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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

A multiscale MDCT image-based breathing lung model with time-varying regional ventilation

A novel algorithm is presented that links local structural variables (regional ventilation and deforming central airways) to global function (total lung volume) in the lung over three imaged lung volumes, to derive a breathing lung model for computational fluid dynamics simulation. The algorithm constitutes the core of an integrative, image-based computational framework for subject-specific simulation of the breathing lung. For the first time, the algorithm is applied to three multi-detector row computed tomography (MDCT) volumetric lung images of the same individual. A key technique in linking global and local variables over multiple images is an in-house mass-preserving image registration method. Throughout breathing cycles, cubic interpolation is employed to ensure C{sub 1} continuity in constructing time-varying regional ventilation at the whole lung level, flow rate fractions exiting the terminal airways, and airway deformation. The imaged exit airway flow rate fractions are derived from regional ventilation with the aid of a three-dimensional (3D) and one-dimensional (1D) coupled airway tree that connects the airways to the alveolar tissue. An in-house parallel large-eddy simulation (LES) technique is adopted to capture turbulent-transitional-laminar flows in both normal and deep breathing conditions. The results obtained by the proposed algorithm when using three lung volume images are compared with those using only one or two volume images. The three-volume-based lung model produces physiologically-consistent time-varying pressure and ventilation distribution. The one-volume-based lung model under-predicts pressure drop and yields un-physiological lobar ventilation. The two-volume-based model can account for airway deformation and non-uniform regional ventilation to some extent, but does not capture the non-linear features of the lung.

42 ENGINEERING↗
DOE OSTI2012

VOYAGER 2 OBSERVES A LARGE DENSITY INCREASE IN THE HELIOSHEATH

Voyager 2 (V2) entered the heliosheath in 2007 August at roughly the same time solar minimum conditions were reaching the outer heliosphere. Soon after crossing the termination shock the solar wind density at Voyager decreased by a factor of two and the temperature decreased by a factor of three. At the beginning of 2011 the plasma density in the heliosheath began to increase and in mid-2012 it was up by more than a factor of two. The temperature rose by about 50% and the speed remained constant, although the flow direction continues to turn tailward. These changes may signal the end of solar minimum conditions at V2 in the heliosheath, although we do not understand why the speed did not decrease. The increased dynamic pressure has lead to an outward movement of the termination shock from its very compressed state at solar minimum.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Paramagnetic Molecular Semiconductors Combining Anisotropic Magnetic Ions with TCNQ Radical Anions

We report the synthesis, magnetic properties, and transport properties of paramagnetic metal complexes, [Co(DMF) 4 (TCNQ) 2 ](TCNQ) 2 (1), [La(DMF) 8 (TCNQ)](TCNQ) 5 (2), and [Nd(DMF) 7 (TCNQ)](TCNQ) 5 (3) (DMF = N,N-dimethylformamide, TCNQ = 7,7,8,8-tetracyanoquinodimethane). All three compounds contain fractionally charged TCNQ δ– anions (0 < δ < 1) and mononuclear complex cations in which the coordination environment of a metal center includes several DMF molecules and one or two terminally coordinated TCNQ δ– anions. The coordinated TCNQ δ– anions participate in π–π stacking interactions with noncoordinated TCNQ δ– anions, forming columnar substructures that provide efficient charge-transporting pathways. Furthermore, temperature-dependent conductivity measurements demonstrate that all three compounds exhibit semiconducting behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Benefits and challenges in deployment of low global warming potential R290 refrigerant for room air conditioning equipment in California

