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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Scattering-based structural inversion of soft materials via Kolmogorov–Arnold networks

Small-angle scattering techniques are indispensable tools for probing the structure of soft materials. However, traditional analytical models often face limitations in structural inversion for complex systems, primarily due to the absence of closed-form expressions of scattering functions. To address these challenges, we present a machine learning framework based on the Kolmogorov–Arnold Network (KAN) for directly extracting real-space structural information from scattering spectra in reciprocal space. This model-independent, data-driven approach provides a versatile solution for analyzing intricate configurations in soft matter. By applying the KAN to lyotropic lamellar phases and colloidal suspensions—two representative soft matter systems—we demonstrate its ability to accurately and efficiently resolve structural collectivity and complexity. Here, our findings highlight the transformative potential of machine learning in enhancing the quantitative analysis of soft materials, paving the way for robust structural inversion across diverse systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Advances in light system engineering across the phototrophic spectrum

Current work in photosynthetic engineering is progressing along the lines of cyanobacterial, microalgal, and plant research. These are interconnected through the fundamental mechanisms of photosynthesis and advances in one field can often be leveraged to improve another. It is worthwhile for researchers specializing in one or more of these systems to be aware of the work being done across the entire research space as parallel advances of techniques and experimental approaches can often be applied across the field of photosynthesis research. This review focuses on research published in recent years related to the light reactions of photosynthesis in cyanobacteria, eukaryotic algae, and plants. Highlighted are attempts to improve photosynthetic efficiency, and subsequent biomass production. Also discussed are studies on cross-field heterologous expression, and related work on augmented and novel light capture systems. This is reviewed in the context of translatability in research across diverse photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improved high-throughput screening technique to rapidly isolate Chlamydomonas transformants expressing recombinant proteins

Abstract The single-celled eukaryotic green alga Chlamydomonas reinhardtii has long been a model system for developing genetic tools for algae, and is also considered a potential platform for the production of high-value recombinant proteins. Identifying transformants with high levels of recombinant protein expression has been a challenge in this organism, as random integration of transgenes into the nuclear genome leads to low frequency of cell lines with high gene expression. Here, we describe the design of an optimized vector for the expression of recombinant proteins in Chlamydomonas , that when transformed and screened using a dual antibiotic selection, followed by screening using fluorescence activated cell sorting (FACS), permits rapid identification and isolation of microalgal transformants with high expression of a recombinant protein. This process greatly reduces the time required for the screening process, and can produce large populations of recombinant algae transformants with between 60 and 100% of cells producing the recombinant protein of interest, in as little as 3 weeks, that can then be used for whole population sequencing or individual clone analysis. Utilizing this new vector and high-throughput screening (HTS) process resulted in an order of magnitude improvement over existing methods, which normally produced under 1% of algae transformants expressing the protein of interest. This process can be applied to other algal strains and recombinant proteins to enhance screening efficiency, thereby speeding up the discovery and development of algal-derived recombinant protein products. Key points • A protein expression vector using double-antibiotic resistance genes was designed • Double antibiotic selection causes fewer colonies with more positive for phenotype • Coupling the new vector with FACS improves microalgal screening efficiency > 60%

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Neuroprotectin D1 Attenuates Blast Overpressure Induced Reactive Microglial Cells in the Cochlea

