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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Discovery and Characterization of a Thioesterase-Specific Monoclonal Antibody That Recognizes the 6-Deoxyerythronolide B Synthase

Assembly line polyketide synthases (PKSs) are large multimodular enzymes responsible for the biosynthesis of diverse antibiotics in bacteria. Structural and mechanistic analysis of these megasynthases can benefit from the discovery of reagents that recognize individual domains or linkers in a site-specific manner. Monoclonal antibodies not only have proven themselves as premier tools in analogous applications but also have the added benefit of constraining the conformational flexibility of their targets in unpredictable but often useful ways. Here we have exploited a library based on the naïve human antibody repertoire to discover a F ab (3A6) that recognizes the terminal thioesterase (TE) domain of the 6-deoxyerythronolide B synthase with high specificity. Biochemical assays were used to verify that 3A6 binding does not inhibit enzyme turnover. The co-crystal structure of the TE–3A6 complex was determined at 2.45 Å resolution, resulting in atomic characterization of this protein–protein recognition mechanism. F ab binding had minimal effects on the structural integrity of the TE. In turn, these insights were used to interrogate via small-angle X-ray scattering the solution-phase conformation of 3A6 complexed to a catalytically competent PKS module and bimodule. Furthermore, we have developed a high-affinity monoclonal antibody tool that recognizes the TE domain of the 6-deoxyerythronolide B synthase while maintaining its native function.

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

Ion-Specific Precipitation of Extractants Enables Rare-Earth Separation and Wastewater Remediation from Solvent Extraction of Critical Elements

The increasing demand for rare-earth elements (REEs) necessitates sustainable recovery strategies, particularly from secondary sources, such as electronic waste. Solvent extraction is the primary industrial method for REE separation; however, the unintentional dissolution of extractants into wastewater poses serious environmental risks, leading to organic contamination and process inefficiencies. Existing wastewater treatment methods struggle to remove these persistent pollutants, underscoring the need for innovative recovery approaches. Herein, we present a ligand-mediated precipitation strategy that simultaneously recovers REEs and removes dissolved extractants from solvent extraction wastewater. We show that residual extractants in the aqueous phase can selectively bind REEs, inducing their precipitation while leaving transition metals in solution. By integrating FTIR spectroscopy, EDS, XPS, EXAFS, and SAXS, we elucidate the mechanism of ion-specific precipitation and the local coordination environment of metal ions in the precipitate. Importantly, we demonstrate that the precipitated extractants can be efficiently recovered and reused, providing a closed-loop solution that enhances sustainability. Applying this method to leachates from samarium–cobalt (Sm–Co) and neodymium–iron–boron (NdFeB) mixed magnets, we achieve highly selective REE precipitation under mild conditions, demonstrating a scalable and cost-effective pathway for REE recovery, wastewater purification, and extractant recycling. In conclusion, by integrating element-specific ligand-mediated precipitation with extractant reuse, this work offers a transformative approach to REE separation that reduces the environmental impact while improving resource efficiency.

E-waste↗
DOE OSTI2019

Facet-Specific Photocatalytic Degradation of Organics by Heterogeneous Fenton Chemistry on Hematite Nanoparticles

Hematite nanoparticles are abundant in the photic zone of aquatic environments, where they play a prominent role in photocatalytic transformations of bound organics. In this work, we examine the photocatalytic degradation of rhodamine B (RhB) by visible light using two different structurally well-defined hematite nanoparticle morphologies. In addition to detailed solids characterization and aqueous kinetics measurements, we also exploit species-selective scavengers in electron paramagnetic spectroscopy (EPR) to sequester specific reaction channels and thereby assess their impact. Photodegradation rates for nanoplates dominated by {001} facets and nanocubes dominated by {012} facets were 0.13 and 0.7 h -1 , respectively, and turn over frequencies for the active sites on {001} and {012} were 7.89 × 10 -3 and 3.07× 10 -3 s -1 , yielding apparent activation energies of 17.13 and 24.94 kcal/mol within the energetic span model. Facet-specific differences appear directly linked not with the simple aerial cation site density but instead with their extent of undercoordination. By establishing this linkage, the findings lay a foundation for predicting the photocatalytic degradation efficiency for the myriad of possible hematite nanoparticle morphologies, and more broadly help unveil key reactions at the interface that may govern photocatalytic organic transformations in natural and engineered aquatic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Autogenerating a Domain-Specific Question-Answering Data Set from a Thermoelectric Materials Database to Enable High-Performing BERT Models

