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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Thermophilic Chassis-Enabled High-Throughput Selection of a Thermostable Fluorogenic Reporter

Thermostable proteins show increased shelf life and performance at elevated temperatures and under harsh conditions, resulting in lower costs for various industrial and biotechnological applications. However, due to a limited understanding of the relationship between stability and function, protein stabilization remains primarily a trial-and-error approach. Therefore, building a combinatorial library of mutations predicted to improve stability, followed by experimental testing, represents a markedly improved methodology. However, the lack of high-throughput approaches to screen even a moderately sized library presents a major bottleneck in the field. Here, in this study, we use a thermophile, Parageobacillus thermoglucosidasius (Ptherm) to rapidly screen combinatorial libraries consisting of rationally designed thermostabilizing mutations (∼10 3 –10 4 ) of a mesophilic fluorescent reporter, Y-FAST. On a Petri dish, microbial growth at an elevated temperature and exposure to fluorogen yielded several colonies of Ptherm that showed distinct fluorescence at 55 and 68 °C in our two sequentially generated libraries using Rosetta and ProteinMPNN, respectively. The Y-FAST variants isolated from fluorescent colonies were brighter than Y-FAST and showed higher resistance to thermal and chemical denaturation. AlphaFold-predicted structures and MD simulations revealed stability-enhancing salt bridges and hydrogen bond networks in the isolated FAST variants. The moderately thermostable FAST (tsFAST) and hyperstable FAST (hsFAST) were then demonstrated as translation reporters for protein expression and folding at elevated temperatures, such as 55 and 68 °C. Our approach of combinatorial library generation and high-throughput screening in a thermophilic chassis could, in principle, be extended to other proteins fused to these translation reporters. Furthermore, the hsFAST protein is small─half the size of the green fluorescent protein─and does not require oxygen for maturation, making it ideal for engineering extremophilic anaerobes for biosensing and bioconversion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo–electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Molecular-Level Insights into the Influence of Ionic Liquids on the Structure and Dynamics of Neutral and Charged Polyimides

We use all-atom molecular dynamics simulations to investigate how increasing ionic functionalization influences polyimide (PI) behavior in ionic liquid (IL) solvation environments. Here, we examine three polymer systems with varying charge densities: a neutral polyimide [N−PI] containing imidazole rings and progressively introduce charge through quaternization to create singly [C−PI] + and doubly charged [C−2PI] 2+ variants across a wide range of IL concentration (0−90 wt %). Through comprehensive structural, mechanical, and electrostatic analyses, we reveal that polymer charge density plays a central role in shaping IL organization and interaction with the polymer matrix. At low IL content, charged systems exhibit strong electrostatic complexation, leading to chain compaction, localized ESP environments, and elevated dielectric constants. As IL concentration increases, the effect of the different polymer charge states becomes less significant. Notably, an intermediate composition regime at approximately 50 wt % IL is associated with changes in IL-rich domain connectivity and overall system behavior across all three PI systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme

A major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are complex plant secondary metabolites with recognized therapeutic value. Due to their difficult synthesis they are regularly sourced by extraction and purification from the low-yielding daffodil Narcissus pseudonarcissus. Here, we propose an efficient biosensor-machine learning technology stack for biocatalyst development, which we apply to engineer an Amaryllidaceae enzyme in Escherichia coli. Directed evolution is used to develop a highly sensitive (EC 50 = 20 μM) and specific biosensor for the key Amaryllidaceae alkaloid branchpoint 4’-O-methylnorbelladine. A structure-based residual neural network (MutComputeX) is subsequently developed and used to generate activity-enriched variants of a plant methyltransferase, which are rapidly screened with the biosensor. Functional enzyme variants are identified that yield a 60% improvement in product titer, 2-fold higher catalytic activity, and 3-fold lower off-product regioisomer formation. A solved crystal structure elucidates the mechanism behind key beneficial mutations.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1988

Electron Diffraction Evidence for the Ordering of Excess Nickel Atoms by Relation to Stoichiometry in Nickel-Rich Beta'-Nial Formation of a Nickel-Aluminum (Ni2al) Superlattices

