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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The application of synthetic antibacterial minerals to combat topical infections: exploring a mouse model of MRSA infection

Abstract The development of new antibiotics has stalled, and novel strategies are needed as we enter the age of antibiotic resistance. Certain naturally occurring clays have been shown to be effective in killing antibiotic resistant bacteria. However, these natural clays are too variable to be used in clinical settings. Our study shows that synthetic antibacterial minerals exhibit potent antibacterial activity against topical MRSA infections and increase the rate of wound closure relative to controls. The antibacterial minerals maintain a redox cycle between Fe 2+ /Fe 3+ and the surfaces of pyrite minerals, which act as a semiconductor and produce reactive oxygen species (ROS), while smectite minerals act as a cation exchange reservoir. Acidic conditions are maintained throughout the application of the hydrated minerals and can mitigate the alkaline pH conditions observed in chronic non-healing wounds. These results provide evidence for the strategy of ‘iron overload’ to combat antibiotic resistant infections through the maintained release of Fe 2+ and generation of ROS via distinct geochemical reactions that can break the chronic wound damage cycle.

58 GEOSCIENCES↗
DOE OSTI2021

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN–nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Single-molecule investigations of single-chain cellulose biosynthesis

Cellulose biosynthesis in sessile bacterial colonies originates in the membrane-integrated bacterial cellulose synthase (Bcs) AB complex. We utilize optical tweezers to measure single-strand cellulose biosynthesis by BcsAB from Rhodobacter sphaeroides . Synthesis depends on uridine diphosphate glucose, Mg 2+ , and cyclic diguanosine monophosphate, with the last displaying a retention time of ∼80 min. Below a stall force of 12.7 pN, biosynthesis is relatively insensitive to force and proceeds at a rate of one glucose addition every 2.5 s at room temperature, increasing to two additions per second at 37°. At low forces, conformational hopping is observed. Single-strand cellulose stretching unveiled a persistence length of 6.2 nm, an axial stiffness of 40.7 pN, and an ability for complexes to maintain a tight grip, with forces nearing 100 pN. Stretching experiments exhibited hysteresis, suggesting that cellulose microstructure underpinning robust biofilms begins to form during synthesis. Cellohexaose spontaneously binds to nascent single cellulose strands, impacting polymer mechanical properties and increasing BcsAB activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response

Protein kinase Gcn2 attenuates protein synthesis in response to amino acid starvation while stimulating translation of a transcriptional activator of amino acid biosynthesis. Gcn2 activation requires a domain related to histidyl-tRNA synthetase (HisRS), the enzyme that aminoacylates tRNA His . While evidence suggests that deacylated tRNA binds the HisRS domain for kinase activation, ribosomal P-stalk proteins have been implicated as alternative activating ligands on stalled ribosomes. We report crystal structures of the HisRS domain ofChaetomium thermophilumGcn2 that reveal structural mimicry of both catalytic (CD) and anticodon-binding (ABD) domains, which in authentic HisRS bind the acceptor stem and anticodon loop of tRNA His . Elements for forming histidyl adenylate and aminoacylation are lacking, suggesting that Gcn2 HisRS was repurposed for kinase activation, consistent with mutations in the CD that dysregulate yeast Gcn2 function. Substituting conserved ABD residues well positioned to contact the anticodon loop or that form a conserved ABD–CD interface impairs Gcn2 function in starved cells. Mimicry in Gcn2 HisRS of two highly conserved structural domains for binding both ends of tRNA—each crucial for Gcn2 function—supports that deacylated tRNAs activate Gcn2 and exemplifies how a metabolic enzyme is repurposed to host new local structures and sequences that confer a novel regulatory function.

Science & Technology - Other Topics↗
DOE OSTI2025

Improved pressure-gradient sensor for the prediction of separation onset in RANS models

Here, we improve upon two key aspects of the Menter shear stress transport (SST) turbulence model: (1) We propose a more robust adverse pressure gradient sensor based on the strength of the pressure gradient in the direction of the local mean flow; (2) We propose two alternative eddy viscosity models to be used in the adverse pressure gradient regions identified by our sensor. Direct numerical simulations of the Boeing Gaussian bump are used to identify the terms in the baseline SST model that need correction, and a posteriori Reynolds-averaged Navier-Stokes calculations are used to calibrate coefficient values, leading to a model that is both physics driven and data informed. The two sensor-equipped models are applied to two thick airfoils representative of modern wind turbine applications, the FFA-W3-301 and the DU00-W-212. The proposed models improve the prediction of stall (onset of separation) with respect to the prediction of the baseline SST model.