We present a method for autogenerating a large domain-specific question-answering (QA) dataset from a thermoelectric materials database. We show that a small language model, BERT, once fine-tuned on this automatically generated dataset of 99,757 QA pairs about thermoelectric materials, affords better performance in the field of thermoelectric materials compared to a BERT model fine-tuned on the generic English-language QA data set, SQuAD-v2. We further show that mixing the two data sets (ours and SQuAD-v2), which have significantly different syntactic and semantic scopes, allows the BERT model to achieve even better performance. The best-performing BERT model fine-tuned on the mixed data set outperforms the models fine-tuned on the other two data sets by scoring an exact match of 67.93% and an F1 score of 72.29% when evaluated on our test data set. This has important implications as it demonstrates the ability to realize high-performing small language models, with modest computational resources, empowered by domain-specific materials data sets which can be generated according to our method.

biological databases↗
DOE OSTI2022

Specific Ion and Electric Field Controlled Diverse Ion Distribution and Electroosmotic Transport in a Polyelectrolyte Brush Grafted Nanochannel

Controlling ion distribution inside a charged nanochannel is central to using such channels in diverse applications. Here, we show the possibility of using a charged polyelectrolyte (PE) brush grafted nanochannel for triggering diverse nanoscopic ion distribution and nanofluidic electroosmotic transport by controlling the valence and size of the counterions (that screen the charges of the PE brushes) and the strength of an externally applied axial electric field. We atomistically simulate separate cases of fully charged Polyacrylic acid (PAA) brush functionalized nanochannels with Na + , Cs + , Ca 2+ , Ba 2+ , and Y 3+ counterions screening the PE charges. Four key findings emerge from our simulations. First, we find that the counterions with a greater valence and a smaller size prefer to remain localized inside the brush layer. Second, for the case where there is an added chloride salt with the same cation (as the screening counterions), there are more coions (Cl - ions) in the brush-free bulk than counterions (for counterions Na + , Ca 2+ , Ba 2+ , Y 3+ ): this is a manifestation of the overscreening (OS) of the PE brush layer. Contrastingly, the number of Cs + ions remain higher than the Cl - ions inside the brush-free bulk, ensuring that there is no OS effect for this case. Third, large applied electric field enables a few Na + , Cs + , and Ba 2+ counterions to leave the brush layer and to go to the bulk: this makes the OS of the PE brush layer disappear for the cases of PE brushes being screened by the Na+ and Ba 2+ ions. On the other hand, no such electric-field-mediated disappearance of OS is observed for the cases of Ca 2+ and Y 3+ screening counterions; we attribute this to the firm attachment of these counterions to the negatively charged monomers. Free energy associated to a counterion binding to a PE chain corroborates this diversity in the counterion-specific response to the applied electric field. Lastly, we demonstrate that such diverse ion distributions, along with specific electric-field-strength-dependent ion properties, lead to (1) EOS transport in nanochannels grafted with PAA brushes screened with Cs + ions to be always counterion dominated, (2) EOS transport in nanochannels grafted with PAA brushes screened with Ca 2+ and Y 3+ ions to be always coion dominated, and (3) EOS transport in nanochannels grafted with PAA brushes screened with Na + and Ba 2+ ions to be coion dominated for smaller electric fields and counterion dominated for larger electric fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cryogenic “Iodide-Tagging” Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids

This work showcases cryogenic and temperature-dependent “iodide-tagging” photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly?I-) as a case study. Multiple Gly?I- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent “iodide-tagging” negative ion photoelectron spectroscopy (NIPES) where iodide was used as the “messenger” to interpret electronic energetics and structural information of various Gly?I- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that “iodide-tagging” NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Predicting Adsorption Properties of Catalytic Descriptors on Bimetallic Nanoalloys with Site-Specific Precision

