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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time‐Resolved X‐Ray Solution Scattering and Markov State Modeling

Understanding protein folding pathways is crucial to deciphering the principles of protein structure and function. Here, the unfolding dynamics of the 35‐residue villin headpiece (HP35) and a norleucine‐substituted variant (2F4K) using a combination of experimental and computational techniques is investigated. Time‐resolved X‐ray solution scattering coupled with equilibrium molecular dynamics simulations and Markov state modeling reveals distinct unfolding mechanisms between the two variants: HP35 and 2F4K. Specifically, HP35 exhibits a two‐state unfolding process, whereas an intermediate state is identified for the 2F4K mutant. A Markov state model constructed from simulations is used to map atomic‐level transitions to experimental observations, providing insights into the role of sequence variations in modulating folding pathways. The findings underscore the importance of integrating experimental and computational approaches to unravel protein unfolding mechanisms between heterogenous structural ensembles.

Nijhawan, Adam K. [Department of Chemistry Northwe↗
DOE OSTI2021

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores

X-ray computed tomography (CT) scanning is used to study the physical characteristics of soil and sediment cores, allowing scientists to analyze stratigraphy without destroying core integrity. Microbiologists often work with geologists to understand the microbial properties in such cores; however, we do not know whether CT scanning alters microbial DNA such that DNA sequencing, a common method of community characterization, changes as a result of X-ray exposure. Our objective was to determine whether CT scanning affects the estimates of the composition of microbial communities that exist in cores. Sediment cores were extracted from a salt marsh and then submitted for CT scanning. We observed a minimal effect of CT scanning on microbial community composition in the sediment cores either when the cores were examined shortly after recovery from the field or after the cores had been stored for several weeks. In contrast, properties such as sediment layer and marsh location did affect microbial community structure. While we observed that CT scanning did not alter microbial community composition as a whole, we identified a few amplicon sequence variants (13 out of 7,037) that showed differential abundance patterns between scanned and unscanned samples among paired sample sets. Our overall conclusion is that the CT-scanning conditions typically used to obtain images for geological core characterization do not significantly alter microbial community structure. We stress that minimizing core exposure to X-rays is important if cores are to be studied for biological properties. Future investigations might consider variables, such as the length and energy of radiation exposure, the volume of the core, or the degree, to which microbial communities are stressed as important factors in assessing the impact of X-rays on microbes in geological cores.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide

Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Guest-Host Interactions in Clathrate Hydrates: Benchmark MP2 and CCSD(T)/CBS Binding Energies of CH4, CO2 and H2S in (H2O)20 Cages

We present benchmark binding energies of naturally occurring gas molecules CH4, CO2, and H2S in the small cage, namely the pentagonal dodecahedron (512) (H2O)20, which is one of the constituent cages of the 3 major lattices (structures I, II and H) of clathrate hydrates. These weak interactions require higher levels of electron correlation and converge slowly with increasing basis set to the Complete Basis Set (CBS) limit, necessitating the use of large basis sets up to the augcc- pV5Z and subsequent correction for Basis Set Superposition Error (BSSE). For the host hollow (H2O)20 cages we have identified a most stable isomer with binding energy of -200.8 ± 2.1 kcal/mol at the CCSD(T)/CBS limit (-199.2 ± 0.5 kcal/mol at the MP2/CBS limit). Additionally, we report converged second order Moller-Plesset (MP2) CBS binding energies for the encapsulation of guests in the (H2O)20 cage of -4.3 ± 0.1 for CH4@(H2O)20, -6.6 ± 0.1 for CO2@(H2O)20 and -8.5 ± 0.1 kcal/mol for H2S@(H2O)20, respectively. For CH4@(H2O)20, exhibiting the weakest encapsulation affinity among the three, we report CCSD(T)/aug-cc-pVTZ binding energies and, based on them, a CCSD(T)/CBS estimate of -4.75 ± 0.1 kcal/mol. To the best of our knowledge, the CCSD(T)/aug-cc-pVTZ calculation for CH4@(H2O)20 is the largest one reported to date (168 valence electrons, 1978 basis functions and the correlation of 84 doubly occupied and 1873 virtual orbitals) and required a scalable implementation of the (T) module on 6144 nodes (350208 cores) of the “Cori” supercomputer at the National Energy Research Supercomputing Center (NERSC) for a total execution time of 195 minutes (for the (T) part). These efficient scalable implementations of highly correlated methods offer the capability to obtain long-lasting benchmarks of intermolecular interactions in complex systems. They also provide a path towards parametrizing classical potentials needed to study the dynamical and transport properties in these complex systems as well as assess the accuracy of lower scaling electronic structure methods such as Density Functional Theory (DFT) and MP2 including its spin-biased variants.

