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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates

Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kβ emission optimized for analysis of dilute biological samples. Here, we further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.

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

Sn-InAs Nanowire Shadow-Defined Josephson Junctions

Hybrid superconductor–semiconductor platforms are foundational to advancing quantum information technologies, motivating the integration of materials with clean interfaces, robust superconductivity, and scalable architectures. Here, in this work, we report the synthesis and analysis of inclined InAs nanowires, conformally coated with β-Sn shells. These nanowires extend in opposite in-plane directions, forming a self-aligned, criss-cross network. This enables the deterministic formation of nanowire-shadow Josephson junctions through angle-controlled, low-temperature Sn deposition. Structural characterization shows uniform polycrystalline β-Sn shells forming a sharp, diffusion-free interface with InAs. Low-temperature transport measurements reveal a hard induced superconducting gap ≈ 600 μeV, switching currents up to ≈ 500 nA, and parallel magnetic field resilience beyond 1T. These results establish β-Sn/InAs nanowire networks as a promising platform for superconducting qubits, low-noise microwave devices, and the exploration of exotic superconducting phases including triplet pairing and topological superconductivity.

B-Sn↗
DOE OSTI2022

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Abstract Lung cancer is frequently caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric EGFR inhibitors offer promise as the next generation of therapeutics, as they are unaffected by common ATP-site resistance mutations and synergize with the drug osimertinib. Here, we examine combinations of ATP-competitive and allosteric inhibitors to better understand the molecular basis for synergy. We identify a subset of irreversible EGFR inhibitors that display positive binding cooperativity and synergy with the allosteric inhibitor JBJ-04-125-02 in several EGFR variants. Structural analysis of these complexes reveals conformational changes occur mainly in the phosphate-binding loop (P-loop). Mutation of F723 in the P-loop reduces cooperative binding and synergy, supporting a mechanism in which F723-mediated contacts between the P-loop and the allosteric inhibitor are critical for synergy. These structural and mechanistic insights will aid in the identification and development of additional inhibitor combinations with potential clinical value.

Beyett, Tyler S. (ORCID:0000000155097004)↗
DOE OSTI2023

Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A

Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na + -dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na + . Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na + -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a “trap-and-flip” mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Importance of Solution Studies for the Structural Characterization of the Enterovirus 5’ Cloverleaf

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5’ cloverleaf (5’CL). Here, we present a biophysical analysis of the 5’CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5’CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed a high propensity for dimerization, which was enhanced by the presence of salts. Enterovirus D70 was observed to be somewhat intermediate, with primarily a monomeric structure, but possessing some potential for dimerization. The equilibrium between the two monomeric and the dimeric conformations is also discussed. These results indicate that the 5’CL conformation may be more complex than the current literature suggests, thus underscoring the need for a combined crystal and solution approach for the accurate representation of the 5’CL conformation, and the conformation of other RNA structural elements, under native conditions.

Virology↗
DOE OSTI2020

Development of a Conditioned System-Level Groundwater Model to Evaluate Long-Term Groundwater Impacts within a Performance Assessment - 20115

A preliminary performance assessment (PA) of single-shell tank Waste Management Area (WMA) A-AX located at the U.S. Department of Energy (DOE)'s Hanford Site in southeastern Washington is being conducted to satisfy the requirements of DOE Order 435.1 [1] as it relates to closure of the single-shell radioactive waste tanks in the WMA A-AX tank farms. A PA assesses the fate, transport, and impacts of radionuclides within a low-level radioactive waste disposal facility in its assumed closure configuration and the subsequent potential doses to humans over a 1,000-year compliance period and a 10,000-year performance evaluation period. The WMA A-AX preliminary PA evaluation is structured around the complementary use of process-level and system-level models to calculate the facility performance against established DOE Order 435.1 [1] performance objectives. Process-level models are those that represent a detailed phenomenological representation of processes of concern in the PA. Process models typically only represent one or a few of the components of the PA, such as groundwater flow and transport, and must be integrated with other modeling elements to perform PA calculations. System-level models are those that are abstracted from the process models, retaining the essential features of the process model, while allowing integration of all aspects of the PA in a single modeling framework. System-level models are often characterized by coarser numerical discretization, lower dimensionality, or other similar simplifications compared to the process-level model. Traditionally, a three-dimensional (3-D) process-level model is utilized primarily to evaluate the long-term impact on groundwater and the potential doses to individuals who consume contaminated groundwater. System-level models are also utilized to evaluate the groundwater pathway in PAs. These models typically have reduced dimensionality (1-D) and are conditioned utilizing flow fields (Darcy fluxes) and moisture content distributions that are abstracted from the process level models. The abstraction approach assures that the flow field in both models is consistent for a specific set of input parameters for flow, differing only in the discretization and dimensionality of the two models. The preliminary WMA A-AX PA incorporates a detailed representation of the geological system and hydraulic properties within the 3-D model STOMP{sup C} numerical code so that the effects of relevant features and processes on water flow and radionuclide transport in the subsurface can be evaluated. The complementary system-level model is developed utilizing the GoldSim{sup C} code to implement a simplified, 1-D equivalent model to represent the groundwater pathway. Contaminant transport through the vadose zone and unconfined aquifer for Tc-99 and I-129 were evaluated in each of the models. Adjustments to the saturated portion of the GoldSim{sup C} 1-D model were required to mimic the dispersion effect captured with the 3-D STOMP{sup C} model. Once this conditioning was conducted, highly similar results for the transport of Tc-99 and I-129 were achieved at the point of calculation, located 100 m downgradient from the WMA A-AX fenceline. These radionuclides represent elements that are regarded as primary dose drivers in the PA groundwater pathway analysis. The high degree of conformance between the two models suggests that the use of the equivalent 1-D system model is suitable for evaluating the full suite of radionuclides that will be released from the tank sources within WMA A-AX over the 1,000-year compliance period and over the 10,000-year evaluation period. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2021

