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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Perspectives on ENCODE

The Encyclopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression. The project has been extended to model organisms, particularly the mouse. Finally, in the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Author Correction: Perspectives on ENCODE

In the original article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Computationally restoring the potency of a clinical antibody against Omicron

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs and revealed how quickly viral escape can curtail effective options. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

An evaporite sequence from ancient brine recorded in Bennu samples

Evaporation or freezing of water-rich fluids with dilute concentrations of dissolved salts can produce brines, as observed in closed basins on Earth and detected by remote sensing on icy bodies in the outer Solar System. The mineralogical evolution of these brines is well understood in regard to terrestrial environments, but poorly constrained for extraterrestrial systems owing to a lack of direct sampling. Here we report the occurrence of salt minerals in samples of the asteroid (101955) Bennu returned by the OSIRIS-REx mission. These include sodium-bearing phosphates and sodium-rich carbonates, sulfates, chlorides and fluorides formed during evaporation of a late-stage brine that existed early in the history of Bennu’s parent body. Discovery of diverse salts would not be possible without mission sample return and careful curation and storage, because these decompose with prolonged exposure to Earth’s atmosphere. Similar brines probably still occur in the interior of icy bodies Ceres and Enceladus, as indicated by spectra or measurement of sodium carbonate on the surface or in plumes.

58 GEOSCIENCES↗
DOE OSTI2022

Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism

Abstract Oilseed rape ( Brassica napus ) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fracture toughness of schist, amphibolite, and rhyolite from the Sanford Underground Research Facility (SURF), Lead, South Dakota

The Cracked Chevron Notched Brazilian Disc (CCNBD) method was selected for Mode I fracture toughness tests on Poorman schist, Yates amphibolite, and rhyolite dikes from the EGS Collab site at the SURF in Lead, South Dakota. The effects of lithology, anisotropy, and loading rate were investigated. Fracture toughness was greatest in amphibolite, with schist and rhyolite having similar toughness values ($K$ amphibolite > $K$ rhyolite ≈ $K$ schist ). The effects of anisotropy on fracture toughness were investigated in the foliated schist samples. Schist samples were prepared in three geometries (divider, arrester, and short transverse) which controlled how the fracture would propagate relative to foliations. The divider geometry was strongest and short transverse geometry was the weakest ($K$ divider > $K$ arrester > $K$ shorttransverse ). Fracture toughness was observed to decrease with decreasing loading rate. Optical and SEM microscopy revealed that for the short transverse geometry, fractures tended to propagate along grain boundaries, whereas in arrester and divider geometries fractures tended to propagate through grains. In foliated samples, the tortuosity of the fracture observed in thin section was greater in arrester and divider geometries than in short transverse geometries.

58 GEOSCIENCES↗
DOE OSTI2020

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt

The intestinal epithelium is replaced weekly by non-quiescent stem cells with kinetics that rely on a rapid loss of stemness and choice for secretory or absorptive lineage differentiation. To determine how the cellular transcriptome and proteome changes during these transitions, we developed a new cell sorting method to purify stem cells, secretory and absorptive progenitor cells, and mature, differentiated cells. Transcriptome analyses revealed that as stem cells transition to the progenitor stage, alternative mRNA splicing and polyadenylation dominate changes in the transcriptome. In contrast, as progenitors differentiate into mature cell types, alterations in gene expression and mRNA levels drive the changes. RNA processing targets mRNAs encoding regulators of cell cycle, RNA regulators, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling of sorted cell populations detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Simulation-guided analysis of resonant soft X-ray scattering for determining the microstructure of triblock copolymers

Resonant soft X-ray scattering (RSoXS) probes structure with chemical sensitivity that is useful for determining the morphology of multiblock copolymers. However, the hyperspectral scattering data produced by this technique can be challenging to interpret. Here, in this study, we use computational scattering simulations to extract the microstructure of a model triblock copolymer from the energy-dependent scattering from RSoXS. An ABC triblock terpolymer formed from poly(4-methylcaprolactone) (P4MCL), poly(2,2,2-trifluoroethylacrylate) (PTFEA), and poly (dodecylacrylate) (PDDA), P4MCL-block-PTFEA-block-PDDA, was synthesized as the model triblock system. Through quantitative evaluation of simulated scattering data from a physics-informed set of candidate structure models against experimental RSoXS data, we find the best agreement with hexagonally packed core–shell cylinders. This result is also consistent with electron-density reconstruction from hard X-ray scattering data evaluated against electron-density maps generated with the same model set. These results demonstrate the utility of simulation-guided scattering analysis to study complex microstructures that are challenging to image by microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effect of poly[oligo(ethylene glycol) methyl ether methacrylate] side chain length on the brush swelling behavior in A/B/A–B ternary blends with polystyrene

