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At least 145 records · Page 8

Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System

Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes and cis -regulatory elements for further functional validations and root growth improvements in grasses.

59 BASIC BIOLOGICAL SCIENCES↗

Chromatographic Modeling of 1-Foot Detritiation Test Column Results for the Optimization of Regeneration Time

This report documents the methods and results of a modeling study on a series of data generated by 1-foot test columns for the Water Detritiation project. In order to compliment modeling work already in progress on this project, a purely empirical curve-fitting approach is used in this study to determine chromatographic performance indicators such as retention time, curve width, and the number of chromatographic stages. The data used in this study comes from four sets of chromatographic test separations performed in March through May of 2017 using 1-foot columns. All are using the same flow rates and temperature (room temperature, nominally 25 C°). The first set of data (referred to in this report as the Column 1 data) is a series of twelve breakthrough curve measurements. Prior to each of these twelve runs, the column was regenerated by flowing hydrogen gas through the column, for increasing amounts of time, ranging from 2 hours to 25 hours. The second set of data (referred to as the Column 2 data) is comprised of five measurements of breakthrough curves measured in similar fashion as the Column 1 data, across a range of regeneration times from 2 to 21 hours. The third set of data (referred to as the Purge data) is of three breakthrough curves, measured after a regeneration time of 8 hours, which takes place after a nitrogen purge of 15, 30, or 45 minutes. The fourth data set is a series of five breakthrough curve measurements using a 2 nd batch of stationary phase, taken after regeneration times ranging from 2 to 20 hours. The overall modeling approach is as follows. First, the data is pre-processed for formatting, artifact removal, and is normalized. The data is then fit by integrated versions of four common chromatographic models. The best model is chosen based on the predictive performance of the model, and chromatographic performance values are calculated based on the best model’s fit parameters. Each of these processes are detailed below.

42 ENGINEERING↗

The CCD/Transit Instrument (CTI) data-analysis system

The automated software system for archiving, analyzing, and interrogating data from the CCD/Transit Instrument (CTI) is described. The CTI collects up to 450 Mbytes of image-data each clear night in the form of a narrow strip of sky observed in two colors. The large data-volumes and the scientific aims of the project make it imperative that the data are analyzed within the 24-hour period following the observations. To this end a fully automatic and self evaluating software system has been developed. The data are collected from the telescope in real-time and then transported to Tucson for analysis. Verification is performed by visual inspection of random subsets of the data and obvious cosmic rays are detected and removed before permanent archival is made to the optical disc. The analysis phase is performed by a pair of linked algorithms, one operating on the absolute pixel-values and the other on the spatial derivative of the data. In this way both isolated and merged images are reliably detected in a single pass. In order to isolate the latter algorithm from the effects of noise spikes a 3x3 Hanning filter is applied to the raw data before the analysis is run. The algorithms reduce the input pixel-data to a database of measured parameters for each image which has been found. A contrast filter is applied in order to assign a detection-probability to each image and then x-y calibration and intensity calibration are performed using known reference stars in the strip. These are added to as necessary by secondary standards boot-strapped from the CTI data itself. The final stages involve merging the new data into the CTI Master-list and History-list and the automatic comparison of each new detection with a set of pre-defined templates in parameter-space to find interesting objects such as supernovae, quasars and variable stars. Each stage of the processing from verification to interesting image selection is performed under a data-logging system which both controls the pipe-lining of data through the system and records key performance monitor parameters which are built into the software. Furthermore, the data from each stage are stored in databases to facilitate evaluation, and all stages offer the facility to enter keyword-indexed free-format text into the data-logging system. In this way a large measure of certification is built into the system to provide the necessary confidence in the end results.

Cawson, M. G. M.↗

Boosted Dark Matter Search with the ICARUS Detector at the Gran Sasso Underground National Laboratory

