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DOE OSTI2022

Reconstructing Sediment Transport by Migrating Bedforms in the Physical and Spectral Domains

Abstract Characteristics of migrating bedforms are often used to indirectly quantify the volumetric sediment flux in fluvial environments. Yet, the range of bedform scales that actually contribute to the sediment transport remains elusive. We performed a series of experiments under four different transport stages in a large‐scale sediment recirculating flume. Three independent variables were simultaneously measured: 2D spatio‐temporal bathymetry z ( x , y , t ), high frequency temporal bed elevations at fixed locations z ( t ), and temporal change of the sediment weight carried by migrating bedforms near the channel outlet q m ( t ). Both the measured spatio‐temporal bed evolution and the sediment discharge were analyzed using bedform tracking and Fourier decomposition. We found that small, rapidly migrating secondary bedforms emerge as a main contributor to the sediment transport and to the propagation of larger primary bedforms that slowly migrate underneath. This critical information allows us to define the range of transport‐contributing scales that must be accounted for in a scale‐dependent sediment mass flux model to enable the estimation of the total bedform transport from bed elevation time series.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Bioreactor Development for CO2-Based In Situ Resource Utilization Manufacturing

Sustainable long-duration manned missions on both the Moon and Mars will require in situ resource utilization (ISRU). Carbon dioxide (CO2) has great potential as a harvestable resource, making up 95% of the atmosphere on Mars and being produced as respiratory waste in spacecraft and future planetary habitats. Through ISRU, biomanufacturing has the capability to produce a near limitless array of products from local space resources, which include pharmaceuticals, bioplastics, chemical feedstocks, and industrial enzymes. Here, a CO2-based ISRU recombinant protein bioreactor and associated biomanufacturing organisms were designed to produce a highly stable carbonic anhydrase (CA). Initial work characterized candidate organisms for growth on acetate and formic acid, carbon substrates that can be synthesized via electrochemical conversion of CO2. To improve growth on the CO2 producing substrate formic acid and for direct integration of ISRU CO2, a synthetic Calvin-Benson-Bassam cycle was designed for use in Cyberlindnera jadinii and Escherichia coli. Genetic modifications in E. coli will be facilitated by a tailored CRISPR/Cas9 and λ red recombineering two-vector system. For expression of CA, a blue light regulated T7 promoter was employed for dynamic and small molecule free induction. Efficient bioproduction through a fed-batch exponential feeding strategy was determined via mass balance calculations from ISRU substrates to biomass and CA yield. Flux balance analysis was used to model ISRU substrate metabolism and metabolic pathway engineering in candidate organisms under cultivation strategy conditions for both metabolism reconstruction and pathway design optimization. Finally, a small-scale, disposable bag bioreactor concept for use in the NASA Bioculture System infrastructure was designed to enable CO2-based CA production in reduced-gravity environments.

Biomanufacturing, Pathway Engineering, Flux Balanc↗

DOE OSTI2022

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2009

Hard X-Ray Flare Source Sizes Measured with the Ramaty High Energy Solar Spectroscopic Imager

Ramaty High Energy Solar Spectroscopic Imager (RHESSI) observations of 18 double hard X-ray sources seen at energies above 25 keV are analyzed to determine the spatial extent of the most compact structures evident in each case. The following four image reconstruction algorithms were used: Clean, Pixon, and two routines using visibilities maximum entropy and forward fit (VFF). All have been adapted for this study to optimize their ability to provide reliable estimates of the sizes of the more compact sources. The source fluxes, sizes, and morphologies obtained with each method are cross-correlated and the similarities and disagreements are discussed. The full width at half-maximum (FWHM) of the major axes of the sources with assumed elliptical Gaussian shapes are generally well correlated between the four image reconstruction routines and vary between the RHESSI resolution limit of approximately 2" up to approximately 20" with most below 10". The FWHM of the minor axes are generally at or just above the RHESSI limit and hence should be considered as unresolved in most cases. The orientation angles of the elliptical sources are also well correlated. These results suggest that the elongated sources are generally aligned along a flare ribbon with the minor axis perpendicular to the ribbon. This is verified for the one flare in our list with coincident Transition Region and Coronal Explorer (TRACE) images. There is evidence for significant extra flux in many of the flares in addition to the two identified compact sources, thus rendering the VFF assumption of just two Gaussians inadequate. A more realistic approximation in many cases would be of two line sources with unresolved widths. Recommendations are given for optimizing the RHESSI imaging reconstruction process to ensure that the finest possible details of the source morphology become evident and that reliable estimates can be made of the source dimensions.

