotrophy, enhancing methane escape from the talik. Remote sensing and numerical modeling indicate the potential for widespread upland talik formation across the pan-arctic Yedoma domain during the 21 st and 22 nd centuries. Contrary to current climate model predictions, these findings imply a positive and much larger permafrost-methane-climate feedback for upland Yedoma.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

ON-OFF neuromorphic ISING machines using Fowler-Nordheim annealers

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using a Fowler-Nordheim quantum mechanical tunneling based threshold-annealing process. The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing dynamics onto a network of integrate-and-fire neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer and the resulting spiking dynamics replicates the optimal escape mechanism and convergence of SA, particularly at low-temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved benchmark combinatorial optimization problems such as MAX-CUT and Max Independent Set. Across multiple runs, NeuroSA consistently generates distribution of solutions that are concentrated around the state-of-the-art results (within 99%) or surpass the current state-of-the-art solutions for Max Independent Set benchmarks. Furthermore, NeuroSA is able to achieve these superior distributions without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform.

42 ENGINEERING↗

DOE OSTI2026

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Generalizable Image Segmentation for Microstructure Characterization Through Integrated SEM and EBSD Analysis

We demonstrate generalizable semantic segmentation using minimal ground truth data. Correlated scanning electron microscopy (SEM) images and electron backscatter diffraction (EBSD) measurements of frictionstir processed 316L stainless steel plates were used to train deep learning models for grain boundary segmentation. Secondary electron (SE) imaging taken at an accelerating voltage of 10 keV correlated to EBSD-derived grain boundaries produced the best performing model. Notably, an ensemble of three models trained on a single SE image produced accurate segmentation over a series of BSE images of samples manufactured under different processing parameters, with a resultant mean absolute error in grain size of 0.34 µm. The striking generalizability of the models likely results from the similar escape depths of the SE training input and the EBSD training output and the reduced probability of dislocation artifacts appearing in the image. This finding highlights the importance of considering the physical principles behind imaging in the development of robust segmentation models for microstructure characterization.

Taufique, Mohammad Fuad Nur↗

DOE OSTI2026

Study of wrap mode impact on Pseudomonas aeruginosa motion in the chemotactic field of fungi

An agent-based discrete computational model biologically calibrated to Pseudomonas aeruginosa migration is used to explore the impacts of bacterial reversals and wrap mode on the efficiency of motion in different environments, both with and without chemotaxis. It is first shown that wrap mode increases the exploration of continuous multimodal chemotactic profiles such as those produced by biologically relevant fungal networks. For cells undergoing a run-reverse pattern, it is shown that the bacteria are likely to remain at the first local chemoattractant maximal production site on a hypha they find. However, with wrap mode, the bacteria can more easily escape these local sites to further explore their neighboring environment along the fungi, suggesting that wrap mode may be beneficial for migration along the fungi in liquid. In a different set of simulations of bacterial motion close to an isolated chemotactic source, wrap mode is shown to increase the ability of a bacterium to reorient toward the source while reducing the overall motion required for similar chemotactic efficiency as a run-reverse strategy, suggesting a potential metabolic benefit. In contrast, model simulations show that wrap mode can increase the rate of dispersal of P. aeruginosa in a nonchemotactic environment.

Hansen, Austin [University of California, Riversid↗

DOE OSTI2025

The variety and origin of materials accreted by Bennu’s parent asteroid

The first bodies to form in the Solar System acquired their materials from stars, the presolar molecular cloud and the protoplanetary disk. Asteroids that have not undergone planetary differentiation retain evidence of these primary accreted materials. However, geologic processes such as hydrothermal alteration can dramatically change their bulk mineralogy, isotopic compositions and chemistry. Here we analyse the elemental and isotopic compositions of samples from asteroid Bennu to uncover the sources and types of material accreted by its parent body. We show that some primary accreted materials escaped the extensive aqueous alteration that occurred on the parent asteroid, including presolar grains from ancient stars, organic matter from the outer Solar System or molecular cloud, refractory solids that formed close to the Sun, and dust enriched in neutron-rich Ti isotopes. We find Bennu to be richer in isotopically anomalous organic matter, anhydrous silicates, and light isotopes of K and Zn than its closest compositional counterparts, asteroid Ryugu and Ivuna-type (CI) carbonaceous chondrite meteorites. We propose that the parent bodies of Bennu, Ryugu and CI chondrites formed from a common but spatially and/or temporally heterogeneous reservoir of materials in the outer protoplanetary disk.