In electron diffraction patterns of nickel-rich beta-NiAl alloys, many anomalies are observed. One of these is the appearance of diffuse intensity maxima between the reflexions of the B2 structure. This is explained by the short-range ordering of the excess nickel atoms on the simple cubic sublattice occupied only by aluminum atoms in the stoichiometric, perfectly ordered NiAl alloy. After annealing Ni 37.5 atomic percent Al and Ni 37.75 atomic percent Al for 1 week at 300 and 400 C, the diffuse intensity maxima transformed into sharp superstructure reflexions. These reflexions are explained by the formation of the four possible variants of an ordered hexagonal superstructure corresponding to the Ni2Al composition. This structure is closely related to the Ni2Al3 structure (same space group) formed by the ordering of vacancies on the nickel sublattice in aluminum-rich beta-NiAl alloys.

Reynaud, F.↗
DOE OSTI2024

Analyzing the Effects of Atmospheric Turbulent Fluctuations on the Wake Structure of Wind Turbines and Their Blade Vibrational Dynamics

In recent trends, a rising demand for renewable energy has driven wind turbines to larger proportions, where lighter blade designs are often adopted to reduce the costs associated with logistics and production. This causes modern utility-scale wind turbine blades to be inherently more flexible, and their amplified aeroelastic sensitivity results in complex multi-physics reactions to variant atmospheric conditions, including dynamic patterns of aerodynamic loading at the rotor and vortex structure evolutions within the wake. In this paper, we analyze the influence of inflow variance for wind turbines with large, flexible rotors through simulations of the National Rotor Testbed (NRT) turbine, located at Sandia National Labs’ Scaled Wind Farm Technology (SWiFT) facility in Lubbock, Texas. The Common Ordinary Differential Equation Framework (CODEF) modeling suite is used to simulate wind turbine aeroelastic oscillatory behavior and wind farm vortex wake interactions for a range of flexible NRT blade variations, operating in differing conditions of variant atmospheric flow. CODEF solutions of turbine operation in Steady-In-The-Average (SITA) wind conditions are compared to SITA wind conditions featuring a controlled gust-like pulse overimposed, to isolate the effects of typical wind fluctuations. Finally, simulations of realistic time-varying wind conditions from SWiFT meteorological tower measurements are compared to the solutions of SITA wind conditions. These increasingly complex atmospheric inflow variations are tested to show the differing effects evoked by various patterns of spatiotemporal atmospheric flow fluctuations. An analysis is presented for solutions of wind turbine aeroelastic response and vortex wake evolution, to elucidate the consequences of variant inflow, which pertain to wind turbine dynamics at an individual and farm-collective scale. The comparisons of simulated farm flow for SITA and measured fluctuating wind conditions show that certain regions of the wake contain up to a 12% difference in normalized axial velocity, due to the introduction of wind fluctuations. The findings of this study prove valuable for practical applications in wind farm control and optimization strategies, with particular significance for modern utility-scale wind power plants operating in variant atmospheric conditions.

Farrell, Alayna (ORCID:000000023555720X)↗
DOE OSTI2026

Engineering Enantiocomplementary Protoglobins for Stereoconvergent Construction of N -Alkylated α-Aminoketones

The synthesis of enantiopure compounds from a mixture of E/Z alkenes represents a notable challenge in synthetic chemistry. While enzymes excel in achieving unparalleled selectivity, their inherent specificity often confines activity to a single stereoisomeric substrate, consequently restricting the overall efficiency of such transformations. Here, we demonstrate that protoglobin-derived hemoproteins can catalyze stereoconvergent intermolecular amination using simple N-alkyl hydroxylamines as nitrene precursors, a transformation which remains elusive in synthetic chemistry. These engineered enzymes process E/Z mixtures of silyl enol ethers, enabling the precise incorporation of N-alkyl amino moieties (−NHAlkyl) into diverse molecular structures (up to 79% yield and 95% ee). Two complementary protoglobin variants were engineered using directed evolution to enable enantiodivergent synthesis of both enantiomers of α-aminoketones. This enzymatic platform achieves stereoconvergent and enantiodivergent transformations, facilitating the conversion of simple chemicals into an array of valuable pharmaceutical compounds featuring aminoketone functionalities.