Dennis, Brian R.↗

DOE OSTI2022

DUNE atmospheric neutrinos: Earth tomography

In this paper we show that the DUNE experiment can measure the Earth’s density profile by analyzing atmospheric neutrino oscillations. The crucial feature that enables such measurement is the detailed event reconstruction capability of liquid argon time projection chambers. This allows for studying the sub-GeV atmospheric neutrino component, which bears a rich oscillation phenomenology, strongly dependent on the matter potential sourced by the Earth. We provide a pedagogical discussion of the MSW and parametric resonances and their role in measuring the core and mantle densities. By performing a detailed simulation, accounting for particle reconstruction at DUNE, nuclear physics effects relevant to neutrino-argon interactions and several uncertainties on the atmospheric neutrino flux, we manage to obtain a robust estimate of DUNE’s sensitivity to the Earth matter profile. We find that DUNE can measure the total mass of the Earth at 9.3% precision with an exposure of 400 kton-year. By accounting for previous measurements of the total mass and moment of inertia of the Earth, the core, lower mantle and upper mantle densities can be determined with 9%, 14% and 22% precision, respectively, for the same exposure. Finally, for a low exposure run of 60 kton-year, which would correspond to two far detectors running for three years, we have found that the core density could be measured by DUNE at ∼ 30% precision.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (k app ) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Altogether, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Uncertainty in land carbon budget simulated by terrestrial biosphere models: the role of atmospheric forcing

Global estimates of the land carbon sink are often based on simulations by terrestrial biosphere models (TBMs). The use of a large number of models that differ in their underlying hypotheses, structure and parameters is one way to assess the uncertainty in the historical land carbon sink. Here we show that the atmospheric forcing datasets used to drive these TBMs represent a significant source of uncertainty that is currently not systematically accounted for in land carbon cycle evaluations. We present results from three TBMs each forced with three different historical atmospheric forcing reconstructions over the period 1850–2015. We perform an analysis of variance to quantify the relative uncertainty in carbon fluxes arising from the models themselves, atmospheric forcing, and model-forcing interactions. We find that atmospheric forcing in this set of simulations plays a dominant role on uncertainties in global gross primary productivity (GPP) (75% of variability) and autotrophic respiration (90%), and a significant but reduced role on net primary productivity and heterotrophic respiration (30%). Atmospheric forcing is the dominant driver (52%) of variability for the net ecosystem exchange flux, defined as the difference between GPP and respiration (both autotrophic and heterotrophic respiration). In contrast, for wildfire-driven carbon emissions model uncertainties dominate and, as a result, model uncertainties dominate for net ecosystem productivity. At regional scales, the contribution of atmospheric forcing to uncertainty shows a very heterogeneous pattern and is smaller on average than at the global scale. We find that this difference in the relative importance of forcing uncertainty between global and regional scales is related to large differences in regional model flux estimates, which partially offset each other when integrated globally, while the flux differences driven by forcing are mainly consistent across the world and therefore add up to a larger fractional contribution to global uncertainty.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

maranasgroup/scRBA

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (kapp) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Overall, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.

Dinh, Hoang↗

NASA NTRS2010

Heat Flux and Wall Temperature Estimates for the NASA Langley HIFiRE Direct Connect Rig

An objective of the Hypersonic International Flight Research Experimentation (HIFiRE) Program Flight 2 is to provide validation data for high enthalpy scramjet prediction tools through a single flight test and accompanying ground tests of the HIFiRE Direct Connect Rig (HDCR) tested in the NASA LaRC Arc Heated Scramjet Test Facility (AHSTF). The HDCR is a full-scale, copper heat sink structure designed to simulate the isolator entrance conditions and isolator, pilot, and combustor section of the HIFiRE flight test experiment flowpath and is fully instrumented to assess combustion performance over a range of operating conditions simulating flight from Mach 5.5 to 8.5 and for various fueling schemes. As part of the instrumentation package, temperature and heat flux sensors were provided along the flowpath surface and also imbedded in the structure. The purpose of this paper is to demonstrate that the surface heat flux and wall temperature of the Zirconia coated copper wall can be obtained with a water-cooled heat flux gage and a sub-surface temperature measurement. An algorithm was developed which used these two measurements to reconstruct the surface conditions along the flowpath. Determinations of the surface conditions of the Zirconia coating were conducted for a variety of conditions.