High global warming potential gases (“high GWP”) are the fastest growing sector of greenhouse gas emissions in the world and in California and are primarily used as refrigerant gases in refrigeration and cooling equipment. Hydrofluorocarbons (HFCs) refrigerants are the dominant type of high GWP gases with GWP values thousands of times larger than CO 2 on a 100-year timescale. Refrigerant-grade propane (“R290”) has a very low GWP (GWP = 3.3) with good thermodynamic properties and good cooling equipment performance but the flammability of any leaked refrigerant makes equipment design, handling, and maintenance critical factors to manage. This paper focuses on the potential climate benefits and costs of transitioning to R290 refrigerant in small room air conditioning (AC) units, specifically window AC, packaged terminal AC/heat pumps (PTAC/PTHP), and mini-split heat pumps. Overall climate impact for a transition to all three types of air conditioning units in the 2022–2051 timeframe is found to be from 15 to 64 million metric tons of greenhouse gas (GHG) savings in California with a cost of saved CO 2 eq that ranges from $14.50 per ton of CO 2 eq saved to -$50.30 per ton of CO 2 eq saved (net savings) depending on whether the baseline refrigerant is R32 or R410A and depending on the relative energy efficiency for R290 units compared to baseline units.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2013

Infrared nanosecond laser-metal ablation in atmosphere: Initial plasma during laser pulse and further expansion

We have investigated the dynamics of the nanosecond laser ablated plasma within and after the laser pulse irradiation using fast photography. A 1064 nm, 15 ns laser beam was focused onto a target made from various materials with an energy density in the order of J/mm{sup 2} in atmosphere. The plasma dynamics during the nanosecond laser pulse were observed, which could be divided into three stages: fast expansion, division into the primary plasma and the front plasma, and stagnation. After the laser terminated, a critical moment when the primary plasma expansion transited from the shock model to the drag model was resolved, and this phenomenon could be understood in terms of interactions between the primary and the front plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Novel Vinculin Binding Site of the IpaA Invasin of Shigella

Internalization of Shigella into host epithelial cells, where the bacteria replicates and spreads to neighboring cells, requires a type 3 secretion system (T3SS) effector coined IpaA. IpaA binds directly to and activates the cytoskeletal protein vinculin after injection in the host cell cytosol, and this was previously thought to be directed by two amphipathic {alpha}-helical vinculin-binding sites (VBS) found in the C-terminal tail domain of IpaA. Here, we report a third VBS, IpaA-VBS3, that is located N-terminal to the other two VBSs of IpaA and show that one IpaA molecule can bind up to three vinculin molecules. Biochemical in vitro Shigella invasion assays and the 1.6 {angstrom} crystal structure of the vinculin {center_dot} IpaA-VBS3 complex showed that IpaA-VBS3 is functionally redundant with the other two IpaA-VBSs in cell invasion and in activating the latent F-actin binding functions of vinculin. Multiple VBSs in IpaA are reminiscent of talin, which harbors 11 VBSs. However, most of the talin VBSs have low affinity and are buried in helix bundles, whereas all three of the VBSs of IpaA are high affinity, readily available, and in close proximity to each other in the IpaA structure. Although deletion of IpaA-VBS3 has no detectable effects on Shigella invasion of epithelial cells, deletion of all three VBSs impaired bacterial invasion to levels found in an ipaA null mutant strain. Thus, IpaA-directed mimicry of talin in activating vinculin occurs through three high affinity VBSs that are essential for Shigella pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains

The endosomal sorting complex required for transport (ESCRT) machinery is responsible for membrane remodeling in a number of biological processes including multivesicular body biogenesis, cytokinesis, and enveloped virus budding. In mammalian cells, efficient abscission during cytokinesis requires proper function of the ESCRT-III protein IST1, which binds to the microtubule interacting and trafficking (MIT) domains of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM). In this paper, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. Crystal structures of the three molecular complexes revealed that IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). Structural comparison revealed that structural features in both MIT and MIM contribute to determine the specific binding mechanism. Within the IST1 MIM sequence, two phenylalanine residues were shown to be important in discriminating MIM1 versus MIM3 binding. Finally, these observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1

Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. Lastly, we consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

