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At least 163 records · Page 9

Data for Transposon Signatures of Allopolyploid Genome Evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

Genomics↗

Unstructured Grid Adaptation: Status, Potential Impacts, and Recommended Investments Toward CFD Vision 2030

Unstructured grid adaptation is a powerful tool to control discretization error for Computational Fluid Dynamics (CFD). It has enabled key increases in the accuracy, automation, and capacity of some fluid simulation applications. Slotnick et al. provides a number of case studies in the CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences to illustrate the current state of CFD capability and capacity. The authors forecast the potential impact of emerging High Performance Computing (HPC) environments forecast in the year 2030 and identify that mesh generation and adaptivity continue to be significant bottlenecks in the CFD work flow. These bottlenecks may persist because very little government investment has been targeted in these areas. To motivate investment, the impacts of improved grid adaptation technologies are identified. The CFD Vision 2030 Study roadmap and anticipated capabilities in complementary disciplines are quoted to provide context for the progress made in grid adaptation in the past fifteen years, current status, and a forecast for the next fifteen years with recommended investments. These investments are specific to mesh adaptation and impact other aspects of the CFD process. Finally, a strategy is identified to diffuse grid adaptation technology into production CFD work flows.

Park, Michael A.↗

Large electron-phonon drag asymmetry and reverse heat flow in the topological semimetal θ-TaN

A broad range of unusual transport behaviors have been discovered in topological semimetals. However, to date, the effect on the thermopower from intrinsic momentum exchange between electrons and phonons has received little attention. Here we report that huge electron-phonon drag enhancements of the thermopower of the to- pological semimetal, θ-phase tantalum nitride (θ-TaN), can occur that persist even up to room temperature. Our first principles calculations also identify a surprising asymmetry in which the large drag-enhanced thermopowers found slightly above the material’s chemical potential disappear just below it. The large thermopower en- hancements result from anomalous drag contributions from high frequency acoustic phonons with unusually small decay rates. The apparent vanishing drag results from (i) the emergence of an exceptionally high electrical conductivity promoted by the steep linear electronic dispersions extending below one of the topological nodal points; (ii) a remarkable cancellation in which momentum transferred from a charge current creates oppositely directed phonon heat currents of nearly equal magnitude, thereby masking the drag contributions. This extraordinary transport behavior is a consequence of an unusual interplay between intrinsic electron and phonon material properties in θ-TaN. Overall, our work gives new insights into the fundamental physical properties of coupled electron-phonon systems and motivates further exploration of drag effects in semimetals.

36 MATERIALS SCIENCE↗

Thermally Insulating, Thermal Shock Resistant Calcium Aluminate Phosphate Cement Composites for Reservoir Thermal Energy Storage

This paper presents the use of hydrophobic silica aerogel (HSA) and hydrophilic fly ash cenosphere (FCS) aggregates for improvements in the thermal insulating and mechanical properties of 100- and 250 °C-autoclaved calcium aluminate phosphate (CaP) cement composites reinforced with micro-glass (MGF) and micro-carbon (MCF) fibers for deployment in medium- (100 °C) and high-temperature (250 °C) reservoir thermal energy storage systems. The following six factors were assessed: (1) Hydrothermal stability of HSA; (2) Pozzolanic activity of the two aggregates and MGF in an alkali cement environment; (3) CaP cement slurry heat release during hydration and chemical reactions; (4) Composite phase compositions and phase transitions; (5) Mechanical behavior; (6) Thermal shock (TS) resistance at temperature gradients of 150 and 225 °C. The results showed that hydrophobic trimethylsilyl groups in trimethylsiloxy-linked silica aerogel structure were susceptible to hydrothermal degradation at 250 °C. This degradation was followed by pozzolanic reactions (PR) of HSA, its dissolution, and the formation of a porous microstructure that caused a major loss in the compressive strength of the composites at 250 °C. The pozzolanic activities of FCS and MGF were moderate, and they offered improved interfacial bonding at cement-FCS and cement-MGF joints through a bridging effect by PR products. Despite the PR of MGF, both MGF and MCF played an essential role in minimizing the considerable losses in compressive strength, particularly in toughness, engendered by incorporating weak HSA. As a result, a FCS/HSA ratio of 90/10 in the CaP composite system was identified as the most effective hybrid insulating aggregate composition, with a persistent compressive strength of more than 7 MPa after three TS tests at a 150 °C temperature gradient. This composite displayed thermal conductivity of 0.28 and 0.35 W/mK after TS with 225 and 150 °C thermal gradients, respectively. These values, below the TC of water (TC water = 0.6 W/mK), were measured under water-saturated conditions for applications in underground reservoirs. However, considering the hydrothermal disintegration of HSA at 250 °C, these CaP composites have potential applications for use in thermally insulating, thermal shock-resistant well cement in a mid-temperature range (100 to 175 °C) reservoir thermal energy storage system.

