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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Nutri‐cereal tissue‐specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet ( Panicum sumatrense )

SUMMARY Little millet (Panicum sumatrenseRoth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress‐tolerant, has a short life cycle, and has a mineral‐rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK‐8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high‐quality, in‐depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user‐friendly interface, allowing interactive visualizations of tissue‐specific gene expression. Using these data, we identified transcripts, the orthologs of which inArabidopsisand rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of “hidden hunger” and to attain nutritional security, making it a valuable asset for translational research.

Plant Sciences↗
DOE OSTI2024

Population‐level gene expression can repeatedly link genes to functions in maize

SUMMARY Transcriptome‐wide association studies (TWAS) can provide single gene resolution for candidate genes in plants, complementing genome‐wide association studies (GWAS) but efforts in plants have been met with, at best, mixed success. We generated expression data from 693 maize genotypes, measured in a common field experiment, sampled over a 2‐h period to minimize diurnal and environmental effects, using full‐length RNA‐seq to maximize the accurate estimation of transcript abundance. TWAS could identify roughly 10 times as many genes likely to play a role in flowering time regulation as GWAS conducted data from the same experiment. TWAS using mature leaf tissue identified known true‐positive flowering time genes known to act in the shoot apical meristem, and trait data from a new environment enabled the identification of additional flowering time genes without the need for new expression data. eQTL analysis of TWAS‐tagged genes identified at least one additional known maize flowering time gene through trans ‐eQTL interactions. Collectively these results suggest the gene expression resource described here can link genes to functions across different plant phenotypes expressed in a range of tissues and scored in different experiments.

Torres‐Rodríguez, J. Vladimir↗
DOE OSTI2025

Comparative transcriptomics uncovers poplar and fungal genetic determinants of ectomycorrhizal compatibility

Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ectomycorrhiza (ECM) first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de novo tree and fungal transcriptional datasets. We identified co-expressed genes enabling ECM symbiosis at early and mature stages of the interaction. These sets of genes can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defenses and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases, and the downregulation of plant cell wall remodeling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene regulation, but also its temporal scale and dynamics seem to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway and nutrient transporters was also studied, revealing constitutive levels of expression and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility, and serve as a data-rich transcriptomic resource to open new research questions in the field.

Marqués‐Gálvez, José Eduardo↗
DOE OSTI2022

Design of a Compact Dry Cooler With an Aluminum Heat Exchanger Core for a Supercritical CO2 Power Cycle Is Evaluated for a Concentrating Solar Power Application

Abstract As the supercritical CO2 power cycle develops and the component technologies mature, there is still a need to reduce the associated capital and operating costs to maintain a competitive levelized cost of electricity (LCOE) in order to enter the market. When considering concentrating solar power (CSP) coupled with an sCO2 power block and sensible thermal storage, the technology presents a clean source for utility-scale power generation to support baseload or peak-load electrical demand. However, the LCOE of the technology is still considered higher than the competing technologies and should be reduced to better compete in the market; 2030 targets for dispatchable solar plants are 5¢/kWh for baseload CSP and 10¢/kWh for peaker plants, as set by the United States Department of Energy. In response to this need, this study is targeting improvements in the power cycle precooler to reduce power block contribution to LCOE. This study considers a dry cooler, as CSP plants are sensitive to water consumption because many installations are slated for remote or arid locations where solar irradiance is very high, but water is scarce. Furthermore, the power block footprint for an sCO2 system is quite compact, especially as compared to a steam cycle. Therefore, there is interest in installing a more compact dry cooler that is proportional to the reduced footprint sCO2 power block, while conventional dry coolers are an order of magnitude larger. The competing goals of size, performance, and cost were considered in this study to develop a compact dry cooler that can easily be packaged with the power block, significantly reducing the installation and transport cost compared to the current state of the art, while maintaining or improving upon the heat transfer performance and impact on plant LCOE. This paper details the high-level findings of a large dry cooler sensitivity study for design point selection, design of the compact dry cooler, expected year-round performance for the dry cooler and the power cycle, and the predicted LCOE for a 30-year plant life. It was found that an aluminum heat exchanger core can be suitably designed to meet the pressure and temperature requirements for a precooler in an sCO2 recompression Brayton cycle. The dry cooler assembly was found to have improved heat transfer performance, allowing for increased cycle efficiencies and a reduced plant LCOE. When coupled with a centrifugal blower and compact transition duct, the dry cooler assembly was able to reduce the installation footprint by over 50%.