Heindel, Joseph↗
DOE OSTI2024

Inhomogeneous Distribution and Coarsening of γ″ Precipitates in a Ni-Based Superalloy and Their Effect on Creep

γ″ was found to be the main precipitate strengthening phase with no detectable g′ in both M725 alloys. After creep, the grip/gage sections of the crept M725-Nb/Ta exhibited preferential coarsening and inhomogeneous distribution of g″ platelets, and sandwich-like structures, comprising of cubic γ′ precipitates with small γ″ discs on each facet. This g″ variant selection behavior taking place in the grip section with no stress applied was different from the typical stress-induced variant selection reported in previous literature.

Hung, Chang-Yu↗
DOE OSTI2025

Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat

The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy of the NHR-targeting entry inhibitor enfuvirtide, no potently neutralizing NHR-directed monoclonal antibodies (mAbs) nor antisera have been identified or elicited to date. The lack of potent NHR-binding mAbs both dampens enthusiasm for vaccine development efforts at this target and presents a barrier to performing passive immunization experiments with NHR-targeting antibodies. To address this challenge, we previously developed an improved variant of the NHR-directed mAb D5, called D5_AR, which is capable of neutralizing diverse tier-2 viruses. Building on that work, here we present the 2.7Å-crystal structure of D5_AR bound to NHR mimetic peptide IQN17. We then utilize protein language models and supervised machine learning to generate small (n < 100) libraries of D5_AR variants that are subsequently screened for improved neutralization potency. We identify a variant with 5-fold improved neutralization potency, D5_FI, which is the most potent NHR-directed monoclonal antibody characterized to date and exhibits broad neutralization of tier-2 and −3 pseudoviruses as well as replicating R5 and X4 challenge strains. Additionally, our work highlights the ability of protein language models to efficiently identify improved mAb variants from relatively small libraries.

Biopolymers↗
DOE OSTI2022

Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids

Abstract Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain ( N RTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the N RTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV N RTD can act as an inhibitor of virus transmission and identify N RTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus N RTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.

Schiltz, Carl J. (ORCID:0000000332030784)↗
DOE OSTI2024

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here, in this work, we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel “dimer of dimers” mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Statistical analysis and degradation pathway modeling of photovoltaic minimodules with varied packaging strategies

Degradation pathway models constructed using network structural equation modeling (netSEM) are used to study degradation modes and pathways active in photovoltaic (PV) system variants in exposure conditions of high humidity and temperature. This data-driven modeling technique enables the exploration of simultaneous pairwise and multiple regression relationships between variables in which several degradation modes are active in specific variants and exposure conditions. Durable and degrading variants are identified from the netSEM degradation mechanisms and pathways, along with potential ways to mitigate these pathways. A combination of domain knowledge and netSEM modeling shows that corrosion is the primary cause of the power loss in these glass/backsheet PV minimodules. We show successful implementation of netSEM to elucidate the relationships between variables in PV systems and predict a specific service lifetime. The results from pairwise relationships and multiple regression show consistency. This work presents a greater opportunity to be expanded to other materials systems.

electrical measurements↗
DOE OSTI2026

Data for "Photoinduced Chemomimetic Biocatalysis for Enantioselective Intermolecular Radical Conjugate Addition"

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Catalysis↗
DOE OSTI2026

RidgeAlloy: A high pressure die casting alloy that captures the approaching wave of automotive body sheet scrap

Oak Ridge National Laboratory (ORNL) has recently launched an effort to economically expand the North American aluminum supply chain by designing and developing a new family of Al-Mg-Si-Fe-Mn structural die cast aluminum alloys that can be made from up to 100% mixed 5xxx and 6xxx series automotive post-consumer sheet scrap and do not require heat treatment. The goal is to develop an alloy capable of capturing the approaching scrap wave of aluminum sheet intensive vehicles (in the 2030’s) into integrated structural high pressure die castings, rather than down-cycling these high-grade sheet alloys into non-structural castings. ORNL discovered a significant gap in the commercial thermodynamic databases that were unable to predict the trends of a key primary intermetallic phase as a function of composition. Experiments were performed to correct this gap and to create a unique, corrected quaternary database for Al-Mg-Si-Fe. High throughput computational methods, including solidification simulations, were used to identify a composition volume capable of avoiding this embrittling primary intermetallic phase, even at higher Fe + Si contents. Laboratory scale castings validated the thermodynamic and solidification predictions and resulted in lab-cast alloys with little primary intermetallic, and which met or exceeded structural casting properties requirements for yield strength and ductility. An accelerated demonstration of an HPDC automotive part was conducted in collaboration with two U.S. small businesses. Ingots made from 100% recycled 5xxx and 6xxx series scrap (plus Fe) were used to die cast one variant of this new family of Al-Mg-Si-Fe-Mn alloys (with high Si + Fe content) into a mid-sized HPDC structural-type automotive component. The HPDC alloy demonstration part showed good properties (especially ductility) and good castability for a complex component.