17 WIND ENERGY↗
DOE OSTI2024

Numerical challenges in modeling gravothermal collapse in Self-Interacting Dark Matter halos

When dark matter has a large cross section for self scattering, halos can undergo a process known as gravothermal core collapse, where the inner core rapidly increases in density and temperature. To date, several methods have been used to implement Self-Interacting Dark Matter (SIDM) in N-body codes, but there has been no systematic study of these different methods or their accuracy in the core-collapse phase. In this paper, we compare three different numerical implementations of SIDM, including the standard methods from the GIZMO and Arepo codes, by simulating idealized dwarf halos undergoing significant dark matter self interactions (σ/m = 50 cm 2 /g). When simulating these halos, we also vary the mass resolution, time-stepping criteria, and gravitational force-softening scheme. The various SIDM methods lead to distinct differences in a halo's evolution during the core-collapse phase, as each results in spurious scattering rate differences and energy gains/losses. The use of adaptive force softening for gravity can lead to numerical heating that artificially accelerates core collapse, while an insufficiently small simulation time step can cause core evolution to stall or completely reverse. Additionally, particle numbers must be large enough to ensure that the simulated halos are not sensitive to noise in the initial conditions. Even for the highest-resolution simulations tested in this study (10 6 particles per halo), we find that variations of order 10% in collapse time are still present. Here, the results of this work underscore the sensitivity of SIDM modeling on the choice of numerical implementation and motivate a careful study of how these results generalize to halos in a cosmological context.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Leading Edge Microspoilers for Load Dumping in Wind Turbine Rotors

As rotor designs have grown in size and flexibility, new design challenges have arisen that could benefit from novel control strategies. Leading edge microspoilers (LEMS) have been shown to effectively reduce forces on airfoils by inducing stall at lower angles of attack. This paper investigates how LEMS can be used to reduce blade loading on large, flexible, downwind rotors during design-limiting design load cases. During shutdown in turbulent flows near cutout speed, LEMS could reduce the tip deflection spikes toward the tower by over 50% and keep flapwise root bending moments below normal operating conditions, thus eliminating these as design-driving load cases. In power producing load cases, deploying LEMS for a short period of time during a load spike can be effective to reduce toward-tower tip deflections without significantly impacting power produced, assuming these load spikes can be identified by a controller. Leveraging this technology could allow for lower specific power machines to be designed.

17 WIND ENERGY↗
DOE OSTI2023

TranSyT , an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE’s release, software development for the automatic integration of transport reactions into models has stalled. Here, in this paper, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Capture and migration of Jupiter and Saturn in mean motion resonance in a gaseous protoplanetary disc

Here, we study the dynamical evolution of Jupiter and Saturn embedded in a gaseous, solar nebula-type disc by means of hydrodynamics simulations with the FARGO2D1D code. We study the evolution for different initial separations of the planets’ orbits, Δa SJ , to investigate whether they become captured in mean motion resonance (MMR) and the direction of the subsequent migration of the planet (inwards or outwards). We also provide an assessment of the planet’s orbital dynamics at different epochs of Saturn’s growth. We find that the evolution of initially compact orbital configurations is dependent on the value of Δa SJ . This implies that an evolution as that proposed in the Grand Tack model depends on the precise initial orbits of Jupiter and Saturn and on the time-scales for their formation. Capture in the 1:2 MMR and inward or (nearly) stalled migration are highly favoured. Within its limits, our work suggests that the reversed migration, associated with the resonance capture of Jupiter and Saturn, may be a low-probability evolutionary scenario, so that other planetary systems with giant planets are not expected to have experienced a Grand Tack-like evolutionary path.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast

Abstract Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.

