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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli .

protofilaments↗
DOE OSTI2020

Containers for Massive Ensemble of I/O Bound Hierarchical Coupled Simulations

We present our experience using containers to scale up a massive ensemble of coupled I/O bound workloads on the NERSC Cori supercomputer. We describe the design of a hierarchical simulation structure using the Integrated Plasma Simulator (IPS) that enables the flexible execution of coupled simulations at the system, node, and core level using the same coupling abstraction and API. The hierarchical design allows for the node-level execution to be efficiently executed using containers while not impacting the structure of the simulation at the system level. We demonstrate the viability of the approach by presenting experimental results from applications in coupled fusion plasma simulations that illustrate the performance impact of using containers to deploy the node-level workloads, in conjunction with the user mountable XFS file systems to ameliorate the load on the Lustre parallel file system. We also present results from production runs showing the ability of the ensemble simulations to scale to hundreds of Cori Haswell nodes, with little or no overhead.

Elwasif, Wael↗
DOE OSTI2020

Zero-energy bound states in the high-temperature superconductors at the two-dimensional limit

Majorana zero modes (MZMs) that obey the non-Abelian statistics have been intensively investigated for potential applications in topological quantum computing. The prevailing signals in tunneling experiments “fingerprinting” the existence of MZMs are the zero-energy bound states (ZEBSs). However, nearly all of the previously reported ZEBSs showing signatures of the MZMs are observed in difficult-to-fabricate heterostructures at very low temperatures and additionally require applied magnetic field. Here, by using in situ scanning tunneling spectroscopy, we detect the ZEBSs upon the interstitial Fe adatoms deposited on two different high-temperature superconducting one-unit-cell iron chalcogenides on SrTiO 3 (001). The spectroscopic results resemble the phenomenological characteristics of the MZMs inside the vortex cores of topological superconductors. Our experimental findings may extend the MZM explorations in connate topological superconductors toward an applicable temperature regime and down to the two-dimensional (2D) limit.

Science & Technology - Other Topics↗
DOE OSTI2021

Observation of bound states in the continuum embedded in symmetry bandgaps

In the past decade, symmetry-protected bound states in the continuum (BICs) have proven to be an important design principle for creating and enhancing devices reliant upon states with high-quality (Q) factors, such as sensors, lasers, and those for harmonic generation. However, as we show, current implementations of symmetry-protected BICs in photonic crystal slabs can only be found at the center of the Brillouin zone and below the Bragg diffraction limit, which fundamentally restricts their use to single-frequency applications. By microprinting a three-dimensional (3D) photonic crystal structure using two-photon polymerization, we demonstrate that this limitation can be overcome by altering the radiative environment surrounding the slab to be a 3D photonic crystal. This allows for the protection of a line of BICs by embedding it in a symmetry bandgap of the crystal. This concept substantially expands the design freedom available for developing next-generation devices with high-Q states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
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 OSTI2021

Error Bounds for Dynamical Spectral Estimation

Dynamical spectral estimation is a well-established numerical approach for estimating eigenvalues and eigenfunctions of the Markov transition operator from trajectory data. Although the approach has been widely applied in biomolecular simulations, its error properties remain poorly understood. Here we analyze the error of a dynamical spectral estimation method called “the variational approach to conformational dynamics" (VAC). We bound the approximation error and estimation error for VAC estimates. Our analysis establishes VAC's convergence properties and suggests new strategies for tuning VAC to improve accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning

This repository contains python scripts and numerical data accompanying the paper: "Leveraging Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning," Tyler Chang, Andrew Gillette, Romit Maulik, 2024. The following subdirectories are included: - "interpolants" contains our interpolation scripts used for all studies - "experiments" contains scripts demonstrating our experiments with synthetic data - "airfoil" contains scripts demonstrating our experiments with the publicly available UIUC airfoil dataset. Further instructions are provided in READMEs within the sub-directories.