58 GEOSCIENCES↗

Comment on the extinct paradox

The extinction paradox is a contradiction between geometrical optics results which predict that at high frequencies the scattering cross section of an object should equal its geometrical cross section and rigorous scattering theory which shows that at high frequencies the scattering cross section approaches twice the geometrical cross section of the object. Confusion about the reason for this paradox persists today even though the nature of the paradox was correctly identified many years ago by Brillouin. The resolution of the paradox is restated and illustrated with an example, and then the implications to the interpretation of scattering cross sections are identified.

Levine, D. M.↗

A Reevaluation of Airborne HO(x) Observations from NASA Field Campaigns

In-situ observations of tropospheric HO(x) (OH and HO2) obtained during four NASA airborne campaigns (SUCCESS, SONEX, PEM-Tropics B and TRACE-P) are reevaluated using the NASA Langley time-dependent photochemical box model. Special attention is given to previously diagnosed discrepancies between observed and predicted HO2 which increase with higher NO(x) levels and at high solar zenith angles. This analysis shows that much of the model discrepancy at high NO(x) during SUCCESS can be attributed to modeling observations at time-scales too long to capture the nonlinearity of HO(x) chemistry under highly variable conditions for NO(x). Discrepancies at high NO(x) during SONEX can be moderated to a large extent by complete use of all available precursor observations. Differences in kinetic rate coefficients and photolysis frequencies available for previous studies versus current recommendations also explain some of the disparity. Each of these causes is shown to exert greater influence with increasing NO(x) due to both the chemical nonlinearity between HO(x) and NO(x) and the increased sensitivity of HO(x) to changes in sources at high NO(x). In contrast, discrepancies at high solar zenith angles will persist until an adequate nighttime source of HO(x) can be identified. It is important to note that this analysis falls short of fully eliminating the issue of discrepancies between observed and predicted HO(x) for high NO(x) environments. These discrepancies are not resolved with the above causes in other data sets from ground-based field studies. Nevertheless, these results highlight important considerations in the application of box models to observationally based predictions of HO(x) radicals.

Olson, Jennifer↗

Persistence Mapping Using EUV Solar Imager Data

We describe a simple image processing technique that is useful for the visualization and depiction of gradually evolving or intermittent structures in solar physics extreme-ultraviolet imagery. The technique is an application of image segmentation, which we call "Persistence Mapping," to isolate extreme values in a data set, and is particularly useful for the problem of capturing phenomena that are evolving in both space and time. While integration or "time-lapse" imaging uses the full sample (of size N ), Persistence Mapping rejects (N - 1)/N of the data set and identifies the most relevant 1/N values using the following rule: if a pixel reaches an extreme value, it retains that value until that value is exceeded. The simplest examples isolate minima and maxima, but any quantile or statistic can be used. This paper demonstrates how the technique has been used to extract the dynamics in long-term evolution of comet tails, erupting material, and EUV dimming regions.

Thompson, B. J.↗

Carbon nanotube biocompatibility in plants is determined by their surface chemistry

Abstract Background Agriculture faces significant global challenges including climate change and an increasing food demand due to a growing population. Addressing these challenges will require the adoption of transformative innovations into biotechnology practice, such as nanotechnology. Recently, nanomaterials have emerged as unmatched tools for their use as biosensors, or as biomolecule delivery vehicles. Despite their increasingly prolific use, plant-nanomaterial interactions remain poorly characterized, drawing into question the breadth of their utility and their broader environmental compatibility. Results Herein, we characterize the response of Arabidopsis thaliana to single walled carbon nanotube (SWNT) exposure with two different surface chemistries commonly used for biosensing and nucleic acid delivery: oligonucleotide adsorbed-pristine SWNTs, and polyethyleneimine-SWNTs loaded with plasmid DNA (PEI-SWNTs), both introduced by leaf infiltration. We observed that pristine SWNTs elicit a mild stress response almost undistinguishable from the infiltration process, indicating that these nanomaterials are well-tolerated by the plant. However, PEI-SWNTs induce a much larger transcriptional reprogramming that involves stress, immunity, and senescence responses. PEI-SWNT-induced transcriptional profile is very similar to that of mutant plants displaying a constitutive immune response or treated with stress-priming agrochemicals. We selected molecular markers from our transcriptomic analysis and identified PEI as the main cause of this adverse reaction. We show that PEI-SWNT response is concentration-dependent and, when persistent over time, leads to cell death. We probed a panel of PEI variant-functionalized SWNTs across two plant species and identified biocompatible SWNT surface functionalizations. Conclusions While SWNTs themselves are well tolerated by plants, SWNTs surface-functionalized with positively charged polymers become toxic and produce cell death. We use molecular markers to identify more biocompatible SWNT formulations. Our results highlight the importance of nanoparticle surface chemistry on their biocompatibility and will facilitate the use of functionalized nanomaterials for agricultural improvement. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative and interpretable order parameters for phase transitions from persistent homology

