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At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Intermediate Temperature Proton‐Conducting Solid Oxide Electrolysis Cells with Improved Performance and Durability

Technical understanding: A high-performance and stable intermediate temperature proton-conducting solid oxide electrolysis cell (PCEC) will add significantly to the hydrogen roadmap of EERE. However, the low electrocatalytic activity of the air electrode and the instability of the electrolyte are technical barriers. In this research, we utilized computational fluid dynamic modeling and materials/microstructure engineering to investigate the complex reaction chain and to improve the performance and reliability of the protonic ceramic electrochemical cells. An active and stable Pr 1.8 Ba 0.2 NiO 4+δ -BaZr 0.1 Ce 0.7 Y 0.1 Yb 0.1 O 3-δ (BZCYYb) scaffold conformal coating electrode was rationally designed where the robust Pr 1.8 Ba 0.2 NiO 4+δ functions both as a catalytic active and a protective layer. The PCECs with porosity-optimized scaffold conformal coating electrodes demonstrate 1.46 Acm -2 under 1.3 V at 600°C, which is among the highest in recent years. The final optimization by computational fluid dynamic modeling and conformal coating technique was applied to evolve the PCEC air electrode from Pr 2 NiO 4+δ to Pr 1.8 Ba 0.2 NiO 4+δ -BaZr 0.1 Ce 0.7 Y 0.1 Yb 0.1 O 3-δ scaffold conformal coating. The electrolysis current was boosted from 0.445A/cm 2 to 1.46A/cm 2 at 600°C and 1.3V. A superior low degradation rate of 1mV/kh was achieved in a 5000-hour of operation. Technical effectiveness and economic feasibility: The effectiveness of this TCO conformal coating on electrolyte backbone as air electrode has been proven by long-term demonstration. Based on the highly conductive BZCYYb electrolyte and the TCO steam electrode PNO, this project rationally took advantage of the existent materials to structure a PCEC device with high TRL and low risk. The solution infiltration method used to structure the conformal coating is a standard method used by the solid oxide cell community. Very minimal adoption is needed in the current SOC fabrication process. It is a cost-effective, scalable method for manufacturing, and brings up remarkable impact on the current technical status of PCEC. Benefit to the public: The findings in the research showed the industry that the severe challenge in PCEC can be overcome in a practical way. A various energy-hydrogen ecosystem is not beyond reach. The success of this technology provides sustainable and affordable H 2 to society. It will stimulate investment from the governmental and private sectors in response to the device manufacture and deployment, and the related infrastructure construction. It will generate high-pay domestic jobs and environmental benefits to the general public in the United States.

08 HYDROGEN↗
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↗
NASA NTRS1994

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Smith, Grant D.↗
NASA NTRS1994

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Smith, Grant D.↗
DOE OSTI2020

Distributions in CFT. Part I. Cross-ratio space

We show that the four-point functions in conformal field theory are defined as distributions on the boundary of the region of convergence of the conformal block expansion. The conformal block expansion converges in the sense of distributions on this boundary, i.e. it can be integrated term by term against appropriate test functions. This can be interpreted as a giving a new class of functionals that satisfy the swapping property when applied to the crossing equation, and we comment on the relation of our construction to other types of functionals. Our language is useful in all considerations involving the boundary of the region of convergence, e.g. for deriving the dispersion relations. We establish our results by elementary methods, relying only on crossing symmetry and the standard convergence properties of the conformal block expansion. This is the first in a series of papers on distributional properties of correlation functions in conformal field theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Surface defects in holographic 5d SCFTs

We use holography to study codimension-2 surface defects in 5d SCFTs engineered by (p, q) 5-brane webs. The three-dimensional defects are realized by D3-branes ending on the brane web. We identify the holographic representation of the defects in Type IIB AdS 6 solutions as probe D3-branes, and study conformal and non-conformal defects which, respectively, preserve one half and one quarter of the supersymmetry. For a sample of 5d SCFTs, including the T N theories, we provide explicit solutions for conformal and non-conformal defects. For the conformal defects we obtain their contribution to the free energy on S 5 .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

$\mathrm{A}$ $\mathrm{CFT}$ distance conjecture

We formulate a series of conjectures relating the geometry of conformal manifolds to the spectrum of local operators in conformal field theories in d > 2 spacetime dimensions. We focus on conformal manifolds with limiting points at infinite distance with respect to the Zamolodchikov metric. Our central conjecture is that all theories at infinite distance possess an emergent higher-spin symmetry, generated by an infinite tower of currents whose anomalous dimensions vanish exponentially in the distance. Stated geometrically, the diameter of a non-compact conformal manifold must diverge logarithmically in the higher-spin gap. In the holographic context our conjectures are related to the Distance Conjecture in the swampland program. Interpreted gravitationally, they imply that approaching infinite distance in moduli space at fixed AdS radius, a tower of higher-spin fields becomes massless at an exponential rate that is bounded from below in Planck units. We discuss further implications for conformal manifolds of superconformal field theories in three and four dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Optimization of operational strategies for rich gas enhanced oil recovery based on a pilot test in the Bakken tight oil reservoir