Objective/Hypothesis We examined a neuroinflammatory response associated with glial activation in the cochlea exposed to blast overpressure and evaluated the potential therapeutic efficacy of specialized pro‐resolving mediators such as neuroprotectin D1, NPD1; (10R, 17S‐dihydroxy‐4Z, 7Z, 11E, 13E, 15Z, 19Z‐docosahexaenoic acid) in a rodent blast‐induced auditory injury model. Study Design Animal Research. Methods A compressed‐air driven shock tube was used to expose anesthetized adult male Long‐Evan rats to shock waves simulating an open‐field blast exposure. Approximately 30 minutes after blast exposure, rats were treated with NPD1 (100 ng/kg body wt.) or vehicle delivered intravenously via tail vein injection. Rats were then euthanized 48 hours after blast exposure. Unexposed rats were included as controls. Tissue sections containing both middle and inner ear were prepared with hematoxylin–eosin staining to elucidate histopathological changes associated with blast exposure. Cochlear tissues were evaluated for relative expression of ionized calcium‐binding adaptor 1 (Iba1), as an indicator of microglial activation by immunohistochemistry and western blot analyses. Results Our animal model resulted in an acute injury mechanism manifested by damage to the tympanic membrane, hemorrhage, infiltration of inflammatory cells, and increased expression of Iba1 protein. Moreover, therapeutic intervention with NPD1 significantly reduced Iba1 expression in the cochlea, suggesting a reduction of a neuroinflammatory response caused by blast overpressure. Conclusions Blast overpressure resulted in an increased expression of proteins involved in gliosis within the auditory system, which were reduced by NPD1. Treatment of NPD1 suggests an effective strategy to reduce or halt auditory microglial cell activation due to primary blast exposure. Level of Evidence NA Laryngoscope , 131:E2018–E2025, 2021

Ríos, José David↗
DOE OSTI2025

Overexpression of plasma membrane SUT1 in poplar alters lateral sucrose partitioning in stem and promotes leaf necrosis

Abstract In Populus and many other tree species, photoassimilate sucrose diffuses down a concentration gradient via symplastically connected mesophyll cells to minor vein phloem for long‐distance transport. There is no evidence for apoplastic phloem‐loading in Populus . However, plasma membrane sucrose transporters (SUT1 and SUT3) orthologous to those associated with apoplastic phloem loading are expressed in vascular tissues of poplar. While SUT3 functions in sucrose import into developing xylem, the role of SUT1 remains unclear. Here, we overexpressed PtaSUT1 in Populus tremula x P. alba to examine the effects on sucrose partitioning in transgenic plants. Overall leaf sucrose levels were similar between wild type and transgenic lines. Stem sucrose levels were not changed in bark but were significantly reduced in the adjacent xylem, suggesting hindered intercellular sucrose trafficking from the phloem to the developing xylem. Fully expanded leaves of transgenic plants deteriorated prematurely with declining photosynthesis prior to severe necrotic spotting. Necrotic spotting advanced most rapidly in the distal portion of mature leaves and was accompanied by sharp hexose increases and sharp sucrose decreases there. Leaf transcriptome profiling and network inference revealed the down‐regulation of copper proteins and elevated expression of copper microRNAs prior to noticeable leaf injury. Our results suggest ectopic expression of PtaSUT1 altered sucrose partitioning in stems with systemic effects on leaf health and copper homeostasis mediated in part by sucrose‐sensitive copper miRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SAGA1 and MITH1 produce matrix-traversing membranes in the CO2-fixing pyrenoid

Abstract Approximately one-third of global CO 2 assimilation is performed by the pyrenoid, a liquid-like organelle found in most algae and some plants. Specialized pyrenoid-traversing membranes are hypothesized to drive CO 2 assimilation in the pyrenoid by delivering concentrated CO 2 , but how these membranes are made to traverse the pyrenoid matrix remains unknown. Here we show that proteins SAGA1 and MITH1 cause membranes to traverse the pyrenoid matrix in the model alga Chlamydomonas reinhardtii . Mutants deficient in SAGA1 or MITH1 lack matrix-traversing membranes and exhibit growth defects under CO 2 -limiting conditions. Expression of SAGA1 and MITH1 together in a heterologous system, the model plant Arabidopsis thaliana , produces matrix-traversing membranes. Both proteins localize to matrix-traversing membranes. SAGA1 binds to the major matrix component, Rubisco, and is necessary to initiate matrix-traversing membranes. MITH1 binds to SAGA1 and is necessary for extension of membranes through the matrix. Our data suggest that SAGA1 and MITH1 cause membranes to traverse the matrix by creating an adhesive interaction between the membrane and matrix. Our study identifies and characterizes key factors in the biogenesis of pyrenoid matrix-traversing membranes, demonstrates the importance of these membranes to pyrenoid function and marks a key milestone toward pyrenoid engineering into crops for improving yields.