Cuda, Vincent, Jr.↗

NASA NTRS2012

Time-Resolved Ultraviolet Spectroscopy of the M-Dwarf GJ 876 Exoplanetary System

Extrasolar planets orbiting M-stars may represent our best chance to discover habitable worlds in the coming decade. The ultraviolet spectrum incident upon both Earth-like and Jovian planets is critically important for proper modeling of their atmospheric heating and chemistry. In order to provide more realistic inputs for atmospheric models of planets orbiting low-mass stars, we present new near- and far-ultraviolet (NUV and FUV) spectroscopy of the M-dwarf exoplanet host GJ 876 (U4V). Using the COS and STIS spectrographs aboard the Hubble Space Telescope, we have measured the 1150 - 3140 Ang. spectrum of GJ 876. We have reconstructed the stellar H I Ly-alpha emission line profile, and find that the integrated Ly-apha flux is roughly equal to the rest of the integrated flux (1150 - 1210 Ang + 1220 - 3140 Ang) in the entire ultraviolet bandpass (F(Ly-alpha)/F(FUV+NUV) approximately equals 0.7). This ratio is approximately 2500 x greater than the solar value. We describe the ultraviolet line spectrum and report surprisingly strong fluorescent emission from hot H2 (T(H2) > 2000 K). We show the light-curve of a chromospheric + transition region flare observed in several far-UV emission lines, with flare/ quiescent flux ratios :2: 10. The strong FUV radiation field of an M-star (and specifically Ly-alpha) is important for determining the abundance of O2 - and the formation of biomarkers - in the lower atmospheres of Earth-like planets in the habitable zones of low-mass stars.

France, Kevin↗

DOE OSTI2020

Improvements to a class of hybrid methods for radiation transport: Nyström reconstruction and defect correction methods

In this study, two modifications are introduced for improving the accuracy, versatility, and robustness of a class of hybrid methods for radiation transport. In general, such methods are constructed by splitting the radiative flux into collided and uncollided components to which low- and high-resolution angular approximations are applied, respectively. In this work we focus on discrete ordinates discretizations of high and low order. The first modification we introduce changes the way in which the collided component is mapped into the uncollided component at the end of each time step in a simulation. The new mapping is a Nyström-type reconstruction that is applicable to arbitrary discrete ordinates quadratures, is guaranteed to preserve positivity of the solution provided that all ordinate weights are positive, is significantly more accurate than previous methods, and can be readily extended to other discretizations such as moment methods, finite element methods, and diffusion approximations. The second modification leverages integral deferred correction (IDC) to iteratively correct for the splitting error introduced by the inconsistency in angular discretization between the collided and uncollided components, in addition to improving the accuracy of the low-order temporal error that is treated by traditional IDC methods. Numerical tests in one- and two-dimensional geometries are used to demonstrate the increased accuracy and efficiency of the proposed modifications. It is found that the two techniques combined yield methods with solution accuracy and memory requirements comparable to that of monolithic discrete ordinates methods while reducing runtime by as much as a factor of between two and ten, depending on the problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Calibration and Performance of the ICARUS Detector at Fermilab

ICARUS is the largest Liquid Argon Time Projection Chamber (LArTPC) in operation and serves as the Far Detector of the Short Baseline Neutrino (SBN) program at Fermilab. Precise detector calibration is essential for reliable energy reconstruction and for maximizing the physics reach of the experiment. In this talk, I will describe the energy and timing calibration procedures developed at ICARUS. Thanks to the abundant flux of cosmic ray muons at the surface, the TPC response to ionization charge has been equalized across the detector, removing non-uniformities and in-transparency effects. A novel data-driven procedure has been used to tune the simulation of ionization signals and electronics noise yielding close agreement between Monte Carlo and data with minimal residual bias in reconstructed charge. In addition, the light detection system has been calibrated to sub-nanosecond timing resolution. This precision enables efficient cosmic background rejection and accurate synchronization of neutrino interactions with the time structure of both the Booster Neutrino Beam (BNB) and Neutrinos at the Main Injector (NuMI) beam. Together, these efforts demonstrate the robust performance of the detector and provide critical experience for future large LArTPCs, such as DUNE.

Vicenzi, Matteo [Brookhaven]↗

DOE OSTI2021

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

First study of neutrino angle reconstruction using quasielasticlike interactions in MicroBooNE

We investigate the expected precision of the reconstructed neutrino direction using a 𝜈 𝜇 -argon quasielasticlike event topology with one muon and one proton in the final state and the reconstruction capabilities of the MicroBooNE liquid argon time projection chamber. This direction is of importance in the context of DUNE sub-GeV atmospheric oscillation studies. MicroBooNE allows for a data-driven quantification of this resolution by investigating the deviation of the reconstructed muon-proton system orientation with respect to the well-known direction of neutrinos originating from the Booster Neutrino Beam with an exposure of 1.3 ×10 21 protons on target. Using simulation studies, we derive the expected sub-GeV DUNE atmospheric-neutrino reconstructed simulated spectrum by developing a reweighting scheme as a function of the true neutrino energy. We further report flux-integrated single- and double-differential cross section measurements of charged-current 𝜈 𝜇 quasielasticlike scattering on argon as a function of the muon-proton system angle using the full MicroBooNE data sets. We also demonstrate the sensitivity of these results to nuclear effects and final state hadronic reinteraction modeling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1992