VLBI OBSERVATIONS OF 10 COMPACT SYMMETRIC OBJECT CANDIDATES: EXPANSION VELOCITIES OF HOT SPOTS

Observations of 10 Compact Symmetric Object (CSO) candidates have been made with the Very Long Baseline Array (VLBA) at 8.4 GHz in 2005 and with a combined Chinese and European Very Long Baseline Interferometry (VLBI) array at 8.4 GHz in 2009. The 2009 observations incorporate for the first time the two new Chinese telescopes at Miyun and Kunming for international astrophysical observations. The observational data, in combination with archival VLBA data from previous epochs, have been used to derive the proper motions of the VLBI components. Because of the long time baseline of {approx}16 years of the VLBI data sets, the expansion velocities of the hot spots can be measured at an accuracy as high as {approx}1.3 {mu}as yr{sup -1}. Six of the ten sources are identified as CSOs with a typical double or triple morphology on the basis of both spectral index maps and their mirror symmetry of proper motions of the terminal hot spots. The compact double source J1324+4048 is also identified as a CSO candidate. Among the three remaining sources, J1756+5748 and J2312+3847 are identified as core-jet sources with proper motions of their jet components relating to systemic source expansion. The third source J0017+5312 is likely also a core-jet source, but a robust detection of a core is needed for an unambiguous identification. The kinematic ages of the CSOs derived from proper motions range from 300 to 2500 years. The kinematic age distribution of the CSOs confirm an overabundance of compact young CSOs with ages less than 500 years. CSOs with known kinematic ages may be used to study the dynamical evolution of extragalactic radio sources at early stages.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Impedance-Based Prediction of Distortions Generated by Resonance in Grid-Connected Converters

Small-signal impedance-based analysis can effectively predict the frequency and damping of resonance modes in power electronic systems. However, it cannot predict the magnitude of resonance or explain resonance-generated distortions in the absence of an external disturbance at the resonance frequency. This paper presents an impedance-based theory for the prediction of the magnitude of resonance or resonance-generated distortions in grid-connected converters. It is discovered that the impedance response of a converter starts changing with the magnitude of resonance at its terminals. The changing converter impedance response may stabilize an unstable growing resonance mode beyond a certain magnitude, at which point the converter enters a limit cycle mode of sustained oscillations. The proposed theory uses large-signal impedance for the prediction of resonance-generated distortions; the large-signal impedance of an electrical equipment represents its impedance response for different magnitudes of perturbation injected at its terminals. Large-signal impedance-based prediction of resonance-generated distortions is demonstrated for a three-phase grid-connected voltage-source converter.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2011

D0 Decommissioning: Storage of depleted uranium modules inside D0 calorimeters after the termination of D0 experiment

Dzero liquid Argon calorimeters contain hadronic modules made of depleted uranium plates. After the termination of D0 detector's operation, liquid Argon will be transferred back to Argon storage Dewar, and all three calorimeters will be warmed up. At this point, there is no intention to disassemble the calorimeters. The depleted uranium modules will stay inside the cryostats. Depleted uranium is a by-product of the uranium enrichment process. It is slightly radioactive, emits alpha, beta and gamma radiation. External radiation hazards are minimal. Alpha radiation has no external exposure hazards, as dead layers of skin stop it; beta radiation might have effects only when there is a direct contact with skin; and gamma rays are negligible - levels are extremely low. Depleted uranium is a pyrophoric material. Small particles (such as shavings, powder etc.) may ignite with presence of Oxygen (air). Also, in presence of air and moisture it can oxidize. Depleted uranium can absorb moisture and keep oxidizing later, even after air and moisture are excluded. Uranium oxide can powder and flake off. This powder is also pyrographic. Uranium oxide may create health problems if inhaled. Since uranium oxide is water soluble, it may enter the bloodstream and cause toxic effects.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Environmental Tuning of Homologs of the Orange Carotenoid Protein-Encoding Gene in the Cyanobacterium Fremyella diplosiphon

