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DOE OSTI2020

Efficient numerical methods to solve sparse linear equations with application to PageRank

Over the last two decades, the PageRank problem has received increased interest from the academic community as an efficient tool to estimate web-page importance in information retrieval. Despite numerous developments, the design of efficient optimization algorithms for the PageRank problem is still a challenge. Here, we propose three new algorithms with a linear time complexity for solving the problem over a bounded-degree graph. The idea behind them is to set up the PageRank as a convex minimization problem over a unit simplex, and then solve it using iterative methods with small iteration complexity. Our theoretical results are supported by an extensive empirical justification using real-world and simulated data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

S K-edge XAS of Cu Ⅱ , Cu Ⅰ , and Zn Ⅱ oxidized Dithiolene complexes: Covalent contributions to structure and the Jahn-Teller effect

We report reduced dithiolene ligands are bound to high valent Mo centers in the active site of the oxotransferase family of enzymes. Related model complexes have been studied with great insight by Prof. Holm and his colleagues. This study focuses on the other limit of dithiolene chemistry: an investigation of the 2-electron oxidized dithiolene bound to low-valent late transition metal (TM) ions (Zn II , Cu I , and Cu II ). The bonding descriptions of the oxidized dithiolene [N,N-dimethyl piperazine 2,3-dithione (Me 2 Dt 0 )] complexes are probed using S K-edge X-ray absorption spectroscopy (XAS) and the results are correlated to density functional theory (DFT) calculations. These experimentally supported calculations are then extended to explain the different geometric structures of the three complexes. The Zn II (Me 2 Dt 0 ) 2 complex has only ligand-ligand repulsion so it is stabilized at the D 2d symmetry limit. The Cu I (Me 2 Dt 0 ) 2 complex has additional weak backbonding thus distorts somewhat from D 2d toward D 2h symmetry. The Cu II (Me 2 Dt 0 ) 2 complex has a strong σ donor bond that leads to both a large Jahn-Teller stabilization to D 2h and an additional covalent contribution to the geometry. The combined strong stabilization results in the square planar, D 2h structure. This study quantifies the competition between the ligand-ligand repulsion and the change in electronic structures in determining the final geometric structures of the oxidized dithiolene complexes, and provides quantitative insights into the Jahn-Teller stabilization energy and its origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Kinetic and structural evidence for specific DMSO interference with reversible binding of uncharged bis-oximes to hAChE and their reactivation kinetics of OP-hAChE

The structural basis of inhibitory effect of organic solvent dimethyl sulfoxide (DMSO) on human acetylcholinesterase (EC 3.1.1.7; hAChE) was inferred from the effect of DMSO on kinetics of reversible inhibition of uncharged, heterocyclic bis-oximes to hAChE, from DMSO effect on rates of reactivation of inactive organophosphate (OP)-hAChE conjugates by bis-oximes and by X-ray structures of bis-oxime and DMSO binding to hAChE. Here, the reversible inhibition constant of DMSO for hAChE in 0.1 M phosphate buffer pH 7.4 at 22 °C, was K i = (0.32 ± 0.04) % (or 45 ± 5 mM). The K i of the bis-oxime LG-703 for hAChE was 3.2-fold larger in 1 % DMSO, consistent with direct competition between LG-703 and DMSO. The X-ray structure of the LG-703∗hAChE complex (PDB ID: 6U3P) shows DMSO and LG-703 bound to individual hAChE monomers, LG-703 in the chain A and DMSO in the chain B. In the co-crystallization both small molecules were present at a similar excess over their corresponding K i values for hAChE (7.8-fold for DMSO and 6.5-fold for LG-703) and formation of two different complexes (DMSO∗hAChE and LG-703∗hAChE), in the same crystal, appears consistent with inhibition kinetics. Furthermore, rates of reactivation of paraoxon-inhibited hAChE (POX-hAChE) and of VX-hAChE by LG-703 and by a novel heterocyclic bis-oxime LG-1922 were reduced 2 – 3-fold in DMSO, consistent with observation of the active-center-bound DMSO molecules in the newly solved structure of the LG-1922∗POX-hAChE complex presented here and in our POX-hAChE structure (PDB ID: 8DT2) showing obstruction of the reactivator access to the conjugated P atom.