Eno-Osher schemes for Euler equations

The combination of the Osher approximate Riemann solver for the Euler equations and various ENO schemes is discussed for one-dimensional flow. The three basic approaches, viz. the ENO scheme using primitive variable reconstruction, either with Cauchy-Kowalewski procedure for time integration or the TVD Runge-Kutta scheme, and the flux-ENO method are tested on different shock tube cases. The shock tube cases were chosen to present a serious challenge to the ENO schemes in order to test their ability to capture flow discontinuities, such as shocks. Also the effect of the ordering of the eigen values, viz. natural or reversed ordering, in the Osher scheme is investigated. The ENO schemes are tested up to fifth order accuracy in space and time. The ENO-Osher scheme using the Cauchy-Kowalewski procedure for time integration is found to be the most accurate and robust compared with the other methods and is also computationally efficient. The tests showed that the ENO schemes perform reasonably well, but have problems in cases where two discontinuities are close together. In that case there are not enough points in the smooth part of the flow to create a non-oscillatory interpolation.

Vandervegt, Jacobus J.↗

NASA NTRS2005

Multi-Dimensional Spectral Difference Method for Unstructured Grids

A new, high-order, conservative, and efficient method for conservation laws on unstructured grids is developed. It combines the best features of structured and unstructured grid methods to attain computational efficiency and geometric flexibility; it utilizes the concept of discontinuous and high-order local representations to achieve conservation and high accuracy; and it is based on the finite-difference formulation for simplicity. Universal reconstructions are obtained by distributing unknowns in a geometrically similar manner for all unstructured cells. Placements of the unknown and flux points with various order of accuracy are given for the line, triangular and tetrahedral elements. The data structure of the new method permits an optimum use of cache memory, resulting in further computational efficiency on modern computers. A new pointer system is developed that reduces memory requirements and simplifies programming for any order of accuracy. Numerical solutions are presented and compared with the exact solutions for wave propagation problems in both two and three dimensions to demonstrate the capability of the method. Excellent agreement has been found. The method is simpler and more efficient than previous discontinuous Galerkin and spectral volume methods for unstructured grids.

Liu, Yen↗

NASA NTRS2023

Extensive Global Wetland Loss Over the Past Three Centuries

Wetlands have long been drained for human use, thereby strongly affecting greenhouse gas fluxes, flood control, nutrient cycling and biodiversity. Nevertheless, the global extent of natural wetland loss remains remarkably uncertain. Here, we reconstruct the spatial distribution and timing of wetland loss through conversion to seven human land uses between 1700 and 2020, by combining national and subnational records of drainage and conversion with land-use maps and simulated wetland extents. We estimate that 3.4 million km 2 (confidence interval 2.9–3.8) of inland wetlands have been lost since 1700, primarily for conversion to croplands. This net loss of 21% (confidence interval 16–23%) of global wetland area is lower than that suggested previously by extrapolations of data disproportionately from high-loss regions. Wetland loss has been concentrated in Europe, the United States and China, and rapidly expanded during the mid-twentieth century. Our reconstruction elucidates the timing and land-use drivers of global wetland losses, providing an improved historical baseline to guide assessment of wetland loss impact on Earth system processes, conservation planning to protect remaining wetlands and prioritization of sites for wetland restoration.

Etienne Fluet-Chouinard↗

DOE OSTI2021

Broadband X-ray ptychography using multi-wavelength algorithm

Ptychography is a rapidly developing scanning microscopy which is able to view the internal structures of samples at a high resolution beyond the illumination size. The achieved spatial resolution is theoretically dose-limited. A broadband source can provide much higher flux compared with a monochromatic source; however, it conflicts with the necessary coherence requirements of this coherent diffraction imaging technique. In this paper, a multi-wavelength reconstruction algorithm has been developed to deal with the broad bandwidth in ptychography. Compared with the latest development of mixed-state reconstruction approach, this multi-wavelength approach is more accurate in the physical model, and also considers the spot size variation as a function of energy due to the chromatic focusing optics. Therefore, this method has been proved in both simulation and experiment to significantly improve the reconstruction when the source bandwidth, illumination size and scan step size increase. It is worth mentioning that the accurate and detailed information of the energy spectrum for the incident beam is not required in advance for the proposed method. Further, we combine multi-wavelength and mixed-state approaches to jointly solve temporal and spatial partial coherence in ptychography so that it can handle various disadvantageous experimental effects. The significant relaxation in coherence requirements by our approaches allows the use of high-flux broadband X-ray sources for high-efficient and high-resolution ptychographic imaging.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