Here, we apply modern methods in computational topology to the task of discovering and characterizing phase transitions. As illustrations, we apply our method to four two-dimensional lattice spin models: the Ising, square ice, XY, and fully frustrated XY models. In particular, we use persistent homology, which computes the births and deaths of individual topological features as a coarse-graining scale or sublevel threshold is increased, to summarize multiscale and high-point correlations in a spin configuration. We employ vector representations of this information called persistence images to formulate and perform the statistical task of distinguishing phases. For the models we consider, a simple logistic regression on these images is sufficient to identify the phase transition. Interpretable order parameters are then read from the weights of the regression. This method suffices to identify magnetization, frustration, and vortex-antivortex structure as relevant features for phase transitions in our models. We also define “persistence” critical exponents and study how they are related to those critical exponents usually considered.

36 MATERIALS SCIENCE↗

One-Dimensional Electron Gas Confined along Nanowrinkles in a Unidirectional Charge Density Wave Material

Two-dimensional (2D) materials inherently exhibit instabilities. Structurally, this may lead to modulations along the third dimension, e.g., wrinkles. Electronically, 2D instabilities can manifest themselves as charge density waves (CDWs). Although wrinkles can alter anisotropic electronic structures susceptible to forming CDWs, less is known about their impact on broken-symmetry ground states. Here, in this study, using scanning tunneling microscopy and spectroscopy, we investigate the CDW states on the wrinkled surface of DyTe 3 . We identify elongated, parallel nanoscale wrinkles stabilized by ribbon-shaped defects. Interestingly, the CDW order persists across the nanowrinkles with a gradual phase shift but is locally suppressed near the defects, where phase windings occur. In addition, these defects induce quantum confinement effects along the nanowrinkles, indicating the presence of one-dimensional metallic states with hole- like dispersion, while angle-resolved photoemission spectroscopy identifies a gap along the wrinkle direction. We ascribe this discrepancy to strain-induced changes in the Fermi surface, which lead to the closure of the gap at the sites of the nanowrinkles. Taken together, our results underscore the complex interplay between structural features and Fermi surface topology, allowing for the deliberate manipulation of quantum states in strongly correlated systems via local crystal deformations.

nanowrinkles↗

Measuring Young Stars in Space and Time. II. The Pre-main-sequence Stellar Content of N44

The Hubble Space Telescope survey Measuring Young Stars in Space and Time (MYSST) entails some of the deepest photometric observations of extragalactic star formation, capturing even the lowest-mass stars of the active star-forming complex N44 in the Large Magellanic Cloud. We employ the new MYSST stellar catalog to identify and characterize the content of young pre-main-sequence (PMS) stars across N44 and analyze the PMS clustering structure. To distinguish PMS stars from more evolved line of sight contaminants, a non-trivial task due to several effects that alter photometry, we utilize a machine-learning classification approach. This consists of training a support vector machine (SVM) and a random forest (RF) on a carefully selected subset of the MYSST data and categorize all observed stars as PMS or non-PMS. Combining SVM and RF predictions to retrieve the most robust set of PMS sources, we find ∼26,700 candidates with a PMS probability above 95% across N44. Employing a clustering approach based on a nearest neighbor surface density estimate, we identify 16 prominent PMS structures at 1σ significance above the mean density with sub-clusters persisting up to and beyond 3σ significance. The most active star-forming center, located at the western edge of N44's bubble, is a subcluster with an effective radius of ∼5.6 pc entailing more than 1100 PMS candidates. Furthermore, we confirm that almost all identified clusters coincide with known H ii regions and are close to or harbor massive young O stars or YSOs previously discovered by MUSE and Spitzer observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Cryostatless high temperature supercurrent bearings for rocket engine turbopumps