Hennacy, Jessica H.↗
DOE OSTI2022

Pressure–strain interaction. II. Decomposition in magnetic field-aligned coordinates

In weakly collisional and collisionless magnetized plasmas, the pressure–strain interaction describes the rate of conversion between bulk flow and thermal energy density. In this study, we derive an analytical expression for the pressure–strain interaction in a coordinate system with an axis aligned with the local magnetic field. The result is eight groups of terms corresponding to different physical mechanisms that can contribute to the pressure–strain interaction. We provide a physical description of each term. Here, the results are immediately of interest to weakly collisional and collisionless magnetized plasmas and the fundamental processes that happen therein, including magnetic reconnection, magnetized plasma turbulence, and collisionless shocks. The terms in the field-aligned coordinate decomposition are likely accessible to measurement with satellite observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil

Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed 13 C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. Here, in cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid–protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microscopic origin of temperature-dependent magnetism in spin-orbit-coupled transition metal compounds

A few 4 d and 5 d transition metal compounds with various electron fillings were recently found to exhibit magnetic susceptibilities χ and magnetic moments that deviate from the well-established Kotani model. This model has been considered for decades to be the canonical expression for descriing the temperature dependence of magnetism in systems with nonnegligible spin-orbit coupling effects. In this paper, we uncover the origin of such discrepancies and determine the applicability and limitations of the Kotani model by calculating the temperature dependence of the magnetic moments of a series of 4 d (Ru-based) and 5 d (W-based) systems at different electron fillings. For this purpose, we perform exact diagonalization of -derived relativistic multiorbital Hubbard models on finite clusters and compute their magnetic susceptibilities. Comparison with experimentally measured magnetic properties indicates that contributions such as a temperature-independent χ 0 background, crystal field effects, Coulomb and Hund's couplings, and intersite interactions—not included in the Kotani model—are especially crucial for correctly describing the temperature dependence of χ and magnetic moments at various electron fillings in these systems. Based on our results, we propose a generalized approach beyond the Kotani model to accurately describe their magnetism. Published by the American Physical Society 2025

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A Method of Moments Wide Band Adaptive Rational Interpolation Method for High-Quality Factor Resonant Cavities

A new adaptive rational interpolation method is proposed to obtain the wideband frequency response of a resonant cavity simulated with the method of moments (MoM). This interpolation method uses both the Loewner matrix to construct a rational expression for the solution vector of MoM’s matrix system and an error estimator generated by the solution vectors and their derivatives. This error estimator is implemented in the adaptive procedure to gain a minimum set of frequencies and solution vectors required in the interpolation. The resulting set of frequencies and solution vectors is applied to interpolate other system variables, such as shielding effectiveness and input impedance. Here numerical results of a slotted cylindrical cavity supporting high-quality factor resonances are presented, showing that the new rational interpolation method is accurate and efficient in interpolating the complicated resonant response of the solution vector functions.

42 ENGINEERING↗
DOE OSTI2024

Rapid and efficient in planta genome editing in sorghum using foxtail mosaic virus‐mediated sgRNA delivery

SUMMARY The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single‐guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR‐associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase ( PDS ), Magnesium‐chelatase subunit I ( MgCh ), 4‐hydroxy‐3‐methylbut‐2‐enyl diphosphate reductase , orthologs of maize Lemon white1 ( Lw1 ) or GFP . The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Data for Rapid and Efficient in planta Genome Editing in Sorghum Using Foxtail Mosaic Virus-mediated sgRNA Delivery

The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single-guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR-associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor . We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase (PDS), Magnesium-chelatase subunit I (MgCh), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, orthologs of maize Lemon white1 (Lw1) or GFP. The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.

