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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2

While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. Here, these results support a model in which the mycobacterial SecA2 works with SecYEG. SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Numerical simulation of falling film sensible heat transfer over round horizontal tubes

Numerical simulations are performed to explore the heat transfer characteristics of falling films over horizontal round tubes with uniform heat flux imposed for a range of Reynolds numbers spanning the droplet, jet, and sheet regimes. Simulations results agree well with available experimental measurements. The study analyzes the local as well as average heat transfer behavior under the different flow modes. The numerical results show that the local Nusselt number (Nu) distribution depends on the flow features in each mode and varies substantially in all directions for the respective mode. In the droplet mode, the Nu value varies significantly as the droplet impinges and the remnant liquid-bridge retracts (peak instantaneous Nu near 6), followed by wave propagation over the tube surface with peak Nu around 0.25. For the jet modes, the local maximum in the heat transfer occurs off-center to the impingement location with magnitudes of peak Nu = 3.1 for the inline jet mode and Nu = 2.7 for the staggered jet mode, while on the rest of the tube surface, it has an inverse relation with the liquid film thickness. Substantial variations in the heat transfer value are also recorded in the middle of the two impinging jets with Nu = 0.95 in the inline jet mode where the neighboring jets do not interact, and Nu = 0.60 in the crest region of the staggered jet mode where the neighboring jets interact with each other. In the sheet mode, the Nu was seen to depend on the thickness of the liquid waves traversing over the tube surface. Lower Nu values were recorded beneath the crest location of the liquid waves, which increases (1.4–11.6% depending on circumferential location) abruptly in magnitude at the advancing fronts of the waves. The temperature distribution in the liquid film in each of the modes was examined to evaluate the mechanism of heat transfer process. This study also compares the local heat transfer coefficient distribution with the analytical heat transfer models derived to predict heat transfer performance over horizontal tube surfaces.

42 ENGINEERING↗
DOE OSTI2014

On the capture of dark matter by neutron stars

We calculate the number of dark matter particles that a neutron star accumulates over its lifetime as it rotates around the center of a galaxy, when the dark matter particle is a self-interacting boson but does not self-annihilate. We take into account dark matter interactions with baryonic matter and the time evolution of the dark matter sphere as it collapses within the neutron star. We show that dark matter self-interactions play an important role in the rapid accumulation of dark matter in the core of the neutron star. We consider the possibility of determining an exclusion region of the parameter space for dark matter mass and dark matter interaction cross section with the nucleons as well as dark matter self-interaction cross section, based on the observation of old neutron stars. We show that for a dark matter density of 10{sup 3} GeV/cm{sup 3}and dark matter mass m{sub χ} ∼< 10 GeV, there is a potential exclusion region for dark matter interactions with nucleons that is three orders of magnitude more stringent than without self-interactions. The potential exclusion region for dark matter self-interaction cross sections is many orders of magnitude stronger than the current Bullet Cluster limit. For example, for high dark matter density regions, we find that for m{sub χ} ∼ 10 GeV when the dark matter interaction cross section with the nucleons ranges from σ{sub χn} ∼ 10{sup −52} cm{sup 2} to σ{sub χn} ∼ 10{sup −57} cm{sup 2}, the dark matter self-interaction cross section limit is σ{sub χχ} ∼< 10{sup −33} cm{sup 2}, which is about ten orders of magnitude stronger than the Bullet Cluster limit.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1979

Interactive color display for multispectral imagery using correlation clustering

A method for processing multispectral data is provided, which permits an operator to make parameter level changes during the processing of the data. The system is directed to production of a color classification map on a video display in which a given color represents a localized region in multispectral feature space. Interactive controls permit an operator to alter the size and change the location of these regions, permitting the classification of such region to be changed from a broad to a narrow classification.

Haskell, R. E.↗
DOE OSTI2026

Iron as a driver of organic carbon fate in permafrost regions

Iron (Fe) and its biogeochemical interactions with organic carbon (OC) exert critical controls over carbon storage and water quality across Arctic and sub-Arctic landscapes. Permafrost thaw affects Fe–organic carbon interactions by exposing thawed material and driving shifts in hydrologic regimes. Here we propose a conceptual framework describing how Fe–OC interactions respond to permafrost thaw and the implications for global carbon cycling. The framework builds on current understanding of hydrologically driven processes that are altered by permafrost thaw, including microbial Fe reduction that influences OC decomposition and carbon emissions; Fe cycling through redox transformations and sulfide oxidation; dissolution and reprecipitation of Fe–OC assemblages; and Fe export to river networks. We put forward four testable hypotheses—on topics from Fe supply to its role in soil OC storage and transfer to rivers—to advance understanding of the coupled environmental controls on pore-scale reactions (that is, microscale reactions at mineral–water–microorganism interfaces) that are central to global Fe–OC cycling. Our framework highlights how soil-profile- and landscape-scale processes, such as hydrologic connectivity and redox dynamics, regulate pore-scale Fe–OC reactions.