The phase behavior of ternary blends composed of two homopolymers (A, B) and their corresponding diblock copolymer (A–B) has been widely studied, with emphasis on the volumetrically symmetric isopleth and the formation of bicontinuous microemulsions. However, almost all the previous studies employed linear polymers, and little is known about the impact of polymer architecture on the phase behavior of such ternary blends. Here, in this work, we report the self-assembly of three sets of ternary blends of polystyrene (PS) and poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA n ), with different lengths of oligo(ethylene glycol) side chains n. Small-angle X-ray scattering was used to probe the phase behavior at different compositions and temperatures. The order-to-disorder transition temperature was found to be impacted by the side chain length. It was also observed that longer side chains lead to poorer miscibility of homopolymers in the corresponding block, resulting in a more “dry-brush” like swelling behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthetic enzymes. In this study, we expressed Arabidopsis phospholipid: diacylglycerol acyltransferase (PDAT1), one of the two major TAG-forming plant enzymes in B. napus DH12075 to evaluate its effect on lipid metabolism in developing seeds and to estimate its flux control coefficient. Despite several-fold increase in PDAT activity, seeds of three independently generated PDAT transgenic events showed a small but consistent decrease in seed oil content and had altered fatty acid composition of phosphoglycerides and TAG, towards less unsaturation. Mass spectrometry imaging of seed sections confirmed the shift in lipid compositions and indicated that PDAT overexpression altered the distinct heterogeneous distributions of phosphatidylcholine (PC) molecular species. Similar, but less pronounced, changes in TAG molecular species distributions were observed. Our data indicate that PDAT exerts a small, negative, flux control on TAG biosynthesis and could have under-appreciated effects in fine-tuning of B. napus seed lipid composition in a tissue-specific manner. This has important implications for efforts to increase oil accumulation in similar crops.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Diacylglycerol enantiomer selectivity of diacylglycerol acyltransferases highlights metabolic specialization in triacylglycerol synthesis across the tree of life

Triacylglycerols are the major energy storage lipids in plants, animals, and microorganisms, and are predominantly produced by acyl-CoA:diacylglycerol (DAG) acyltransferases (DGATs). Two enantiomers of the DAG substrate, sn -1,2 and sn -2,3, can be produced by different biological mechanisms; however, little is known about which species produce each enantiomer, the selectivity of DGAT isoforms for either enantiomer, or whether DGAT enantiomer selectivity varies across organisms. Here, DAG enantiomer selectivity of DGAT1 and DGAT2 was measured from eight seed plants, two mammals, one oleaginous yeast, and one photosynthetic microalga using enantiomer-specific in vitro DGAT assays. Across most plants, DGAT1 favored sn -1,2-DAG, whereas DGAT2 preferentially utilized sn -2,3-DAG. However, there were several exceptions. Mammalian DGAT1, DGAT2, and microbial DGAT1s efficiently used both DAG enantiomers, while microbial DGAT2s had unique selectivity. The selectivity of several DGATs for combined acyl-CoA and DAG enantiomer molecular species were also evaluated for biotechnical applications. Therefore, DGAT DAG enantiomer selectivity is common yet strongly dependent on lineage and isoform and likely shaped in part by species-specific metabolic context of triacylglycerol synthesis, turnover, and remodeling. This work expands our understanding of DGAT function and establishes a foundation for leveraging enantiomer-selective acyltransferases in metabolic engineering of tailored lipid products.

Arabidopsis thaliana↗
DOE OSTI2021

Using silicon-vacancy centers in diamond to probe the full strain tensor

An ensemble of silicon vacancy (SiV−) centers in diamond is probed using two-pulse correlation spectroscopy and multidimensional coherent spectroscopy. Two main distinct families of SiV− centers are identified, and these families are paired with two orientation groups by comparing spectra from different linear polarizations of the incident laser. By tracking the peak centers in the measured spectra, the full diamond strain tensor is calculated local to the laser spot. Measurements are made at multiple points on the sample surface, and variations in the strain tensor are observed.