14 SOLAR ENERGY↗
DOE OSTI2020

Attached Jet Velocity Profiles in Mixing Tanks

Free jets have been studied in detail over much of the last century, but the theory for offset and attached jets remains incomplete. Attached jets differ from free jets in that they lose momentum to nearby surfaces, attenuating their velocities. The velocity profiles of free circular jets are nearly Gaussian, with quantitative mathematical descriptions derived from first principles by Goertler and Tollmien (Rajaratnam, 1976). In contrast, mathematical descriptions of three-dimensional attached jets from circular nozzles remain much less mature. Agelin-Chaab and Tachie (2011) used particle imaging velocimetry of a three-dimensional attached jet to show that the scaled velocity decays with scaled distance from the nozzle with a power law exponent between -1.15 and -1.21, which is larger in magnitude than that of a free jet. However, quantitative analytical expressions for the velocity profiles of attached jets similar to those of free jets remain elusive. This paper addresses this critical gap. Here we evaluate the velocity profiles of three-dimensional offset jets emerging from circular nozzles that that become attached jets. These jets lose momentum due to interactions with nearby surfaces and are important to evaluating flows in mixing vessels and to suspending solids and trapped gases in radioactive waste tanks. Despite the importance of attached jets, prior insight has been purely experimental, limited to overly simplistic analytical models, or restricted to computationally expensive computational fluid dynamics case studies. We compare the expression of Verhoff (1963) to experimental results to find reasonable quantitative agreement. As stated by Agelin-Chaab and Tachie (2011), “detailed velocity measurements of 3D offset jets are rare.” Such remains the case. This study adds to the literature by providing information at two additional Reynolds numbers (1.43 106 and 1.87 106) and evaluating simple but accurate expressions for velocity profiles. These Reynolds numbers are an order of magnitude higher than prior reports. The semi-empirical stream wise velocity profile perpendicular to the surface proposed by Verhoff (1963) is in approximate agreement with these velocity profiles, which is surprising because these attached jets are three-dimensional instead of two-dimensional as evaluated by Verhoff. However, additional work is necessary to fully describe these profiles quantitatively.

jet, attached jet, offset jet↗
DOE OSTI2021

MODELING AND TESTING OF A NOVEL ULTRA-LOW TEMPERATURE SCO2 OPPOSING PISTON EXPANDER

The Flameless Pressurized Oxy-Combustion (FPO) cycle, a novel flexible fuel technology, is being developed into a large pilot. This effort seeks to complete the preliminary engineering and planning of a 25 MWth Pilot Plant that will demonstrate the technology for scale-up to a commercial unit. The technology, pioneered by ITEA at the 5 MWth scale, must be brought to a higher technology readiness level (TRL) to be viable at the commercial scale. The 25 MWth pilot cycle was optimized for cost and technology development and demonstration. Preliminary drawings, layouts, and plans were defined. Process flow diagrams were used to describe the pilot configuration in greater detail. A heat and mass balance with stream data was created. A master equipment list specified the operating conditions for major pieces of equipment within the pilot using this heat and mass balance. The 25 MWth FPO pilot is assessed for environmental performance. A test campaign is developed to assess the type of test and number of hours required for pilot demonstration. The environmental performance is compared against projected performance at the commercial scale. This project builds upon extensive evaluation of the techno-economic performance of the FPO technology already performed by ITEA. This includes system improvements, such as the addition of a turbo-expander to the flue gas stream. Some of the performance-enhancing components are not as well defined as others. The primary goal of this effort was to bring all of the core cycle components to the same level of design maturity. A techno-economic assessment (TEA) evaluated the FPO technology at the commercial scale in comparison to the NETL baseline cases. The reference plants were used in combination with proprietary equipment estimates to build a plant capital cost and cost of electricity evaluation. FPO performed better than the sub-bituminous post-combustion capture cases. Further preliminary estimates of improvements to the FPO cycle show even further gains when compared to conventional carbon capture methods.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2020

