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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Biotransformation of Phenolics in Spent Liquor from Aqueous Ammonia Pretreatment

Spent liquors of biomass pretreatment provide a source for renewable chemical production. These liquors require treatment before being discharged; otherwise, they negatively impact the environment. Herein, spent liquors from aqueous ammonia pretreatment of poplar wood are characterized for phenolic content via liquid chromatography–mass spectrometry and nuclear magnetic resonance spectroscopy. The main phenolics are phenol, p-hydroxybenzamide (pHBAm), and p-hydroxybenzoic acid (pHBA), of which pHBAm and pHBA are produced from the ester-linked p-hydroxybenzoates in poplar wood. Phenol is produced from pHBA via decarboxylation. The potential biotransformation of the extracted phenolics into 2-pyrone-4,6-dicarboxylic acid (PDC) is assessed using an engineered strain of Novosphingobium aromaticivorans DSM12444 (PDC strain). Biotransformation of pHBAm to PDC is shown to be possible in the presence of pHBA, but not when pHBAm is the sole phenolic substrate, this is the first reported observation of N. aromaticivorans producing PDC from an aromatic amide. The phenol present is not transformed to PDC and does not inhibit PDC production. This study demonstrates that the phenolic amide in spent liquor from ammonia pretreatment can be valorized via biotransformation using N. aromaticivorans, which adds to the growing versatility of N. aromaticivorans as a microbial chassis for converting plant-derived compounds to useful products.

biomass↗
DOE OSTI2025

Biomanufacturing from gaseous C1 feedstocks: A perspective on opportunities and challenges

Single-carbon (C1) substrates including carbon dioxide, carbon monoxide, and methane are abundantly available from natural and anthropogenic sources and present potential feedstocks for biomanufacturing. Utilizing these C1 gas feedstocks in bioprocesses for sustainable production of chemicals and fuels could prove pivotal in removing excess carbon from the atmosphere. This perspective describes the spectrum and sources of CO2, CO, and CH4 and examines emerging opportunities in microbial bioconversion and bioelectrochemical processes for these feedstocks. We discuss existing challenges in bioprocess development that currently restrict the commercialization of C1 biomanufacturing technologies. We detail different aerobic and anaerobic bioconversion approaches for C1 feedstocks employing pure and mixed cultures and examine the suitability of each scenario for producing specific molecules. Beyond strain engineering and bioprocess constraints, we address often overlooked factors that limit the development of efficient and reliable bioprocesses, including technology availability for research and safety considerations. We then discuss and recommend the necessary safety features and technological research tools for developing fast, safe, and efficient bioprocesses using gaseous feedstocks to support the scale-up and commercialization of C1 biomanufacturing technologies. This perspective provides an overview of the current scientific and industrial state of the art and offers insights into future technological needs that must be addressed to realize the potential of biomanufacturing from gaseous feedstocks. Synopsis: C1 gases offer a sustainable feedstock for biomanufacturing of fuels and chemicals. This work analyzes bioconversion methods, challenges, and safety considerations, and emphasizes the need for improved technology to enable commercialization.

Biomanufacturing↗
DOE OSTI2024

Adaptive laboratory evolution and metabolic engineering of Cupriavidus necator for improved catabolism of volatile fatty acids

Bioconversion of high-volume waste streams into value-added products will be an integral component of the growing bioeconomy. Volatile fatty acids (VFAs) (e.g., butyrate, valerate, and hexanoate) are an emerging and promising waste-derived feedstock for microbial carbon upcycling. Cupriavidus necator H16 is a favorable host for conversion of VFAs into various bioproducts due to its diverse carbon metabolism, ease of metabolic engineering, and use at industrial scales. Here, in this study, we report that a common strategy to improve product titers in C. necator, deletion of the polyhydroxybutyrate (PHB) biosynthetic operon, results in a significant growth defect on VFA substrates. Using adaptive laboratory evolution, we identify mutations to the regulator gene phaR, the two-component response regulator-histidine kinase pair encoded by H16_A1372/H16_A1373, and the tripartite transporter assembly encoded by H16_A2296-A2298 as causative for improved growth on VFA substrates. Deletion of phaR and H16_A1373 led to significantly reduced NADH abundance accompanied by large changes to expression of genes involved in carbon metabolism, balance of electron carriers, and oxidative stress tolerance that may be responsible for improved growth of these engineered strains. These results provide insight into the role of PHB biosynthesis in carbon and energy metabolism and highlight a key role for the regulator PhaR in global regulatory networks. By combining mutations, we generated platform strains with significant growth improvements on VFAs, which can enable improved conversion of waste-derived VFA substrates to target bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2025