Plotkowski, Alex [ORNL] (ORCID:0000000154718681)↗
DOE OSTI2025

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Design principles for site-selective hydroxylation by a Rieske oxygenase

Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tensor network investigation of the double layer Kagome compound Ca 10 Cr 7 O 28

Quantum spin liquids are exotic quantum phases of matter that do not order even at zero temperature. While there are several toy models and simple Hamiltonians that could host a quantum spin liquid as their ground state, it is very rare to find actual, realistic materials that exhibit their properties. At the same time, the classical simulation of such instances of strongly correlated systems is intricate and reliable methods are scarce. Here, in this work, we investigate the quantum magnet Ca 10 Cr 7 O 28 that has recently been discovered to exhibit properties of a quantum spin liquid in inelastic neutron scattering experiments. This compound has a distorted bilayer Kagome lattice crystal structure consisting of Cr 5+ ions with spin- moments. Coincidentally, the lattice structure renders a tensor network algorithm in 2D applicable that can be seen as a new variant of a projected entangled simplex state algorithm in the thermodynamic limit. In this first numerical investigation of this material that takes into account genuine quantum correlations, good agreement with the experimental findings is found. Our study contributes to uplifting tensor networks from conceptual tools to methods to describe real two-dimensional quantum materials.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Quantitative SANS and multi-model analysis of spacer-dependent micellization of urea-based gemini surfactants

The micellization behavior of urea-based cationic gemini surfactants was investigated using small-angle neutron scattering (SANS) with multi-model form factor analysis. A homologous series of surfactants with urea group included in the hydrophobic tail and polymethylene spacers consisting of two to ten methylene units was analyzed using three form factor models: a core–shell ellipsoid and two variants of homogeneous ellipsoids. The results from all models show a consistent trend of the micelle structures, confirming that the spacer length critically influences micellar geometry, aggregation number, and hydration. The surfactant with four CH 2 groups in the spacer formed the largest micelles with the highest aggregation number, while longer spacers led to progressively smaller, more compact aggregates. The shell hydration—quantified as the volume fraction of heavy water within the hydrophilic region—decreased systematically with increasing spacer length due to enhanced hydrophobicity of the headgroup-spacer region. Intermicellar interactions, modeled as screened Coulomb interaction using the rescaled mean spherical approximation (RMSA), revealed the strongest electrostatic repulsion for the case of four methylene groups in the spacer, corresponding to the highest micellar charge and largest interparticle spacing. The observed spacer-dependent trends were robust across all modeling approaches, demonstrating that the spacer length serves as a key structural determinant of self-assembly in this type of urea-based gemini systems. These findings provide insight into the design of gemini surfactants with tailored aggregation behavior for applications in drug delivery, nanostructure templating, and solubilization technologies.

Core–shell ellipsoid model↗
DOE OSTI2020

Using hole injection layers for decreased metastability and higher performance in Cu(In,Ga)Se 2 devices

In this work, modifications to the buffer structure in Cu(In,Ga)Se 2 (CIGS) solar cells are examined in terms of power conversion efficiency and metastability. Varying amounts of thin hole-injecting layers are introduced at different locations in the CIGS/Zn(O,S) device structure. It is found that such layers simultaneously increase performance and decrease metastability. The most effective variant produces devices without metastability and with higher efficiency than the CdS-only controls. The most effective location for hole injection is found to be between the Zn(O,S) buffer and the transparent conductor. At this location, passivation of the CIGS surface is not a function of the hole injection layer, and thus a variety of materials with appropriate band-edge energies should achieve the same purpose.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An African-Specific Variant of TP5 3 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression

TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53–PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Preemptive optimization of a clinical antibody for broad neutralization of SARS-CoV-2 variants and robustness against viral escape

Most previously authorized clinical antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lost neutralizing activity to recent variants due to rapid viral evolution. To mitigate such escape, we preemptively enhance AZD3152, an antibody authorized for prophylaxis in immunocompromised individuals. Using deep mutational scanning (DMS) on the SARS-CoV-2 antigen, we identify AZD3152 vulnerabilities at antigen positions F456 and D420. Through two iterations of computational antibody design that integrates structure-based modeling, machine-learning, and experimental validation, we co-optimize AZD3152 against 24 contemporary and previous SARS-CoV-2 variants, as well as 20 potential future escape variants. Our top candidate, 3152-1142, restores full potency (100-fold improvement) against the more recently emerged XBB.1.5+F456L variant that escaped AZD3152, maintains potency against previous variants of concern, and shows no additional vulnerability as assessed by DMS. This preemptive mitigation demonstrates a generalizable approach for optimizing existing antibodies against potential future viral escape.

59 BASIC BIOLOGICAL SCIENCES↗