MoorDyn V2: New Capabilities in Mooring System Components and Load Cases

MoorDyn, an open-source mooring dynamics model, is being expanded with capabilities for additional mooring system features and load cases. As floating wind turbine technology matures, mooring systems are becoming more sophisticated and more complex scenarios need to be considered in the design process. Mooring systems may have synthetic line materials, ballast/buoyancy bodies along the lines, or interconnections between platforms. Failure modes may involve multiple cascading line failures that depend on mooring system dynamics. Features recently added to MoorDyn aim to address these emerging needs. MoorDyn’s linear elasticity model has been supplemented to support user-defined stress-strain curves, which can be adjusted to represent synthetic mooring materials. Rigid six-degree-of-freedom bodies in the mooring system can now be modeled using two new model objects. “Rod” objects provide an option for rigid cylindrical bodies. They use the existing Morison equation-based hydrodynamics model and can be connected to mooring lines at either end. “Body” objects provide a generic six-degree-of-freedom rigid-body representation based on a lumped-parameter model of translational and rotational properties. Rod objects can be added to Body objects and mooring lines can be attached at any location, allowing a wide variety of submerged structures to be integrated into the mooring system. Lastly, a means of dynamically simulating mooring line failures has been implemented. These new features, currently in the C++ version of MoorDyn, are described and then demonstrated on a two-turbine shared-mooring array. A qualitative view of the results suggests the new features are functioning as expected.

49 EE - Wind and Water Power Program - Wind (EE-4W↗
DOE OSTI2025

An Open-Source Python Package for CFD Solution Verification

Informed decision-making using computational fluid dynamics (CFD) results requires quantifying the errors and uncertainties of a simulation. Verification, validation, and uncertainty quantification (VVUQ) methods were developed to address this need and have matured. However, these VVUQ analyses are often non-trivial and require CFD analysts and practitioners to have specific skill sets. This has led to the uneven adoption of VVUQ analyses, in part, based on the availability of software tools to aid CFD analysts and practitioners. Solution verification, a procedure to evaluate the accuracy of a simulation by estimating potential errors arising from the computational model and computing the uncertainties without comparing to results from a physical system, is one of the lagging VVUQ analyses as the absence of software has forced CFD analysts and practitioners to develop their own codes or piece together incomplete software from across the internet. This work presents an opensource Python package, CFDverify, to lower the barrier of entry and fill in the technological gap in solution verification. CFDverify also provides a streamlined framework to remove some potential errors in post-processing CFD results. The hope is that CFDverify can improve the quality and quantity of CFD solution verification in scientific and research studies and attract interest in developing a communal tool. This paper describes the design, features, and an example use of CFDverify.

Weinmeister, Justin [ORNL] (ORCID:0000000160090237↗
DOE OSTI2023

Improved noise performance from the next-generation buried-channel p-MOSFET SiSeROs

The Single electron Sensitive Read Out (SiSeRO) is a novel on-chip charge detector output stage for charge-coupled device (CCD) image sensors. Developed at MIT Lincoln Laboratory, this technology uses a p-MOSFET transistor with a depleted internal gate beneath the transistor channel. The transistor source-drain current is modulated by the transfer of charge into the internal gate. At Stanford, we have developed a readout module based on the drain current of the on-chip transistor to characterize the device. In our earlier work, we characterized a number of first prototype SiSeROs with the MOSFET transistor channels at the surface layer. An equivalent noise charge (ENC) of around 15 electrons root mean square (RMS) was obtained. In this work, we examine the first buried-channel SiSeRO. Here we have achieved substantially improved noise performance of around 4.5 electrons root mean square (RMS) and a full width half maximum (FWHM) energy resolution of 132 eV at 5.9 keV, for a readout speed of 625 kpixel/s. We also discuss how digital filtering techniques can be used to further improve the SiSeRO noise performance. Additional measurements and device simulations will be essential to further mature the SiSeRO technology. This new device class presents an exciting new technology for the next-generation astronomical X-ray telescopes requiring fast, low-noise, radiation-hard megapixel imagers with moderate spectroscopic resolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Line emission mapper microcalorimeter spectrometer