The quest to discover dark matter is one of the most pressing topics in modern physics. Evidence of gravitational anomalies is present at different cosmological scales, spanning the stability and rotation of galaxies to the overall density profile of the entire observable Universe. Due to the discrepancy between the mass measured and the gravitational influence on the mass, if General Relativity is to correctly describe gravity at different scales, extra electromagnetically invisible matter termed dark matter must exist. In recent decades, many experiments have been performed to detect dark matter with masses that span many orders of magnitude, from Mass Compact Halo Objects (MACHOs) with masses several orders of magnitude that of our sun to very light particles on the order of $\sim\mu$eV. However, experiments have only been able to constrain the possible parameter space of dark matter models and, in general, probe dark matter models with single constituent dark matter like Weakly Interacting Massive Particles (WIMPs). In the Boosted Dark Matter (BDM) paradigm, there are four particles in the dark sector: $\chi_0$, $\chi_1$, $\chi_2$, and the dark photon $X$. WIMP-like properties are ascribed to $\chi_0$ to describe the physics of the gravitational anomalies, while relativistic components are assigned to $\chi_1$ and $\chi_2$. The inelastic boosted dark matter (iBDM) channel $\chi_1 e^-\rightarrow \chi_2 e^-\rightarrow \chi_1 Xe^-\rightarrow \chi_1 (e^+ e^- ) e^-$, where $\chi_2$ is an excited state of $\chi_1$, has a unique signature that is distinguishable from neutrino interactions, making neutrino experiments a viable search environment for BDM. Using data collected by the ICARUS collaboration with ICARUS T-600 Liquid Argon Time Projection Chamber (LArTPC) during its operation at the Gran Sasso Underground Laboratory (LNGS), the first-ever LArTPC dark matter search using the ICARUS detector is presented. With a total detector exposure of 0.13 kton$\cdot$year, a total of 4 iBDM candidate events were identified by several stages of data scanning. All were rejected due to defined selection criteria and a wire-by-wire $dE/dx$ evaluation, giving a null result. Exclusion plots at 90\%C.L. for the dark photon ($m_X$, $\epsilon$) parameter space for fixed ($m_0,m_1,m_2$) DM mass sets are presented, setting new limits on the dark photon visible decay parameter space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Daily evaluation of 26 precipitation datasets using Stage-IV gauge-radar data for the CONUS

New precipitation (P) datasets are released regularly, following innovations in weather forecasting models, satellite retrieval methods, and multi-source merging techniques. Using the conterminous US as a case study, we evaluated the performance of 26 gridded (sub-)daily P datasets to obtain insight into the merit of these innovations. The evaluation was performed at a daily timescale for the period 2008–2017 using the Kling–Gupta efficiency (KGE), a performance metric combining correlation, bias, and variability. As a reference, we used the high-resolution (4 km) Stage-IV gauge-radar P dataset. Among the three KGE components, the P datasets performed worst overall in terms of correlation (related to event identification). In terms of improving KGE scores for these datasets, improved P totals (affecting the bias score) and improved distribution of P intensity (affecting the variability score) are of secondary importance. Among the 11 gauge-corrected P datasets, the best overall performance was obtained by MSWEP V2.2, underscoring the importance of applying daily gauge corrections and accounting for gauge reporting times. Several uncorrected P datasets outperformed gauge-corrected ones. Among the 15 uncorrected P datasets, the best performance was obtained by the ERA5-HRES fourth-generation reanalysis, reflecting the significant advances in earth system modeling during the last decade. The (re)analyses generally performed better in winter than in summer, while the opposite was the case for the satellite-based datasets. IMERGHH V05 performed substantially better than TMPA-3B42RT V7, attributable to the many improvements implemented in the IMERG satellite P retrieval algorithm. IMERGHH V05 outperformed ERA5-HRES in regions dominated by convective storms, while the opposite was observed in regions of complex terrain. The ERA5-EDA ensemble average exhibited higher correlations than the ERA5-HRES deterministic run, highlighting the value of ensemble modeling. The WRF regional convection-permitting climate model showed considerably more accurate P totals over the mountainous west and performed best among the uncorrected datasets in terms of variability, suggesting there is merit in using high-resolution models to obtain climatological P statistics. Our findings provide some guidance to choose the most suitable P dataset for a particular application.

Hylke E. Beck↗

Identification and correction of temporal and spatial distortions in scanning transmission electron microscopy

Scanning transmission electron microscopy (STEM) has become the technique of choice for quantitative characterization of atomic structure of materials, where the minute displacements of atomic columns from high-symmetry positions can be used to map strain, polarization, octahedra tilts, and other physical and chemical order parameter fields. The latter can be used as inputs into mesoscopic and atomistic models, providing insight into the correlative relationships and generative physics of materials on the atomic level. However, these quantitative applications of STEM necessitate understanding the microscope induced image distortions and developing the pathways to compensate them both as part of a rapid calibration procedure for in situ imaging, and the post-experimental data analysis stage. Here, we explore the spatiotemporal structure of the microscopic distortions in STEM using multivariate analysis of the atomic trajectories in the image stacks. Based on the behavior of principal component analysis (PCA), we develop the Gaussian process (GP)-based regression method for quantification of the distortion function. The limitations of such an approach and possible strategies for implementation as a part of in-line data acquisition in STEM are discussed. Here, the analysis workflow is summarized in a Jupyter notebook that can be used to retrace the analysis and analyze the reader's data.