Herndon, Elizabeth [ORNL] (ORCID:0000000291945493)↗
DOE OSTI2017

The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1

Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding. The large subunit, Cac1 organizes the assembly of CAF-1. Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. These results define direct structural roles for yeast CAF-1 subunits and uncover a previously unknown critical function of the middle subunit in CAF-1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Measurement of the $M_A^{QE}$ parameter using multiple quasi-elastic dominated sub-samples in the minos near detector

The Main Injector Neutrino Oscillation Search (MINOS) is a two detector, long baseline neutrino oscillation experiment. The MINOS near detector is an ironscintillator tracking/sampling calorimeter and has recorded the world’s largest data set of neutrino interactions in the 0-5 GeV region. This high statistics data set is used to make precision measurements of neutrino interaction cross-sections on iron. The Q 2 dependence in charged current quasi-elastic (CCQE) scattering probes the axial and vector structure (form factor) of the nucleon/nuclear target, and nuclear effects in neutrino scattering. Presented here is a study of the MINOS Data that will introduce a method that improves the existing MINOS CCQE analysis. This analysis uses an additional CCQE dominated sub-sample from a different kinematic region to reduce correlations between fit parameters in the existing MINOS CCQE analysis. The measured value of the axial-vector mass is M QE A = 1.312 +0.037 -0.038 (fit) +0.123 -0.265 (syst.) GeV.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1994

Vortex distortion during vortex-surface interaction in a Mach 3 stream

An experimental study has been conducted in Mach 3 wind tunnel to investigate the behavior of supersonic vortices as they interact with a wedge surface placed in their passage. The experimental setup was arranged so that interactions resulted in a close encounter of the vortex core and the wedge leading edge. Spark shadow photographs of the flowfield along the pressure measurements on the wedge surface were used to study the interaction problem. In their most organized form, distortion of streamwise vortices upon interacting with the wedge was found to result in formation of symmetric detached shock fronts far upstream of the wedge leading edge followed by an apparent slip surface separating a subsonic region from a supersonic zone. Interaction experiments leading to substantial changes in the structure of vortices revealed that the supersonic vortex distortion has strong resemblances to the incompressible 'B-breakdown' reported in the literature. Experimental results also indicate that the interaction strongly depends on the vortex strength and vortex proximity to the wedge leading edge, and the generated flowfield was found to be highly unsteady. Interaction of concentrated streamwise vortices with the oblique shock formed over the wedge surface resulted in formation of a locally three-dimensional shock wave with a limited subsonic region downstream of the shock.

Kalkhoran, Iraj M.↗
DOE OSTI2016

INTERACTIONS OF THE INFRARED BUBBLE N4 WITH ITS SURROUNDINGS

The physical mechanisms that induce the transformation of a certain mass of gas in new stars are far from being well understood. Infrared bubbles associated with H ii regions have been considered to be good samples for investigating triggered star formation. In this paper we report on the investigation of the dust properties of the infrared bubble N4 around the H ii region G11.898+0.747, analyzing its interaction with its surroundings and star formation histories therein, with the aim of determining the possibility of star formation triggered by the expansion of the bubble. Using Herschel PACS and SPIRE images with a wide wavelength coverage, we reveal the dust properties over the entire bubble. Meanwhile, we are able to identify six dust clumps surrounding the bubble, with a mean size of 0.50 pc, temperature of about 22 K, mean column density of 1.7 × 10{sup 22} cm{sup −2}, mean volume density of about 4.4 × 10{sup 4} cm{sup −3}, and a mean mass of 320 M{sub ⊙}. In addition, from PAH emission seen at 8 μm, free–free emission detected at 20 cm, and a probability density function in special regions, we could identify clear signatures of the influence of the H ii region on the surroundings. There are hints of star formation, though further investigation is required to demonstrate that N4 is the triggering source.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1983

A search for nebulosity around G61-29

The apparent nebulosity in the region around the twin degenerate interacting binary G61-29 is studied. It has been assumed that this nebulosity represents material ejected from the system. However, a direct image of the region shows that the apparent nebulosity is actually a grouping of faint stars unrelated to the G61-29.