Horizontal well drilling and multistage hydraulic fracturing have been demonstrated as effective approaches for stimulating oil production in the Bakken tight oil reservoir. However, after multiple years of production, primary oil recovery in the Bakken is generally less than 10% of the estimated original oil in place. Gas huff ‘n’ puff (HnP) has been tested in the Bakken Formation as an enhanced oil recovery (EOR) method; however, most field pilot test results showed no significant incremental oil production. One of the factors affecting HnP EOR performance is premature gas breakthrough, which is one of the most critical issues observed in the field because of the presence of interwell fractures. Consequently, injected gas rapidly reaches adjacent production wells without contacting reservoir rock and increasing oil recovery. Proper conformance control is therefore needed to avoid early gas breakthrough and improve EOR performance. In this study, a rich gas EOR pilot in the Bakken was carefully analyzed to collect the essential reservoir and operational data. A simulation model with 16 wells was then developed to reproduce the production history and predict the EOR performance with and without conformance control. EOR operational strategies, including single- and multiple-well HnP, with different gas injection constraints were investigated. The simulation results of single-well HnP without conformance control showed that a rich gas injection rate of at least 10 MMscfd was needed to yield meaningful incremental oil production. The strategy of conformance control via water injection could significantly improve oil production in the HnP well, but injecting an excessive amount of water also leads to water breakthrough and loss of oil production in the offset wells. By analyzing the production performance of the wells individually, the arrangement of wells was optimized for multiple-well HnP EOR. The multiwell results showed that rich gas EOR could improve oil production up to 7.4% by employing conformance control strategies. Furthermore, replacing rich gas with propane as the injection gas could result in 14% of incremental oil production.

02 PETROLEUM↗
DOE OSTI2020

Cyclic Topology Enhancing Structural Ordering and Stability of Comb-Shaped Polypeptoid Thin Films against Melt-Induced Dewetting

We investigated the effect of cyclic chain topology on the molecular ordering and thermal stability of comb-shaped polypeptoid thin films on silicon (Si) substrates. Cyclic and linear poly(N-decylglycine) (PNDG) bearing long n-decyl side chains were synthesized by ring-opening polymerization of N-decylglycine-derived N-carboxyanhydrides. When the spin-coated thin films were subjected to thermal annealing at temperatures above the melting temperature (T > T m ), the cyclic PNDG films exhibited significantly enhanced stability against melt-induced dewetting than the linear counterparts (l-PNDG). When recrystallized at temperatures below the crystallization temperature (T < T c ), the homogeneous c-PNDG films exhibit enhanced crystalline ordering relative to the macroscopically dewetted l-PNDG films. Both cyclic and linear PNDG molecules adopt cis-amide conformations in the crystalline film, which transition into trans-amide conformations upon melting. A top-down solvent leaching treatment of both l/c-PNDG films revealed the formation of an irreversibly physisorbed monolayer with similar thickness (ca. 3 nm) on the Si substrate. The physisorbed monolayers are more disordered relative to the respective thicker crystalline films for both cyclic and linear PNDGs. Upon heating above T m , the adsorbed c-PNDG chains adopt trans-amide backbone conformation identical with the free c-PNDG molecules in the molten film. By contrast, the backbone conformations of l-PNDG chains in the adsorbed layers are notably different from those of the free chains in the molten film. We postulate that the conformational disparity between the chains in the physically adsorbed layers versus the free chains in the molten film is an important factor to account for the difference in the thermal stability of PNDG thin films. These findings highlight the use of cyclic chain topology to suppress the melt-induced dewetting in polymer thin films.