Kuiper belt↗

DOE OSTI2024

Observation of the antimatter hypernucleus $^4_{\bar{\Lambda}}\overline{\hbox{H}}$

Matter-antimatter asymmetry is a research topic of fundamental interest, as it is the basis for the existence of the matter world, which survived annihilation with antimatter in the early Universe. High energy nuclear collisions create conditions similar to the Universe microseconds after the Big Bang, with comparable amounts of matter and antimatter. Much of the antimatter created escapes the rapidly expanding fireball without annihilation, making such collisions an effective experimental tool to create heavy antimatter nuclear objects and study their properties. In this paper, we report the first observation of the antimatter hypernucleus $^4_{\bar{\Lambda}}\overline{\hbox{H}}$, composed of an $\bar{\Lambda}$, an antiproton and two antineutrons. The discovery was made through its two-body decay after production in ultrarelativistic heavy ion collisions by the STAR experiment at the Relativistic Heavy Ion Collider. In total, 15.6 candidate $^4_{\bar{\Lambda}}\overline{\hbox{H}}$ antimatter hypernuclei are obtained with an estimated background count of 6.4. Lifetimes of the antihypernuclei $^3_{\bar{\Lambda}}\overline{\hbox{H}}$ and $^4_{\bar{\Lambda}}\overline{\hbox{H}}$ are measured and compared with lifetimes of their corresponding hypernuclei, testing the symmetry between matter and antimatter. Various production yield ratios among (anti)hypernuclei and (anti)nuclei are also measured and compared with theoretical model predictions, shedding light on their production mechanism.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Unlocking saponin biosynthesis in soapwort

Abstract Soapwort ( Saponaria officinalis ) is a flowering plant from the Caryophyllaceae family with a long history of human use as a traditional source of soap. Its detergent properties are because of the production of polar compounds (saponins), of which the oleanane-based triterpenoid saponins, saponariosides A and B, are the major components. Soapwort saponins have anticancer properties and are also of interest as endosomal escape enhancers for targeted tumor therapies. Intriguingly, these saponins share common structural features with the vaccine adjuvant QS-21 and, thus, represent a potential alternative supply of saponin adjuvant precursors. Here, we sequence the S . officinalis genome and, through genome mining and combinatorial expression, identify 14 enzymes that complete the biosynthetic pathway to saponarioside B. These enzymes include a noncanonical cytosolic GH1 (glycoside hydrolase family 1) transglycosidase required for the addition of d- quinovose. Our results open avenues for accessing and engineering natural and new-to-nature pharmaceuticals, drug delivery agents and potential immunostimulants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

X-ray photoelectron spectroscopy of surfactants on sub-micron aqueous aerosols

Organic molecules at the aqueous interfaces of droplets and aerosols can influence multiphase chemistry and cloud condensation nuclei activity. While surface tension measurements on flat surfaces are commonly used to quantify organic partitioning and structure, extending these measurements to more realistic aerosols that might exist in metastable, supercooled and supersaturated states remains a challenge. Here, we use aerosol velocity map imaging X-ray photoelectron spectroscopy (A-VMI-XPS), a surface-sensitive and in situ technique, to study the partitioning and structure of a model surfactant (n-octyl β-D-thioglucopyranoside, OTG) in submicron aqueous aerosols with a mean radius of 116 nm. After accounting for finite size effects and evaporative cooling, we find the bulk concentrations of OTG in the aerosol are depleted 600-fold relative to macroscopic solutions. At the low temperatures of the experiment (ca. ∼188 K), we obtain a Langmuir equilibrium constant of 700 m3 mol-1, which corresponds to 4.9 m3 mol-1 at room temperature; a value that is consistent with prior literature reports. Analysis of photoelectron angular distributions, peak areas, and secondary electron escape barriers indicates a transition from a disordered surfactant layer at low [OTG] to a more structured layer at high [OTG]. These results link macroscopic surface tension measurements to nanoparticle surfactant behavior and demonstrate the utility of A-VMI-XPS in probing surfactant coating structure on free aerosols, with implications for understanding the impact of organic coatings on cloud formation and atmospheric chemistry.

Deal, Alexandra M↗

DOE OSTI2026

A skyrmionic topology perspective on Lehmann clusters

When two parallel coplanar dislocations with opposite Burgers vectors are brought into collision by the action of stress in solid crystals, they annihilate each other. In cholesterics with pitch p, under certain conditions, colliding dislocations with Burgers vectors b = p and b = − p are immune against annihilation and form stable twin-like pairs known as Lehmann clusters. We point out that this immunity is due to the escape of the director field into the third dimension. We show that from a topological point of view, Lehmann clusters can be seen as skyrmion tubes embedded in a helicoidal background, and their extremities have the topology of monopoles.

Pieranski, Pawel [Univ. Paris-Saclay, Orsay (Franc↗