Carvalho Borges, Pâmela C. (ORCID:0000000244919874↗
DOE OSTI2026

Sparsomycin inhibits translation through a conserved mechanism across all domains of life

Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

Paranjpe, Madhura N [Department of Biological Scie↗
DOE OSTI2022

Shock revival in core-collapse supernovae assisted by heavy axionlike particles

We report axionlike particles (ALPs) are a class of hypothetical pseudoscalar particles which feebly interact with ordinary matter. The hot plasma of core-collapse supernovae is a possible laboratory to explore physics beyond the standard model including ALPs. Once produced, some of the ALPs can be absorbed by the supernova matter and affect energy transfer. In this study, we calculate the ALP emission in core-collapse supernovae and the backreaction on supernova dynamics consistently. It is found that the stalled bounce shock can be revived if the coupling between ALPs and photons is as high as $g_{aγ}$ ~ 10 -9 GeV -1 and the ALP mass is 40–400 MeV. Most of the models result in more energetic explosions than the average observed supernova. While this can be used to place constraints on those ALPs, long-term simulations across multiple progenitors need to be further investigated to place robust limits.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Gravitational-wave signature of core-collapse supernovae

Here, we calculate the gravitational-wave (GW) signatures of detailed 3D core-collapse supernova sim ulations spanning a range of massive stars. Most of the simulations are carried out to times late enough to capture more than 95% of the total GW emission. We find that the f/g-mode and f-mode of proto-neutron star oscillations carry away most of the GW power. The f-mode frequency inex orably rises as the proto-neutron star (PNS) core shrinks. We demonstrate that the GW emission is excited mostly by accretion plumes onto the PNS that energize modal oscillations and also high frequency (“haze”) emission correlated with the phase of violent accretion. The duration of the major phase of emission varies with exploding progenitor and there is a strong correlation between the total GW energy radiated and the compactness of the progenitor. Moreover, the total GW emissions vary by as much as three orders of magnitude from star to star. For black-hole formation, the GW signal tapers off slowly and does not manifest the haze seen for the exploding models. For such failed models, we also witness the emergence of a spiral shock motion that modulates the GW emission at a frequency near ~100 Hertz that slowly increases as the stalled shock sinks. We find significant angular anisotropy of both the high- and low-frequency (memory) GW emissions, though the latter have very little power.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Graph Analytics on Jellyfish topology

Because large unstructured datasets is important for many science domains, distributed graph analytics is critical to many scientists. Unfortunately, obtaining scaling and performance for irregular communication is challenging because contemporary network interconnects are primarily designed to maximize bandwidths of fixed-neighborhoods large-message exchanges (e.g., stencils). Although there is no consensus on the “best” network topologies for irregular communication, unstructured graph-based interconnects can be more suitable. We analyze three popular graph workloads – clustering, pattern enumeration, and traversal — on comparable networks (in terms of resources and costs) constructed from Jellyfish Random Regular, Dragonfly and Fat tree topologies, varying the routing algorithms. Using packet-level simulations, we demonstrate up to 60% improvement in communication time with Jellyfish due to diversity of the short paths between arbitrary endpoints, which can reduce overall network stalls and congestion.

Graph Analytics, network topology, interconnect, H↗
DOE OSTI2022

Accelerating Flash-X Simulations with Asynchronous I/O

Most high-fidelity physics simulation codes, such as Flash-X, need to save intermediate results (checkpoint files) to restart or gain insights into the evolution of the simulation. These simulation codes save such intermediate files synchronously, where computation is stalled while the data is written to storage. Depending on the problem size and computational requirements, this file write time can be a substantial portion of the total simulation time. In order to hide the I/O latency of checkpointing, asynchronous I/O methods have been introduced. These methods use background threads for performing I/O while the main threads continue with the simulation. The usage of background threads can compete for resources on the node as well as with communication. In this paper, we evaluate the overheads and the overall benefit of asynchronous I/O in HDF5 to simulations. Results from real-world high-fidelity simulations on the Summit supercomputer show that I/O operation is overlapped with application communication or computation or both, effectively hiding some or all of the I/O latency. Our evaluation shows that while using asynchronous I/O adds overhead to the application, the I/O time reduction is more significant, resulting in overall up to 1.5X performance speedup.

Jain, Rajeev↗