The line emission mapper (LEM) is a probe-class mission concept that is designed to detect x-ray emission lines from hot ionized gas (T > 10 6 K) that will enable us to test galaxy evolution theories. It will permit us to study the effects of stellar and black-hole feedback and flows of baryonic matter into and out of galaxies. The key to being able to study the hot gases that are otherwise invisible to current imaging x-ray spectrometers is that the energy resolution is sufficient to use cosmological redshift to separate extragalactic source lines from foreground Milky Way emission. LEM incorporates a large-format microcalorimeter array instrument called the LEM microcalorimeter spectrometer (LMS) with a light-weight x-ray optic with 10” half power diameter angular resolution. The LMS microcalorimeter array has pixels with 15" pixel pitch over a 33' field of view (FOV) optimized for the 0.3 to 2 keV energy band. The central 7' region of the array has an energy resolution of 1.3 eV at 1 keV and the rest of the FOV has 2.5 eV energy resolution at 1 keV. The array will be read out with state-of-the-art time-division multiplexing. We present an overview of the LMS instrument, including details of the entire detection chain, the focal plane assembly, as well as the cooling system and overall mechanical and thermal design. For each of the key technologies, we discuss the current technology readiness level and the plan to advance them to be ready for flight. We also describe the current system design and our estimate for the mass, power, and data rate of the instrument. The design details presented concentrate primarily on the unique aspects of the LMS design compared with prior missions and confirm that the type of microcalorimeter instrument needed for LEM is not only feasible but also technically mature.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Development of the microcalorimeter and anticoincidence detector for the Line Emission Mapper x-ray probe

The Line Emission Mapper (LEM) is an x-ray probe mission concept that is designed to provide unprecedented insight into the physics of galaxy formation, including stellar and black-hole feedback and flows of baryonic matter into and out of galaxies. LEM incorporates a light-weight x-ray optic with a large-format microcalorimeter array. The LEM detector utilizes a 14k pixel array of transition-edge sensors (TESs) that will provide <2.5 eV spectral resolution over the energy range 0.2 to 2 keV, along with a field-of-view of 30 arcmin. The microcalorimeter array and readout builds upon the technology developed for the European Space Agency’s (ESA’s) Athena/x-ray Integral Field Unit. Here, we present a detailed overview of the base- line microcalorimeter design, its performance characteristics, including a detailed energy resolution budget and the expected count-rate capability. In addition, we outline the current status and plan for continued technology maturation. Behind the LEM array sits a high-efficiency TES-based anticoincidence (antico) detector that will reject cosmic-ray background events. We will briefly describe the design of the antico and plan for continued development.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Image transformers for classifying acute lymphoblastic leukemia

Cancer is the leading cause of death by disease in American children. Each year, nearly 16,000 children in the United States and over 300,000 children globally are diagnosed with cancer. Leukemia is a form of blood cancer that originates in the bone marrow and accounts for one-third of pediatric cancers. This disease occurs when the bone marrow contains 20% or more immature white blood cell blasts. Acute lymphoblastic leukemia is the most prevalent leukemia type found in children, with half of all annual cases in the U.S. diagnosed for subjects under 20 years of age. To diagnose acute lymphoblastic leukemia, pathologists often conduct a morphological bone marrow assessment. This assessment determines whether the immature white blood cell blasts in bone marrow display the correct morphological characteristics, such as size and appearance of nuclei. Pathologists also use immunophenotyping via multi-channel flow cytometry to test whether certain antigens are present on the surface of blast cells; the antigens are used to identify the cell lineage of acute lymphoblastic leukemia. These manual processes require well-trained personnel and medical professionals, thus being costly in time and expenses. Computerized decision support via machine learning can accelerate the diagnosis process and reduce the cost. Training a reliable classification model to distinguish between mature and immature white blood cells is essential to the decision support system. Here, we adopted the Vision Transformer model to classify white blood cells. The Vision Transformer achieved superb classification performance compared to state-of-the-art convolutional neural networks while requiring less computational resources for training. Additionally, the latent self-attention architecture provided attention maps for a given image, providing clues as to which portion(s) of the image were significant in decision-making. We applied the Vision Transformer model and a convolutional neural network model to an acute lymphoblastic leukemia classification dataset of 12,528 samples and achieved accuracies of 88.4% and 86.2%.