Acetylcholinesterase inhibition↗

DOE OSTI2022

U(VI) binding onto electrospun polymers functionalized with phosphonate surfactants

We previously observed that phosphonate functionalized electrospun nanofibers can uptake U(VI), making them promising materials for sensing and water treatment applications. Here, we investigate the optimal fabrication of these materials and their mechanism of U(VI) binding under the influence of environmentally relevant ions (e.g., Ca 2+ and CO 3 2- ). We found that U(VI) uptake was greatest on polyacrylonitrile (PAN) functionalized with longer-chain phosphonate surfactants (e.g., hexa- and octadecyl phosphonate; HDPA and ODPA, respectively), which were better retained in the nanofiber after surface segregation. Subsequent uptake experiments to better understand specific solid-liquid interfacial interactions were carried out using 5 mg of HDPA-functionalized PAN mats with 10 μM U at pH 6.8 in four systems with different combinations of solutions containing 5 mM calcium (Ca 2+ ) and 5 mM bicarbonate (HCO 3 -). U uptake was similar in control solutions containing no Ca 2+ and HCO 3 - (resulting in 19 ± 3% U uptake), and in those containing only 5 mM Ca2+ (resulting in 20 ± 3% U uptake). A decrease in U uptake (10 ± 4% U uptake) was observed in experiments with HCO 3 -, indicating that UO 2 -CO 3 complexes may increase uranium solubility. Results from shell-by-shell EXAFS fitting, aqueous extractions, and surface-enhanced Raman scattering (SERS) indicate that U is bound to phosphonate as a monodentate inner sphere surface complex to one of the hydroxyls in the phosphonate functional groups. New knowledge derived from this study on material fabrication and solid-liquid interfacial interactions will help to advance technologies for use in the in-situ detection and treatment of U in water.

42 ENGINEERING↗

DOE OSTI2024

M IV /Co –I (M = Zr, Hf) Bis(phosphinoamide) Complexes with η 6 - and η 4 -Arenes

Despite their relevance to catalysis, low-/subvalent cobalt complexes are difficult to synthesize and isolate. Consequently, very few “cobaltate” complexes are known and there is a lack of architectural diversity in this field. Lewis acidic d 0 group IV metals have been demonstrated to stabilize Co –I centers via metal–metal bonds. Herein, we report the synthesis of bis(phosphinoamide) heterobimetallic M IV /Co –I arene complexes (M = Zr, Hf). The driving force to maintain the aromaticity of the arenes dictates the hapticity of the Co-bound arene ligands and influences the binding arrangement of the phosphinoamide ligands. Benzene and toluene were observed to bind η 6 to the Co –I center, forcing dissociation of one of the phosphinoamide ligands, whereas η 4 -coordination of anthracene allows both phosphinoamide ligands to remain bound to the Co center. The identity of both the arene and the group IV metal ion starkly influence the lability of the arene. For instance, the Co-bound benzene ligand in the Zr IV /Co –I benzene complex rapidly exchanges with C 6 D 6 in solution, whereas toluene/C 6 D 6 exchange is much slower and appreciable C 6 H 6 /C 6 D 6 exchange is not observed for the Hf analogue. The Zr IV /Co –I benzene complex loses benzene upon repeated exposure to vacuum to form an arene-free tetrametallic dimer.

aromatic compounds↗

DOE OSTI2026

Hamiltonian simulation in Zeno subspaces

Here, we investigate the quantum Zeno effect as a framework for designing and analyzing quantum algorithms for Hamiltonian simulation. We show that frequent projective measurements of an ancilla qubit register can be used to simulate quantum dynamics on a target qubit register with a circuit complexity similar to randomized approaches. The classical sampling overhead in the latter approaches is traded for ancilla qubit overhead in Zeno-based approaches. A second-order Zeno sequence is developed to improve scaling and implementations through unitary kicks are discussed. We derive rigorous error bounds that allow for identifying the associated circuit complexities for the first- and second-order Zeno sequences. We show that the circuits over the combined register can be identified as a subroutine commonly used in post-Trotter Hamiltonian simulation methods. We build on this observation to reveal connections between different Hamiltonian simulation algorithms.