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

High-energy X-ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long-range order, but is underutilized for molecular complexes in solution. Here we demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal...metal distances separated by over 12 Å. The metal…metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub-Ångström conformational differences by direct comparison of solution phase and solid-state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

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

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

Abstract High‐energy X‐ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long‐range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub‐Ångström conformational differences by direct comparison of solution phase and solid‐state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

Xie, Zhu‐Lin↗
DOE OSTI2026

Transient hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation. I. Conformer- and isomer-resolved infrared spectra

Transient carbon-centered hydroperoxyalkyl intermediates (•QOOH) in isopentane oxidation are characterized by infrared (IR) action spectroscopy under jet-cooled conditions with selective detection of hydroxyl (OH) radical products. Two distinct •QOOH isomers with radical sites at a primary carbon of one of the methyl groups (β-Me) or a secondary carbon (β-Et) of the ethyl group are identified by comparison with theoretically calculated IR absorption features for multiple conformers, including C–O, ethyl, and O–O torsions of the two isomers. Here, a master-equation analysis is developed and utilized to explore the conformational cooling process and the resultant conformer population distributions of the two isomers. Most of the IR features observed, including those in the strong fundamental and first overtone OH stretch regions as well as weaker combination bands involving OH stretch with torsion or OOH bend, are in good accord with computed anharmonic frequencies for the most populated conformers of the •QOOH_Et isomer. Relatively weak IR features most evident in the fundamental and first overtone OH stretch regions are ascribed to multiple conformers of the less stable •QOOH_Me isomer, along with a weak feature that is uniquely attributed to a combination band involving asymmetric CH 2 stretch and HCH bend of •QOOH_Me.

Chemical reaction jet spectroscopy↗
DOE OSTI2020

Fabrication Lessons Learned of Transportation Packaging from the Perspective of a Design Authority - 20322

This paper presents lessons learned regarding fabricating packaging systems from the perspective of a design authority (DA). Capturing and implementing lessons learned is critical for an organization to reduce systematic project risk and thereby promote the likelihood of project success. This paper defines the design authority as the organization responsible for technical design, resolving technical design issues, quality assurance program, and maintenance of the packaging system license. A package system is defined as the packaging, its contents, and auxiliary equipment. Packages are certified by the NRC under 10 CFR 71[1] for transportation by ground. The following lessons learned subjects are presented in the paper: quality assurance, interpretation of drawing dimensional requirements, execution of manufacturing processes, hardware dimensional inspection, and leakage rate testing. All discrepancies presented in this paper have been resolved as described in the appropriate final data package. All described package systems are in compliance with their Safety Analysis Report (SAR) and certificate of conformance requirements. The intent of this paper is to identify opportunities for improving the outcome of future projects and to mitigate fabrication challenges proactively. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

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

Unveiling horizons in quantum critical collapse

Critical gravitational collapse offers a unique window into regimes of arbitrarily high curvature, culminating in a naked singularity arising from smooth initial data — thus providing a dynamical counterexample to weak cosmic censorship. Near the critical regime, quantum effects from the collapsing matter are expected to intervene before full quantum gravity resolves the singularity. Despite its fundamental significance, a self-consistent treatment has so far remained elusive. In this work, we perform a one-loop semiclassical analysis using the robust anomaly-based method in the canonical setup of Einstein gravity minimally coupled to a free, massless scalar field. Focusing on explicitly solvable near-critical solutions in both 2 + 1 and 3 + 1 dimensions, we analytically solve the semiclassical Einstein equations and obtain controlled, quantitative results for several long-standing questions within the dominant s-wave sector. We find that regularity uniquely selects a Boulware-like quantum state, encoding genuine vacuum polarization effects from the collapsing matter. Remarkably, the resulting quantum corrections manifest as a growing mode. Horizon-tracing analyses, incorporating both classical and quantum modes, reveal the emergence of a finite mass gap, signaling a phase transition from classical Type II to quantum-modified Type I behavior, thereby providing a quantum enforcement of the weak cosmic censorship. The most non-trivial aspect of our analysis involves dealing with non-conformal matter fields in explicitly time-dependent critical spacetimes. Along the way, we uncover intriguing and previously underexplored features of quantum field theory in curved spacetime.

2D Gravity↗
DOE OSTI2021

CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin

Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.

59 BASIC BIOLOGICAL SCIENCES↗