MechBERT: Language Models for Extracting Chemical and Property Relationships about Mechanical Stress and Strain

Language models are transforming materials-aware naturallanguage processing by enabling the extraction of dynamic, context-rich information from unstructured text, thus, moving beyond the limitations of traditional information-extraction methods. Moreover, small language models are on the rise because some of them can perform better than large language models (LLMs) when given domain-specific questionanswer tasks, especially about an application area that relies on a highly specialized vernacular, such as materials science. We therefore present a new class of MechBERT language models for understanding mechanical stress and strain in materials. These employ Bidirectional Encoder Representations for transformer (BERT) architectures. We showcase four MechBERT models, all of which were pretrained on a corpus of documents that are textually rich in chemicals and their stress–strain properties and were fine-tuned on question-answering tasks. We evaluated the level of performance of our models on domain-specific as well as general English-language question-answer tasks and also explored the influence of the size and type of BERT architectures on model performance. We find that our MechBERT models outperform BERT-based models of the same size and maintain relevancy better than much larger BERT-based models when tasked with domain-specific question-answering tasks within the stress–strain engineering sector. These small language models also enable much faster processing and require a much smaller fraction of data to pretrain them, affording them greater operational efficiency and energy sustainability than LLMs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation

The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.

Singh, Nitin Kumar [Michigan State Univ., East Lan↗
DOE OSTI2025

Single-Atom-Resolved Vibrational Spectroscopy of a Dislocation

Dislocations in III-nitride semiconductors impede heat transport, leading to localized overheating, which severely limits the performance and reliability of optoelectronic and power devices. Current research on phonon–dislocation interactions primarily addresses bulk materials, focusing on the average effects at specific dislocation densities. However, phonon resistance from dislocation scattering arises from both short-range core interactions and long-range strain field interactions, which remain largely unexplored. Here, in this study, electron energy-loss spectroscopy is used to investigate a GaN dislocation. Vibrational modes localized on specific core atoms are revealed, reflecting short-range interactions. Additionally, phonon energy shifts driven by strain fields surrounding the dislocation are observed, reflecting long-range interactions. Ab initio calculations support these findings and draw out additional details. This work establishes a paradigm for probing defect-induced phonon scattering at the single-atom level, revealing how dislocations affect phonon behavior through atomic reconstruction and strain engineering, thus offering insights for designing improved material functionalities.

III-nitride semiconductors↗
DOE OSTI2026

Strain in Metal Halide Perovskite Thin Films - Interfacial Mechanical Coupling

Hybrid organic−inorganic metal halide perovskites (MHPs) are promising semiconductors for photovoltaics and optoelectronics, but their commercial viability is limited by instability, particularly strain induced by mismatch in coefficients of thermal expansion (CTE) between the perovskite film and substrate. Here, we investigate strain development and relaxation in MHP thin films using in situ bending and Grazing Incidence Wide-Angle X-ray Scattering (GIWAXS). We quantify the film− substrate interfacial mechanical coupling and identify interfacial slippage beyond a critical strain (∼0.4%), with Br-2PACz exhibiting comparatively stronger interfacial mechanical coupling among common interface modifiers. Time-resolved GIWAXS reveals reversible macrostrain during thermal cycling driven by CTE mismatch. Leveraging this behavior, we introduce a prestrain process that induces persistent compressive strain after cooling, with partial relaxation over time. These results provide insight into interfacial mechanical coupling and strain dynamics, offering a framework for strain engineering in perovskite devices.

metals↗
DOE OSTI2026

Rapid Evaluation of Amine-Functionalized Solvents for Biomass Deconstruction Using High-Throughput Screening and One-Pot Enzymatic Saccharification