Bates, Kelsey M. (ORCID:0000000324961124)↗
DOE OSTI2022

Imaging dynamic exciton interactions and coupling in transition metal dichalcogenides

Transition metal dichalcogenides (TMDs) are regarded as a possible material platform for quantum information science and related device applications. In TMD monolayers, the dephasing time and inhomogeneity are crucial parameters for any quantum information application. In TMD heterostructures, coupling strength and interlayer exciton lifetimes are also parameters of interest. However, many demonstrations in TMDs can only be realized at specific spots on the sample, presenting a challenge to the scalability of these applications. Here, using multi-dimensional coherent imaging spectroscopy, we shed light on the underlying physics—including dephasing, inhomogeneity, and strain—for a MoSe 2 monolayer and identify both promising and unfavorable areas for quantum information applications. We, furthermore, apply the same technique to a MoSe 2 /WSe 2 heterostructure. Despite the notable presence of strain and dielectric environment changes, coherent and incoherent coupling and interlayer exciton lifetimes are mostly robust across the sample. This uniformity is despite a significantly inhomogeneous interlayer exciton photoluminescence distribution that suggests a bad sample for device applications. This robustness strengthens the case for TMDs as a next-generation material platform in quantum information science and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Suppressing parametric instabilities in direct-drive inertial-confinement-fusion plasmas using broadband laser light

It has long been recognized that broadband laser light has the potential to control parametric instabilities in inertial-confinement-fusion (ICF) plasmas. Here, we use results from laser-plasma-interaction simulations to estimate the bandwidth requirements for mitigating the three predominant classes of instabilities in direct-drive ICF implosions: cross-beam energy transfer (CBET), two-plasmon decay (TPD), and stimulated Raman scattering (SRS). We find that for frequency-tripled, Nd:glass laser light, a bandwidth of 8.5 THz can significantly increase laser absorption by suppressing CBET, while ∼13 THz is needed to mitigate absolute TPD and SRS on an ignition-scale platform. None of the glass lasers used in contemporary ICF experiments, however, possess a bandwidth greater than 1 THz and reaching larger values requires the use of an auxiliary broadening technique such as optical parametric amplification or stimulated-rotational-Raman scattering. An arguably superior approach is the adoption of an argon-fluoride (ArF) laser as an ICF driver. Besides having a broad bandwidth of ∼10 THz, the ArF laser also possesses the shortest wavelength (193 nm) that can scale to the high energy/power required for ICF—a feature that helps to mitigate parametric instabilities even further. We show that these native properties of ArF laser light are sufficient to eliminate nearly all CBET scattering in a direct-drive target and also raise absolute TPD and SRS thresholds well above those for broadband glass lasers. The effective control of parametric instabilities with broad bandwidth is potentially a “game changer” in ICF because it would enable higher laser intensities and ablation pressures in future target designs.

Bates, J. W. (ORCID:0000000188087240)↗
DOE OSTI2025

Absolute Hugoniot measurements in low-density plastic foams on the NIKE shock compression platform

The propagation of Mbar-range shock waves in low-density foam materials is of interest to target design in all approaches to inertial confinement fusion, high energy density physics, and laboratory astrophysics. We report absolute Hugoniot measurements for CH 1.72 N 0.086 O 0.37 plastic foams with 73 and 94 mg/cm 3 densities in the 32–107 km/s shock velocity range. The experiments were performed on the shock compression platform developed on the NIKE KrF laser facility at the U.S. Naval Research Laboratory. NIKE's 4 or 8-ns long flat-top laser pulses drive steady shock waves into foam targets at the ablative pressures of 1–7 Mbar. The propagation of the ablation and shock fronts is tracked continuously in time using streaked side-on monochromatic x-ray imaging radiography. The straight x−t trajectories of the shock and ablation fronts in the recorded streak images confirmed their steadiness. The SESAME tabulated equation of state predictions generally agrees with our Hugoniot data within a 95% confidence band. The experimental uncertainty of the evaluated shock density compression ratios remains large, indicating the need for more experiments and improved theoretical understanding of the strong shock propagation mechanisms in dry foams.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Engineering Li/Na selectivity in 12-Crown-4–functionalized polymer membranes

Significance Lithium is a key ingredient in batteries, which are integral components of next-generation automobiles, airplanes, grid energy storage, and electronic devices. Unfortunately, lithium extraction from natural sources is laborious, slow, and costly, motivating the search for more efficient isolation techniques. While polymeric membranes could reduce the cost of lithium recovery, current membrane materials lack sufficient lithium-ion selectivity. To address this challenge, we introduce a class of polymeric membranes that incorporate ion binding sites, which significantly increases the transport selectivity of LiCl over NaCl. These studies provide guidelines and practical considerations for incorporating specific interactants into polymers that mediate selective ion transport.

36 MATERIALS SCIENCE↗