Gillette, Andrew↗
DOE OSTI2024

Tight Practical Bounds for Subgraph Densities in Ego-centric Networks

SAND2025-11782O Tight Practical Bounds for Subgraph Densities in Ego-centric Networks is a software tool for calculating the “subgraph spread ratio” for social network analysis. This value is useful in network analysis for determining the amount of exogenous and endogenous pressure on a graph. It can distinguish between networks coming from different sources, e.g. distinguishing a graph of Facebook data versus a graph of Wikipedia data. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Mattes, Connor↗
DOE OSTI2023

Structure of coagulation factor VIII bound to a patient-derived anti-C1 domain antibody inhibitor

The development of pathogenic antibody inhibitors against coagulation factor VIII (FVIII) occurs in ~30% of congenital hemophilia A patients receiving FVIII replacement therapy as well as in all cases of acquired hemophilia A. KM33 is an anti-C1 domain antibody inhibitor previously isolated from a severe hemophilia A patient. In addition to potently blocking FVIII binding to von Willebrand factor and phospholipid surfaces, KM33 disrupts FVIII binding to lipoprotein receptor-related protein 1 (LRP1), which drives FVIII hepatic clearance and antigen presentation in dendritic cells. Here, we report on the structure of FVIII bound to NB33, a recombinant derivative of KM33, by single-particle cryo-electron microscopy. Furthermore, structural analysis reveals the NB33 epitope localizes to FVIII residues R2090-S2094 and I2158-R2159 which constitute membrane-binding loops in the C1 domain. Further analysis reveals multiple FVIII lysine and arginine residues, previously shown to mediate binding to LRP1, dock onto an acidic cleft at the NB33 variable domain interface, thus blocking a putative LRP1 binding site. Together, these results demonstrate a novel mechanism of FVIII inhibition by a patient-derived antibody inhibitor and provide structural evidence toward engineering FVIII with reduced LRP1-mediated clearance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for Simultaneous Suppression of Lignin, Tricin and Wall-Bound Phenolic Biosynthesis via the Expression of Monolignol 4- O -Methyltransferases in Rice

Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross-link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro-industrial applications. In the present study, we assess the applications of two engineered monolignol 4- O -methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para-methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan-bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol-extractable 4- O -methylated ferulic acid and 5–7 μmol/g 4- O -methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de-starched rice straw biomass after diluted acid-pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar-based production of biofuel and bio-chemicals.

Biomass Analytics↗
DOE OSTI2021

Achieving extreme light confinement in low-index dielectric resonators through quasi-bound states in the continuum

Obtaining large field enhancement in low-refractive-index dielectric materials is highly relevant to many photonic and quantum optics applications. However, confining light in these materials is challenging, owing to light leakage through coupling to continuum modes in the surrounding environment. Here, we investigate the possibility of achieving high quality factors in low-index dielectric resonators through the bound states in the continuum (BIC). Our simulations demonstrate that destructive interference between leaky modes can be achieved by tuning the geometrical parameters of the resonator arrays, leading to the emergence of quasi-BIC in resonators that have a small index contrast to the underlying substrates. The resultant large field enhancement gives rise to giant quality factors and Purcell effects. By introducing vertical mirror symmetry, the quasi-BIC can be tuned into an ideal BIC. In addition, the quasi-BIC can modify the emission patterns of the coupled emitters, rendering highly directional and focused far-field emission. These findings may provide a path for the practical implementation of photonic and quantum devices based on low-index dielectric materials.

42 ENGINEERING↗
DOE OSTI2022

X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain

Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biogeochemical reactions and release of iron-bound organic carbon during the redox processes. Final report

Accurate simulation and prediction for reactions of soil organic carbon (OC) under different biogeochemical conditions remain a grand challenge. This project aims to investigate the transformation and degradation of OC under anaerobic and aerobic conditions as well as anaerobic-aerobic transitions, as well as its coupling with reactions for iron (Fe) oxide minerals. We determined that OC can serve as electron shuttle (including pyrogenic OC) and donor for accelerating the reduction of Fe oxide. The presence of OC can inhibit the transformation of poor crystalline Fe oxide (ferrihydrite) to other more crystalline forms. Reduction of Fe oxide can lead to the mobilization of OC, depending on the ratio of OC/Fe. More condensed aromatic OC can be selectively associated with Fe oxide and also resistant to the reduction release, enhancing their stability during the anaerobic reactions. Under aerobic condition, the association with Fe oxide can inhibit the degradation of OC and also its priming effects on the degradation of indigenous soil OC. During an anaerobic-aerobic transition, OC mineralization was inhibited substantially compared to controls incubated only aerobically. Our field measurement in the Arctic region revealed the importance of deep soil temperature in regulating the generation of CO 2 and CH 4 . These results highlighted the importance of redox reactions in controlling the fate and stability of soil OC. For future studies, investigations are required to fill in the knowledge gap regarding the structure and chemical nature of important organic ligands for Fe, accurate quantification of Fe-bound OC in soils, the long-term effects of anaerobic-aerobic transitions on the OC mineralization as well as response of microbial communities to redox transitions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Bound Constrained Partial DifferentialEquation Inverse Problem Solution by theSemi-Smooth Newton Method