Efficient and sustainable pretreatment of lignocellulosic biomass is critical for biofuel and biochemical production, yet its optimization is often hindered by slow, labor-intensive experimental methods. Here, we report the first demonstration of a custom-built, miniaturized, high-throughput screening platform integrated with one-pot enzymatic saccharification, enabling parallel evaluation of solvent type, feedstock, and temperature with minimal material use and high reproducibility. As a proof-of-concept, the HTX platform was used to screen five amine-functionalized solvents, including isopropanolamine, butylamine, N-methylbutylamine, ethanolamine, and ethanolamine acetate across three bioenergy crops (sorghum, poplar, and switchgrass) and pretreatment temperatures ranging from 80 to 140 °C. Vacuum drying successfully removed more than 99% of the solvents from the pretreated biomass, eliminating the need for water washing prior to saccharification. Isopropanolamine and N-methylbutylamine yielded the highest glucose (70–80%) and xylose (58–67%) release, with trends reflecting feedstock recalcitrance. The produced hydrolysates supported robust growth of an engineered strain of the yeast Rhodosporidium toruloides, confirming biocompatibility. This high-throughput platform provides a scalable, feedstock-agnostic framework for rapid pretreatment screening, accelerating solvent–feedstock pairing and process optimization. Its ability to integrate pretreatment, solvent removal, saccharification, and microbial conversion in a miniaturized format offers significant advantages for cost-competitive biorefinery development.

Biomass↗
DOE OSTI2026

Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas mobilis

The conversion of lignocellulosic biomass to biofuels and bioproducts is limited by small inhibitory molecules generated during the pretreatment process. The diverse compounds within the cell wall hydrolysate including aldehydes, carboxylic acids, phenolics, and alcohols inhibit microbial growth by disrupting microbial membranes. Although Zymomonas mobilis combines high ethanol productivity with hopanoid-rich membranes that confer solvent tolerance, hydrolysate compounds still inhibit microbial growth. One proposed mitigation strategy is to pump these molecules out through active transport processes, reducing direct toxicity. However, if passive permeation rates are high, active transport would create a futile cycle where the exported molecules diffuse back in, creating a net drag on fitness. To investigate this hypothesis, we measure the passive permeation for thirty-three lignocellulose derived compounds using atomistic molecular dynamics simulations with enhanced sampling. Permeability coefficients determined spanned more than eight orders of magnitude driven largely by the balance between hydrophobicity and polarity. Hydrophobic inhibitors such as aromatic acids, aldehydes, and short chain alcohols readily partitioned into the membrane and showed high permeability consistent with rapid passive influx and strong toxicity. Most polar molecules have lower but still appreciable permeation rates, with only the most polar sugars having low permeabilities. By integrating these predictions together with hydrolysate composition information, we find that most of these molecules are so permeable that futile cycles where passive permeation overwhelms efflux is highly likely. These findings provide a predictive framework for strain engineering, highlighting that, for highly permeable inhibitors, reducing extracellular inhibitor concentrations through hydrolysate detoxification, pretreatment optimization, or dilution may be necessary to mitigate futile cycling and improve microbial productivity in industrial biorefineries.

Zymomonas mobilis↗
DOE OSTI2025

Systematic Mapping of Bacterial CRISPRa Systems for Synergistic Gene Activation Reveals Antagonistic Effects

CRISPR gene activation (CRISPRa) tools have shown great promise for bacterial strain engineering but often require customization for each intended application. Our goal is to create generalizable CRISPRa tools that can overcome previous limitations of gene activation in bacteria. In eukaryotic cells, multiple activators can be combined for synergistic gene activation. To identify potential effectors for synergistic activation in bacteria, we systematically characterized bacterial activator proteins with a set of engineered synthetic promoters. We found that optimal target sites for different activators could vary by up to 200 bases in the region upstream of the transcription start site (TSS). These optimal target sites qualitatively matched previous reports for each activator, but the precise targeting rules varied between different promoters. By characterizing targeting rules in the same promoter context, we were able to test activator combinations with each effector positioned at its optimal target site. We did not find any activator combinations that produced synergistic activation, and we found that many combinations were antagonistic. Furthermore, this systematic investigation highlights fundamental mechanistic differences between bacterial and eukaryotic transcriptional activation systems and suggests that alternative strategies will be necessary for strong bacterial gene activation at arbitrary endogenous targets.