Stover, R. J.↗
DOE OSTI2015

Nonstationary oscillations in gyrotrons revisited

Development of gyrotrons requires careful understanding of different regimes of gyrotron oscillations. It is known that in the planes of the generalized gyrotron variables: cyclotron resonance mismatch and dimensionless current or cyclotron resonance mismatch and dimensionless interaction length complicated alternating sequences of regions of stationary, periodic, automodulation, and chaotic oscillations exist. In the past, these regions were investigated on the supposition that the transit time of electrons through the interaction space is much shorter than the cavity decay time. This assumption is valid for short and/or high diffraction quality resonators. However, in the case of long and/or low diffraction quality resonators, which are often utilized, this assumption is no longer valid. In such a case, a different mathematical formalism has to be used for studying nonstationary oscillations. One example of such a formalism is described in the present paper.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

System of Schwinger-Dyson equations and asymptotic behavior in the Euclidean region

A system of Schwinger-Dyson equations for the model of scalar-field interaction is studied in a deep Euclidean region. It is shown that there exists a critical coupling constant that separates the weak-coupling region characterized by the asymptotically free behavior and the strong-coupling region, where the asymptotic behavior of field propagators becomes ultralocal.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2020

Historical and Future Changes in Air Pollutants from CMIP6 Models

Poor air quality is currently responsible for large impacts on human health across the world. In addition, the air pollutants ozone (O3) and particulate matter less than 2.5 µm in diameter (PM2.5) are also radiatively active in the atmosphere and can influence Earth's climate. It is important to understand the effect of air quality and climate mitigation measures over the historical period and in different future scenarios to ascertain any impacts from air pollutants on both climate and human health. The Coupled Model Intercomparison Project Phase 6 (CMIP6) presents an opportunity to analyse the change in air pollutants simulated by the current generation of climate and Earth system models that include a representation of chemistry and aerosols (particulate matter). The shared socio-economic pathways (SSPs) used within CMIP6 encompass a wide range of trajectories in precursor emissions and climate change, allowing for an improved analysis of future changes to air pollutants. Firstly, we conduct an evaluation of the available CMIP6 models against surface observations of O3 and PM2.5. CMIP6 models consistently overestimate observed surface O3 concentrations across most regions and in most seasons by up to 16 ppb, with a large diversity in simulated values over Northern Hemisphere continental regions. Conversely, observed surface PM2.5 concentrations are consistently underestimated in CMIP6 models by up to 10 µg m−3, particularly for the Northern Hemisphere winter months, with the largest model diversity near natural emission source regions. The biases in CMIP6 models when compared to observations of O3 and PM2.5 are similar to those found in previous studies. Over the historical period (1850–2014) large increases in both surface O3 and PM2.5 are simulated by the CMIP6 models across all regions, particularly over the mid to late 20th century, when anthropogenic emissions increase markedly. Large regional historical changes are simulated for both pollutants across East and South Asia with an annual mean increase of up to 40 ppb for O3 and 12 µg m−3 for PM2.5. In future scenarios containing strong air quality and climate mitigation measures (ssp126), annual mean concentrations of air pollutants are substantially reduced across all regions by up to 15 ppb for O3 and 12 µg m−3 for PM2.5. However, for scenarios that encompass weak action on mitigating climate and reducing air pollutant emissions (ssp370), annual mean increases in both surface O3 (up 10 ppb) and PM2.5 (up to 8 µg m−3) are simulated across most regions, although, for regions like North America and Europe small reductions in PM2.5 are simulated due to the regional reduction in precursor emissions in this scenario. A comparison of simulated regional changes in both surface O3 and PM2.5 from individual CMIP6 models highlights important regional differences due to the simulated interaction of aerosols, chemistry, climate and natural emission sources within models. The projection of regional air pollutant concentrations from the latest climate and Earth system models used within CMIP6 shows that the particular future trajectory of climate and air quality mitigation measures could have important consequences for regional air quality, human health and near-term climate. Differences between individual models emphasise the importance of understanding how future Earth system feedbacks influence natural emission sources, e.g. response of biogenic emissions under climate change.