The orange carotenoid protein (OCP) family of proteins are light-activated proteins that function in dissipating excess energy absorbed by accessory light-harvesting complexes, i.e., phycobilisomes (PBSs), in cyanobacteria. Some cyanobacteria contain multiple homologs of the OCP-encoding gene ( ocp ). Fremyella diplosiphon , a cyanobacterium studied for light-dependent regulation of PBSs during complementary chromatic acclimation (CCA), contains several OCP homologs – two full-length OCPs, three Helical Carotenoid Proteins (HCPs) with homology to the N-terminus of OCP, and one C-terminal domain-like carotenoid protein (CCP) with homology to the C-terminus of OCP. We examined whether these homologs are distinctly regulated in response to different environmental factors, which could indicate distinct functions. We observed distinct patterns of expression for some OCP, HCP, and CCP encoding genes, and have evidence that light-dependent aspects of ocp homolog expression are regulated by photoreceptor RcaE which controls CCA. RcaE-dependent transcriptional regulator RcaC is also involved in the photoregulation of some hcp genes. Apart from light, additional environmental factors associated with cellular redox regulation impact the mRNA levels of ocp homologs, including salt, cold, and disruption of electron transport. Analyses of conserved sequences in the promoters of ocp homologs were conducted to gain additional insight into regulation of these genes. Several conserved regulatory elements were found across multiple ocp homolog promoters that potentially control differential transcriptional regulation in response to a range of environmental cues. The impact of distinct environmental cues on differential accumulation of ocp homolog transcripts indicates potential functional diversification of this gene family in cyanobacteria. These genes likely enable dynamic cellular protection in response to diverse environmental stress conditions in F . diplosiphon .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Dissociative double-photoionization of butadiene in the 25-45 eV energy range using 3-D multi-coincidence ion momentum imaging spectrometry

Dissociative double-photoionization of butadiene in the 25-45 eV energy range has been studied with tunable synchrotron radiation using full three-dimensional ion momentum imaging. Using ab initio calculations, the electronic states of the molecular dication below 33 eV are identified. The results of the measurement and calculation show that double ionization from π orbitals selectively triggers twisting about the terminal or central C–C bonds. We show that this conformational rearrangement depends upon the dication electronic state, which effectively acts as a gateway for the dissociation reaction pathway. For photon energies above 33 eV, three-body dissociation channels where neutral H-atom evaporation precedes C–C charge-separation in the dication species appear in the correlation map. The fragment angular distributions support a model where the dication species is initially aligned with the molecular backbone parallel to the polarization vector of the light, indicating a high probability for double-ionization to the “gateway states” for molecules with this orientation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II

Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using novel, direct, and quantitative chemical tools. We determine the proline isomeric preference of three CTD phosphatases: Ssu72 as cis-proline specific, Scp1 and Fcp1 as strongly trans-preferred. Due to this inherent characteristic, these phosphatases respond differently to enzymes that catalyze the isomerization of proline, like Ess1/Pin1. We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. This leads to diversified phosphorylation states of CTD in vitro and in cells. In conclusion, we provide the chemical tools to investigate proline isomerization and its ability to selectively enhance signaling in transcription and other biological contexts.

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

Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes

Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting Staphylococcus aureus Cas9 (SauCas9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13–AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13–AcrIIA15 as unique bifunctional inhibitors of SauCas9.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Role for first zinc finger of WT1 in DNA sequence specificity: Denys–Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites

Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1–4). An alternative splicing of Wt1 can add three additional amino acids—lysine (K), threonine (T) and serine (S)—between ZF3 and ZF4. In the –KTS isoform, ZF2–4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type –KTS isoform ZF1–4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2–4, ZF1 can be positioned continuously in the DNA major groove forming a ‘near-cognate’ complex. Second, while ZF2–4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys–Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.

59 BASIC BIOLOGICAL SCIENCES↗