CRISPR activation↗
DOE OSTI2026

Engineering Escherichia coli for Urease-Driven Synthesis of Metal Oxide Nanomaterials

The development of functional nanomaterials with controlled morphologies is essential for advancements in medicine, electronics and computing, energy, catalysis, and environmental applications. However, conventional synthesis methods often demand high energy input and pose significant environmental challenges. Urease-based biomineralization presents an efficient, eco-friendly alternative for nanomaterial production under mild conditions. In this study, we engineered Escherichia coli ( E. coli ) to express a urease gene cluster from Sporosarcina pasteurii using CRAGE-Duet technology. The engineered strain successfully synthesized calcium carbonate and calcium phosphate crystals. Expanding the approach, we synthesized metal oxide nanoparticles, including hematite (Fe 2 O 3 ), and nanocrystalline anatase titanium dioxide (TiO 2 ). These nanomaterials were characterized by electron microscopy, demonstrating the potential of E. coli as a sustainable and versatile platform for green nanomaterial synthesis.

bacteria↗
DOE OSTI2026

Bio-based oxalic acid production in Issatchenkia orientalis enables sustainable rare earth recovery

The growing demand for rare earth elements (REEs) in clean energy and high-tech industries underscores the need for sustainable recovery methods and a reliable supply of processing chemicals. Here, we establish a microbial platform using the acid-tolerant yeast Issatchenkia orientalis SD108 to produce bio-oxalic acid for REE recovery. By introducing an oxaloacetate cleavage pathway and applying metabolic engineering, the engineered strain produces 39.53 g·L -1 oxalic acid at pH 4.0 in fed-batch fermentation. The crude fermentation broth, used without purification, efficiently precipitates over 99% neodymium (Nd), 99% dysprosium (Dy), and 98% lanthanum (La) from individual REE chloride solutions. Recovery from a low-grade ore leachate achieves over 99% total recovery. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) confirm that REE oxalates precipitated with bio-oxalic acid closely resemble those obtained using commercial oxalic acid. Techno-economic analysis (TEA) and life cycle assessment (LCA) further demonstrate that bio-oxalic acid can be produced at a competitive price of $1.79·kg -1 while reducing carbon intensity (CI) by 112% to 63.5% with and without electricity displacement, respectively, relative to the fossil-based benchmark. These results highlight bio-oxalic acid as a green, economically viable alternative to synthetic oxalate for sustainable REE recovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Imaging supermoiré relaxation in helical trilayer graphene

In twisted van der Waals materials, local atomic relaxation can alter the underlying electronic structure. Characterizing lattice reconstruction and its susceptibility to strain is essential for understanding emergent electronic states, especially in multilayers in which interference between moiré lattices yields larger supermoiré patterns whose energy is highly sensitive to local stacking. Here, in this study, we image spatial modulations in the electronic character of helical trilayer graphene, which indicate relaxation into a superstructure of large domains with uniform moiré periodicity. We show that the supermoiré domain size is increased by strain and can be altered in the same device while preserving the local properties within each domain. Finally, we observe a higher conductance at the domain boundaries, consistent with predictions that they host counterpropagating edge modes. Our work provides a real-space visualization of moiré-periodic domains, reveals two independently tunable length scales and demonstrates strain engineering as a route towards designing correlated topological networks at the supermoiré scale.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Magnetic compressibility of layered ferromagnet under pressure

This study systematically investigates the magnetic properties of the layered ferromagnet MnPt 5 As under pressure through a combination of experimental measurements and theoretical simulations. MnPt 5 As exhibits a ferromagnetic transition at approximately 301 K. Neutron diffraction measurements under applied pressures up to ∼4.9 GPa were performed over a temperature range from 320 to 100 K to probe its magnetic behavior. The results confirm that the Mn atoms maintain a ferromagnetic order under applied pressures, consistent with the ambient-pressure findings. However, magnetic anisotropy is notably suppressed. To further elucidate the compressibility of magnetic anisotropy in MnPt 5 As, x-ray diffraction under pressure was conducted. The results reveal that the c-axis undergoes a greater and more rapid compression compared to the ab -plane, which may contribute to the observed suppression of Mn ferromagnetic ordering along the c -axis. Additionally, theoretical calculations indicate that magnetic ordering exhibits a similar pressure-induced trend under applied pressure, supporting the experimental observations. These findings offer insights into the pressure-dependent magnetic properties and anisotropy of MnPt 5 As, with potential implications for strain engineering in Mn-based magnetic devices.