Air pollutants↗
DOE OSTI2018

Testosterone complex and non-steroidal ligands of human aromatase

Cytochrome P450 aromatase (AROM) catalyzes the biosynthesis of estrogen from androgen. Previously crystal structures of human AROM in complex with the substrate androstenedione, and inhibitors exemestane, as well as the newly designed steroidal compounds, have been reported. Here, in this paper, we report the first crystal structure of testosterone complex of human placental AROM. Testosterone binds at the androgen-specific heme distal pocket. The polar and hydrophobic interactions with the surrounding residues resemble the interactions observed for other ligands. The heme proximal region comprises the intermolecular interface in AROM, and also the putative interaction surface of its redox partner cytochrome P450 reductase. Unreported previously, the proximal region is characterized by a large surface cavity, unlike most known P450’s. Using five best X-ray data sets from androstenedione and testosterone complexes of AROM, we now unequivocally show the presence of an unexplained ligand electron density inside the proximal cavity. The density is interpreted as ordered five ethylene glycol units of polyethylene glycols used as a solvent for steroids and also in crystallization. Interestingly, polyethylene glycol exhibits weak inhibition of AROM enzyme activity in a time dependent manner. Besides its critical role in the redox partner coupling and electron transfer process, the proximal cavity possibly serves as the interaction site for other molecules that may have regulatory effects on AROM activity. In addition, the new data also reveal a previously unidentified water channel linking the active site to the lipid interface. The channel could be the predicted passage for water molecules involved in catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Distinctive Spatial Configuration of a Class Microwave Flaring Sources

We discuss a particular spatial configuration of a class of microwave flaring regions in which the primary energy release results from the interaction between emerging magnetic flux and an existing overlying region. Such events typically exhibit radio and X-ray emission at the main flare site (the site of interaction) and in addition radio emission at a remote site up to 10 (exp 05) km away in another active region. We have identified and studied more than a dozen microwave flares in this class, in order to arrive at some general conclusions on reconnection and energy release in such solar flares.

Kundu, Mukul R.↗
DOE OSTI2013

Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery

The 3' untranslated region (3' UTR) of hepatitis C virus (HCV) messenger RNA stimulates viral translation by an undetermined mechanism. We identified a high affinity interaction, conserved among different HCV genotypes, between the HCV 3' UTR and the host ribosome. The 3' UTR interacts with 40S ribosomal subunit proteins residing primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry and exit sites. This region partially overlaps with the site where the HCV internal ribosome entry site was found to bind, with the internal ribosome entry site-40S subunit interaction being dominant. Despite its ability to bind to 40S subunits independently, the HCV 3' UTR only stimulates translation in cis, without affecting the first round translation rate. These observations support a model in which the HCV 3' UTR retains ribosome complexes during translation termination to facilitate efficient initiation of subsequent rounds of translation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Complex Fracture Nucleation and Evolution with Nonlocal Elastodynamics

A mechanical model is introduced for predicting the initiation and evolution of complex fracture patterns without the need for a damage variable or law. The model, a continuum variant of Newton’s second law, uses integral rather than partial differential operators where the region of integration is over finite domain. The force interaction is derived from a novel nonconvex strain energy density function, resulting in a nonmonotonic material model. The resulting equation of motion is proved to be mathematically well-posed. The model has the capacity to simulate nucleation and growth of multiple, mutually interacting dynamic fractures. In the limit of zero region of integration, the model reproduces the classic Griffith model of brittle fracture. As a result, the simplicity of the formulation avoids the need for supplemental kinetic relations that dictate crack growth or the need for an explicit damage evolution law.

36 MATERIALS SCIENCE↗
NASA NTRS2000

Retinex Preprocessing for Improved Multi-Spectral Image Classification

The goal of multi-image classification is to identify and label "similar regions" within a scene. The ability to correctly classify a remotely sensed multi-image of a scene is affected by the ability of the classification process to adequately compensate for the effects of atmospheric variations and sensor anomalies. Better classification may be obtained if the multi-image is preprocessed before classification, so as to reduce the adverse effects of image formation. In this paper, we discuss the overall impact on multi-spectral image classification when the retinex image enhancement algorithm is used to preprocess multi-spectral images. The retinex is a multi-purpose image enhancement algorithm that performs dynamic range compression, reduces the dependence on lighting conditions, and generally enhances apparent spatial resolution. The retinex has been successfully applied to the enhancement of many different types of grayscale and color images. We show in this paper that retinex preprocessing improves the spatial structure of multi-spectral images and thus provides better within-class variations than would otherwise be obtained without the preprocessing. For a series of multi-spectral images obtained with diffuse and direct lighting, we show that without retinex preprocessing the class spectral signatures vary substantially with the lighting conditions. Whereas multi-dimensional clustering without preprocessing produced one-class homogeneous regions, the classification on the preprocessed images produced multi-class non-homogeneous regions. This lack of homogeneity is explained by the interaction between different agronomic treatments applied to the regions: the preprocessed images are closer to ground truth. The principle advantage that the retinex offers is that for different lighting conditions classifications derived from the retinex preprocessed images look remarkably "similar", and thus more consistent, whereas classifications derived from the original images, without preprocessing, are much less similar.

Thompson, B.↗