The rocket engine systems examined include SSME, ALS, and CTV systems. The liquid hydrogen turbopumps in the SSME and ALS vehicle systems are identified as potentially attractive candidates for development of Supercurrent Bearings since the temperatures around the bearings is about 30 K, which is considerably lower than the 95 K transition temperatures of HTS materials. At these temperatures, the current HTS materials are shown to be capable of developing significantly higher current densities. This higher current density capability makes the development of supercurrent bearings for rocket engines an attractive proposition. These supercurrent bearings are also shown to offer significant advantages over conventional bearings used in rocket engines. They can increase the life and reliability over rolling element bearings because of noncontact operation. They offer lower power loss over conventional fluid film bearings. Compared to conventional magnetic bearings, they can reduce the weight of controllers significantly, and require lower power because of the use of persistent currents. In addition, four technology areas that require further attention have been identified. These are: Supercurrent Bearing Conceptual Design Verification; HTS Magnet Fabrication and Testing; Cryosensors and Controller Development; and Rocket Engine Environmental Compatibility Testing.

Rao, Dantam K.↗

Quantification of Brønsted Acid Sites in Zeolites by Water Desorption Thermogravimetry

The many studies that have been conducted on water adsorption on zeolites were carried out in “adsorption” mode, from adsorption isotherms or single-point measurements, with the samples being first degassed at high temperature, and then exposed to water vapor at variable partial pressure. Here, we report Thermogravimetric Analysis (TGA) studies of HZSM-5 saturated with water at room temperature, thus studying water adsorption in “desorption” mode. In this work, TGA was used to ascertain the amount of water remaining as a function of the pretreatment temperature, and to identify the temperature at which one water molecule per framework Al atom persists. Solid-state 1H NMR spectroscopy, combined with molecular modeling, provided evidence for water molecules hydrogen bonded to Brønsted acid sites and formation of oxonium species for distinct water per framework Al atom. TGA is shown to be a simple and expeditious technique to measure the number of Brønsted acid sites in aluminosilicate zeolites, with advantages over the traditional methods of IR or TPD of dangerous adsorbed ammonia or pyridine. TGA of adsorbed water also provides information on the water clusters formed at the acid sites of HZSM-5, which are proportional to the number of acid sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Changes and Reversibility Upon Deintercalation of Li from LiCoPO 4 Derivatives

In an effort to improve the cycle life and rate capability of olivine LiCoPO 4 , Cr, Fe, and Si were added to produce nominal Li 1.025 Co 0.84 Fe 0.10 Cr 0.05 Si 0.01 (PO 4 ) 1.025 . This cathode material has an energy density comparable to LiCoPO 4 , with markedly improved electrochemical performance. Here, we apply operando X-ray diffraction to gain an understanding of the crystallographic delithiation mechanism of this new substituted electrode material, compared to both LiCo 0.75 Fe 0.25 PO 4 and LiCo 0.75 Fe 0.25 PO 4 . Throughout charging, the extent of solid-solution domains was significantly increased in Li 1.025 Co 0.84 Fe 0.10 Cr 0.05 Si 0.01 (PO 4 ) 1.025 and LiCo 0.75 Fe 0.25 PO 4 compared to LiCoPO 4 . These domains reduce the mechanical strain during electrode function, providing a clear explanation for the high durability with Co substitution. Li 1.025 Co 0.84 Fe 0.10 Cr 0.05 Si 0.01 (PO 4 ) 1.025 operated at notably higher average potential than LiCo 0.75 Fe 0.25 PO 4 , which would increase the energy density of the cell. Ex situ measurements reveal the persistence of structural irreversibilities in the substituted phase after the first cycle, identifying avenues for further improvement in durability. Overall, this finding sheds light on the strategies for judicious cation substitution in LiCoPO 4 electrodes to maximize the cycle life while preserving high energy density, especially compared to LiFePO 4 .

25 ENERGY STORAGE↗

Impact of neutrino flavor conversions on neutron star merger dynamics, ejecta, nucleosynthesis, and multimessenger signals

We present numerical relativity simulations of binary neutron star mergers incorporating neutrino flavor transformations triggered by fast flavor instability, quantum many-body effects, or potential beyond standard model physics. In both long-lived and short-lived remnant scenarios, neutrino flavor conversions modify species-dependent neutrino luminosities and mean energies, and drive the matter towards more neutron rich conditions. They produce up to more neutron rich ejecta and significantly boost the r-process yields, especially in low-density, near-equatorial outflows. We identify regions unstable to fast flavor instabilities and find that these instabilities persist despite flavor conversions. We further test the sensitivity to the equilibration timescale of the flavor conversions, finding that slower flavor conversions can interact with thermodynamic equilibration, and increase the neutron richness of the ejecta. Flavor conversions may also contribute to stronger gravitational wave and neutrino emissions, pointing to a correlation between neutrino transport and merger dynamics. Furthermore, these results highlight the potential impact of flavor conversions while motivating future work to improve on theoretical understanding of flavor instabilities in global simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