36 MATERIALS SCIENCE↗

From Science to e-Science to Semantic e-Science: A Heliosphysics Case Study

The past few years have witnessed unparalleled efforts to make scientific data web accessible. The Semantic Web has proven invaluable in this effort; however, much of the literature is devoted to system design, ontology creation, and trials and tribulations of current technologies. In order to fully develop the nascent field of Semantic e-Science we must also evaluate systems in real-world settings. We describe a case study within the field of Heliophysics and provide a comparison of the evolutionary stages of data discovery, from manual to semantically enable. We describe the socio-technical implications of moving toward automated and intelligent data discovery. In doing so, we highlight how this process enhances what is currently being done manually in various scientific disciplines. Our case study illustrates that Semantic e-Science is more than just semantic search. The integration of search with web services, relational databases, and other cyberinfrastructure is a central tenet of our case study and one that we believe has applicability as a generalized research area within Semantic e-Science. This case study illustrates a specific example of the benefits, and limitations, of semantically replicating data discovery. We show examples of significant reductions in time and effort enable by Semantic e-Science; yet, we argue that a "complete" solution requires integrating semantic search with other research areas such as data provenance and web services.

Narock, Thomas↗

Geologic Mapping of Vesta

We report on a preliminary global geologic map of Vesta, based on data from the Dawn spacecraft's High- Altitude Mapping Orbit (HAMO) and informed by Low-Altitude Mapping Orbit (LAMO) data. This map is part of an iterative mapping effort; the geologic map has been refined with each improvement in resolution. Vesta has a heavily-cratered surface, with large craters evident in numerous locations. The south pole is dominated by an impact structure identified before Dawn's arrival. Two large impact structures have been resolved: the younger, larger Rheasilvia structure, and the older, more degraded Veneneia structure. The surface is also characterized by a system of deep, globe-girdling equatorial troughs and ridges, as well as an older system of troughs and ridges to the north. Troughs and ridges are also evident cutting across, and spiraling arcuately from, the Rheasilvia central mound. However, no volcanic features have been unequivocally identified. Vesta can be divided very broadly into three terrains: heavily-cratered terrain; ridge-and-trough terrain (equatorial and northern); and terrain associated with the Rheasilvia crater. Localized features include bright and dark material and ejecta (some defined specifically by color); lobate deposits; and mass-wasting materials. No obvious volcanic features are evident. Stratigraphy of Vesta's geologic units suggests a history in which formation of a primary crust was followed by the formation of impact craters, including Veneneia and the associated Saturnalia Fossae unit. Formation of Rheasilvia followed, along with associated structural deformation that shaped the Divalia Fossae ridge-and-trough unit at the equator. Subsequent impacts and mass wasting events subdued impact craters, rims and portions of ridge-and-trough sets, and formed slumps and landslides, especially within crater floors and along crater rims and scarps. Subsequent to the formation of Rheasilvia, discontinuous low-albedo deposits formed or were emplaced; these lie stratigraphically above the equatorial ridges that likely were formed by Rheasilvia. The last features to be formed were craters with bright rays and other surface mantling deposits. Executed progressively throughout data acquisition, the iterative mapping process provided the team with geologic proto-units in a timely manner. However, interpretation of the resulting map was hampered by the necessity to provide the team with a standard nomenclature and symbology early in the process. With regard to mapping and interpreting units, the mapping process was hindered by the lack of calibrated mineralogic information. Topography and shadow played an important role in discriminating features and terrains, especially in the early stages of data acquisition.

Vesta↗

Radio Sources Associated with Intermediate X-ray Luminosity Objects in Merging Galaxy Systems

We present new, high-resolution 6, 3.6, and 2 cm radio images of a time-ordered sequence of merging galaxy systems. The new data have a resolution of less than 100pc and a sensitivity comparable to a few x Cas A. We detect compact radio sources in all systems, generally embedded in more diffuse radio emission at the longer wavelengths. Several of the compact radio sources are coincident with compact Intermediate-luminosity X-ray Objects (IXOs) in these systems, and many more are within the 3$/sigma$ Chandra position errors for other IXOs. The fraction of radio identifications and the nature of the radio sources changes as a function of merger stage. These data suggest that the IXOs are associated with complexes of supernova remnants, and therefore with star formation that has occurred within the last $/sim$10$circumflex7$ yr, but are not located in HII regions where copious star formation is occurring currently.