Bimetallic nanoparticles present a vastly tunable structural and compositional design space rendering them promising materials for catalytic and energy applications. Yet it remains an enduring challenge to efficiently screen candidate alloys with atomic level specificity while explicitly accounting for their inherent stabilities under reaction conditions. Herein, by leveraging correlations between binding energies of metal adsorption sites and metal–adsorbate complexes, we predict adsorption energies of typical catalytic descriptors (OH*, CH 3 *, CH*, and CO*) on bimetallic alloys with site-specific resolution. We demonstrate that our approach predicts adsorption energies on top and bridge sites of bimetallic nanoparticles having generic morphologies and chemical environments with errors between 0.09 and 0.18 eV. By forging a link between the inherent stability of an alloy and the adsorption properties of catalytic descriptors, we can now identify active site motifs in nanoalloys that possess targeted catalytic descriptor values while being thermodynamically stable under working conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular Basis of Broad Spectrum N -Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2

Immunoglobulin G (IgG) glycosylation critically modulates antibody effector functions. Streptococcus pyogenes secretes a unique endo-β-N-acetylglucosaminidase, EndoS2, which deglycosylates the conserved N-linked glycan at Asn297 on IgG Fc to eliminate its effector functions and evade the immune system. EndoS2 and specific point mutants have been used to chemoenzymatically synthesize antibodies with customizable glycosylation for gain of functions. EndoS2 is useful in these schemes because it accommodates a broad range of N-glycans, including high-mannose, complex, and hybrid types; however, its mechanism of substrate recognition is poorly understood. We present crystal structures of EndoS2 alone and bound to complex and high-mannose glycans; the broad N-glycan specificity is governed by critical loops that shape the binding site of EndoS2. Furthermore, hydrolytic experiments, domain-swap chimeras, and hydrogen–deuterium exchange mass spectrometry reveal the importance of the carbohydrate-binding module in the mechanism of IgG recognition by EndoS2, providing insights into engineering enzymes to catalyze customizable glycosylation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

Peptide antibiotics represent a class of conformationally-constrained natural products of growing pharmaceutical interest. Plantazolicin (PZN) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, Bacillus anthracis. The bioactivity of PZN is contingent on dimethylation of its N-terminal Arg residue by an S-adenosylmethionine-dependent methyltransferase. Here in this paper, we explore the substrate tolerances of two homologous PZN methyltransferases by carrying out kinetic analyses of the enzymes against a synthetic panel of truncated PZN analogs containing the N-terminal Arg residue. X-ray cocrystal structures of the PZN methyltransferases with each of these heterocycle-containing substrates provide a rationale for understanding the strict substrate specificity of these enzymes. Kinetic studies of structure-guided, site-specific variants allowed for the assignment of residues governing catalysis and substrate scope. Microbiological testing further revealed that upon dimethylation of the N-terminal Arg, a pentaheterocyclized PZN analog retained potent anti-B. anthracis activity, nearly equal to that of full-length PZN. These studies may be useful in the biosynthetic engineering of natural product analogs with different bioactivity profiles, as demonstrated by our identification of a truncated plantazolicin derivative that is active against methicillin-resistant Staphylococcus aureus (MRSA).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Optical Control of Dopamine D2-like Receptors with Cell-Specific Fast-Relaxing Photoswitches

Dopamine D2-like receptors (D2R, D3R, and D4R) control diverse physiological and behavioral functions and are important targets for the treatment of a variety of neuropsychiatric disorders. Their complex distribution and activation kinetics in the brain make it difficult to target specific receptor populations with sufficient precision. We describe a new toolkit of light-activatable, fast-relaxing, covalently taggable chemical photoswitches that fully activate, partially activate, or block D2-like receptors. This technology combines the spatiotemporal precision of a photoswitchable ligand (P) with cell type and spatial specificity of a genetically encoded membrane anchoring protein (M) to which the P tethers. These tools set the stage for targeting endogenous D2-like receptor signaling with molecular, cellular, and spatiotemporal precision using only one wavelength of light.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Co‐Evolution of Specific Stiffness and Permeability of Rock Fractures Offset in Shear