Alcohols↗
DOE OSTI2020

Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids

The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. We report experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.

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

Advances and Challenges of SCAN and r 2 SCAN Density Functionals in Transition‐Metal Compounds

ABSTRACT Transition‐metal compounds (TMCs) with open‐shell d ‐electrons are characterized by a complex interplay of lattice, charge, orbital, and spin degrees of freedom, giving rise to various fascinating applications. Often exhibiting exotic properties, these compounds are commonly classified as correlated systems due to strong inter‐electronic interactions called Hubbard U . This inherent complexity presents significant challenges to Kohn‐Sham density functional theory (KS‐DFT), the most widely used electronic structure method in condensed matter physics and materials science. While KS‐DFT is, in principle, exact for the ground‐state total energy, its exchange‐correlation energy must be approximated in practice. The mean‐field nature of KS implementations, combined with the limitations of current exchange‐correlation density functional approximations, has led to the perception that DFT is inadequate for correlated systems, particularly TMCs. Consequently, a common workaround involves augmenting DFT with an on‐site Hubbard‐like U correction. In recent years, the strongly constrained and appropriately normed (SCAN) density functional, along with its refined variant r 2 SCAN, has achieved remarkable progress in accurately describing the structural, energetic, electronic, magnetic, and vibrational properties of TMCs, challenging the traditional perception of DFT's limitations. This review explores the design principles of SCAN and r 2 SCAN, highlights their key advancements in studying TMCs, explains the mechanisms driving these improvements, and addresses the remaining challenges in this evolving field.

Zhang, Yubo [Minjiang Collaborative Center for The↗
DOE OSTI2020

Flat bands in the CoSn-type compounds

Quantum interference on the kagome lattice generates electronic bands with narrow bandwidth, called flat bands. Crystal structures incorporating this lattice can host strong electron correlations with nonstandard ingredients, but only if these bands lie at the Fermi level. In the six compounds with the CoSn structure type (FeGe, FeSn, CoSn, NiIn, RhPb, and PtTl) the transition metals form a kagome lattice. The two iron variants are robust antiferromagnets so we focus on the latter four and investigate their thermodynamic and transport properties. We consider these results and calculated band structures to locate and characterize the flat bands in these materials. Finally, we propose that CoSn and RhPb deserve the community's attention for exploring flat-band physics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Machine learning guided selection of broad-spectrum epitope-specific functional antibodies for "Disease X"

Our project established and demonstrated a transfer learning framework that enables prediction of antibody–antigen interactions across related viruses. The approach focused on three major activities: 1. Conserved region and epitope identification – We compared viral protein structures and sequences to identify shared receptor-binding domains and neutralizing epitope regions across variants and related viruses. These conserved features formed the foundation for discovering broadly functional antibodies. 2. Machine learning model development – We built neural network–based models that integrate epitope features with antibody sequence information. Instead of relying solely on structural or physical properties, the models learned transferable patterns that describe antibody binding potential across different viral families. 3. Transfer learning and validation – Using SARS-CoV-2 and Ebola as source systems, we successfully transferred learned epitope features to predict antibody interactions for SARS CoV-1 and Marburg virus. Iterative cycles of dataset generation, retraining, and evaluation improved generalization and predictive power, ensuring the framework can adapt to new threats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

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

Challenges for a QCD axion at the 10 MeV scale

We report on an interesting realization of the QCD axion, with mass in the range $\mathcal{O}$(10) MeV. It has previously been shown that although this scenario is stringently constrained from multiple sources, the model remains viable for a range of parameters that leads to an explanation of the Atomki experiment anomaly. In this article we study in more detail the additional constraints proceeding from recent low energy experiments and study the compatibility of the allowed parameter space with the one leading to consistency of the most recent measurements of the electron anomalous magnetic moment and the fine structure constant. We further provide an ultraviolet completion of this axion variant and show the conditions under which it may lead to the observed quark masses and CKM mixing angles, and remain consistent with experimental constraints on the extended scalar sector appearing in this Standard Model extension. In particular, the decay of the Standard Model-like Higgs boson into two light axions may be relevant and leads to a novel Higgs boson signature that may be searched for at the LHC in the near future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Electron transfer in polysaccharide monooxygenase catalysis

Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C–H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from Myceliophthora thermophila ( Mt PMO9E). When Y62, a buried residue 12 Å from the active site, is mutated to F, lower activity is observed with O 2 . However, a WT-level activity is observed with H 2 O 2 as a cosubstrate indicating an important role in ET for O 2 activation. To better understand the structural effects of mutations to Y62 and axial copper ligand Y168, crystal structures were solved of the wild type Mt PMO9E and the variants Y62W, Y62F, and Y168F. A bioinformatic analysis revealed that position 62 is conserved as either Y or W in the AA9 family. The Mt PMO9E Y62W variant has restored activity with O 2 . Overall, the use of redox-active residues to supply electrons for the reaction with O 2 appears to be widespread in the AA9 family. Furthermore, the results provide a molecular framework to understand catalysis with O 2 versus H 2 O 2 .

Sayler, Richard I. (ORCID:000000017252707X)↗
DOE OSTI2020

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

35S rDNA evolution↗
DOE OSTI2023

Recognition of centromere‐specific histone Cse4 by the inner kinetochore Okp1‐Ame1 complex

Abstract Successful mitosis depends on the timely establishment of correct chromosomal attachments to microtubules. The kinetochore, a modular multiprotein complex, mediates this connection by recognizing specialized chromatin containing a histone H3 variant called Cse4 in budding yeast and CENP‐A in vertebrates. Structural features of the kinetochore that enable discrimination between Cse4/CENP‐A and H3 have been identified in several species. How and when these contribute to centromere recognition and how they relate to the overall structure of the inner kinetochore are unsettled questions. More generally, this molecular recognition ensures that only one kinetochore is built on each chromatid and that this happens at the right place on the chromatin fiber. We have determined the crystal structure of a Cse4 peptide bound to the essential inner kinetochore Okp1‐Ame1 heterodimer from budding yeast. The structure and related experiments show in detail an essential point of Cse4 contact and provide information about the arrangement of the inner kinetochore.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Carbonate-Catalyzed CO 2 Insertion into Hydrocarbon C-H Bonds (Final Technical Report)

The development of methods to utilize CO 2 as a feedstock for chemical and fuel synthesis is critical for creating renewable alternatives to fossil fuel-based products. This project investigated a class of catalyst materials known as "dispersed carbonates", which are composed of alkali carbonate salts (e.g. potassium carbonate) dispersed in porous support materials. These catalysts react with CO 2 and organic molecules to form chemicals known as carboxylates that have wide applications in the chemical industry. The project used a combination of spectroscopic and reactivity studies to provide fundamental insight into the structure and mechanism of dispersed carbonates in these reactions, leading to variants with greater reactivity. In addition, dispersed carbonates were investigated for CO 2 hydrogenation catalysis, which is critical for processes under development for making sustainable fuels. The dispersed carbonates proved to be highly active and selective catalysts for the reverse water gas shift reaction in which CO 2 is hydrogenated to CO. The dispersed carbonates provide a compelling alternative to conventional metal-based catalysts for reverse water gas shift that could enable new process designs with higher efficiency and lower complexity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Adjustable lossless image compression based on a natural splitting of an image into drawing, shading, and fine-grained components

The compression, or efficient coding, of single band or multispectral still images is becoming an increasingly important topic. While lossy compression approaches can produce reconstructions that are visually close to the original, many scientific and engineering applications require exact (lossless) reconstructions. However, the most popular and efficient lossless compression techniques do not fully exploit the two-dimensional structural links existing in the image data. We describe here a general approach to lossless data compression that effectively exploits two-dimensional structural links of any length. After describing in detail two main variants on this scheme, we discuss experimental results.

Novik, Dmitry A.↗