Cho, Priscilla↗
DOE OSTI2020

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

Characterizing relationships between cell structures and functions requires mesoscale mapping of intact cells showing subcellular rearrangements following stimulation; however, current approaches are limited in this regard. Here, we report a unique application of soft x-ray tomography to generate three-dimensional reconstructions of whole pancreatic β cells at different time points following glucose-stimulated insulin secretion. Reconstructions following stimulation showed distinct insulin vesicle distribution patterns reflective of altered vesicle pool sizes as they travel through the secretory pathway. Our results show that glucose stimulation caused rapid changes in biochemical composition and/or density of insulin packing, increased mitochondrial volume, and closer proximity of insulin vesicles to mitochondria. Costimulation with exendin-4 (a glucagon-like peptide-1 receptor agonist) prolonged these effects and increased insulin packaging efficiency and vesicle maturation. This study provides unique perspectives on the coordinated structural reorganization and interactions of organelles that dictate cell responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Digital quantum simulation of NMR experiments

Simulations of nuclear magnetic resonance (NMR) experiments can be an important tool for extracting information about molecular structure and optimizing experimental protocols but are often intractable on classical computers for large molecules such as proteins and for protocols such as zero-field NMR. We demonstrate the first quantum simulation of an NMR spectrum, computing the zero-field spectrum of the methyl group of acetonitrile using four qubits of a trapped-ion quantum computer. We reduce the sampling cost of the quantum simulation by an order of magnitude using compressed sensing techniques. We show how the intrinsic decoherence of NMR systems may enable the zero-field simulation of classically hard molecules on relatively near-term quantum hardware and discuss how the experimentally demonstrated quantum algorithm can be used to efficiently simulate scientifically and technologically relevant solid-state NMR experiments on more mature devices. Our work opens a practical application for quantum computation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

High-throughput identification of spin-photon interfaces in silicon

Color centers in host semiconductors are prime candidates as spin-photon interfaces for quantum applications. Finding an optimal spin-photon interface in silicon would move quantum information technologies toward a mature semiconducting host. However, the space of possible charged defects is vast, making the identification of candidates from experiments alone extremely challenging. Here, we use high-throughput first-principles computational screening to identify spin-photon interfaces among more than 1000 charged defects in silicon. The use of a single-shot hybrid functional approach is critical in enabling the screening of many quantum defects with a reasonable accuracy. We identify three promising spin-photon interfaces as potential bright emitters in the telecom band: Ti$^+_i$, Fe$^0_i$, and Ru$^0_i$. These candidates are excited through defect-bound excitons, stressing the importance of such defects in silicon for telecom band operations. Our work paves the way to further large-scale computational screening for quantum defects in semiconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Time-resolved tracking of cellulose biosynthesis and assembly during cell wall regeneration in live Arabidopsis protoplasts

Cellulose, the most abundant polysaccharide on earth composing plant cell walls, is synthesized by coordinated action of multiple enzymes in cellulose synthase complexes embedded within the plasma membrane. Multiple chains of cellulose fibrils form intertwined extracellular matrix networks. It remains largely unknown how newly synthesized cellulose is assembled into an intricate fibril network on cell surfaces. Here, we have established an in vivo time-resolved imaging platform to continuously visualize cellulose biosynthesis and fibril network assembly onArabidopsis thalianaprotoplast surfaces as the primary cell wall regenerates. Our observations provide the basis for a model of cellulose fibril network development in protoplasts driven by an interplay of multiscale dynamics that includes rapid diffusion and coalescence of nascent cellulose fibrils, processive elongation of single fibrils, and cellulose fibrillar network rearrangement during maturation. This study provides fresh insights into the dynamic and mechanistic aspects of cell wall synthesis at the single-cell level.

Science & Technology - Other Topics↗
DOE OSTI2020

Structural basis of a shared antibody response to SARS-CoV-2

Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti–SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53–neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)–binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.

59 BASIC BIOLOGICAL SCIENCES↗