Neff, S. G.↗

Modeling of streamflow in a 30 km long reach spanning 5 years using OpenFOAM 5.x

Abstract. Developing accurate and efficient modeling techniques for streamflow at the tens-of-kilometers spatial scale and multi-year temporal scale is critical for evaluating and predicting the impact of climate- and human-induced discharge variations on river hydrodynamics. However, achieving such a goal is challenging because of limited surveys of streambed hydraulic roughness, uncertain boundary condition specifications, and high computational costs. We demonstrate that accurate and efficient three-dimensional (3-D) hydrodynamic modeling of natural rivers at 30 km and 5-year scales is feasible using the following three techniques within OpenFOAM, an open-source computational fluid dynamics platform: (1) generating a distributed hydraulic roughness field for the streambed by integrating water-stage observation data, a rough wall theory, and a local roughness optimization and adjustment strategy; (2) prescribing the boundary condition for the inflow and outflow by integrating precomputed results of a one-dimensional (1-D) hydraulic model with the 3-D model; and (3) reducing computational time using multiple parallel runs constrained by 1-D inflow and outflow boundary conditions. Streamflow modeling for a 30 km long reach in the Columbia River (CR) over 58 months can be achieved in less than 6 d using 1.1 million CPU hours. The mean error between the modeled and the observed water stages for our simulated CR reach ranges from −16 to 9 cm (equivalent to approximately ±7 % relative to the average water depth) at seven locations during most of the years between 2011 and 2019. We can reproduce the velocity distribution measured by the acoustic Doppler current profiler (ADCP). The correlation coefficients of the depth-averaged velocity between the model and ADCP measurements are in the range between 0.71 and 0.83 at 75 % of the survey cross sections. With the validated model, we further show that the relative importance of dynamic pressure versus hydrostatic pressure varies with discharge variations and topography heterogeneity. Given the model's high accuracy and computational efficiency, the model framework provides a generic approach to evaluate and predict the impacts of climate- and human-induced discharge variations on river hydrodynamics at tens-of-kilometers and decadal scales.

58 GEOSCIENCES↗

Countercurrent Actinide Lanthanide Separation Process (ALSEP) Demonstration Test with a Simulated PUREX Raffinate in Centrifugal Contactors on the Laboratory Scale

An Actinide Lanthanide Separation Process (ALSEP) for the separation of trivalent actinides (An(III)) from simulated raffinate solution was successfully demonstrated using a 32-stage 1 cm annular centrifugal contactor setup. The ALSEP solvent was composed of a mixture of 2-ethylhexylphosphonic acid mono-2-ethylhexyl ester (HEH[EHP]) and N,N,N',N'-tetra-(2-ethylhexyl)-diglycolamide (T2EHDGA) in n-dodecane. Flowsheet calculations and evaluation of the results were done using the Argonne’s Model for Universal Solvent Extraction (AMUSE) code using single-stage distribution data. The co-extraction of Zr(IV) and Pd(II) was prevented using CDTA (trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid) as a masking agent in the feed. For the scrubbing of co-extracted Mo; citrate-buffered acetohydroxamic acid was used. The separation of An(III) from the trivalent lanthanides (Ln(III)) was achieved using citrate-buffered diethylene-triamine-N,N,N',N",N"-pentaacetic acid (DTPA), and Ln(III) were efficiently back extracted using N,N,N',N'-tetraethyl-diglycolamide (TEDGA). A clean An(III) product was obtained with a recovery of 95% americium and curium. The Ln(III) were efficiently stripped; but the Ln(III) product contained 5% of the co-stripped An(III). The carryover of Am and Cm into the Ln(III) product is attributed to too few actinide stripping stages, which was constrained by the number of centrifugal contactors available. Improved separation would be achieved by increasing the number of An strip stages. The heavier lanthanides (Pr, Nd, Sm, Eu, and Gd) and yttrium were mainly routed to the Ln product, whereas the lighter lanthanides (La and Ce) were mostly routed to the raffinate.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Chemical Looping of Manganese to Synthesize Ammonia at Atmospheric Pressure: Sodium as Promoter

