Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “partner”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Exploring the roles of microbes in facilitating plant adaptation to climate change

Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant–microbe–environment interactions. In this perspective, we highlight some of the key factors influencing plant–microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant–microbe–environment interactions under a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

WLCG Authorisation from X.509 to Tokens

The WLCG Authorisation Working Group was formed in July 2017 with the objective to understand and meet the needs of a future-looking Authentication and Authorisation Infrastructure (AAI) for WLCG experiments. Much has changed since the early 2000s when X.509 certificates presented the most suitable choice for authorisation within the grid; progress in token based authorisation and identity federation has provided an interesting alternative with notable advantages in usability and compatibility with external (commercial) partners. The need for interoperability in this new model is paramount as infrastructures and research communities become increasingly interdependent. Over the past two years, the working group has made significant steps towards identifying a system to meet the technical needs highlighted by the community during staged requirements gathering activities. Enhancement work has been possible thanks to externally funded projects, allowing existing AAI solutions to be adapted to our needs. A cornerstone of the infrastructure is the reliance on a common token schema in line with evolving standards and best practices, allowing for maximum compatibility and easy cooperation with peer infrastructures and services. We present the work of the group and an analysis of the anticipated changes in authorisation model by moving from X.509 to token based authorisation. A concrete example of token integration in Rucio is presented.

Bockelman, Brian↗
DOE OSTI2024

WLCG Transition from X.509 to Tokens. Status, Plans, and Timeline

Since 2017, the Worldwide LHC Computing Grid (WLCG) has been working towards enabling token-based authentication and authorization throughout its entire middleware stack. Following the initial publication of the WLCG Token Schema v1.0 in 2019, OAuth2.0 token workflows have been integrated across grid middleware. There are many complex challenges to be addressed before the WLCG can be end-to-end token-based, including not just technical hurdles but also interoperability with the wider authentication and authorization landscape. This paper presents the status of the WLCG coordination and deployment work, and how it relates to software providers and partner communities. The authors also detail how the WLCG token transition timeline has progressed, and how it has changed since its publication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Bromide as the Directing Group for β-Arylation of Thiophenes

Direct β-arylation of thiophene derivatives with bromide as directing group is disclosed. The reaction is conducted with PdCl 2 /(p-tolyl) 3 P as catalyst, silver carbonate as additive, and aryl iodide as coupling partner, affording brominated biaryl compounds as product. Control experiments indicated that the presence of bromide group enhances the reactivity of the C–H bond, enabling β-arylation. Additionally, the C–Br bond can be easily converted into many useful functional groups through a wide range of methodologies. The mechanistic study suggests that silver salt plays a key role in the C–H bond-activation step.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Furthermore, following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Prediction challenge: First principles simulation of the ultrafast electron diffraction spectrum of cyclobutanone

Computer simulation has long been an essential partner of ultrafast experiments, allowing the assignment of microscopic mechanistic detail to low-dimensional spectroscopic data. However, the ability of theory to make a priori predictions of ultrafast experimental results is relatively untested. Herein, as a part of a community challenge, we attempt to predict the signal of an upcoming ultrafast photochemical experiment using state-of-the-art theory in the context of preexisting experimental data. Specifically, we employ ab initio Ehrenfest with collapse to a block mixed quantum–classical simulations to describe the real-time evolution of the electrons and nuclei of cyclobutanone following excitation to the 3s Rydberg state. The gas-phase ultrafast electron diffraction (GUED) signal is simulated for direct comparison to an upcoming experiment at the Stanford Linear Accelerator Laboratory. Following initial ring-opening, dissociation via two distinct channels is observed: the C3 dissociation channel, producing cyclopropane and CO, and the C2 channel, producing CH2CO and C2H4. Direct calculations of the GUED signal indicate how the ring-opened intermediate, the C2 products, and the C3 products can be discriminated in the GUED signal. We also report an a priori analysis of anticipated errors in our predictions: without knowledge of the experimental result, which features of the spectrum do we feel confident we have predicted correctly, and which might we have wrong?

Chemistry↗
DOE OSTI2025

A perspective on lessons learned and future needs for wind energy field campaigns

This perspective paper provides motivation and guidance to the wind energy community for suggested future investments and a long-term strategy for wind-energy-related field campaigns that will provide much-needed observations for improving wind energy science and model validation. We synthesize key lessons learned from past field campaigns, identify critical science gaps that we think should drive future field efforts, and provide a suggested pipeline on how future endeavors should be developed. When considering future grand field campaigns, we stress the need for international cooperation across funding bodies, research institutes, and industry partners to collect observations to overcome current and future grand challenges for wind energy.