We present the mathematical derivation, software implementation details, and computational results for a semi-smooth Newton method applied to two inverse problems governed by partial differential equations with bound constraints. The two problems share mathematical structural similarities to density-based topology optimization problems. The semi-smooth Newton method provides a mesh independent solution computation for the two test problems. A key step is that the complementarity part of the necessary optimality conditions are reformulated with the use of a complementarity functionφsuch that the complementarity conditions are satisfied if and only if a zero of a nonsmooth function has been obtained. The modular finite element package MFEM is utilized for the software implementation. In addition we constructed a matrix-free Operator to enable the use of efficient Krylov subspace IterativeSolver of MFEM for the solution of our two target problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

DNS/LES Study of Representative Wall-Bounded Turbulent Flows using SIERRA/Fuego

This report summarizes a series of SIERRA/Fuego validation efforts of turbulent flow models on canonical wall-bounded configurations. In particular, direct numerical simulations (DNS) and large eddy simulations (LES) turbulence models are tested on a periodic channel, a periodic pipe, and an open jet for which results are compared to the velocity profiles obtained theoretically or experimentally. Velocity inlet conditions for channel and pipe flows are developed for application to practical simulations. To show this capability, LES is performed over complex terrain in the form of two natural hills and the results are compared with other flow solvers. The practical purpose of the report is to document the creation of inflow boundary conditions of fully developed turbulent flows for other LES calculations where the role of inflow turbulence is critical.

42 ENGINEERING↗
DOE OSTI2021

DOE Plasma Science Center - Predictive Control of Plasma Kinetics: Multi-Phase and Bounded Systems (Final Report DE-SC0001939)

Low temperature plasmas (LTPs) are the plasmas of electron-volt (eV) physics and eV technologies. LTPs have characteristic electron temperatures of a few eV and fractional ionizations that are typically small. Since LTPs have electron temperatures commensurate with the threshold energies of excited states in neutral atoms and molecules, power transfer from electrons to these atoms and molecules efficiently produces activated species (e.g., radicals, excited states, photons). Acceleration of ions in the sheaths of LTPs to energies of tens to hundreds of eV enable activation of surface modifying processes – sputtering, etching, deposition. With such properties, LTPs are often and beneficially used in technological devices, ranging from etching and deposition in microelectronics and solar cell fabrication, to hardening of surgical instruments. LTPs harbor fundamental science issues that are intellectually challenging and rewarding. At the same time, there are enormous societal benefits that are enabled by LTPs. The entire present-day and future information technology infrastructure owes its very existence to LTPs. Renewable energy sources, such as solar cell arrays, could not be economically produced in the absence of deposition and etching by LTPs. In acknowledgment of the importance of LTPs, the DOE Office of Fusion Energy Sciences supported the Plasma Science Center for Predictive Control of Plasma Kinetics: Multi-Phase and Bounded Systems from August 2009 to July 2021, consisting of an initial 5-year grant, 3 funded extensions and 2 no-cost extensions. This is the final report of the Center in which the productivity of the Center is discussed in terms of publications, impact and personnel. High-lights of the research performed in the Center are provided.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Penetration Bounds For Azimuthal Slot On Infinite Cylinder With Finite Length Backing Cylindrical Cavity

We examine coupling into azimuthal slots on an infinite cylinder with a infinite length interior cavity operating both at the fundamental cavity modal frequencies, with small slots and a resonant slot, as well as higher frequencies. The coupling model considers both radiation on an infinite cylindrical exterior as well as a half space approximation. Bounding calculations based on maximum slot power reception and interior power balance are also discussed in detail and compared with the prior calculations. For higher frequencies limitations on matching are imposed by restricting the loads ability to shift the slot operation to the nearest slot resonance; this is done in combination with maximizing the power reception as a function of angle of incidence. Finally, slot power mismatch based on limited cavity load quality factor is considered below the first slot resonance.

42 ENGINEERING↗