Abstract Affordable synthetic ammonia (NH 3 ) enables the production of nearly half of the food we eat and is emerging as a renewable energy carrier. Sodium‐promoted chemical looping NH 3 synthesis at atmospheric pressure using manganese (Mn) is here demonstrated. The looping process may be advantageous when inexpensive renewable hydrogen from electrolysis is available. Avoiding the high pressure of the Haber‐Bosch process by chemical looping using earth‐abundant materials may reduce capital cost, facilitate intermittent operation, and allow operation in geographic areas where infrastructure is less sophisticated. At this early stage, the data suggest that 0.28 m 3 of a 50 % porosity solid Mn bed may suffice to produce 100 kg NH 3 per day by chemical looping, with abundant opportunities for improvement.

Aframehr, Wrya Mohammadi↗

Efficient lattice QCD computation of radiative-leptonic-decay form factors at multiple positive and negative photon virtualities

In previous work [D. Giusti, Methods for high-precision determinations of radiative-leptonic decay form factors using lattice QCD, Phys. Rev. D 107, 074507 (2023)], we showed that form factors for radiative leptonic decays of pseudoscalar mesons can be determined efficiently and with high precision from lattice QCD using the “three-dimensional (3D) method,” in which three-point functions are computed for all values of the current insertion time and the time integral is performed at the data-analysis stage. Here, we demonstrate another benefit of the 3D method: the form factors can be extracted for any number of nonzero photon virtualities from the same three-point functions at no extra cost. We present results for the $D_s → ℓνγ*$ vector form factor as a function of photon energy and photon virtuality, for both positive and negative virtuality, for a single ensemble with 340 MeV pion mass and 0.11 fm lattice spacing. In our analysis, we separately consider the two different time orderings and the different quark flavors in the electromagnetic current. We discuss in detail the behavior of the unwanted exponentials contributing to the three-point functions, as well as the choice of fit models and fit ranges used to remove them for various values of the virtuality. While positive photon virtuality is relevant for decays to multiple charged leptons, negative photon virtuality suppresses soft contributions and is of interest in QCD-factorization studies of the form factors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ti-6Al-4V to over 1.2 TPa: Shock Hugoniot experiments, ab initio calculations, and a broad-range multiphase equation of state

Titanium alloys are used in a large array of applications. In this work we focus our attention on the most used alloy, Ti-6Al-4V (Ti64), which has excellent mechanical and biocompatibility properties with applications in aerospace, defense, biomedical, and other fields. Here we present high-fidelity experimental shock compression data measured on Sandia’s Z machine. We extend the principal shock Hugoniot for Ti64 to more than threefold compression, up to over 1.2 TPa. We use the data to validate our ab initio molecular dynamics simulations and to develop a highly reliable, multiphase equation of state (EOS) for Ti64, spanning a broad range of temperature and pressures. The first-principles simulations show very good agreement with Z data and with previous three-stage gas gun data from Sandia’s STAR facility. The resulting principal Hugoniot and the broad-range EOS and phase diagram up to 10 TPa and 10 5 K are suitable for use in shock experiments and in hydrodynamic simulations. The high-precision experimental results and high-fidelity simulations demonstrate that the Hugoniot of the Ti64 alloy is stiffer than that of pure Ti and reveal that Ti64 melts on the Hugoniot at a significantly lower pressure and temperature than previously modeled.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Towards Diverse and Representative Global Pretraining Datasets for Remote Sensing Foundation Models

The design of a pretraining dataset is emerging as a critical component for the generality of foundation models. In the remote sensing realm, large volumes of imagery and benchmark datasets exist that can be leveraged to pretrain foundation models, however using this imagery in absence of a well-crafted sampling strategy is inefficient and has the potential to create biased and less generalizable models. Here, we provide a discussion and vision for the curation and assessment of pretraining datasets for remote sensing geospatial foundation models. We highlight the importance of geographic, temporal, and image acquisition diversity and review possible strategies to enable such diversity at global scale. In addition to these characteristics, support for various spatial-temporal pretext tasks within the dataset is also critical. Ultimately, our primary objective is to place emphasis on and draw attention to the data curation stage of the foundation model development pipeline. By doing so, we think it is possible to reduce biases of geospatial foundation models, as well as enable broader generalization to downstream remote sensing tasks and applications.

Arndt, Jacob↗