Electronic band structure↗
DOE OSTI2025

Modeling strain and quantum confinement in GaAs/Ga x In 1−x P superlattices for spin-polarized electron sources

In this study, we systematically design and simulate a series of GaAs-based superlattice configurations aimed at enhancing heavy-hole–light-hole band splitting while simultaneously optimizing band alignment to reduce the conduction band barrier, thereby facilitating efficient electron transport. These combined effects are crucial for achieving high electron spin polarization and high quantum efficiency, the two key performance metrics of next-generation spin-polarized electron sources. We investigated three types of superlattice architectures: (1) compressively strained GaAs wells on GaInP barriers, yielding a maximum band splitting of 140 meV, (2) lattice-matched GaAs/GaInP structures, resulting in the maximum band splitting of 75 meV, and (3) tensile strained GaAs wells on GaInP barriers, with a maximum band splitting of 40 meV. The results demonstrate the tunability of heavy-hole–light-hole band splitting and establish a design framework for high-performance spin-polarized photocathodes based on a combination of strain engineering, quantum confinement, and optimized heterostructure design.

Electron sources↗
DOE OSTI2025

How transparent is graphene? A surface science perspective on remote epitaxy

Remote epitaxy is the synthesis of a single crystalline film on a graphene-covered substrate, where the film adopts epitaxial registry to the substrate as if the graphene is transparent. Despite many exciting applications for flexible electronics, strain engineering, and heterogeneous integration, an understanding of the fundamental synthesis mechanisms remains elusive. Here we offer a perspective on the synthesis mechanisms, focusing on the foundational assumption of graphene transparency. We identify challenges for quantifying the strength of the remote substrate potential that permeates through graphene, and propose Fourier and beating analysis as a bias-free method for decomposing the lattice potential contributions from the substrate, from graphene, and from surface reconstructions, each at different frequencies. We highlight the importance of graphene-induced reconstructions on epitaxial templating, drawing comparison to moiré epitaxy. We highlight the role of the remote potential in tuning surface diffusion and adatom kinetics on graphene, which are crucial for navigating the competition between remote epitaxy and defect-seeded mechanisms like pinhole epitaxy. In light of this weak remote potential, we re-evaluate the current state-of-the-art experimental evidence, highlighting why it remains challenging to experimentally validate a ‘remote’ epitaxy mechanism that cannot be explained by alternatives, such as pinhole-seeded epitaxy or serial van der Waals epitaxy. We end with one experimental example that, to out knowledge, cannot be explained by competing mechanisms: a different long-range epitaxial relationship for GdPtSb films grown on graphene/sapphire, compared to direct epitaxy on sapphire. We suggest for future experiments that directly measure the remote potential and impact of tuneable growth kinetics.

epitaxy↗
DOE OSTI2024

Theory of nonlinear terahertz susceptibility in ferroelectrics

An analytical theory is developed for predicting the nonlinear susceptibility of ionic polarization to continuous electromagnetic waves in both bulk and strained thin film ferroelectrics. Using a perturbation method for solving the nonlinear equation of motion for ionic polarization within the framework of Landau-Ginzburg-Devonshire theory, the full second-order nonlinear susceptibility tensor is derived as a function of frequency, temperature, and strain. Here, the theory predicts the coexistence of a significantly enhanced second-order dielectric susceptibility and a relatively low dielectric loss in BaTiO 3 films with a strain-stabilized monoclinic ferroelectric phase and in a strained SrTiO 3 film near its temperature-driven second-order ferroelectric-to-paraelectric phase transition. In this paper, we establish a theoretical framework for predicting and exploiting nonlinear interactions between terahertz waves and ferroelectric materials and, more generally, suggest exciting opportunities to strain-engineer nonlinear dynamical properties of ferroelectrics beyond the static and quasistatic limits.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Strain-tunable microwave-resonance technique for quantum materials

By integrating a dielectric microwave resonator with a piezoelectric-based strain device, we develop an in situ strain-tunable microwave spectroscopy technique that enables contactless measurements of material properties under strain. To demonstrate the capability of this device, we measure the strain-dependent microwave surface impedance of the representative iron-based superconductor Ba⁢Fe 2 (As 1−𝑥 ⁢P 𝑥 ) 2 at the slightly overdoped composition. We successfully control and observe the suppression of superconductivity under both compressive and tensile anisotropic lattice distortions along the tetragonal [110] T direction, as manifested by changes in the quality factor and resonance frequency shifts of microwave resonance. Furthermore, strain-induced changes in microwave surface resistivity, an extension of conventional DC-limit transport elastoresistivity to the microwave regime, provide information on electronic anisotropy equivalent to that of DC elastoresistivity, while offering a contactless alternative. Furthermore, our strain-tunable cavity therefore serves as a powerful, contactless probe of fundamental material properties under strain and may also potentially facilitate the design of hybrid quantum systems with strain-engineered quantum degrees of freedom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