36 MATERIALS SCIENCE↗
NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗
DOE OSTI2020

The cosmological bootstrap: inflationary correlators from symmetries and singularities

Scattering amplitudes at weak coupling are highly constrained by Lorentz invariance, locality and unitarity, and depend on model details only through coupling constants and the particle content of the theory. For example, four-particle amplitudes are analytic for contact interactions and have simple poles with appropriately positive residues for tree-level exchange. In this paper, we develop an understanding of inflationary correlators which parallels that of flat-space scattering amplitudes. Specifically, we study slow-roll inflation with weak couplings to extra massive particles, for which all correlation functions are controlled by an approximate conformal symmetry on the boundary of the spacetime. After systematically classifying all possible contact terms in de Sitter space, we derive an analytic expression for the four-point function of conformally coupled scalars mediated by the tree-level exchange of massive scalars. Conformal symmetry implies that the correlator satisfies a pair of differential equations with respect to spatial momenta, encoding bulk time evolution in purely boundary terms. The absence of unphysical singularities (and the correct normalization of physical ones) completely fixes this correlator. Moreover, a “spin-raising” operator relates it to the correlators associated with the exchange of particles with spin, while “weight-shifting” operators map it to the four-point function of massless scalars. We explain how these de Sitter four-point functions can be perturbed to obtain inflationary three-point functions. Using our formalism, we reproduce many classic results in the literature, such as the three-point function of slow-roll inflation, and provide a complete classification of all inflationary three- and four-point functions arising from weakly broken conformal symmetry. Remarkably, the inflationary bispectrum associated with the exchange of particles with arbitrary spin is completely characterized by the soft limit of the simplest scalar-exchange four-point function of conformally coupled scalars and a series of contact terms. Finally, we demonstrate that the inflationary correlators contain flat-space scattering amplitudes via a suitable analytic continuation of the external momenta, which can also be directly connected with the signals for particle production seen in the squeezed limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Modeling receptor flexibility in the structure-based design of KRAS G12C inhibitors

KRAS has long been referred to as an ‘undruggable’ target due to its high affinity for its cognate ligands (GDP and GTP) and its lack of readily exploited allosteric binding pockets. Recent progress in the development of covalent inhibitors of KRAS G12C has revealed that occupancy of an allosteric binding site located between the α3-helix and switch-II loop of KRAS G12C —sometimes referred to as the ‘switch-II pocket’—holds great potential in the design of direct inhibitors of KRAS G12C . In studying diverse switch-II pocket binders during the development of sotorasib (AMG 510), the first FDA-approved inhibitor of KRAS G12C , we found the dramatic conformational flexibility of the switch-II pocket posing significant challenges toward the structure-based design of inhibitors. Here, we present our computational approaches for dealing with receptor flexibility in the prediction of ligand binding pose and binding affinity. For binding pose prediction, we modified the covalent docking program CovDock to allow for protein conformational mobility. This new docking approach, termed as FlexCovDock, improves success rates from 55 to 89% for binding pose prediction on a dataset of 10 cross-docking cases and has been prospectively validated across diverse ligand chemotypes. For binding affinity prediction, we found standard free energy perturbation (FEP) methods could not adequately handle the significant conformational change of the switch-II loop. We developed a new computational strategy to accelerate conformational transitions through the use of targeted protein mutations. Using this methodology, the mean unsigned error (MUE) of binding affinity prediction were reduced from 1.44 to 0.89 kcal/mol on a set of 14 compounds. These approaches were of significant use in facilitating the structure-based design of KRAS G12C inhibitors and are anticipated to be of further use in the design of covalent (and noncovalent) inhibitors of other conformationally labile protein targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

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

Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis

The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463–785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovery of Multiple Light-Harvesting States of the Photosynthetic Protein PE545

Cryptophytes are photosynthetic microalga that flourish in a remarkable diversity of natural environments by using pigment-containing proteins with absorption maxima tuned to each ecological niche. While this diversity in the absorption has been well established, the subsequent photophysics is highly sensitive to the local protein environment and so may exhibit similar variation. Thermal fluctuations of the protein conformation are expected to introduce photophysical heterogeneity of the pigments that may have evolved important functional properties in a manner similar to that of the absorption. However, such heterogeneity is averaged out in ensemble measurements and, therefore, has not yet been probed. Here, we report single-molecule measurements of phycoerythrin 545 (PE545), the prototypical cryptophyte antenna protein, in its native dimeric form. A conformational ensemble was resolved consisting of distinct photophysical states with different light-harvesting properties. Proteins that did not quench, partially quenched, or fully quenched absorbed light were observed. Light intensity increased the quenched-state population of the dimer, potentially as a mechanism to deal with the extreme light intensities found in aqueous environments. Cross-linking, which mimics local interactions, introduces this light-dependent functionality while also suppressing other conformational dynamics. The cellular organization can, therefore, actively modulate the protein conformation and dynamics, selecting for distinct levels of light harvesting. Furthermore, the complex conformational equilibrium provides an additional mechanism for cryptophytes and likely other photosynthetic organisms to optimize solar energy capture and conversion.

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

Retrieving functional pathways of biomolecules from single-particle snapshots

Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer

Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Vanilloid-dependent TRPV1 opening trajectory from cryo EM ensemble analysis

Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis.

59 BASIC BIOLOGICAL SCIENCES↗