Hamiltonian simulation↗

DOE OSTI2020

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1972

The interaction of moderately strong shock waves with thick perforated walls of low porosity

A theoretical prediction is given of the flow through thick perforated walls of low porosity resulting from the impingement of a moderately strong traveling shock wave. The model was a flat plate positioned normal to the direction of the flow. Holes bored in the plate parallel to the direction of the flow provided nominal hole length-to-diameter ratios of 10:1 and an axial porosity of 25 percent of the flow channel cross section. The flow field behind the reflected shock wave was assumed to behave as a reservoir producing a quasi-steady duct flow through the model. Rayleigh and Fanno duct flow theoretical computations for each of three possible auxiliary wave patterns that can be associated with the transmitted shock (to satisfy contact surface compatibility) were used to provide bounding solutions as an alternative to the more complex influence coefficients method. Qualitative and quantitative behavior was verified in a 1.5- by 2.0-in. helium shock tube. High speed Schlieren photography, piezoelectric pressure-time histories, and electronic-counter wave speed measurements were used to assess the extent of correlation with the theoretical flow models. Reduced data indicated the adequacy of the bounding theory approach to predict wave phenomena and quantitative response.

Grant, D. J.↗

DOE OSTI2020

Cross‐Coupling between Hydrazine and Aryl Halides with Hydroxide Base at Low Loadings of Palladium by Rate‐Determining Deprotonation of Bound Hydrazine

Abstract Reported here is the Pd‐catalyzed C–N coupling of hydrazine with (hetero)aryl chlorides and bromides to form aryl hydrazines with catalyst loadings as low as 100 ppm of Pd and KOH as base. Mechanistic studies revealed two catalyst resting states: an arylpalladium(II) hydroxide and arylpalladium(II) chloride. These compounds are present in two interconnected catalytic cycles and react with hydrazine and base or hydrazine alone to give the product. The selectivity of the hydroxide complex with hydrazine to form aryl over diaryl hydrazine was lower than that of the chloride complex, as well as the catalytic reaction. In contrast, the selectivity of the chloride complex closely matched that of the catalytic reaction, indicating that the aryl hydrazine is derived from this complex. Kinetic studies showed that the coupling process occurs by rate‐limiting deprotonation of a hydrazine‐bound arylpalladium(II) chloride complex to give an arylpalladium(II) hydrazido complex.

Wang, Justin Y.↗

DOE OSTI2020

Cross‐Coupling between Hydrazine and Aryl Halides with Hydroxide Base at Low Loadings of Palladium by Rate‐Determining Deprotonation of Bound Hydrazine

Wang, Justin Y.↗

DOE OSTI2026

Discovery and engineering of enzymes for new-to-nature photobiocatalysis

Photobiocatalysis integrates enzymatic catalysis with photochemistry, enabling challenging radical transformations with high selectivity under mild conditions. Early developments in this field were largely driven by the discovery that enzyme-bound cofactors can form photoactive charge–transfer complexes with substrates, thereby initiating radical chemistry upon light irradiation. Recent advances, however, have substantially expanded the mechanistic landscape of photobiocatalysis through diverse mechanisms. This review summarizes major developments in photobiocatalysis reported since 2024. Rather than cataloging individual reactions, we focus on the fundamental mechanisms of radical generation and interception within enzyme active sites, and discuss how these mechanistic principles guide the discovery, engineering, and design of enzymes for new-to-nature photobiocatalysis.

Bai, Zibo [University of Illinois Urbana-Champaign↗

DOE OSTI2022

Chemical Amplification of Subthreshold Base Triggers To Drive Sol–Gel Transitions in Polymers

Chemical amplification has been widely applied in applications ranging from stimuli sensing to advanced photoresists, but it is rarely utilized to drive productive mechanical property changes. Here, we demonstrate the use of a base amplifier to drive the gelation of a functional polymer solution, in response to a subthreshold base trigger through a mechanism whereby the trigger drives a dramatic increase in the base concentration driven by base amplification, resulting in complexation of Fe(III) and polymer-bound catechol groups and subsequent gelation of the polymer solution. Furthermore, the concomitant crystallization of dibenzofulvene, which is a byproduct of base amplification, led to significant stiffening of the resultant gel and an unexpected temperature-sensitive change of gel stiffness.