17 WIND ENERGY↗
DOE OSTI2026

Single-shot ultrafast dynamics of nanosecond pulsed plasmas: Transition from ps–ns nonequilibrium to near-full ionization

The ultrafast multi-stage evolution of state-defining properties in atmospheric-pressure nanosecond pulsed plasmas is quantified using single-discharge, jitter-free, continuous streak-sweep spectroscopy of N 2 (C → B) molecular and N + /O + ionic species with a single-shot time resolution as short as ∼160 ps. An early period of extreme nonequilibrium is observed with vibrational temperatures [T V (C)] dropping from ∼8000 K at <200 ps after plasma breakdown to <4000 K within ∼1 ns, with near-ambient rotational temperatures [T R (C)] ∼ 300 K due to limited collisional energy transfer. This early-time T V (C) trend is representative of a direct and unquenched look into the high-energy tail of the electron energy distribution function; thus, it tracks real-time changes in the mean electron energy via the N2(C) emission signatures. This is followed by the rapid onset of N + /O + ionic emission after a distinct time delay of ∼14.9 ns due to multistep chemical kinetics. The ionic emission enables determination of electron densities (n e ) >2 × 10 19 cm −3 and electron temperatures (T e ) >36 000 K, indicating the transition to a nearly fully ionized regime. The ps–ns temporal dynamics are also compared between air and N 2 plasmas to assess the influence of collisional partners, as well as across the anode, cathode, and central gap regions to identify spatial variations in plasma behavior. Finally, this work demonstrates versatile continuously probing approach capable of spectro-temporal and spatially resolved single-shot measurements of key state variables in the ps–ns evolution of atmospheric-pressure nanosecond pulsed plasmas.

Electric discharges↗
DOE OSTI2019

Direct visualization of degradation microcompartments at the ER membrane

To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non–membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga Chlamydomonas reinhardtii , we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER–Golgi interface. These non–membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control.

Science & Technology - Other Topics↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of “undruggability” for an intracellular target. Structural studies reveal extensive protein–WDB002 and protein–protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise “undruggable” targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evolution of a σ–(c-di-GMP)–anti-σ switch

Filamentous actinobacteria of the genus Streptomyces have a complex lifecycle involving the differentiation of reproductive aerial hyphae into spores. We recently showed c-di-GMP controls this transition by arming a unique anti-σ, RsiG, to bind the sporulation-specific σ, WhiG. The Streptomyces venezuelae RsiG–(c-di-GMP) 2 –WhiG structure revealed that a monomeric RsiG binds c-di-GMP via two E(X) 3 S(X) 2 R(X) 3 Q(X) 3 D repeat motifs, one on each helix of an antiparallel coiled-coil. Here we show that RsiG homologs are found scattered throughout the Actinobacteria. Strikingly, RsiGs from unicellular bacteria descending from the most basal branch of the Actinobacteria are small proteins containing only one c-di-GMP binding motif, yet still bind their WhiG partners. Our structure of a Rubrobacter radiotolerans (RsiG) 2 –(c-di-GMP) 2 –WhiG complex revealed that these single-motif RsiGs are able to form an antiparallel coiled-coil through homodimerization, thereby allowing them to bind c-di-GMP similar to the monomeric twin-motif RsiGs. Further data show that in the unicellular actinobacterium R. radiotolerans , the (RsiG) 2 –(c-di-GMP) 2 –WhiG regulatory switch controls type IV pilus expression. Phylogenetic analysis indicates the single-motif RsiGs likely represent the ancestral state and an internal gene-duplication event gave rise to the twin-motif RsiGs inherited elsewhere in the Actinobacteria. Thus, these studies show how the anti-σ RsiG has evolved through an intragenic duplication event from a small protein carrying a single c-di-GMP binding motif, which functions as a homodimer, to a larger protein carrying two c-di-GMP binding motifs, which functions as a monomer. Consistent with this, our structures reveal potential selective advantages of the monomeric twin-motif anti-σ factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ADP enhances the allosteric activation of eukaryotic elongation factor 2 kinase by calmodulin

Protein translation, one of the most energy-consumptive processes in a eukaryotic cell, requires robust regulation, especially under energy-deprived conditions. A critical component of this regulation is the suppression of translational elongation through reduced ribosome association of the GTPase eukaryotic elongation factor 2 (eEF-2) resulting from its specific phosphorylation by the calmodulin (CaM)-activated α–kinase eEF-2 kinase (eEF-2K). It has been suggested that the eEF-2K response to reduced cellular energy levels is indirect and mediated by the universal energy sensor AMP-activated protein kinase (AMPK) through direct stimulatory phosphorylation and/or downregulation of the eEF-2K-inhibitory nutrient-sensing mTOR pathway. Here, we provide structural, biochemical, and cell-biological evidence of a direct energy-sensing role of eEF-2K through its stimulation by ADP. A crystal structure of the nucleotide-bound complex between CaM and the functional core of eEF-2K phosphorylated at its primary stimulatory site (T348) reveals ADP bound at a unique pocket located on the face opposite that housing the kinase active site. Within this basic pocket (BP), created at the CaM/eEF-2K interface upon complex formation, ADP is stabilized through numerous interactions with both interacting partners. Biochemical analyses using wild-type eEF-2K and specific BP mutants indicate that ADP stabilizes CaM within the active complex, increasing the sensitivity of the kinase to CaM. Induction of energy stress through glycolysis inhibition results in significantly reduced enhancement of phosphorylated eEF-2 levels in cells expressing ADP-binding compromised BP mutants compared to cells expressing wild-type eEF-2K. These results suggest a direct energy-sensing role for eEF-2K through its cooperative interaction with CaM and ADP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units

Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding

The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein eIF4E for promoting cap-independent genome translation. However, the structural basis of such 5' cap-binding protein recognition by the uncapped RNA remains largely unknown. Here, we have determined the crystal structure of a 3' CITE, panicum mosaic virus-like translation enhancer (PTE) from the saguaro cactus virus (SCV), using a Fab crystallization chaperone. The PTE RNA folds into a three-way junction architecture with a pseudoknot between the purine-rich R domain and pyrimidine-rich Y domain, which organizes the overall structure to protrude out a specific guanine nucleotide, G18, from the R domain that comprises a major interaction site for the eIF4E binding. The superimposable crystal structures of the wild-type, G18A, G18C, and G18U mutants suggest that the PTE scaffold is preorganized with the flipped-out G18 ready to dock into the eIF4E 5' cap-binding pocket. The binding studies with wheat and human eIF4Es using gel electrophoresis and isothermal titration calorimetry, and molecular docking computation for the PTE–eIF4E complex demonstrated that the PTE structure essentially mimics the mRNA 5' cap for eIF4E binding. Such 5' cap mimicry by the uncapped and structured viral RNA highlights how viruses can exploit RNA structures to mimic the host protein-binding partners and bypass the canonical mechanisms for their genome translation, providing opportunities for a better understanding of virus-host interactions and non-canonical translation mechanisms found in many pathogenic RNA viruses.

3' cap-independent translation enhancers↗
DOE OSTI2024

Electrochemical cofactor recycling of bacterial microcompartments

Bacterial microcompartments (BMCs) are prokaryotic organelles that consist of a protein shell which sequesters metabolic reactions in its interior. While most of the substrates and products are relatively small and can permeate the shell, many of the encapsulated enzymes require cofactors that must be regenerated inside. We have analyzed the occurrence of an enzyme previously assigned as a cobalamin (vitamin B 12 ) reductase and, curiously, found it in many unrelated BMC types that do not employ B 12 cofactors. We propose Nicotinamide adenine dinucleotide (NAD+) regeneration as the function of this enzyme and name it Metabolosome Nicotinamide Adenine Dinucleotide Hydrogen (NADH) dehydrogenase (MNdh). Its partner shell protein BMC-T SE (tandem domain BMC shell protein of the single layer type for electron transfer) assists in passing the generated electrons to the outside. We support this hypothesis with bioinformatic analysis, functional assays, Electron Paramagnetic Resonance spectroscopy, protein voltammetry, and structural modeling verified with X-ray footprinting. This finding represents a paradigm for the BMC field, identifying a new, widely occurring route for cofactor recycling and a new function for the shell as separating redox environments.

bacterial microcompartment↗
DOE OSTI2020

Verification of Arms Control Treaties with Resonance Phenomena

Nuclear disarmament treaties remain insufficient to neutralize the existential threat of the nuclear weapons. Technologies are necessary for verifying the authenticity of the nuclear warheads undergoing dismantlement before counting them toward a treaty partner’s obligation. Here we present a review of concepts involving isotope-specific resonance processes, Nuclear Resonance Fluorescence (NRF) [1] and Neutron Resonance Transmission Analysis (NRTA) [2, 3], used to authenticate a warhead’s fissile components by comparing them to a previously authenticated template. All information is encrypted in the physical domain by the addition of an encrypting filter to the target, leading to measurements with an outcome similar to an equation with two unknowns. Using Monte Carlo simulations and experiments we show that the measurements readily detect hoaxing attempt, while no vital isotopic or geometric information about the weapon is released. These nuclear techniques can be used to dramatically increase the reach and trustworthiness of future nuclear disarmament treaties.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2021

A world without pythons would be so simple

We show that bulk operators lying between the outermost extremal surface and the asymptotic boundary admit a simple boundary reconstruction in the classical limit. This is the converse of the Python's lunch conjecture, which proposes that operators with support between the minimal and outermost (quantum) extremal surfaces—e.g. the interior Hawking partners—are highly complex. Our procedure for reconstructing this 'simple wedge' is based on the HKLL construction, but uses causal bulk propagation of perturbed boundary conditions on Lorentzian timefolds to expand the causal wedge as far as the outermost extremal surface. As a corollary, we establish the Simple Entropy proposal for the holographic dual of the area of a marginally trapped surface as well as a similar holographic dual for the outermost extremal surface. Here, we find that the simple wedge is dual to a particular coarse-grained CFT state, obtained via averaging over all possible Python's lunches. An efficient quantum circuit converts this coarse-grained state into a 'simple state' that is indistinguishable in finite time from a state with a local modular Hamiltonian. Under certain circumstances, the simple state modular Hamiltonian generates an exactly local flow; we interpret this result as a holographic dual of black hole uniqueness.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