Feedstock Production↗
DOE OSTI2020

Theoretical Review of the MFIX Fluid and Two-Fluid Models

MFIX (Multiphase Flow with Interphase eXchanges) is a general purpose code that can be used for describing the hydrodynamics, chemical reactions, and heat transfer of dense or dilute multiphase fluid flows. MFIX calculations give detailed information on pressure, temperature, composition, and velocity distributions in the defined system. This report provides an overview of MFIX’s expressions for single phase flow and continuous dispersed multiphase flow (i.e., the two-fluid model). In addition to the two fluid model (MFIX-TFM), MFIX contains a discrete element model (MFIX-DEM) and a multi-phase particle in cell model (MFIX-PIC) that are not reviewed within this document.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Transcriptomics (ACS-DP1)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5), immortalized human lung fibroblasts cells (MRC5) (MOI5), and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue. Sample data was acquired using an Illumina HiSeq 2000 sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Generation of Pseudomonas putida KT2440 Strains with Efficient Utilization of Xylose and Galactose via Adaptive Laboratory Evolution

While Pseudomonas putida KT2440 has great potential for biomass-converting processes, its inability to utilize the biomass abundant sugars xylose and galactose has limited its applications. Here, in this study, we utilized Adaptive Laboratory Evolution (ALE) to optimize engineered KT2440 with heterologous expression of xylD encoding xylonate dehydratase from Caulobacter crescentus and galETKM encoding UDP-glucose 4-epimerase, galactose-1-phosphate uridylyltransferase, galactokinase, and galactose-1-epimerase from Escherichia coli K-12 MG1655. Poor starting strain growth (<0.1 h –1 or none) was evolutionarily optimized to rates of up to 0.25 h –1 on xylose and 0.52 h –1 on galactose. Whole-genome sequencing, transcriptomic analysis, and growth screens revealed significant roles of kguT encoding a 2-ketogluconate operon repressor and 2-ketogluconate transporter, and gtsABCD encoding an ATP-binding cassette (ABC) sugar transporting system in xylose and galactose growth conditions, respectively. Finally, we expressed the heterologous indigoidine production pathway in the evolved and unevolved engineered strains and successfully produced 3.2 g/L and 2.2 g/L from 10 g/L of either xylose or galactose in the evolved strains whereas the unevolved strains did not produce any detectable product. Thus, the generated KT2440 strains have the potential for broad application as optimized platform chassis to develop efficient microorganism-based biomass-utilizing bioprocesses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Software-Defined Network for End-to-end Networked Science at the Exascale

Domain science applications and workflow processes are currently forced to view the network as an opaque infrastructure into which they inject data and hope that it emerges at the destination with an acceptable Quality of Experience. There is little ability for applications to interact with the network to exchange information, negotiate performance parameters, discover expected performance metrics, or receive status/troubleshooting information in real time. The work we presen here is motivated by a vision for a new smart network and smart application ecosystem that will provide a more deterministic and interactive environment for domain science workflows. The Software-Defined Network for End-to-end Networked Science at Exascale (SENSE) system includes a model-based architecture, implementation, and deployment which enables automated end-to-end network service instantiation across administrative domains. An intent based interface allows applications to express their high-level service requirements, an intelligent orchestrator and resource control systems allow for custom tailoring of scalability and real-time responsiveness based on individual application and infrastructure operator requirements. This allows the science applications to manage the network as a first-class schedulable resource as is the current practice for instruments, compute, and storage systems. Deployment and experiments on production networks and testbeds have validated SENSE functions and performance. Emulation based testing verified the scalability needed to support research and education infrastructures. Key contributions of this work include an architecture definition, reference implementation, and deployment. This provides the basis for further innovation of smart network services to accelerate scientific discovery in the era of big data, cloud computing, machine learning and artificial intelligence.

97 MATHEMATICS AND COMPUTING↗