Patterns of helicity in solar active regions

Using 46 vector magnetograms from the Stokes Polarimeter of Mees Solar Observatory (MSO), we studied patterns of local helicity in three diverse solar active regions. From these magnetograms we computed maps of the local helicity parameter alpha = J(sub z)/B(sub z). Although such maps are noisy, we found patterns at the level approximately 2 to 3 sigma(sub J(sub z)), which repeat in successive magnetograms for up to several days. Typically, the alpha maps of any given active region contain identifiable patches with both positive and negative values of alpha. Even within a single sunspot complex, several such alpha patches can often be seen. We followed 68 alpha patches that could be identified on at least two successive alpha maps. We found that the persistence fraction of such patches decrease exponentially, with a characteristic time approximately 27 hr.

Pevtsov, Alexei A.↗

Essential SpaceWire Hardware Capabilities for a Robust Network

The Geostationary Operational Environmental Satellite R-Series Program (GOES-R) mission is a joint program between National Oceanic & Atmospheric Administration (NOAA) and National Aeronautics & Space Administration (NASA) Goddard Space Flight Center (GSFC). GOES-R project selected SpaceWire as the best solution to satisfy the desire for simple and flexible instrument to spacecraft command and telemetry communications. GOES-R development and integration is complete and the observatory is scheduled for launch October 2016. The spacecraft design was required to support redundant SpaceWire links for each instrument side, as well as to route the fewest number of connections through a Slip Ring Assembly necessary to support Solar pointing instruments. The final design utilized two different router designs. The SpaceWire standard alone does not ensure the most practical or reliable network. On GOES-R a few key hardware capabilities were identified that merit serious consideration for future designs. Primarily these capabilities address persistent port stalls and the prevention of receive buffer overflows. Workarounds were necessary to overcome shortcomings that could be avoided in future designs if they utilize the capabilities, discussed in this paper, above and beyond the requirements of the SpaceWire standard.

SpaceWire↗

Diabatic Eddy Forcing Increases Persistence and Opposes Propagation of the Southern Annular Mode in MERRA-2

Abstract As a dominant mode of jet variability on subseasonal time scales, the Southern Annular Mode (SAM) provides a window into how the atmosphere can produce internal oscillations on longer-than-synoptic time scales. While SAM’s existence can be explained by dry, purely barotropic theories, the time scale for its persistence and propagation is set by a lagged interaction between barotropic and baroclinic mechanisms, making the exact physical mechanisms challenging to identify and to simulate, even in latest generation models. By partitioning the eddy momentum flux convergence in MERRA-2 using an eddy–mean flow interaction framework, we demonstrate that diabatic processes (condensation and radiative heating) are the main contributors to SAM’s persistence in its stationary regime, as well as the key for preventing propagation in this regime. In SAM’s propagating regime, baroclinic and diabatic feedbacks also dominate the eddy–jet feedback. However, propagation is initiated by barotropic shifts in upper-level wave breaking and then sustained by a baroclinic response, leading to a roughly 60-day oscillation period. This barotropic propagation mechanism has been identified in dry, idealized models, but here we show evidence of this mechanism for the first time in reanalysis. The diabatic feedbacks on SAM are consistent with modulation of the storm-track latitude by SAM, altering the emission temperature and cloud cover over individual waves. Therefore, future attempts to improve the SAM time scale in models should focus on the storm-track location, as well as the roles of the cloud and moisture parameterizations. Significance Statement As they circumnavigate the planet, the tropospheric jet streams slowly drift north and south over about 30 days, longer than the normal limit of weather prediction. Understanding the source of this “memory” could improve our knowledge of how the atmosphere organizes itself and our ability to make long-term forecasts. Current theories have identified several possible internal atmospheric interactions responsible for this memory. Yet most of the theories for understanding the jets’ behavior assume that this behavior is only weakly influenced by atmospheric water vapor. We show that this assumption is not enough to understand jet persistence. Instead, clouds and precipitation are more important contributors in reanalysis data than internal “dry” mechanisms to this memory of the Southern Hemisphere jet.

54 ENVIRONMENTAL SCIENCES↗