Abstract Fractures and faults represent planes of weakness and compliance in rock masses that serve as focal points for both microearthquakes and fluid transport, with seismicity and permeability evolution closely linked. Contact stiffness is highly stress‐sensitive and directly influences permeability. We explore the co‐evolution of specific stiffness and permeability of rough fractures under normal stress and shear offset using numerical simulations. Individual rough fractures are represented by variable amplitude (Root mean square) and wavelength ( λ ) using a granular mechanics model. Contacting rough surfaces are mated, offset in shear, and then compacted in displacement mode. The compacting fractures generate stress‐dependent changes in contact porosity, which govern both permeability and stiffness evolution. We establish a universal dimensionless relationship linking specific stiffness and permeability that inherently incorporates the effects of surface roughness, shear offset, and microcracking. The observed cracking effect—where local stress redistribution and pressure‐driven microcrack propagation dynamically alter the aperture field—introduces a nonlinear permeability response at high stress. Increased roughness amplitude and larger shear offsets reduce stiffness while dampening permeability sensitivity to stress, demonstrating a strong interplay between surface texture and hydro‐mechanical behavior. While the model captures this behavior effectively, deviations emerge at very low porosities due to extreme aperture sensitivity in this limit.

He, Xinxin [Energy and Mineral Engineering Pennsyl↗
DOE OSTI2016

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF 2 molecules following X-ray absorption at the Xe site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The critical role of point defects in improving the specific capacitance of δ-MnO 2 nanosheets

3D porous nanostructures built from 2D δ-MnO 2 nanosheets are an environmentally friendly and industrially scalable class of supercapacitor electrode material. While both the electrochemistry and defects of this material have been studied, the role of defects in improving the energy storage density of these materials has not been addressed. In this work, δ-MnO 2 nanosheet assemblies with 150 m 2 g -1 specific surface area are prepared by exfoliation of crystalline K x MnO 2 and subsequent reassembly. Equilibration at different pH introduces intentional Mn vacancies into the nanosheets, increasing pseudocapacitance to over 300 F g -1 , reducing charge transfer resistance as low as 3 Ω, and providing a 50% improvement in cycling stability. X-ray absorption spectroscopy and high-energy X-ray scattering demonstrate a correlation between the defect content and the improved electrochemical performance. The results show that Mn vacancies provide ion intercalation sites which concurrently improve specific capacitance, charge transfer resistance and cycling stability.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate

The majority of the eukaryotic genome is transcribed, generating a significant number of long intergenic noncoding RNAs (lincRNAs). Although lincRNAs represent the most poorly understood product of transcription, recent work has shown lincRNAs fulfill important cellular functions. In addition to low sequence conservation, poor understanding of structural mechanisms driving lincRNA biology hinders systematic prediction of their function. Here we report the molecular requirements for the recognition of steroid receptors (SRs) by the lincRNA growth arrest-specific 5 (Gas5), which regulates steroid-mediated transcriptional regulation, growth arrest and apoptosis. We identify the functional Gas5-SR interface and generate point mutations that ablate the SR-Gas5 lincRNA interaction, altering Gas5-driven apoptosis in cancer cell lines. Further, we find that the Gas5 SR-recognition sequence is conserved among haplorhines, with its evolutionary origin as a splice acceptor site. This study demonstrates that lincRNAs can recognize protein targets in a conserved, sequence-specific manner in order to affect critical cell functions.

Hudson, William H.↗
DOE OSTI2015

Allelic variation contributes to bacterial host specificity

Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Methylamine-specific methyltransferase paralogs in Methanosarcina are functionally distinct despite frequent gene conversion

Abstract Sequenced archaeal genomes are mostly smaller and more streamlined than typical bacterial genomes; however, members of the Methanosarcina genus within the Euryarchaeaota are a significant exception, with M. acetivorans being the largest archaeal genome (5.8 Mbp) sequenced thus far. This finding is partially explained by extensive gene duplication within Methanosarcina spp. Significantly, the evolutionary pressures leading to gene duplication and subsequent genome expansion have not been well investigated, especially with respect to biological methane production (methanogenesis), which is the key biological trait of these environmentally important organisms. In this study, we address this question by specifically probing the functional evolution of two methylamine-specific methyltransferase paralogs in members of the Methanosarcina genus. Using the genetically tractable strain, M. acetivorans, we first show that the two paralogs have distinct cellular functions: one being required for methanogenesis from methylamine, the other for use of methylamine as a nitrogen source. Subsequently, through comparative sequence analyses, we show that functional divergence of paralogs is primarily mediated by divergent evolution of the 5′ regulatory region, despite frequent gene conversion within the coding sequence. This unique evolutionary paradigm for functional divergence of genes post-duplication underscores a divergent role for an enzyme singularly associated with methanogenic metabolism in other aspects of cell physiology.

59 BASIC BIOLOGICAL SCIENCES↗