Aromatic compounds↗

DOE OSTI2020

Structural and Enzymatic Analyses Reveal the Binding Mode of a Novel Series of Francisella tularensis Enoyl Reductase (FabI) Inhibitors

Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.

Mehboob, Shahila↗

DOE OSTI2025

Dynamics and activation of membrane-bound B cell receptor assembly

B-cell receptor (BCR) complexes are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes have been published that validates the asymmetric organization of the BCR complex. Here, we carry out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identify two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding causes increased flexibility in regions distal to the antigen binding site. Second, antigen binding alters the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements lead to changes in localized lipid composition. Our work indirectly supports the conformational-change induced models of BCR activation and contributes to the understanding of the antigen-dependent activation mechanism of BCRs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles.

Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus ( Ca. ) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.

Volland, Jean-Marie↗

DOE OSTI2024

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction

Abstract mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti–MHC-I mAb, we determined X-ray crystal structures of four complexes of anti–MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti–H2-Dd mAb, two anti–MHC-I α3 domain mAbs, and an anti–β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.

Immunology↗

NASA NTRS1997

Some Decomposable Codes: The |a + x|b + x|a + b + x| Construction

Codes with decomposable structure allow the use of multistage decoding procedures to achieve suboptimum bounded-distance error performance with reduced decoding complexity. This correspondence presents some new decomposable codes, including a class of distance-8 codes, that are constructed based on the|a + x|b + x|a + b + x| construction method. Some existing best codes are shown to be decomposable and hence can be decoded with multistage decoding.

Fossorier, Marc P. C.↗

NASA NTRS2012

Progress Toward Affordable High Fidelity Combustion Simulations Using Filtered Density Functions for Hypersonic Flows in Complex Geometries

Significant progress has been made in the development of subgrid scale (SGS) closures based on a filtered density function (FDF) for large eddy simulations (LES) of turbulent reacting flows. The FDF is the counterpart of the probability density function (PDF) method, which has proven effective in Reynolds averaged simulations (RAS). However, while systematic progress is being made advancing the FDF models for relatively simple flows and lab-scale flames, the application of these methods in complex geometries and high speed, wall-bounded flows with shocks remains a challenge. The key difficulties are the significant computational cost associated with solving the FDF transport equation and numerically stiff finite rate chemistry. For LES/FDF methods to make a more significant impact in practical applications a pragmatic approach must be taken that significantly reduces the computational cost while maintaining high modeling fidelity. An example of one such ongoing effort is at the NASA Langley Research Center, where the first generation FDF models, namely the scalar filtered mass density function (SFMDF) are being implemented into VULCAN, a production-quality RAS and LES solver widely used for design of high speed propulsion flowpaths. This effort leverages internal and external collaborations to reduce the overall computational cost of high fidelity simulations in VULCAN by: implementing high order methods that allow reduction in the total number of computational cells without loss in accuracy; implementing first generation of high fidelity scalar PDF/FDF models applicable to high-speed compressible flows; coupling RAS/PDF and LES/FDF into a hybrid framework to efficiently and accurately model the effects of combustion in the vicinity of the walls; developing efficient Lagrangian particle tracking algorithms to support robust solutions of the FDF equations for high speed flows; and utilizing finite rate chemistry parametrization, such as flamelet models, to reduce the number of transported reactive species and remove numerical stiffness. This paper briefly introduces the SFMDF model (highlighting key benefits and challenges), and discusses particle tracking for flows with shocks, the hybrid coupled RAS/PDF and LES/FDF model, flamelet generated manifolds (FGM) model, and the Irregularly Portioned Lagrangian Monte Carlo Finite Difference (IPLMCFD) methodology for scalable simulation of high-speed reacting compressible flows.

Drozda, Tomasz G.↗